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
WASH7P	653635	broad.mit.edu	37	1	16487	16487	+	Intron	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16487T>C	uc009vis.2	-						WASH7P_uc009vit.2_Intron|WASH7P_uc001aae.3_Intron|WASH7P_uc009viu.2_Intron|WASH7P_uc001aab.3_Intron|WASH7P_uc001aah.3_Intron|WASH7P_uc009vir.2_Intron|WASH7P_uc009viq.2_Intron|WASH7P_uc001aac.3_Intron|WASH7P_uc009viv.2_RNA|WASH7P_uc009viw.2_RNA|WASH7P_uc009vix.2_Intron|WASH7P_uc009vjd.2_Intron					Homo sapiens cDNA FLJ31670 fis, clone NT2RI2004984.												0						GAACAAGATATTTGAAATGGA	0.428													3	8	---	---	---	---	PASS
KIAA1751	85452	broad.mit.edu	37	1	1888064	1888064	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1888064T>G	uc001aim.1	-	17	2167	c.2011A>C	c.(2011-2013)AAA>CAA	p.K671Q	KIAA1751_uc009vkz.1_Missense_Mutation_p.K671Q	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	671										pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		CTCACTAATTTCAGGGCAGAC	0.572													25	25	---	---	---	---	PASS
C1orf212	113444	broad.mit.edu	37	1	35320643	35320643	+	3'UTR	SNP	C	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35320643C>G	uc001byb.2	-	2						NM_138428	NP_612437			hypothetical protein LOC113444												0		Myeloproliferative disorder(586;0.0393)				AAGATTCGATCATTATGGTTC	0.408													18	26	---	---	---	---	PASS
ZYG11B	79699	broad.mit.edu	37	1	53282280	53282280	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53282280C>T	uc001cuj.2	+	13	2218	c.2023C>T	c.(2023-2025)CAA>TAA	p.Q675*	ZYG11B_uc009vzg.2_RNA|ZYG11B_uc010onj.1_Nonsense_Mutation_p.Q596*|ZYG11B_uc009vzh.2_Nonsense_Mutation_p.Q97*	NM_024646	NP_078922	Q9C0D3	ZY11B_HUMAN	zyg-11 homolog B	675							protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						TTGGGCCATGCAACATGTCTG	0.363													5	284	---	---	---	---	PASS
SNX7	51375	broad.mit.edu	37	1	99225719	99225719	+	3'UTR	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99225719A>G	uc010ouc.1	+	9					SNX7_uc001dsa.2_3'UTR|SNX7_uc010oud.1_3'UTR	NM_015976	NP_057060	Q9UNH6	SNX7_HUMAN	sorting nexin 7 isoform a						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		GATCTTTGGGAGACAGCATTT	0.398													6	206	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	104260636	104260636	+	Silent	SNP	A	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104260636A>T	uc010our.1	+	4	383	c.261A>T	c.(259-261)CCA>CCT	p.P87P		NM_000699	NP_000690			pancreatic amylase alpha 2A precursor																		GGGTTGGGCCACCAAATAATA	0.403													10	145	---	---	---	---	PASS
CAPZA1	829	broad.mit.edu	37	1	113192053	113192053	+	Silent	SNP	A	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113192053A>T	uc001ecj.1	+	3	509	c.117A>T	c.(115-117)CTA>CTT	p.L39L		NM_006135	NP_006126	P52907	CAZA1_HUMAN	F-actin capping protein alpha-1 subunit	39					actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex|WASH complex	actin 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)		TTCGGCTACTACTTAATAATG	0.358													24	267	---	---	---	---	PASS
TCHH	7062	broad.mit.edu	37	1	152083904	152083904	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152083904T>C	uc001ezp.2	-	2	1789	c.1789A>G	c.(1789-1791)AGG>GGG	p.R597G	TCHH_uc009wne.1_Missense_Mutation_p.R597G	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	597	9 X 28 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCTCGAGCCTCTCTTCCTGC	0.682													6	8	---	---	---	---	PASS
OR10J3	441911	broad.mit.edu	37	1	159284265	159284265	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159284265A>G	uc010piu.1	-	1	185	c.185T>C	c.(184-186)TTC>TCC	p.F62S		NM_001004467	NP_001004467	Q5JRS4	O10J3_HUMAN	olfactory receptor, family 10, subfamily J,	62	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_hematologic(112;0.0429)					GCACAGGAAGAAGTACATGGG	0.473													12	324	---	---	---	---	PASS
CASQ1	844	broad.mit.edu	37	1	160160522	160160522	+	5'UTR	SNP	A	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160160522A>C	uc010pja.1	+	1						NM_001231	NP_001222	P31415	CASQ1_HUMAN	calsequestrin 1							mitochondrial matrix|sarcoplasmic reticulum lumen|smooth endoplasmic reticulum	calcium ion binding			central_nervous_system(1)	1	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGGAGAGCCAACCCAGATCCC	0.622													11	28	---	---	---	---	PASS
RGS4	5999	broad.mit.edu	37	1	163039314	163039314	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163039314A>G	uc009wuy.2	+	1	551	c.40A>G	c.(40-42)AGG>GGG	p.R14G	RGS4_uc001gcl.3_Missense_Mutation_p.R111G|RGS4_uc009wuz.2_Missense_Mutation_p.R14G|RGS4_uc009wva.2_5'Flank	NM_005613	NP_005604	P49798	RGS4_HUMAN	regulator of G-protein signaling 4 isoform 2	14					inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	plasma membrane	calmodulin binding|GTPase activator activity|signal transducer activity			ovary(2)|central_nervous_system(1)	3						TTCTTGCTTGAGGAGGTAAGA	0.423											OREG0013952	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	72	---	---	---	---	PASS
F5	2153	broad.mit.edu	37	1	169528479	169528479	+	Silent	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169528479T>C	uc001ggg.1	-	5	787	c.642A>G	c.(640-642)CTA>CTG	p.L214L	F5_uc010plr.1_RNA	NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	214	F5/8 type A 1.|Plastocyanin-like 2.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	ACACAGCAAATAGTAGCACGA	0.453													52	118	---	---	---	---	PASS
FAM5C	339479	broad.mit.edu	37	1	190129986	190129986	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190129986C>G	uc001gse.1	-	7	1228	c.996G>C	c.(994-996)ATG>ATC	p.M332I	FAM5C_uc010pot.1_Missense_Mutation_p.M230I	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	332						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)					GGAAATAATTCATAGGTAGCC	0.299													7	260	---	---	---	---	PASS
CRB1	23418	broad.mit.edu	37	1	197404477	197404477	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197404477C>A	uc001gtz.2	+	9	3619	c.3484C>A	c.(3484-3486)CAT>AAT	p.H1162N	CRB1_uc010poz.1_Missense_Mutation_p.H1138N|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Missense_Mutation_p.H1050N|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Missense_Mutation_p.H643N|CRB1_uc001gub.1_Missense_Mutation_p.H811N	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	1162	Extracellular (Potential).|EGF-like 15.				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9						TAGCTCTTATCATTGCTCCTG	0.463													81	145	---	---	---	---	PASS
FAM177B	400823	broad.mit.edu	37	1	222922743	222922743	+	Intron	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222922743T>C	uc001hnt.2	+						uc001hnr.1_Intron|FAM177B_uc009xeb.2_RNA	NM_207468	NP_997351	A6PVY3	F177B_HUMAN	hypothetical protein LOC400823											ovary(1)	1						ACTCTGGGCATCTCAACTGAT	0.368													4	102	---	---	---	---	PASS
RGS7	6000	broad.mit.edu	37	1	240969479	240969479	+	Silent	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240969479G>A	uc001hyv.2	-	15	1560	c.1230C>T	c.(1228-1230)AAC>AAT	p.N410N	RGS7_uc010pyh.1_Silent_p.N384N|RGS7_uc010pyj.1_Silent_p.N326N|RGS7_uc001hyu.2_Silent_p.N410N|RGS7_uc009xgn.1_Silent_p.N357N|RGS7_uc001hyw.2_Silent_p.N410N|RGS7_uc001hyt.2_Silent_p.N242N	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7	410	RGS.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			GTTCCTTCACGTTCTGTGTGG	0.483													33	279	---	---	---	---	PASS
ASAP2	8853	broad.mit.edu	37	2	9484692	9484692	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9484692G>A	uc002qzh.2	+	10	1221	c.881G>A	c.(880-882)AGC>AAC	p.S294N	ASAP2_uc002qzi.2_Missense_Mutation_p.S294N	NM_003887	NP_003878	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH	294					regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0						ACAGCTTATAGCTTACATCAG	0.458													73	194	---	---	---	---	PASS
CAPN13	92291	broad.mit.edu	37	2	30964652	30964652	+	Intron	SNP	T	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30964652T>G	uc002rnn.2	-						CAPN13_uc002rnm.2_Intron|CAPN13_uc002rno.2_3'UTR	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					GAGAGGCAGGTAAAATAGTCC	0.582													6	19	---	---	---	---	PASS
HNRPLL	92906	broad.mit.edu	37	2	38809099	38809099	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38809099T>C	uc002rqw.2	-	6	1168	c.758A>G	c.(757-759)GAC>GGC	p.D253G	HNRPLL_uc002rqv.2_5'UTR|HNRPLL_uc002rqx.2_Missense_Mutation_p.D248G	NM_138394	NP_612403	Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	253					mRNA processing|positive regulation of RNA splicing	nucleus|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding			skin(1)	1		all_hematologic(82;0.248)				ACTGTCATTGTCATTCCTAAT	0.333													7	505	---	---	---	---	PASS
PCYOX1	51449	broad.mit.edu	37	2	70502693	70502693	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70502693G>T	uc002sgn.3	+	5	820	c.754G>T	c.(754-756)GGT>TGT	p.G252C	PCYOX1_uc010fdo.2_Missense_Mutation_p.G175C|PCYOX1_uc010yqu.1_Missense_Mutation_p.G234C	NM_016297	NP_057381	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1 precursor	252					prenylated protein catabolic process	lysosome|very-low-density lipoprotein particle	prenylcysteine oxidase activity			central_nervous_system(1)	1						GGCAGTAGAAGGTGGCAATAA	0.433													67	204	---	---	---	---	PASS
RMND5A	64795	broad.mit.edu	37	2	86980658	86980658	+	Silent	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86980658C>T	uc010ytm.1	+	4	875	c.498C>T	c.(496-498)GTC>GTT	p.V166V	RMND5A_uc002srs.3_Intron|RMND5A_uc002srr.2_Silent_p.V166V	NM_022780	NP_073617	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog	166	CTLH.									ovary(1)|skin(1)	2						CATTAAAGGTCAGAGTTCTGA	0.373													207	447	---	---	---	---	PASS
IL1F8	27177	broad.mit.edu	37	2	113788647	113788647	+	Silent	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113788647A>G	uc002tiq.1	-	3	203	c.99T>C	c.(97-99)CCT>CCC	p.P33P	IL1F8_uc002tir.1_Silent_p.P33P	NM_014438	NP_055253	Q9NZH7	IL36B_HUMAN	interleukin 1 family, member 8 isoform 1	33					immune response	extracellular space	cytokine activity|interleukin-1 receptor binding			ovary(1)	1						TGCGGCTAAGAGGAGCTGCTA	0.493													5	194	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125521709	125521709	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125521709C>T	uc002tno.2	+	16	2879	c.2515C>T	c.(2515-2517)CGA>TGA	p.R839*	CNTNAP5_uc010flu.2_Nonsense_Mutation_p.R840*	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	839	Laminin G-like 3.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		AGACTTCATTCGACTCGAAAT	0.289													9	267	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	140990809	140990809	+	Silent	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140990809C>T	uc002tvj.1	-	91	14718	c.13746G>A	c.(13744-13746)AGG>AGA	p.R4582R		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4582	Cytoplasmic (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GCAGTTCTTTCCTTTCATCAA	0.328										TSP Lung(27;0.18)			5	594	---	---	---	---	PASS
DPP4	1803	broad.mit.edu	37	2	162902066	162902066	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162902066A>C	uc002ubz.2	-	5	903	c.342T>G	c.(340-342)ATT>ATG	p.I114M	DPP4_uc010fpb.2_Translation_Start_Site|DPP4_uc002uca.1_RNA|DPP4_uc002ucb.1_RNA	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV	114	Extracellular (Potential).				cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	ATTCTAAGAGAATAAACTGCC	0.303													91	224	---	---	---	---	PASS
PGAP1	80055	broad.mit.edu	37	2	197777686	197777686	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197777686T>G	uc002utw.2	-	4	683	c.569A>C	c.(568-570)AAG>ACG	p.K190T	PGAP1_uc002utx.2_Missense_Mutation_p.K16T|PGAP1_uc002uty.1_Missense_Mutation_p.K190T|PGAP1_uc010zgv.1_RNA|PGAP1_uc010fsj.2_Missense_Mutation_p.K16T	NM_024989	NP_079265	Q75T13	PGAP1_HUMAN	GPI deacylase	190	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4						CAGATCATGCTTAAAATTTTT	0.378													66	176	---	---	---	---	PASS
UNC80	285175	broad.mit.edu	37	2	210640619	210640619	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210640619G>C	uc010zjc.1	+	3	228	c.148G>C	c.(148-150)GAG>CAG	p.E50Q	UNC80_uc002vdj.1_Missense_Mutation_p.E50Q	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1	50						integral to membrane					0						ACAGTCCTTTGAGCGAGTGTT	0.358													35	60	---	---	---	---	PASS
AGFG1	3267	broad.mit.edu	37	2	228396862	228396862	+	Intron	SNP	A	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228396862A>C	uc002vpc.2	+						AGFG1_uc002vpd.2_Missense_Mutation_p.M275L|AGFG1_uc002vpe.2_Intron|AGFG1_uc002vpf.2_Intron	NM_004504	NP_004495	P52594	AGFG1_HUMAN	HIV-1 Rev binding protein isoform 2						cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4						AGCATTTAGAATGCTTTCATC	0.333													7	703	---	---	---	---	PASS
KIF1A	547	broad.mit.edu	37	2	241662861	241662861	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241662861C>T	uc002vzy.2	-	40	4276	c.4130G>A	c.(4129-4131)TGG>TAG	p.W1377*	KIF1A_uc010fzk.2_Nonsense_Mutation_p.W1478*|KIF1A_uc002vzz.1_Nonsense_Mutation_p.W1486*|KIF1A_uc002vzw.2_Nonsense_Mutation_p.W38*|KIF1A_uc002vzx.2_Nonsense_Mutation_p.W104*	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	1377					anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		CTCCAGCTCCCACTGGTGGTC	0.627													3	18	---	---	---	---	PASS
HDLBP	3069	broad.mit.edu	37	2	242168842	242168842	+	3'UTR	SNP	C	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242168842C>A	uc002waz.2	-	28					HDLBP_uc002wba.2_3'UTR|HDLBP_uc002wbb.2_3'UTR	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein						cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		CACGGCCAGGCCTGGAGGAGC	0.622													5	55	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191558	10191558	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191558T>C	uc003bvc.2	+	3	764	c.551T>C	c.(550-552)CTC>CCC	p.L184P	VHL_uc003bvd.2_Missense_Mutation_p.L143P	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	184			L -> P (in VHLD; type I).|L -> R (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.L184P(4)|p.S183*(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTCAGGTCGCTCTACGAAGAT	0.517		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				39	41	---	---	---	---	PASS
LOC100125556	100125556	broad.mit.edu	37	3	125647387	125647387	+	RNA	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125647387G>A	uc003eif.3	+	5		c.561G>A			LOC100125556_uc003eid.3_RNA|LOC100125556_uc003eie.3_RNA	NR_024251				Homo sapiens family with sequence similarity 86, member A pseudogene, mRNA (cDNA clone IMAGE:4425123).												0						ACCAGAAACTGTTTCCCTATG	0.502													5	41	---	---	---	---	PASS
LOC100125556	100125556	broad.mit.edu	37	3	125647396	125647396	+	RNA	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125647396T>C	uc003eif.3	+	5		c.570T>C			LOC100125556_uc003eid.3_RNA|LOC100125556_uc003eie.3_RNA	NR_024251				Homo sapiens family with sequence similarity 86, member A pseudogene, mRNA (cDNA clone IMAGE:4425123).												0						TGTTTCCCTATGAAGAGCACT	0.502													5	44	---	---	---	---	PASS
MBD4	8930	broad.mit.edu	37	3	129150264	129150264	+	3'UTR	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129150264A>G	uc003emh.1	-	8					uc003emg.2_5'Flank|MBD4_uc003emi.1_3'UTR|MBD4_uc003emj.1_3'UTR|MBD4_uc003emk.1_3'UTR	NM_003925	NP_003916	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4						depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding			ovary(1)|lung(1)	2						CTATGGCTGGAAAGGTGGTTG	0.373								BER_DNA_glycosylases					22	100	---	---	---	---	PASS
PFN2	5217	broad.mit.edu	37	3	149684007	149684007	+	3'UTR	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149684007G>A	uc003ext.1	-	3					PFN2_uc003exs.1_Missense_Mutation_p.L75F|PFN2_uc003exu.1_Missense_Mutation_p.L124F|PFN2_uc011bnu.1_Missense_Mutation_p.L124F	NM_053024	NP_444252	P35080	PROF2_HUMAN	profilin 2 isoform a						actin cytoskeleton organization|regulation of actin polymerization or depolymerization	actin cytoskeleton|cytoplasm	actin binding|phosphatidylinositol-4,5-bisphosphate binding				0			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TTCTTGTTAAGTGTGCCTCCG	0.453													192	113	---	---	---	---	PASS
MED12L	116931	broad.mit.edu	37	3	151100523	151100523	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151100523G>T	uc003eyp.2	+	31	4603	c.4565G>T	c.(4564-4566)CGC>CTC	p.R1522L	MED12L_uc011bnz.1_Missense_Mutation_p.R1382L|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Missense_Mutation_p.R685L	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1522					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TTGCAACTCCGCCTAAATTTG	0.388													11	165	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164754179	164754179	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164754179T>G	uc003fei.2	-	22	2575	c.2513A>C	c.(2512-2514)AAA>ACA	p.K838T		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	838	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	AGACTTACCTTTAGTTTCTCC	0.338										HNSCC(35;0.089)			136	275	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195509939	195509939	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195509939G>T	uc011bto.1	-	3	8588	c.8128C>A	c.(8128-8130)CCT>ACT	p.P2710T	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGGGATGGTGACA	0.592													16	31	---	---	---	---	PASS
DOK7	285489	broad.mit.edu	37	4	3478155	3478155	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3478155T>G	uc003ghd.2	+	4	488	c.418T>G	c.(418-420)TTG>GTG	p.L140V	DOK7_uc003ghe.2_Silent_p.S5S	NM_173660	NP_775931	Q18PE1	DOK7_HUMAN	downstream of tyrosine kinase 7 isoform 1	140	IRS-type PTB.				positive regulation of protein tyrosine kinase activity	cell junction|synapse	insulin receptor binding|protein kinase binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TGTCCTCGTCTTGGCCAGGGA	0.592													15	37	---	---	---	---	PASS
TMEM128	85013	broad.mit.edu	37	4	4242116	4242116	+	Silent	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4242116T>C	uc003ghr.1	-	3	360	c.330A>G	c.(328-330)GGA>GGG	p.G110G	TMEM128_uc003ghq.1_Silent_p.G86G|TMEM128_uc003ghs.2_Silent_p.G110G|TMEM128_uc011bvv.1_Silent_p.G110G|TMEM128_uc011bvw.1_Silent_p.G110G	NM_032927	NP_116316	Q5BJH2	TM128_HUMAN	transmembrane protein 128	110						integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)		CATCATATTCTCCAATTCCAC	0.408													7	363	---	---	---	---	PASS
MIR218-1	407000	broad.mit.edu	37	4	20529994	20529994	+	RNA	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20529994C>T	hsa-mir-218-1|MI0000294	+			c.97C>T			SLIT2_uc003gpr.1_Intron|SLIT2_uc003gps.1_Intron|uc011bxl.1_RNA																	0						TGGAACGTCACGCAGCTTTCT	0.413													88	198	---	---	---	---	PASS
PLRG1	5356	broad.mit.edu	37	4	155463398	155463398	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155463398T>C	uc003iny.2	-	8	691	c.628A>G	c.(628-630)ATT>GTT	p.I210V	PLRG1_uc003inz.2_Missense_Mutation_p.I201V|PLRG1_uc011cil.1_Missense_Mutation_p.I49V	NM_002669	NP_002660	O43660	PLRG1_HUMAN	pleiotropic regulator 1 (PRL1 homolog,	210	WD 1.					catalytic step 2 spliceosome|nuclear speck	protein binding|signal transducer activity|transcription corepressor activity				0	all_hematologic(180;0.215)	Renal(120;0.0854)				TCCACAGCAATACATCGAACC	0.373													6	307	---	---	---	---	PASS
ODZ3	55714	broad.mit.edu	37	4	183714853	183714853	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183714853A>G	uc003ivd.1	+	25	7065	c.7028A>G	c.(7027-7029)TAT>TGT	p.Y2343C		NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	2343	Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		GGTGGCCTGTATGACCCACTC	0.403													96	203	---	---	---	---	PASS
CLPTM1L	81037	broad.mit.edu	37	5	1331925	1331925	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1331925G>A	uc003jch.2	-	8	1011	c.965C>T	c.(964-966)TCC>TTC	p.S322F	CLPTM1L_uc003jcg.2_Missense_Mutation_p.S189F	NM_030782	NP_110409	Q96KA5	CLP1L_HUMAN	CLPTM1-like	322	Cytoplasmic (Potential).				apoptosis	integral to membrane				breast(1)|central_nervous_system(1)	2	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		TGCCTTGGTGGACATGCCGAT	0.552													45	116	---	---	---	---	PASS
MARCH6	10299	broad.mit.edu	37	5	10407230	10407230	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10407230T>C	uc003jet.1	+	17	1652	c.1469T>C	c.(1468-1470)ATT>ACT	p.I490T	MARCH6_uc011cmu.1_Missense_Mutation_p.I442T|MARCH6_uc003jeu.1_Missense_Mutation_p.I188T|MARCH6_uc011cmv.1_Missense_Mutation_p.I385T	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6	490	Helical; (Potential).				protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						TTTGGCTCCATTGTCCTCCTG	0.418													197	453	---	---	---	---	PASS
SFRS12	140890	broad.mit.edu	37	5	65455077	65455077	+	5'UTR	SNP	C	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65455077C>G	uc003juo.2	+	4					SFRS12_uc003jun.2_Missense_Mutation_p.S109C|SFRS12_uc010iwy.2_5'UTR	NM_139168	NP_631907	Q8WXA9	SREK1_HUMAN	splicing factor, arginine/serine-rich 12 isoform						mRNA processing|RNA splicing	spliceosomal complex	nucleic acid binding|nucleotide binding|protein binding				0		Lung NSC(167;9.34e-06)|Prostate(74;0.00187)|Ovarian(174;0.0545)|Breast(144;0.0928)|Colorectal(97;0.234)		Lung(70;0.00449)		AAAGCCCTCTCTTTATTGGCT	0.428													71	167	---	---	---	---	PASS
TAF9	6880	broad.mit.edu	37	5	68647926	68647926	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68647926T>C	uc003jwa.2	-	5	573	c.481A>G	c.(481-483)AAA>GAA	p.K161E	TAF9_uc003jwb.2_Missense_Mutation_p.K158E	NM_016283	NP_057367	Q16594	TAF9_HUMAN	TAF9 RNA polymerase II, TATA box binding	Error:Variant_position_missing_in_Q16594_after_alignment					histone H3 acetylation|negative regulation of apoptosis|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of cell growth|positive regulation of response to cytokine stimulus|positive regulation of transcription from RNA polymerase II promoter|response to interleukin-1|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	MLL1 complex|PCAF complex|pre-snoRNP complex|STAGA complex|transcription factor TFIID complex|transcription factor TFTC complex	activating transcription factor binding|C2H2 zinc finger domain binding|p53 binding|transcription coactivator activity|transcription regulatory region DNA binding				0		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.1e-56)|Epithelial(20;9.54e-53)|all cancers(19;2.2e-48)|Lung(70;0.0176)		TCAATCCATTTCAAGATCTGA	0.373													5	231	---	---	---	---	PASS
AGGF1	55109	broad.mit.edu	37	5	76348572	76348572	+	Silent	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76348572T>C	uc003ket.2	+	9	1767	c.1407T>C	c.(1405-1407)TAT>TAC	p.Y469Y		NM_018046	NP_060516	Q8N302	AGGF1_HUMAN	angiogenic factor VG5Q	469	FHA.				angiogenesis|cell adhesion|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|RNA processing|vasculogenesis	extracellular region|perinuclear region of cytoplasm	eukaryotic cell surface binding|nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		TACAAAGTTATGTCCTTGTGG	0.299													124	291	---	---	---	---	PASS
MEGF10	84466	broad.mit.edu	37	5	126793028	126793028	+	3'UTR	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126793028G>T	uc003kuh.3	+	26					MEGF10_uc003kui.3_3'UTR	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor						cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		GGACCGCTTGGTAGCCACTGG	0.418													6	41	---	---	---	---	PASS
TGFBI	7045	broad.mit.edu	37	5	135382106	135382106	+	Silent	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135382106G>A	uc003lbf.3	+	4	542	c.381G>A	c.(379-381)AAG>AAA	p.K127K	TGFBI_uc003lbg.3_5'UTR|TGFBI_uc003lbh.3_5'UTR|TGFBI_uc011cyb.1_5'UTR	NM_000358	NP_000349	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	127	FAS1 1.				angiogenesis|cell adhesion|cell proliferation|negative regulation of cell adhesion|response to stimulus|visual perception	extracellular space|proteinaceous extracellular matrix	integrin binding			breast(3)|ovary(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCACGGAGAAGCTGAGGCCTG	0.617													10	22	---	---	---	---	PASS
TGFBI	7045	broad.mit.edu	37	5	135382107	135382107	+	Silent	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135382107C>T	uc003lbf.3	+	4	543	c.382C>T	c.(382-384)CTG>TTG	p.L128L	TGFBI_uc003lbg.3_5'UTR|TGFBI_uc003lbh.3_5'UTR|TGFBI_uc011cyb.1_5'UTR	NM_000358	NP_000349	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	128	FAS1 1.				angiogenesis|cell adhesion|cell proliferation|negative regulation of cell adhesion|response to stimulus|visual perception	extracellular space|proteinaceous extracellular matrix	integrin binding			breast(3)|ovary(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CACGGAGAAGCTGAGGCCTGA	0.622													10	23	---	---	---	---	PASS
STK32A	202374	broad.mit.edu	37	5	146619114	146619114	+	5'UTR	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146619114G>A	uc010jgn.1	+	2					STK32A_uc003lol.3_5'UTR|STK32A_uc003lom.2_5'UTR|STK32A_uc011dbw.1_5'UTR	NM_001112724	NP_001106195	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A isoform 1								ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCCAACTAAGGCTTCGGGAC	0.448													4	131	---	---	---	---	PASS
CNOT6	57472	broad.mit.edu	37	5	179994125	179994125	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179994125T>C	uc003mlx.2	+	8	1104	c.755T>C	c.(754-756)GTA>GCA	p.V252A	CNOT6_uc010jld.2_Missense_Mutation_p.V252A|CNOT6_uc010jle.2_Missense_Mutation_p.V247A	NM_015455	NP_056270	Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	252					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	exonuclease activity|metal ion binding|protein binding|RNA binding				0	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		TTTTTTCTGGTAGAGCTGAAA	0.363													110	318	---	---	---	---	PASS
HIST1H1A	3024	broad.mit.edu	37	6	26017495	26017495	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26017495C>A	uc003nfo.2	-	1	546	c.466G>T	c.(466-468)GCT>TCT	p.A156S		NM_005325	NP_005316	Q02539	H11_HUMAN	histone cluster 1, H1a	156					nucleosome assembly|spermatogenesis	nucleosome|nucleus	DNA binding			ovary(2)	2						GGCTTTTTAGCCTTTTTCGGA	0.463													116	304	---	---	---	---	PASS
MAPK14	1432	broad.mit.edu	37	6	36043701	36043701	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36043701C>A	uc003olp.2	+	7	1053	c.572C>A	c.(571-573)CCT>CAT	p.P191H	MAPK14_uc011dth.1_Missense_Mutation_p.P191H|MAPK14_uc003olo.2_Missense_Mutation_p.P191H|MAPK14_uc003olq.2_Missense_Mutation_p.P191H|MAPK14_uc003olr.2_Missense_Mutation_p.P191H|MAPK14_uc011dti.1_Missense_Mutation_p.P114H	NM_001315	NP_001306	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14 isoform 1	191	Protein kinase.				activation of MAPK activity|cellular component movement|cellular response to ionizing radiation|chemotaxis|innate immune response|mRNA metabolic process|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of muscle cell differentiation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|signal transduction in response to DNA damage|stress-activated MAPK cascade|stress-induced premature senescence|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase activity|MAP kinase kinase activity|protein binding			ovary(2)|stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	6						TACAGGGCTCCTGAGATCATG	0.468													89	201	---	---	---	---	PASS
SUPT3H	8464	broad.mit.edu	37	6	44921067	44921067	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44921067G>C	uc003oxo.2	-	11	1132	c.814C>G	c.(814-816)CAG>GAG	p.Q272E	SUPT3H_uc003oxn.1_Missense_Mutation_p.Q261E|SUPT3H_uc011dvv.1_Missense_Mutation_p.Q109E|SUPT3H_uc003oxp.2_Missense_Mutation_p.Q261E|SUPT3H_uc011dvw.1_Missense_Mutation_p.Q175E	NM_181356	NP_852001	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog isoform 2	343					histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3						TTGTGATACTGAATGAAGGTT	0.393													65	187	---	---	---	---	PASS
BMP5	653	broad.mit.edu	37	6	55620443	55620443	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55620443C>A	uc003pcq.2	-	7	1965	c.1253G>T	c.(1252-1254)TGT>TTT	p.C418F	BMP5_uc011dxf.1_Missense_Mutation_p.C381F	NM_021073	NP_066551	P22003	BMP5_HUMAN	bone morphogenetic protein 5 preproprotein	418					cartilage development|cell differentiation|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(2)	2	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			TGGAGCACAACAAGGCTTTGG	0.333													17	302	---	---	---	---	PASS
ZUFSP	221302	broad.mit.edu	37	6	116987986	116987986	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116987986T>C	uc003pxf.1	-	2	616	c.370A>G	c.(370-372)ACT>GCT	p.T124A	ZUFSP_uc010kef.1_Intron	NM_145062	NP_659499	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	124						intracellular	zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		CTAGATTCAGTTAAGTTCTCT	0.353													7	417	---	---	---	---	PASS
RSPO3	84870	broad.mit.edu	37	6	127517220	127517220	+	3'UTR	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127517220C>T	uc003qar.2	+	5					RSPO3_uc003qas.1_Intron	NM_032784	NP_116173	Q9BXY4	RSPO3_HUMAN	R-spondin 3 precursor							extracellular region	heparin binding				0				GBM - Glioblastoma multiforme(226;0.0555)		GACAGGTGCTCTAGCCATTAG	0.418													12	142	---	---	---	---	PASS
NUP43	348995	broad.mit.edu	37	6	150047983	150047983	+	3'UTR	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150047983T>C	uc003qmz.2	-	8					NUP43_uc003qmx.3_RNA|NUP43_uc011eee.1_RNA|NUP43_uc011eef.1_3'UTR	NM_198887	NP_942590	Q8NFH3	NUP43_HUMAN	nucleoporin 43kDa						carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			upper_aerodigestive_tract(1)	1		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;4.71e-13)|GBM - Glioblastoma multiforme(68;0.101)		TTGACATTAATGGTAGTTTAC	0.373													4	10	---	---	---	---	PASS
HGC6.3	100128124	broad.mit.edu	37	6	168377135	168377135	+	Silent	SNP	T	C	C	rs75642682		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168377135T>C	uc010kks.1	-	1	485	c.198A>G	c.(196-198)CAA>CAG	p.Q66Q		NM_001129895	NP_001123367	Q9UM08	Q9UM08_HUMAN	hypothetical protein LOC100128124	66											0						CTGCAGTGTGTTGGGAGGAGG	0.622													5	32	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91670309	91670309	+	Intron	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91670309G>T	uc003ulg.2	+						AKAP9_uc003ule.2_3'UTR|AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TATTTTTTATGTAGCCATAAT	0.343			T	BRAF	papillary thyroid								5	46	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121637955	121637955	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121637955C>G	uc003vjy.2	+	10	1530	c.1135C>G	c.(1135-1137)CTA>GTA	p.L379V	PTPRZ1_uc003vjz.2_Missense_Mutation_p.L379V	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	379	Extracellular (Potential).|Fibronectin type-III.				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						CAATAATTTGCTACCCAATAT	0.348													94	124	---	---	---	---	PASS
TMEM229A	730130	broad.mit.edu	37	7	123672832	123672832	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123672832G>T	uc011kob.1	-	1	692	c.226C>A	c.(226-228)CGC>AGC	p.R76S	uc011koc.1_Intron	NM_001136002	NP_001129474	B2RXF0	T229A_HUMAN	transmembrane protein 229A	76						host cell nucleus|integral to membrane	sequence-specific DNA binding transcription factor activity				0						CGGGCGAAGCGCCGGGCCGAG	0.677													4	16	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131866156	131866156	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131866156G>A	uc003vra.3	-	18	3705	c.3476C>T	c.(3475-3477)ACG>ATG	p.T1159M		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1159	IPT/TIG 4.|Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						GATGATGGGCGTGCCAGGCTT	0.582													57	202	---	---	---	---	PASS
C7orf13	129790	broad.mit.edu	37	7	156432294	156432294	+	3'UTR	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156432294G>T	uc003wmm.2	-	1					C7orf13_uc003wmn.1_RNA|RNF32_uc003wmo.2_5'Flank|RNF32_uc010lql.1_5'Flank|RNF32_uc010lqm.2_5'Flank|RNF32_uc003wmp.2_5'Flank|RNF32_uc003wmq.2_5'Flank	NR_026865				RecName: Full=Uncharacterized protein C7orf13;												0						gggaagcaGCGAGCCAGAGTA	0.303													39	129	---	---	---	---	PASS
C7orf13	129790	broad.mit.edu	37	7	156432295	156432295	+	3'UTR	SNP	A	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156432295A>T	uc003wmm.2	-	1					C7orf13_uc003wmn.1_RNA|RNF32_uc003wmo.2_5'Flank|RNF32_uc010lql.1_5'Flank|RNF32_uc010lqm.2_5'Flank|RNF32_uc003wmp.2_5'Flank|RNF32_uc003wmq.2_5'Flank	NR_026865				RecName: Full=Uncharacterized protein C7orf13;												0						ggaagcaGCGAGCCAGAGTAT	0.308													38	129	---	---	---	---	PASS
GPR124	25960	broad.mit.edu	37	8	37688398	37688398	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37688398C>T	uc003xkj.2	+	7	1252	c.889C>T	c.(889-891)CTC>TTC	p.L297F	GPR124_uc010lvy.2_Missense_Mutation_p.L297F	NM_032777	NP_116166	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124 precursor	297	Extracellular (Potential).|Ig-like.				central nervous system development|endothelial cell migration|neuropeptide signaling pathway|regulation of angiogenesis|regulation of chemotaxis|sprouting angiogenesis	integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(2)|ovary(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			GGCGGGCATCCTCCTGGCCGA	0.647													5	22	---	---	---	---	PASS
C8orf22	492307	broad.mit.edu	37	8	49987949	49987949	+	3'UTR	SNP	G	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49987949G>C	uc003xqq.3	+	5						NM_001007176	NP_001007177	Q8WWR9	PDPFL_HUMAN	hypothetical protein LOC492307												0		all_cancers(86;0.0452)|all_epithelial(80;0.000863)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				CAAGATCACAGCAGCCACTGA	0.433													10	37	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55540593	55540593	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55540593T>G	uc003xsd.1	+	4	4299	c.4151T>G	c.(4150-4152)TTT>TGT	p.F1384C	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1384					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AAAAATGGATTTAATACATTG	0.328													25	73	---	---	---	---	PASS
C8orf38	137682	broad.mit.edu	37	8	96070133	96070133	+	Silent	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96070133T>C	uc003yhj.2	+	9	986	c.970T>C	c.(970-972)TTG>CTG	p.L324L	C8orf38_uc003yhf.2_Silent_p.L232L|C8orf38_uc011lgs.1_Intron|C8orf38_uc003yhi.2_Silent_p.L272L|C8orf38_uc003yhk.2_RNA|C8orf38_uc003yhl.2_Silent_p.L232L	NM_152416	NP_689629	Q330K2	CH038_HUMAN	hypothetical protein LOC137682 precursor	324					biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)					TCCATTATATTTGTATATTCA	0.264													8	264	---	---	---	---	PASS
KCNV1	27012	broad.mit.edu	37	8	110980370	110980370	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110980370C>T	uc003ynr.3	-	3	1792	c.1450G>A	c.(1450-1452)GGC>AGC	p.G484S	KCNV1_uc010mcw.2_Missense_Mutation_p.G484S	NM_014379	NP_055194	Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	484	Cytoplasmic (Potential).					voltage-gated potassium channel complex	ion channel inhibitor activity|potassium channel regulator activity|voltage-gated potassium channel activity			lung(1)|kidney(1)	2	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			CTTTCTCTGCCTTTCAGTCGC	0.378													5	217	---	---	---	---	PASS
ZNF623	9831	broad.mit.edu	37	8	144733782	144733782	+	3'UTR	SNP	A	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144733782A>C	uc003yzd.2	+	1					ZNF623_uc011lkp.1_3'UTR|ZNF623_uc003yzc.2_3'UTR	NM_014789	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			AGTGGGTGCCACCTGCCACTG	0.517													6	3	---	---	---	---	PASS
DENND4C	55667	broad.mit.edu	37	9	19296056	19296056	+	Silent	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19296056A>G	uc003znq.2	+	2	177	c.144A>G	c.(142-144)CTA>CTG	p.L48L	DENND4C_uc011lnc.1_5'UTR	NM_017925	NP_060395	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	48						integral to membrane				ovary(1)|skin(1)	2						GGGAACTTCTATCAGAGAAAC	0.373													7	291	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66499770	66499770	+	Missense_Mutation	SNP	G	T	T	rs75046133		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66499770G>T	uc004aee.1	+	1	580	c.580G>T	c.(580-582)GCC>TCC	p.A194S	LOC442421_uc004aed.1_RNA					Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).												0						CAACCTGGTGGCCATCGTGGT	0.582													3	20	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79325303	79325303	+	Silent	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79325303G>T	uc010mpk.2	-	8	2011	c.1887C>A	c.(1885-1887)CTC>CTA	p.L629L		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	629					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						CTTCTGTATAGAGTGAGGCTG	0.493													21	239	---	---	---	---	PASS
EPB41L4B	54566	broad.mit.edu	37	9	112005948	112005948	+	Silent	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112005948A>G	uc004bdz.1	-	15	1654	c.1359T>C	c.(1357-1359)CCT>CCC	p.P453P	EPB41L4B_uc004bea.2_Silent_p.P453P	NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	453						cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|skin(1)	3						GATGGATATTAGGATGATATT	0.453													113	241	---	---	---	---	PASS
ST6GALNAC4	27090	broad.mit.edu	37	9	130678772	130678772	+	5'UTR	SNP	A	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130678772A>C	uc004bss.2	-	2					ST6GALNAC4_uc004bst.2_Intron	NM_175039	NP_778204	Q9H4F1	SIA7D_HUMAN	sialyltransferase 7D isoform a						glycolipid metabolic process|protein glycosylation	integral to Golgi membrane|nucleus|soluble fraction	(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity				0						GGAGCCGGGCACCTGCCAAGA	0.617													12	25	---	---	---	---	PASS
C9orf78	51759	broad.mit.edu	37	9	132595900	132595900	+	Intron	SNP	G	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132595900G>C	uc004byp.2	-						C9orf78_uc004byo.2_5'Flank|C9orf78_uc004byq.1_5'UTR|USP20_uc004bys.2_5'Flank|USP20_uc004byr.2_5'Flank|USP20_uc004byt.1_5'Flank	NM_016520	NP_057604	Q9NZ63	CI078_HUMAN	chromosome 9 open reading frame 78												0		Ovarian(14;0.00556)				TGCAGGGAGGGCTGCCATAAC	0.473													6	69	---	---	---	---	PASS
CACNB2	783	broad.mit.edu	37	10	18823091	18823091	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18823091C>G	uc001ipr.2	+	11	1201	c.1141C>G	c.(1141-1143)CCA>GCA	p.P381A	CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Missense_Mutation_p.P357A|CACNB2_uc001ipt.2_Missense_Mutation_p.P343A|CACNB2_uc001ipu.2_Missense_Mutation_p.P353A|CACNB2_uc001ipv.2_Missense_Mutation_p.P329A|CACNB2_uc009xka.1_Missense_Mutation_p.P315A|CACNB2_uc001ipw.2_Missense_Mutation_p.P288A|CACNB2_uc001ipx.2_Missense_Mutation_p.P326A|CACNB2_uc001ipz.2_Missense_Mutation_p.P303A|CACNB2_uc001ipy.2_Missense_Mutation_p.P327A|CACNB2_uc010qco.1_Missense_Mutation_p.P295A|CACNB2_uc001iqa.2_Missense_Mutation_p.P333A|NSUN6_uc001iqb.2_Intron	NM_201596	NP_963890	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2	381					axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	AATTAATCATCCAGCTCAACT	0.403													7	221	---	---	---	---	PASS
LOC441666	441666	broad.mit.edu	37	10	42833429	42833429	+	RNA	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42833429A>G	uc010qey.1	-	3		c.546T>C				NR_024380				Homo sapiens noncoding mRNA sequence.												0						TCTTCTCCTAAGTCTATTTGA	0.333													4	8	---	---	---	---	PASS
SIRT1	23411	broad.mit.edu	37	10	69651246	69651246	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69651246T>A	uc001jnd.2	+	4	929	c.876T>A	c.(874-876)GAT>GAA	p.D292E	SIRT1_uc010qis.1_5'UTR|SIRT1_uc009xpp.2_Missense_Mutation_p.D100E|SIRT1_uc001jne.2_5'UTR	NM_012238	NP_036370	Q96EB6	SIRT1_HUMAN	sirtuin 1 isoform a	292	Deacetylase sirtuin-type.				apoptosis|cell aging|cellular response to hydrogen peroxide|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|histone H3 deacetylation|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation	chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin	bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|mitogen-activated protein kinase binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|zinc ion binding				0						ATCTTCCAGATCCTCAAGCGA	0.408													136	297	---	---	---	---	PASS
SIRT1	23411	broad.mit.edu	37	10	69651247	69651247	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69651247C>T	uc001jnd.2	+	4	930	c.877C>T	c.(877-879)CCT>TCT	p.P293S	SIRT1_uc010qis.1_5'UTR|SIRT1_uc009xpp.2_Missense_Mutation_p.P101S|SIRT1_uc001jne.2_5'UTR	NM_012238	NP_036370	Q96EB6	SIRT1_HUMAN	sirtuin 1 isoform a	293	Deacetylase sirtuin-type.				apoptosis|cell aging|cellular response to hydrogen peroxide|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|histone H3 deacetylation|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation	chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin	bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|mitogen-activated protein kinase binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|zinc ion binding				0						TCTTCCAGATCCTCAAGCGAT	0.403													134	296	---	---	---	---	PASS
LIPM	340654	broad.mit.edu	37	10	90562629	90562629	+	5'UTR	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90562629A>G	uc009xtm.1	+	1					LIPM_uc009xtn.1_5'UTR	NM_001128215	NP_001121687	Q5VYY2	LIPM_HUMAN	lipase, family member M precursor						lipid catabolic process	extracellular region	hydrolase activity			central_nervous_system(1)	1						CATTGGCAGGAAAAAATAAAT	0.383													10	172	---	---	---	---	PASS
KIF20B	9585	broad.mit.edu	37	10	91518521	91518521	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91518521A>G	uc001kgs.1	+	27	4634	c.4562A>G	c.(4561-4563)GAA>GGA	p.E1521G	KIF20B_uc001kgr.1_Missense_Mutation_p.E1481G|KIF20B_uc001kgt.1_Missense_Mutation_p.E732G|KIF20B_uc009xtw.1_RNA	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	1521					cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						TGGCGAGAAGAACGAGATCAA	0.343													5	195	---	---	---	---	PASS
C10orf4	118924	broad.mit.edu	37	10	95459948	95459948	+	Intron	SNP	A	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95459948A>C	uc001kiz.1	-						C10orf4_uc001kiv.1_Intron|C10orf4_uc001kja.1_Intron|C10orf4_uc001kjb.1_5'UTR|C10orf4_uc009xuh.1_Intron	NM_145246	NP_660289	Q70Z53	F10C1_HUMAN	FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)				gttatcttaaacagccacaat	0.149													15	51	---	---	---	---	PASS
CNNM1	26507	broad.mit.edu	37	10	101151192	101151192	+	Splice_Site	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101151192A>G	uc001kpp.3	+	11	3066	c.2777_splice	c.e11-2	p.S926_splice	CNNM1_uc010qpi.1_Splice_Site_p.S947_splice|CNNM1_uc009xwf.2_Splice_Site_p.S876_splice|CNNM1_uc009xwg.2_Splice_Site_p.S326_splice	NM_020348	NP_065081	Q9NRU3	CNNM1_HUMAN	cyclin M1						ion transport	integral to membrane|plasma membrane					0		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		TGTTTTTTTCAGGTGGCCAAA	0.438													41	84	---	---	---	---	PASS
MKI67	4288	broad.mit.edu	37	10	129906122	129906122	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129906122C>T	uc001lke.2	-	13	4177	c.3982G>A	c.(3982-3984)GGC>AGC	p.G1328S	MKI67_uc001lkf.2_Missense_Mutation_p.G968S|MKI67_uc009yav.1_Missense_Mutation_p.G903S|MKI67_uc009yaw.1_Missense_Mutation_p.G478S	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	1328	16 X 122 AA approximate repeats.|3.				cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTCTTGCTGCCGGTTAAGTTC	0.502													101	108	---	---	---	---	PASS
OR5AR1	219493	broad.mit.edu	37	11	56431824	56431824	+	Silent	SNP	C	A	A	rs144241394		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56431824C>A	uc010rjm.1	+	1	663	c.663C>A	c.(661-663)ATC>ATA	p.I221I		NM_001004730	NP_001004730	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR,	221	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						ATACCTTTATCCTTGTTGCAA	0.483													57	153	---	---	---	---	PASS
LOC645332	645332	broad.mit.edu	37	11	67560717	67560717	+	Silent	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67560717G>A	uc001omt.3	-	4	380	c.357C>T	c.(355-357)AAC>AAT	p.N119N	LOC645332_uc001omu.3_Silent_p.N69N	NR_024249				SubName: Full=cDNA FLJ57700, weakly similar to Protein FAM86A;												0						TAGGGAAACAGTTTCTGGTCA	0.512													19	53	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	102988374	102988374	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102988374A>G	uc001pho.2	+	6	925	c.781A>G	c.(781-783)AGG>GGG	p.R261G	DYNC2H1_uc001phn.1_Missense_Mutation_p.R261G|DYNC2H1_uc009yxe.1_Missense_Mutation_p.R261G	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	261	Stem (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TTCATTTGGAAGGTTTGTTCA	0.284													7	654	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108115600	108115600	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108115600C>T	uc001pkb.1	+	7	1133	c.748C>T	c.(748-750)CGA>TGA	p.R250*	ATM_uc009yxr.1_Nonsense_Mutation_p.R250*	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	250			R -> Q.		cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		CTTTCGAATTCGAGTGTGTGA	0.338			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			128	309	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108127062	108127062	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108127062G>A	uc001pkb.1	+	14	2630	c.2245G>A	c.(2245-2247)GCC>ACC	p.A749T	ATM_uc009yxr.1_Missense_Mutation_p.A749T	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	749					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		ATTCCAGAAAGCCAAGGTAGG	0.348			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			108	224	---	---	---	---	PASS
EXPH5	23086	broad.mit.edu	37	11	108383643	108383643	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108383643C>A	uc001pkk.2	-	6	2702	c.2591G>T	c.(2590-2592)TGC>TTC	p.C864F	EXPH5_uc010rvy.1_Missense_Mutation_p.C676F|EXPH5_uc010rvz.1_Missense_Mutation_p.C708F|EXPH5_uc010rwa.1_Missense_Mutation_p.C788F	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	864					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)		AGTTAACTTGCATTTTGAGTA	0.383													27	625	---	---	---	---	PASS
APOC3	345	broad.mit.edu	37	11	116703621	116703621	+	3'UTR	SNP	A	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116703621A>C	uc001ppt.1	+	4						NM_000040	NP_000031	P02656	APOC3_HUMAN	apolipoprotein C-III precursor						Cdc42 protein signal transduction|cholesterol efflux|cholesterol homeostasis|chylomicron remnant clearance|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle remodeling|lipoprotein metabolic process|negative regulation of cholesterol import|negative regulation of fatty acid biosynthetic process|negative regulation of high-density lipoprotein particle clearance|negative regulation of lipoprotein lipase activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor-mediated endocytosis|negative regulation of triglyceride catabolic process|negative regulation of very-low-density lipoprotein particle clearance|negative regulation of very-low-density lipoprotein particle remodeling|phospholipid efflux|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle assembly	chylomicron|intermediate-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	high-density lipoprotein particle receptor binding|lipase inhibitor activity|phospholipid binding				0	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		CCCCAAGTCCACCTGCCTATC	0.557													10	33	---	---	---	---	PASS
SC5DL	6309	broad.mit.edu	37	11	121177308	121177308	+	Intron	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121177308G>T	uc001pxu.2	+						SC5DL_uc001pxt.2_Missense_Mutation_p.S186I|SC5DL_uc001pxv.2_Intron	NM_006918	NP_008849	O75845	SC5D_HUMAN	sterol-C5-desaturase						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	C-5 sterol desaturase activity|iron ion binding|lathosterol oxidase activity			ovary(1)	1		Breast(109;0.00328)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	OV - Ovarian serous cystadenocarcinoma(1;0.0334)	BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.144)		AAATGTCTAAGTAGCCATAAT	0.333													3	19	---	---	---	---	PASS
KDM5A	5927	broad.mit.edu	37	12	394401	394401	+	3'UTR	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:394401T>C	uc001qif.1	-	28					KDM5A_uc001qie.1_3'UTR	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						ACATGAAATATTGGCTGTTGT	0.428			T 	NUP98	AML								5	3	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	8048099	8048099	+	Silent	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8048099C>T	uc001qtp.1	+	2	87	c.7C>T	c.(7-9)CTG>TTG	p.L3L						RecName: Full=Putative homeobox protein NANOG2;																		CTCCATGGATCTGCCTATTCA	0.398													6	125	---	---	---	---	PASS
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	T	T	rs121913529		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25398284C>T	uc001rgp.1	-	2	216	c.35G>A	c.(34-36)GGT>GAT	p.G12D	KRAS_uc001rgq.1_Missense_Mutation_p.G12D|KRAS_uc001rgr.2_RNA	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	12	GTP.		G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G12D(7175)|p.G12V(4780)|p.G12C(2482)|p.G12A(1180)|p.G12S(1119)|p.G12R(691)|p.G12?(50)|p.G12F(34)|p.G12N(6)|p.G12G(6)|p.G12L(5)|p.G12I(4)|p.G12_G13insG(4)|p.G12E(3)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12fs*3(1)		large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	21052	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12D(HPAC_PANCREAS)|G12V(SW403_LARGE_INTESTINE)|G12D(HPAFII_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12V(NCIH441_LUNG)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(PK1_PANCREAS)|G12V(KP3_PANCREAS)|G12D(PANC0813_PANCREAS)|G12A(SW1116_LARGE_INTESTINE)|G12D(LS180_LARGE_INTESTINE)|G12V(NCIH727_LUNG)|G12V(PATU8988S_PANCREAS)|G12V(CAPAN2_PANCREAS)|G12D(KP4_PANCREAS)|G12D(LS513_LARGE_INTESTINE)|G12D(SNUC2A_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(COLO668_LUNG)|G12D(COLO678_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12D(PANC0203_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(SW900_LUNG)|G12V(LCLC97TM1_LUNG)|G12V(SW620_LARGE_INTESTINE)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12V(SH10TC_STOMACH)|G12V(A498_KIDNEY)|G12D(PK59_PANCREAS)|G12D(HEC1A_ENDOMETRIUM)|G12D(PANC0504_PANCREAS)|G12V(SNGM_ENDOMETRIUM)|G12A(RERFLCAD1_LUNG)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12D(ASPC1_PANCREAS)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12V(RCM1_LARGE_INTESTINE)|G12V(CORL23_LUNG)|G12D(SW1990_PANCREAS)|G12D(HEYA8_OVARY)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12V(HUPT4_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(HEC50B_ENDOMETRIUM)|G12V(YAPC_PANCREAS)|G12V(NCIH2444_LUNG)|G12V(HCC56_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12V(DANG_PANCREAS)|G12V(SHP77_LUNG)|G12D(AGS_STOMACH)|G12D(SKLU1_LUNG)|G12V(QGP1_PANCREAS)|G12D(L33_PANCREAS)|G12V(PANC0327_PANCREAS)|G12D(PANC1_PANCREAS)|G12V(RKN_OVARY)|G12V(PATU8902_PANCREAS)	119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			10	281	---	---	---	---	PASS
SLC11A2	4891	broad.mit.edu	37	12	51394164	51394164	+	Silent	SNP	A	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51394164A>T	uc001rxe.3	-	6	565	c.468T>A	c.(466-468)GCT>GCA	p.A156A	SLC11A2_uc001rxd.3_Silent_p.A5A|SLC11A2_uc001rxc.3_Silent_p.A156A|SLC11A2_uc001rxf.2_RNA|SLC11A2_uc010smx.1_Silent_p.A152A|SLC11A2_uc001rxh.1_Silent_p.A156A|SLC11A2_uc001rxj.1_Silent_p.A156A|SLC11A2_uc001rxi.2_Silent_p.A156A|SLC11A2_uc001rxk.1_Silent_p.A185A|SLC11A2_uc010smy.1_Silent_p.A119A	NM_000617	NP_000608	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled	156	Helical; (Potential).				activation of caspase activity|cellular iron ion homeostasis|cellular response to oxidative stress|detection of oxygen|ferrous iron import|multicellular organismal iron ion homeostasis|response to hypoxia|response to iron ion	apical plasma membrane|basal part of cell|cell surface|cytoplasmic vesicle|early endosome|late endosome|late endosome membrane|lysosomal membrane|lysosome|nucleus|paraferritin complex|perinuclear region of cytoplasm|perinuclear region of cytoplasm|plasma membrane|recycling endosome|trans-Golgi network	cadmium ion transmembrane transporter activity|cadmium ion transmembrane transporter activity|cobalt ion transmembrane transporter activity|copper ion transmembrane transporter activity|ferrous iron transmembrane transporter activity|ferrous iron transmembrane transporter activity|lead ion transmembrane transporter activity|lead ion transmembrane transporter activity|manganese ion transmembrane transporter activity|manganese ion transmembrane transporter activity|nickel ion transmembrane transporter activity|protein binding|solute:hydrogen symporter activity|vanadium ion transmembrane transporter activity|zinc ion transmembrane transporter activity			large_intestine(1)	1						AGCCGATGATAGCCAACTCCA	0.443													9	163	---	---	---	---	PASS
TENC1	23371	broad.mit.edu	37	12	53449821	53449821	+	Intron	SNP	G	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53449821G>C	uc001sbp.2	+						uc001sbk.1_5'Flank|TENC1_uc001sbl.2_Intron|TENC1_uc001sbm.2_3'UTR|TENC1_uc001sbn.2_Intron|TENC1_uc001sbo.1_Intron|TENC1_uc001sbq.2_5'Flank|TENC1_uc001sbr.2_5'Flank	NM_170754	NP_736610	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase						intracellular signal transduction|negative regulation of cell proliferation	focal adhesion	metal ion binding|phosphoprotein phosphatase activity|protein binding			ovary(1)|pancreas(1)	2						GTTTCCTGGGGCAGCCACAAA	0.328													5	1	---	---	---	---	PASS
BBS10	79738	broad.mit.edu	37	12	76739560	76739560	+	3'UTR	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76739560A>G	uc001syd.1	-	2						NM_024685	NP_078961	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10						cellular protein metabolic process|nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	cilium	ATP binding			ovary(1)|skin(1)	2						CTTGAGTTAGATGAAAAGTTT	0.348									Bardet-Biedl_syndrome				76	196	---	---	---	---	PASS
TMTC2	160335	broad.mit.edu	37	12	83424647	83424647	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83424647A>G	uc001szt.2	+	9	2573	c.2141A>G	c.(2140-2142)TAC>TGC	p.Y714C	TMTC2_uc010suk.1_Missense_Mutation_p.Y469C	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat	714	TPR 8.					endoplasmic reticulum|integral to membrane	binding			ovary(2)	2						GGAAACTGTTACATGCATTAT	0.393													6	493	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88496844	88496844	+	Intron	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88496844C>T	uc001tar.2	-						CEP290_uc001taq.2_Translation_Start_Site|CEP290_uc001tat.2_Intron	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						TGGTCAAGCACTAGCCACTTT	0.299													9	21	---	---	---	---	PASS
ACAD10	80724	broad.mit.edu	37	12	112147524	112147524	+	Intron	SNP	A	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112147524A>C	uc001tsq.2	+						ACAD10_uc009zvw.2_3'UTR|ACAD10_uc001tso.3_Intron|ACAD10_uc001tsp.2_Intron|ACAD10_uc009zvx.2_Intron|ACAD10_uc001tsr.2_5'Flank	NM_025247	NP_079523	Q6JQN1	ACD10_HUMAN	acyl-Coenzyme A dehydrogenase family, member 10								acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2						CCTCCCATGCACCAGCCACTA	0.388													5	39	---	---	---	---	PASS
DKFZp686A1627	266695	broad.mit.edu	37	13	19625310	19625310	+	RNA	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19625310G>A	uc001umb.1	-	8		c.3213C>T				NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0						CCTTGAGCACGTGGTACCAGG	0.607													5	13	---	---	---	---	PASS
FRY	10129	broad.mit.edu	37	13	32711103	32711103	+	Silent	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32711103C>T	uc001utx.2	+	11	1669	c.1173C>T	c.(1171-1173)AAC>AAT	p.N391N	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	391					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GCTTGTCCAACCTTAAAGTTA	0.438													4	199	---	---	---	---	PASS
NDFIP2	54602	broad.mit.edu	37	13	80122465	80122465	+	Silent	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80122465T>C	uc001vlf.2	+	6	923	c.843T>C	c.(841-843)TTT>TTC	p.F281F	NDFIP2_uc010tib.1_Silent_p.F261F|NDFIP2_uc001vlg.2_Intron	NM_019080	NP_061953	Q9NV92	NFIP2_HUMAN	Nedd4 family interacting protein 2 isoform 1	281	Cytoplasmic (Potential).				negative regulation of gene expression|negative regulation of protein transport|negative regulation of transporter activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of protein ubiquitination	endoplasmic reticulum|Golgi membrane|integral to membrane|mitochondrion|multivesicular body membrane|perinuclear region of cytoplasm	signal transducer activity|WW domain binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0196)		CTCCATAGTTTTCTGATTATT	0.269													7	836	---	---	---	---	PASS
PCCA	5095	broad.mit.edu	37	13	100982868	100982868	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100982868G>T	uc001voo.2	+	17	1521	c.1483G>T	c.(1483-1485)GTA>TTA	p.V495L	PCCA_uc010aga.2_Missense_Mutation_p.V469L|PCCA_uc010tiz.1_Missense_Mutation_p.V495L|PCCA_uc001vop.2_RNA	NM_000282	NP_000273	P05165	PCCA_HUMAN	propionyl-Coenzyme A carboxylase, alpha	495	Biotin carboxylation.				fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	CTCACGCTTTGTAAAAGGAGA	0.308													5	464	---	---	---	---	PASS
RPGRIP1	57096	broad.mit.edu	37	14	21789516	21789516	+	Silent	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21789516C>T	uc001wag.2	+	12	1566	c.1566C>T	c.(1564-1566)ACC>ACT	p.T522T	RPGRIP1_uc001wah.2_Silent_p.T164T|RPGRIP1_uc001wai.2_Silent_p.T164T|RPGRIP1_uc001waj.1_5'UTR|RPGRIP1_uc001wak.2_5'UTR|RPGRIP1_uc010aim.2_5'Flank|RPGRIP1_uc001wal.2_5'Flank|RPGRIP1_uc001wam.2_5'Flank	NM_020366	NP_065099	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator	522	Potential.				response to stimulus|visual perception	cilium				ovary(4)|breast(2)|pancreas(1)	7	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		TAGAAAAGACCAGGGACATGC	0.458													12	346	---	---	---	---	PASS
GMFB	2764	broad.mit.edu	37	14	54948128	54948128	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54948128G>A	uc010tqz.1	-	4	298	c.199C>T	c.(199-201)CGC>TGC	p.R67C	GMFB_uc001xaw.1_RNA	NM_004124	NP_004115	P60983	GMFB_HUMAN	glia maturation factor, beta	67	ADF-H.				nervous system development|protein phosphorylation	intracellular	actin binding|enzyme activator activity|growth factor activity|protein kinase inhibitor activity|signal transducer activity				0						AAAGGATATCGAGGTTGTCGT	0.363													131	331	---	---	---	---	PASS
PRKCH	5583	broad.mit.edu	37	14	61997229	61997229	+	Silent	SNP	A	G	G	rs150403406		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61997229A>G	uc001xfn.2	+	12	1982	c.1677A>G	c.(1675-1677)GAA>GAG	p.E559E	PRKCH_uc010tsa.1_Silent_p.E398E|PRKCH_uc010tsb.1_Silent_p.E127E	NM_006255	NP_006246	P24723	KPCL_HUMAN	protein kinase C, eta	559	Protein kinase.				intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		CAGAGAACGAAGATGACCTCT	0.517													5	163	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64682878	64682878	+	Intron	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64682878T>C	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc001xgn.2_Intron|SYNE2_uc001xgo.2_Intron|SYNE2_uc010aqa.2_Intron|SYNE2_uc001xgq.2_Intron|SYNE2_uc001xgr.2_Intron|SYNE2_uc010tsi.1_Intron|SYNE2_uc001xgs.2_Intron|SYNE2_uc001xgt.2_5'UTR	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GCTGCAGAACTCATTTTCATA	0.448													4	63	---	---	---	---	PASS
ADAM21P1	145241	broad.mit.edu	37	14	70714061	70714061	+	5'UTR	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70714061G>A	uc010ttg.1	-	1						NR_003951				SubName: Full=ADAM21-like protein;												0						ACAGTCATCTGGGATGAAGAG	0.473													35	123	---	---	---	---	PASS
ADAM21	8747	broad.mit.edu	37	14	70924533	70924533	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70924533C>T	uc001xmd.2	+	1	317	c.317C>T	c.(316-318)CCA>CTA	p.P106L		NM_003813	NP_003804	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21 preproprotein	106					proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding			pancreas(1)|skin(1)	2				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		CTCTTCATCCCAGATGACTGT	0.473													5	90	---	---	---	---	PASS
KCNK10	54207	broad.mit.edu	37	14	88658594	88658594	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88658594G>A	uc001xwo.2	-	5	1284	c.827C>T	c.(826-828)ACG>ATG	p.T276M	KCNK10_uc001xwm.2_Missense_Mutation_p.T281M|KCNK10_uc001xwn.2_Missense_Mutation_p.T281M	NM_021161	NP_066984	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	276					signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|skin(2)|pancreas(1)	5						AAAGCCCACCGTGGTCAGAGT	0.537													43	60	---	---	---	---	PASS
SMEK1	55671	broad.mit.edu	37	14	91942053	91942053	+	Intron	SNP	C	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91942053C>A	uc001xzn.2	-						SMEK1_uc001xzm.2_Intron|SMEK1_uc001xzo.2_Intron|SMEK1_uc010atz.2_Intron|SMEK1_uc001xzp.1_Intron|SMEK1_uc001xzq.1_Silent_p.V332V	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1							microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		ATTATGGCTACACTTTTCCCA	0.284													8	32	---	---	---	---	PASS
CLMN	79789	broad.mit.edu	37	14	95688029	95688029	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95688029T>C	uc001yef.2	-	4	439	c.323A>G	c.(322-324)AAT>AGT	p.N108S		NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin	108	Actin-binding.|CH 1.					integral to membrane	actin binding				0				Epithelial(152;0.193)		AACACTTACATTGCTATCTTC	0.423													60	125	---	---	---	---	PASS
SETD3	84193	broad.mit.edu	37	14	99876467	99876467	+	Intron	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99876467A>G	uc001ygc.2	-						SETD3_uc001ygd.2_3'UTR	NM_032233	NP_115609	Q86TU7	SETD3_HUMAN	SET domain containing 3 isoform a						peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|peptidyl-lysine trimethylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone methyltransferase activity (H3-K36 specific)|transcription coactivator activity				0		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				acgctggaggaggtctatgag	0.000													4	71	---	---	---	---	PASS
WDR25	79446	broad.mit.edu	37	14	100934461	100934461	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100934461G>A	uc010avx.2	+	3	1019	c.926G>A	c.(925-927)AGT>AAT	p.S309N	WDR25_uc001yhm.2_Missense_Mutation_p.S301N|WDR25_uc001yhn.2_Missense_Mutation_p.S309N|WDR25_uc010avy.2_Intron|WDR25_uc001yho.2_Missense_Mutation_p.S52N	NM_001161476	NP_001154948	Q64LD2	WDR25_HUMAN	WD repeat domain 25	309	WD 2.										0		Melanoma(154;0.212)				CGCATCCTCAGTGGTGGCTTT	0.642													26	56	---	---	---	---	PASS
PLDN	26258	broad.mit.edu	37	15	45879557	45879557	+	5'UTR	SNP	G	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45879557G>C	uc001zvq.2	+	1					PLDN_uc001zvr.2_RNA|PLDN_uc001zvs.2_5'Flank	NM_012388	NP_036520	Q9UL45	PLDN_HUMAN	pallidin						post-Golgi vesicle-mediated transport|synaptic vesicle docking involved in exocytosis	BLOC-1 complex|endomembrane system|membrane	identical protein binding|syntaxin-13 binding			skin(1)	1		Lung NSC(122;1.6e-06)|all_lung(180;1.13e-05)|Melanoma(134;0.027)		all cancers(107;6.58e-18)|GBM - Glioblastoma multiforme(94;5.91e-07)		TCTTCTGTCCGGCCAGCCGCT	0.622													5	12	---	---	---	---	PASS
LACTB	114294	broad.mit.edu	37	15	63421946	63421946	+	Intron	SNP	A	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63421946A>C	uc002alw.2	+						LACTB_uc002alv.2_3'UTR	NM_032857	NP_116246	P83111	LACTB_HUMAN	lactamase, beta isoform a							mitochondrion	hydrolase activity				0						TCCAAAATCAACCTGCCACAT	0.323													8	6	---	---	---	---	PASS
TLE3	7090	broad.mit.edu	37	15	70351055	70351055	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70351055A>T	uc002asm.2	-	11	1984	c.865T>A	c.(865-867)TCG>ACG	p.S289T	TLE3_uc002ask.2_Missense_Mutation_p.S233T|TLE3_uc002asl.2_Missense_Mutation_p.S294T|TLE3_uc010ukd.1_Missense_Mutation_p.S282T|TLE3_uc010bik.1_Intron|TLE3_uc010bil.1_Missense_Mutation_p.S289T|TLE3_uc002asn.2_Missense_Mutation_p.S289T|TLE3_uc002asp.2_Missense_Mutation_p.S289T|TLE3_uc002aso.2_Missense_Mutation_p.S289T	NM_005078	NP_005069	Q04726	TLE3_HUMAN	transducin-like enhancer protein 3 isoform a	289	Pro/Ser-rich.				organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding			lung(2)	2						GAGGCCACCGAGGCAGGGCTG	0.632													18	40	---	---	---	---	PASS
ZNF213	7760	broad.mit.edu	37	16	3188358	3188358	+	Intron	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3188358G>A	uc010uws.1	+						ZNF213_uc002cud.2_RNA|ZNF213_uc010btf.2_3'UTR|ZNF213_uc010bth.2_Intron|ZNF213_uc010uwt.1_Intron	NM_004220	NP_004211	O14771	ZN213_HUMAN	zinc finger protein 213						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TTCCCAGGGAGTAAACTCTGT	0.597													4	4	---	---	---	---	PASS
ABCC6P1	653190	broad.mit.edu	37	16	18586426	18586426	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18586426C>T	uc002dfg.2	+	4	453	c.253C>T	c.(253-255)CTC>TTC	p.L85F	ABCC6P1_uc010vam.1_Missense_Mutation_p.L28F	NR_003569				SubName: Full=cDNA FLJ51267, highly similar to Multidrug resistance-associated protein 6;												0						TTACTGGCTTCTCTGCTTTGT	0.572													4	68	---	---	---	---	PASS
DNAH3	55567	broad.mit.edu	37	16	21136611	21136611	+	Nonsense_Mutation	SNP	G	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21136611G>C	uc010vbe.1	-	9	1289	c.1289C>G	c.(1288-1290)TCA>TGA	p.S430*	DNAH3_uc002die.2_Nonsense_Mutation_p.S401*	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	430	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		GTTTCGACTTGAGTCATAGTT	0.483													51	110	---	---	---	---	PASS
PKD1L3	342372	broad.mit.edu	37	16	71967417	71967417	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71967417A>G	uc010vmm.1	-	29	4832	c.4832T>C	c.(4831-4833)CTG>CCG	p.L1611P		NM_181536	NP_853514			polycystin 1-like 3 precursor												0						TCCAAACAGCAGGTTAAACTG	0.483													49	123	---	---	---	---	PASS
ZNF778	197320	broad.mit.edu	37	16	89288521	89288521	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89288521C>T	uc002fmv.2	+	3	386	c.47C>T	c.(46-48)TCA>TTA	p.S16L	ZNF778_uc010vpf.1_RNA|ZNF778_uc002fmw.1_Intron|ZNF778_uc010vpg.1_5'UTR	NM_182531	NP_872337	Q96MU6	ZN778_HUMAN	zinc finger protein 778	16					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0269)		TCTAGGGACTCAGTCTGCCTT	0.453													13	330	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10429940	10429940	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10429940C>T	uc010coi.2	-	30	4291	c.4163G>A	c.(4162-4164)CGC>CAC	p.R1388H	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.R1388H|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1388	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle	p.R1388H(1)		ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						CTCCTCTGTGCGCTGGATGGC	0.512													66	124	---	---	---	---	PASS
ALDH3A1	218	broad.mit.edu	37	17	19641666	19641666	+	Silent	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19641666C>T	uc010cqu.2	-	9	1647	c.1317G>A	c.(1315-1317)CTG>CTA	p.L439L	ALDH3A1_uc010vzd.1_Silent_p.L439L|ALDH3A1_uc002gwj.2_Silent_p.L439L|ALDH3A1_uc010cqv.2_Silent_p.L438L|ALDH3A1_uc002gwk.2_Silent_p.L556L|ALDH3A1_uc002gwl.1_Silent_p.L366L	NM_001135168	NP_001128640	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3A1	439					cellular aldehyde metabolic process	cytosol|endoplasmic reticulum	alcohol dehydrogenase (NADP+) activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(1)|pancreas(1)	2	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)	NADH(DB00157)	ATCTGACCTTCAGGCCTTCAT	0.632													3	27	---	---	---	---	PASS
ERAL1	26284	broad.mit.edu	37	17	27182269	27182269	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27182269T>C	uc002hcy.1	+	1	227	c.217T>C	c.(217-219)TTC>CTC	p.F73L	ERAL1_uc002hcx.1_Missense_Mutation_p.F73L|ERAL1_uc002hcz.1_RNA|ERAL1_uc002hda.1_5'Flank|ERAL1_uc002hdb.1_5'Flank	NM_005702	NP_005693	O75616	ERAL1_HUMAN	Era-like 1	73					ribosomal small subunit assembly	mitochondrial inner membrane|mitochondrial matrix	GTP binding|ribosomal small subunit binding|rRNA binding			skin(1)	1	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.12e-05)|all cancers(11;5.32e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.105)			CCTGGACCACTTCCTCGGATT	0.627													3	19	---	---	---	---	PASS
C17orf75	64149	broad.mit.edu	37	17	30660439	30660439	+	Silent	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30660439T>C	uc002hhg.2	-	9	1003	c.972A>G	c.(970-972)CTA>CTG	p.L324L		NM_022344	NP_071739	Q9HAS0	NJMU_HUMAN	hypothetical protein LOC64149	324					spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			TAATTACCTTTAGTTTAAAGT	0.373													106	193	---	---	---	---	PASS
UNC45B	146862	broad.mit.edu	37	17	33477188	33477188	+	Silent	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33477188G>A	uc002hja.2	+	4	424	c.327G>A	c.(325-327)CGG>CGA	p.R109R	UNC45B_uc002hjb.2_Silent_p.R109R|UNC45B_uc002hjc.2_Silent_p.R109R|UNC45B_uc010cto.2_Silent_p.R109R	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	109	TPR 3.				cell differentiation|muscle organ development	cytosol	binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)				TCGAGCCACGGAACCAGAACT	0.602													21	41	---	---	---	---	PASS
TLK2	11011	broad.mit.edu	37	17	60598172	60598172	+	Silent	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60598172C>T	uc010ddp.2	+	3	388	c.120C>T	c.(118-120)TGC>TGT	p.C40C	TLK2_uc002izx.3_5'UTR|TLK2_uc002izz.3_Silent_p.C40C|TLK2_uc002jaa.3_Silent_p.C40C|TLK2_uc010wpd.1_Silent_p.C40C	NM_006852	NP_006843	Q86UE8	TLK2_HUMAN	tousled-like kinase 2 isoform A	40					cell cycle|chromatin modification|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|kidney(1)	2						AGAGCTTGTGCAGCGTCGGAT	0.323													5	194	---	---	---	---	PASS
TLK2	11011	broad.mit.edu	37	17	60598179	60598179	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60598179G>A	uc010ddp.2	+	3	395	c.127G>A	c.(127-129)GGA>AGA	p.G43R	TLK2_uc002izx.3_5'UTR|TLK2_uc002izz.3_Missense_Mutation_p.G43R|TLK2_uc002jaa.3_Missense_Mutation_p.G43R|TLK2_uc010wpd.1_Missense_Mutation_p.G43R	NM_006852	NP_006843	Q86UE8	TLK2_HUMAN	tousled-like kinase 2 isoform A	43					cell cycle|chromatin modification|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|kidney(1)	2						GTGCAGCGTCGGATCCTTGAG	0.308													4	209	---	---	---	---	PASS
HELZ	9931	broad.mit.edu	37	17	65144746	65144746	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65144746C>T	uc010wqk.1	-	20	2750	c.2563G>A	c.(2563-2565)GCT>ACT	p.A855T	HELZ_uc002jfv.3_RNA|HELZ_uc002jfx.3_Missense_Mutation_p.A854T	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					GGGAACTCAGCAGGGTAATGC	0.473													4	136	---	---	---	---	PASS
DNAH17	8632	broad.mit.edu	37	17	76421493	76421493	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76421493T>C	uc010dhp.1	-	25	4297	c.4075A>G	c.(4075-4077)AAA>GAA	p.K1359E	DNAH17_uc002jvq.2_Missense_Mutation_p.K644E|DNAH17_uc002jvs.2_RNA					SubName: Full=DNAH17 variant protein; Flags: Fragment;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TCTCGGTTTTTCTTGGTCACC	0.567													11	61	---	---	---	---	PASS
CIRBP	1153	broad.mit.edu	37	19	1271824	1271824	+	Intron	SNP	T	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1271824T>G	uc002lrr.3	+						C19orf23_uc010xgk.1_5'Flank|CIRBP_uc010dsg.1_3'UTR|CIRBP_uc002lrt.2_Intron|CIRBP_uc010xgl.1_Intron|CIRBP_uc002lrv.3_Intron|CIRBP_uc002lru.2_Intron	NM_001280	NP_001271	Q14011	CIRBP_HUMAN	cold inducible RNA binding protein						mRNA stabilization|positive regulation of translation|response to cold|response to UV|stress granule assembly	nucleoplasm|stress granule	mRNA 3'-UTR binding|nucleotide binding|protein binding|SSU rRNA binding|translation repressor activity				0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GACAGGCTGGTGGAGATTTTG	0.627													8	13	---	---	---	---	PASS
PLIN4	729359	broad.mit.edu	37	19	4510945	4510945	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4510945T>A	uc002mar.1	-	3	2985	c.2985A>T	c.(2983-2985)AAA>AAT	p.K995N	PLIN4_uc010dub.1_Missense_Mutation_p.K19N	NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN	plasma membrane associated protein, S3-12	995						lipid particle|plasma membrane					0						GGACGGCCCCTTTGGCCATGC	0.627													18	41	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9000513	9000513	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9000513G>C	uc002mkp.2	-	54	40675	c.40471C>G	c.(40471-40473)CGG>GGG	p.R13491G	MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Missense_Mutation_p.R308G|MUC16_uc010xki.1_RNA	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TCCTCATACCGCAGGTTAGTG	0.473													144	392	---	---	---	---	PASS
UQCRFS1	7386	broad.mit.edu	37	19	29699033	29699033	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29699033T>C	uc002nsd.2	-	2	358	c.247A>G	c.(247-249)ATC>GTC	p.I83V		NM_006003	NP_005994	P47985	UCRI_HUMAN	ubiquinol-cytochrome c reductase, Rieske	83					respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain complex III	2 iron, 2 sulfur cluster binding|metal ion binding|ubiquinol-cytochrome-c reductase activity				0	Breast(6;0.0545)|Esophageal squamous(110;0.239)		Lung(7;0.092)			GGCACCTTGATGTCTGTGTGG	0.423													8	49	---	---	---	---	PASS
SUPT5H	6829	broad.mit.edu	37	19	39965287	39965287	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39965287C>T	uc002olo.3	+	28	3132	c.2953C>T	c.(2953-2955)CAG>TAG	p.Q985*	SUPT5H_uc002olp.3_Nonsense_Mutation_p.Q985*|SUPT5H_uc002olq.3_Nonsense_Mutation_p.Q981*|SUPT5H_uc002oln.3_Nonsense_Mutation_p.Q985*|SUPT5H_uc002olr.3_Nonsense_Mutation_p.Q985*|SUPT5H_uc002ols.1_Nonsense_Mutation_p.Q608*	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	985					cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CACTGACATTCAGGTGAAGGT	0.612													10	35	---	---	---	---	PASS
ZNF227	7770	broad.mit.edu	37	19	44732560	44732560	+	Intron	SNP	T	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44732560T>A	uc002oyu.2	+						ZNF227_uc010xwu.1_Intron|ZNF227_uc002oyv.2_Intron|ZNF227_uc010xwv.1_Intron|ZNF227_uc010xww.1_Intron|ZNF227_uc002oyw.2_Intron|ZNF227_uc010ejh.2_Intron|ZNF235_uc002oyx.1_RNA	NM_182490	NP_872296	Q86WZ6	ZN227_HUMAN	zinc finger protein 227						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0435)				TAGTGAAGGTTGGTTGTAAGA	0.433													15	297	---	---	---	---	PASS
ZNF845	91664	broad.mit.edu	37	19	53856702	53856702	+	Missense_Mutation	SNP	G	A	A	rs150688663	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53856702G>A	uc010ydv.1	+	4	2891	c.2774G>A	c.(2773-2775)CGT>CAT	p.R925H	ZNF845_uc010ydw.1_Missense_Mutation_p.R925H	NM_138374	NP_612383	Q96IR2	ZN845_HUMAN	zinc finger protein 845	925	C2H2-type 26.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AAAACCTTCCGTCACAATTCA	0.363													5	75	---	---	---	---	PASS
ZNF845	91664	broad.mit.edu	37	19	53856730	53856730	+	Silent	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53856730G>A	uc010ydv.1	+	4	2919	c.2802G>A	c.(2800-2802)AAG>AAA	p.K934K	ZNF845_uc010ydw.1_Silent_p.K934K	NM_138374	NP_612383	Q96IR2	ZN845_HUMAN	zinc finger protein 845	934	C2H2-type 26.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TAATTCATAAGACAATTCATA	0.368													5	82	---	---	---	---	PASS
SIRPB1	10326	broad.mit.edu	37	20	1552666	1552666	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1552666C>T	uc010gai.2	-	3	550	c.451G>A	c.(451-453)GTG>ATG	p.V151M	SIRPB1_uc002wfk.3_Intron	NM_006065	NP_006056	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1 isoform 1	151	Ig-like C1-type 1.|Extracellular (Potential).				cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding			ovary(1)	1						CCCGATACCACGGGGGCAGAG	0.478													61	120	---	---	---	---	PASS
RRBP1	6238	broad.mit.edu	37	20	17640580	17640580	+	Silent	SNP	T	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17640580T>G	uc010zrq.1	-	3	927	c.573A>C	c.(571-573)ACA>ACC	p.T191T	RRBP1_uc002wpu.2_5'Flank|RRBP1_uc002wpv.1_Intron|RRBP1_uc002wpw.1_Intron|RRBP1_uc010gcl.1_Intron|RRBP1_uc010zrr.1_Silent_p.T191T			Q9P2E9	RRBP1_HUMAN	SubName: Full=RRBP1 protein; Flags: Fragment;	191	Cytoplasmic (Potential).				protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1						CAGTGGCTGGTGTGTTGCCCT	0.572													9	20	---	---	---	---	PASS
NAPB	63908	broad.mit.edu	37	20	23361900	23361900	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23361900A>G	uc002wta.2	-	8	733	c.616T>C	c.(616-618)TTC>CTC	p.F206L	NAPB_uc002wtc.2_Missense_Mutation_p.F112L|NAPB_uc002wtb.2_Missense_Mutation_p.F210L|NAPB_uc002wtd.3_RNA|NAPB_uc010zss.1_Missense_Mutation_p.F93L|NAPB_uc010zst.1_Missense_Mutation_p.F167L	NM_022080	NP_071363	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment	206					intracellular protein transport|vesicle-mediated transport	membrane				ovary(1)	1	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					GCTTTGAAGAAGTAATCCTTT	0.398													5	204	---	---	---	---	PASS
TOP1	7150	broad.mit.edu	37	20	39741521	39741521	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39741521A>G	uc002xjl.2	+	14	1654	c.1408A>G	c.(1408-1410)ATG>GTG	p.M470V	uc002xjn.1_Intron	NM_003286	NP_003277	P11387	TOP1_HUMAN	DNA topoisomerase I	470					DNA topological change|interspecies interaction between organisms|phosphorylation|programmed cell death|response to drug	chromosome|nucleolus|nucleoplasm	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity|protein binding			breast(3)|ovary(2)|central_nervous_system(1)|kidney(1)	7		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Topotecan(DB01030)	GTCCAAAGAGATGAAAGTCCG	0.498			T	NUP98	AML*								57	105	---	---	---	---	PASS
CTSA	5476	broad.mit.edu	37	20	44521907	44521907	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44521907T>C	uc002xqj.3	+	7	1123	c.649T>C	c.(649-651)TCC>CCC	p.S217P	NEURL2_uc002xqg.1_5'Flank|CTSA_uc002xqh.2_Missense_Mutation_p.S235P|CTSA_uc002xqi.2_RNA|CTSA_uc010zxi.1_Missense_Mutation_p.S218P|CTSA_uc002xqk.3_Missense_Mutation_p.S217P	NM_001127695	NP_001121167	P10619	PPGB_HUMAN	cathepsin A isoform b precursor	217					intracellular protein transport|proteolysis	endoplasmic reticulum|lysosome|nucleus	enzyme activator activity|protein binding|serine-type carboxypeptidase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				GAATGACAACTCCCTGGTCTA	0.557													45	130	---	---	---	---	PASS
PMEPA1	56937	broad.mit.edu	37	20	56227136	56227136	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56227136C>G	uc002xyq.2	-	4	1230	c.837G>C	c.(835-837)AAG>AAC	p.K279N	PMEPA1_uc002xyr.2_Missense_Mutation_p.K229N|PMEPA1_uc002xys.2_Missense_Mutation_p.K244N|PMEPA1_uc002xyt.2_Missense_Mutation_p.K229N	NM_020182	NP_064567	Q969W9	PMEPA_HUMAN	transmembrane prostate androgen-induced protein	279	Cytoplasmic (Potential).				androgen receptor signaling pathway	integral to membrane|plasma membrane	WW domain binding			pancreas(1)	1						TCTGTTTATCCTTCTCTTTGC	0.622													17	44	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47981523	47981523	+	Intron	SNP	T	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47981523T>G	uc002zjo.2	+						DIP2A_uc011afz.1_Intron|DIP2A_uc002zjs.2_5'UTR|DIP2A_uc002zjt.2_5'Flank	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a						multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TCATGGCAGGTGTGCTGTGGA	0.557													13	23	---	---	---	---	PASS
PRAME	23532	broad.mit.edu	37	22	22893221	22893221	+	Silent	SNP	A	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22893221A>C	uc002zwf.2	-	3	468	c.312T>G	c.(310-312)CTT>CTG	p.L104L	LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_Silent_p.L88L|PRAME_uc010gtr.2_Silent_p.L104L|PRAME_uc002zwg.2_Silent_p.L104L|PRAME_uc002zwh.2_Silent_p.L104L|PRAME_uc002zwi.2_Silent_p.L104L|PRAME_uc002zwj.2_Silent_p.L104L|PRAME_uc002zwk.2_Silent_p.L104L	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	104					apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|regulation of growth|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		GGAGCACATCAAGTCCATCAA	0.597													16	34	---	---	---	---	PASS
DEPDC5	9681	broad.mit.edu	37	22	32150850	32150850	+	5'UTR	SNP	A	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32150850A>G	uc003als.2	+	2					DEPDC5_uc011als.1_5'UTR|DEPDC5_uc011alu.1_5'UTR|DEPDC5_uc011alv.1_RNA|DEPDC5_uc003alt.2_5'Flank|DEPDC5_uc003alr.1_5'UTR|DEPDC5_uc011alt.1_5'UTR	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8						TGTGGCAGGGAGGCAAGATGA	0.443											OREG0003494	type=REGULATORY REGION|Gene=DEPDC5|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	20	234	---	---	---	---	PASS
RBX1	9978	broad.mit.edu	37	22	41368620	41368620	+	3'UTR	SNP	G	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41368620G>T	uc003azk.2	+	5						NM_014248	NP_055063	P62877	RBX1_HUMAN	ring-box 1						DNA repair|interspecies interaction between organisms|protein neddylation|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	Cul3-RING ubiquitin ligase complex|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytosol|nucleus|SCF ubiquitin ligase complex	NEDD8 ligase activity|protein binding|zinc ion binding			skin(1)	1						TGCTGTTTCTGTAGCCATATT	0.348													17	199	---	---	---	---	PASS
EFCAB6	64800	broad.mit.edu	37	22	44079660	44079660	+	Silent	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44079660C>T	uc003bdy.1	-	12	1433	c.1218G>A	c.(1216-1218)GCG>GCA	p.A406A	EFCAB6_uc003bdz.1_Silent_p.A254A|EFCAB6_uc010gzi.1_Silent_p.A254A|EFCAB6_uc010gzk.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Silent_p.A403A	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	406	EF-hand 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				TCTTCAGTGACGCAGAGTGAT	0.358													6	735	---	---	---	---	PASS
NXF3	56000	broad.mit.edu	37	X	102334162	102334162	+	Silent	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102334162C>T	uc004eju.2	-	16	1436	c.1365G>A	c.(1363-1365)GGG>GGA	p.G455G	NXF3_uc010noi.1_Silent_p.G305G	NM_022052	NP_071335	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	455	NTF2.					cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3						CCTTGAACACCCCGTTGACAG	0.582													4	166	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13195	13195	+	RNA	SNP	T	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13195T>C	uc004cox.3	+	1		c.859T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		TCACCACTCTGTTCGCAGCAG	0.443													5	139	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13268	13268	+	RNA	SNP	G	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13268G>A	uc004cox.3	+	1		c.932G>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		AAGTCAACTAGGACTCATAAT	0.458													49	122	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15035	15035	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15035C>T	uc004coy.2	+	1	275	c.200C>T	c.(199-201)ACA>ATA	p.T67I	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		GCCTCTTCCTACACATCGGGC	0.458													17	125	---	---	---	---	PASS
DFFB	1677	broad.mit.edu	37	1	3800477	3800477	+	3'UTR	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3800477delG	uc001alc.2	+	7					DFFB_uc001ale.2_RNA|DFFB_uc009vlp.2_RNA|DFFB_uc001alb.2_RNA|DFFB_uc010nzn.1_3'UTR|DFFB_uc009vlq.2_RNA|DFFB_uc009vlr.2_3'UTR|DFFB_uc001ald.2_3'UTR	NM_004402	NP_004393	O76075	DFFB_HUMAN	DNA fragmentation factor, 40 kD, beta						apoptotic chromosome condensation|DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction	cytosol|nucleoplasm	deoxyribonuclease activity|enzyme binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		CTGAATTGTTGGGGttttttt	0.169													4	2	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	6997450	6997452	+	Intron	DEL	ACT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6997450_6997452delACT	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		acttaccaccactatcatcacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	14332306	14332307	+	IGR	DEL	CC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14332306_14332307delCC								PRDM2 (180734 upstream) : KAZ (592906 downstream)																							ACTTAAAGTTCCAGGTGTTGTT	0.455													4	2	---	---	---	---	
AHDC1	27245	broad.mit.edu	37	1	27888206	27888207	+	Intron	INS	-	AG	AG			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27888206_27888207insAG	uc009vsy.2	-						AHDC1_uc009vsz.1_Intron|AHDC1_uc001boh.1_Intron	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1								DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		gaggaaaagacagagagagaga	0.233													4	2	---	---	---	---	
CYP4A22	284541	broad.mit.edu	37	1	47609382	47609382	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47609382delC	uc001cqv.1	+						CYP4A22_uc009vyo.2_Intron|CYP4A22_uc009vyp.2_Intron	NM_001010969	NP_001010969	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A,							endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding			skin(2)|ovary(1)|breast(1)	4						CATTCTACTTCCGGGTAATGG	0.517													31	26	---	---	---	---	
C1orf87	127795	broad.mit.edu	37	1	60506428	60506428	+	Intron	DEL	T	-	-	rs71582611		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60506428delT	uc001czs.1	-							NM_152377	NP_689590	Q8N0U7	CA087_HUMAN	hypothetical protein LOC127795								calcium ion binding			ovary(1)|breast(1)	2						CTGTCTTTAATTTTttttttt	0.199													3	3	---	---	---	---	
NEXN	91624	broad.mit.edu	37	1	78395422	78395422	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78395422delG	uc001dic.3	+						NEXN_uc001dia.3_Intron|NEXN_uc009wcb.1_Intron|NEXN_uc001dib.3_Intron|NEXN_uc001did.1_Intron|NEXN_uc001dif.1_Intron	NM_144573	NP_653174	Q0ZGT2	NEXN_HUMAN	nexilin (F actin binding protein)						regulation of cell migration|regulation of cytoskeleton organization	cytoskeleton|Z disc	actin filament binding|structural constituent of muscle			ovary(2)	2				Colorectal(170;0.114)		CACAAAGGATGGAATATTATC	0.348													4	2	---	---	---	---	
AMY1A	276	broad.mit.edu	37	1	104202831	104202832	+	Intron	INS	-	TA	TA			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104202831_104202832insTA	uc001duu.2	+						AMY1A_uc001duv.2_Intron	NM_001008221	NP_001008222	P04745	AMY1_HUMAN	salivary amylase alpha 1A precursor						carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding|protein binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)		gtgtgtgtgtgtATATATATAT	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	104935552	104935552	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104935552delT								AMY1A (728380 upstream) : None (None downstream)																							tcacatcaggttttttttttg	0.000													4	2	---	---	---	---	
OVGP1	5016	broad.mit.edu	37	1	111970551	111970552	+	5'Flank	INS	-	CC	CC			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111970551_111970552insCC	uc001eba.2	-						OVGP1_uc001eaz.2_5'Flank|OVGP1_uc010owb.1_5'Flank|OVGP1_uc010owc.1_5'Flank	NM_002557	NP_002548	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1 precursor						chitin catabolic process|female pregnancy|single fertilization	transport vesicle	cation binding|chitinase activity			ovary(4)|large_intestine(1)	5		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		TCCCTCTCCAACAAAGCAACAG	0.436													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	113822450	113822450	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113822450delT								LRIG2 (155108 upstream) : MAGI3 (111025 downstream)																							AAAAGTTACCTTTTTTTTTCC	0.383													3	3	---	---	---	---	
PTPN22	26191	broad.mit.edu	37	1	114374189	114374189	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114374189delA	uc001eds.2	-						PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron	NM_015967	NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TATCTATTGCAAAAAAAAAAT	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116100866	116100866	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116100866delC								NGF (220009 upstream) : VANGL1 (83708 downstream)																							GTGTTCAAGGCCCCACGCTAG	0.373													4	2	---	---	---	---	
SPAG17	200162	broad.mit.edu	37	1	118584465	118584465	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118584465delT	uc001ehk.2	-	21	3083	c.3015delA	c.(3013-3015)GAAfs	p.E1005fs		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1005						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GGGGGGACTCTTCTGTTACTT	0.383													959	430	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120560007	120560008	+	Intron	INS	-	A	A	rs138352700	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120560007_120560008insA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		cctctgttcttataaccctgag	0.035			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142608175	142608176	+	IGR	DEL	TG	-	-	rs141317539		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142608175_142608176delTG								None (None upstream) : None (None downstream)																							tgacaaaaactgcatgattatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142802411	142802412	+	Intron	INS	-	AAC	AAC			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142802411_142802412insAAC	uc001eiw.1	+						uc001ejc.2_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																		TTAGCCAGAGTAACACACTGAT	0.455													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142804582	142804582	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142804582delT	uc001eiw.1	+						uc001ejb.2_RNA|uc001ejc.2_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		TATTGGCGTGTGTTTTAATAA	0.259													6	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144519342	144519343	+	Intron	INS	-	A	A	rs151085852	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144519342_144519343insA	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|LOC728875_uc001eky.3_Intron|LOC728875_uc001ela.3_Intron|LOC728875_uc001ekz.3_Intron|uc001elb.3_RNA	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						ACCACTCATTGAAAAAAAAAAT	0.396													5	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145436575	145436575	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145436575delA	uc001emp.3	+						TXNIP_uc001enn.3_5'Flank|TXNIP_uc001enm.1_5'Flank|TXNIP_uc010oys.1_5'Flank	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		attccaccttaaaaaaaaaaa	0.189													6	3	---	---	---	---	
PRPF3	9129	broad.mit.edu	37	1	150325178	150325178	+	Intron	DEL	T	-	-	rs78725366		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150325178delT	uc001eum.3	+						PRPF3_uc010pca.1_Intron|PRPF3_uc010pcb.1_Intron	NM_004698	NP_004689	O43395	PRPF3_HUMAN	PRP3 pre-mRNA processing factor 3 homolog						nuclear mRNA splicing, via spliceosome	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding			ovary(1)	1	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)		GAGGTCACAATTTTTTTTTAA	0.189													4	2	---	---	---	---	
PGLYRP4	57115	broad.mit.edu	37	1	153311854	153311855	+	Intron	INS	-	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153311854_153311855insG	uc001fbo.2	-						PGLYRP4_uc001fbp.2_Intron	NM_020393	NP_065126	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein-I-beta						defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(3)|skin(1)	4	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCTACTAAAATGGGGACAGAGA	0.490													4	2	---	---	---	---	
SLC25A44	9673	broad.mit.edu	37	1	156179712	156179712	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156179712delT	uc001fnp.2	+						SLC25A44_uc010phc.1_Intron|SLC25A44_uc009wrr.2_Intron|SLC25A44_uc010phd.1_Intron|SLC25A44_uc010phe.1_Intron	NM_014655	NP_055470	Q96H78	S2544_HUMAN	solute carrier family 25, member 44						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding			ovary(1)	1	Hepatocellular(266;0.158)					tttatgaatattttttttttc	0.055													4	2	---	---	---	---	
PRCC	5546	broad.mit.edu	37	1	156740872	156740872	+	Intron	DEL	G	-	-	rs11264545	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156740872delG	uc001fqa.2	+						PRCC_uc001fqb.2_Intron	NM_005973	NP_005964	Q92733	PRCC_HUMAN	papillary renal cell carcinoma						cell cycle|mitotic cell cycle checkpoint	nucleus	protein binding		PRCC/TFE3(25)	kidney(25)|central_nervous_system(2)	27	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ggagccctctggggggagatg	0.000			T	TFE3	papillary renal 								4	2	---	---	---	---	
RGS4	5999	broad.mit.edu	37	1	163042903	163042903	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163042903delA	uc009wuy.2	+						RGS4_uc001gcl.3_Intron|RGS4_uc009wuz.2_Intron|RGS4_uc009wva.2_Intron	NM_005613	NP_005604	P49798	RGS4_HUMAN	regulator of G-protein signaling 4 isoform 2						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	plasma membrane	calmodulin binding|GTPase activator activity|signal transducer activity			ovary(2)|central_nervous_system(1)	3						CGGAAGAGAGAAAAAAAATGA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163235927	163235928	+	IGR	INS	-	CT	CT	rs148816018	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163235927_163235928insCT								RGS5 (63055 upstream) : NUF2 (55795 downstream)																							gggatctgctcctgtttttatt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166440902	166440903	+	IGR	INS	-	A	A	rs151102656	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166440902_166440903insA								FAM78B (304696 upstream) : FMO9P (132250 downstream)																							ttcccctgcccaaaaaaactgc	0.000													14	8	---	---	---	---	
C1orf112	55732	broad.mit.edu	37	1	169791102	169791102	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169791102delA	uc001ggp.2	+						C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggq.2_Intron|C1orf112_uc009wvt.2_Intron|C1orf112_uc010plu.1_Intron|C1orf112_uc009wvu.1_Intron|C1orf112_uc001ggr.2_Intron|C1orf112_uc010plv.1_Intron	NM_018186	NP_060656	Q9NSG2	CA112_HUMAN	hypothetical protein LOC55732												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CTTAGAAAGTAAAAAAAAAAT	0.154													6	3	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	185866788	185866788	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185866788delC	uc001grq.1	+							NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						ggtcacctttccagataaacc	0.000													4	2	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	186072428	186072428	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186072428delT	uc001grq.1	+							NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						GATCCATCCCTTTTGAAAGTG	0.323													4	2	---	---	---	---	
PTPRC	5788	broad.mit.edu	37	1	198693806	198693807	+	Intron	DEL	TC	-	-	rs111822544		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198693806_198693807delTC	uc001gur.1	+						PTPRC_uc001gus.1_Intron|PTPRC_uc001gut.1_Intron|PTPRC_uc009wzf.1_Intron|PTPRC_uc010ppg.1_Intron	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C						axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12						CCATCCTGATtctctctctctc	0.257													4	2	---	---	---	---	
PFKFB2	5208	broad.mit.edu	37	1	207208507	207208507	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207208507delT	uc010psc.1	+						C1orf116_uc001hfd.2_5'Flank|C1orf116_uc009xcb.1_5'Flank			O60825	F262_HUMAN	SubName: Full=cDNA FLJ53941, highly similar to 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2;						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity			ovary(1)	1	Prostate(682;0.19)					CCAGCTCACCTGACTCATCTG	0.438													4	2	---	---	---	---	
CAMK1G	57172	broad.mit.edu	37	1	209756830	209756831	+	5'Flank	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209756830_209756831delCA	uc001hhd.2	+						CAMK1G_uc001hhf.3_5'Flank|CAMK1G_uc001hhe.2_5'Flank	NM_020439	NP_065172	Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG							Golgi membrane|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			breast(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		cacacagactcacacacacaca	0.332													4	2	---	---	---	---	
C1orf115	79762	broad.mit.edu	37	1	220871098	220871098	+	3'UTR	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220871098delG	uc001hmp.1	+	2						NM_024709	NP_078985	Q9H7X2	CA115_HUMAN	hypothetical protein LOC79762							integral to membrane					0				GBM - Glioblastoma multiforme(131;0.0273)		CAGATGTGAAGGAAATGGAAA	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	230710568	230710569	+	IGR	DEL	TG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230710568_230710569delTG								PGBD5 (197201 upstream) : COG2 (67633 downstream)																							atgtgtgtgttgtgtgttgttt	0.178													4	6	---	---	---	---	
FMN2	56776	broad.mit.edu	37	1	240497102	240497102	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240497102delG	uc010pyd.1	+						FMN2_uc010pye.1_Intron|FMN2_uc010pyf.1_Intron|FMN2_uc010pyg.1_Intron	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GTATATACATGAATTCACTAG	0.303													13	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8336028	8336028	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8336028delT	uc010eww.1	-											Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																		CTTCCAGTCATGTCTTTGATG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15210963	15210966	+	IGR	DEL	GGAA	-	-	rs151030505		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15210963_15210966delGGAA								FAM84A (420030 upstream) : NBAS (96066 downstream)																							CAGTTTCTTTGGAAGAAGAAAGAG	0.377													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16690354	16690354	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16690354delC								MYCN (603226 upstream) : FAM49A (43547 downstream)																							AGCTCCAGAACCCCCAGGCAG	0.363													4	2	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28490306	28490307	+	Intron	DEL	AC	-	-	rs113134916		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28490306_28490307delAC	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					acacacacatacacacacacac	0.198													4	2	---	---	---	---	
GALNT14	79623	broad.mit.edu	37	2	31253206	31253206	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31253206delA	uc002rnr.2	-						GALNT14_uc002rnq.2_Intron|GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					GGCTGGATGGAAAAAAAAATC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35907268	35907268	+	IGR	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35907268delG								None (None upstream) : CRIM1 (676129 downstream)																							TGACAAAGGTGGGGTGGTATC	0.348													4	2	---	---	---	---	
HEATR5B	54497	broad.mit.edu	37	2	37292363	37292364	+	Intron	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37292363_37292364insT	uc002rpp.1	-							NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)				TAGAAGTCTTCAACAAATTTTA	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38413019	38413019	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38413019delA								C2orf58 (4028 upstream) : ATL2 (109012 downstream)																							GGAAAAAAAGAGCAAATGTCT	0.368													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	45942786	45942786	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45942786delT	uc002rut.2	+						PRKCE_uc002ruu.2_Intron	NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			GTCAAGTCCCTTTTAAAAACA	0.448													4	2	---	---	---	---	
TTC7A	57217	broad.mit.edu	37	2	47246874	47246878	+	Intron	DEL	TTTGC	-	-	rs72136538		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47246874_47246878delTTTGC	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron|TTC7A_uc002rvq.2_Intron|TTC7A_uc002rvr.2_Intron	NM_020458	NP_065191	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GAAGCTGGCATTTGCTGAGCAGAAG	0.459													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	52224570	52224571	+	IGR	INS	-	A	A	rs145414839	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:52224570_52224571insA								NRXN1 (964896 upstream) : None (None downstream)																							GAATATTGGGGAAAAAAAACCA	0.317													3	4	---	---	---	---	
ACYP2	98	broad.mit.edu	37	2	54353735	54353737	+	Intron	DEL	AAA	-	-	rs146851096		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54353735_54353737delAAA	uc002rxq.3	+							NM_138448	NP_612457	P14621	ACYP2_HUMAN	acylphosphatase 2						phosphate metabolic process		acylphosphatase activity				0						tcaaatttgcaaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
EML6	400954	broad.mit.edu	37	2	55082747	55082747	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55082747delG	uc002ryb.3	+							NM_001039753	NP_001034842	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like							cytoplasm|microtubule					0						GGCACACAGAGGGCATCTGCA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	63911687	63911690	+	IGR	DEL	AAGG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63911687_63911690delAAGG								LOC388955 (61528 upstream) : UGP2 (156408 downstream)																							TAATGCCCACAAGGTACTCTGTGG	0.446													36	21	---	---	---	---	
PAIP2B	400961	broad.mit.edu	37	2	71432194	71432194	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71432194delA	uc002shu.2	-							NM_020459	NP_065192	Q9ULR5	PAI2B_HUMAN	poly(A) binding protein interacting protein 2B						negative regulation of translational initiation		protein binding|translation repressor activity, nucleic acid binding				0						agaaagaaagaaaaaaaaaaC	0.299													4	2	---	---	---	---	
C2orf3	6936	broad.mit.edu	37	2	75907050	75907050	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75907050delT	uc002sno.2	-						C2orf3_uc010ffs.2_Intron|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						TGATTACCACTCCTATCACAG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85752005	85752005	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85752005delC								SH2D6 (87855 upstream) : MAT2A (14283 downstream)																							CTTCTCCCAACAAACACCTTT	0.478													4	2	---	---	---	---	
IMMT	10989	broad.mit.edu	37	2	86373489	86373493	+	Intron	DEL	ATATA	-	-	rs147978838	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86373489_86373493delATATA	uc002sqz.3	-						IMMT_uc002sqy.3_Intron|IMMT_uc002srb.3_Intron|IMMT_uc002sra.3_Intron|IMMT_uc010ytd.1_Intron|IMMT_uc010yte.1_Intron|IMMT_uc002src.1_Intron	NM_006839	NP_006830	Q16891	IMMT_HUMAN	inner membrane protein, mitochondrial isoform 1							integral to mitochondrial inner membrane	protein binding			skin(1)	1						TATTTGATGTATATAATATAttttt	0.185													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90461803	90461804	+	IGR	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90461803_90461804insA								None (None upstream) : None (None downstream)																							gaccctgtctcaaaaaaaaaaa	0.193													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91797028	91797028	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91797028delC								None (None upstream) : LOC654342 (8164 downstream)																							gccttggcctcccaaactgtt	0.000													4	2	---	---	---	---	
RFX8	731220	broad.mit.edu	37	2	102051196	102051196	+	Intron	DEL	A	-	-	rs66539076		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102051196delA	uc010yvx.1	-						RFX8_uc002tbb.1_Intron	NM_001145664	NP_001139136	Q6ZV50	RFX8_HUMAN	regulatory factor X, 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0						GACAGCAACCAAGGTAATACA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106998899	106998900	+	IGR	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106998899_106998900insA								UXS1 (188104 upstream) : PLGLA (3869 downstream)																							AATAATGGGTGACTTTTCAAAT	0.381													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108570132	108570134	+	IGR	DEL	CAA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108570132_108570134delCAA								RGPD4 (61133 upstream) : SLC5A7 (32861 downstream)																							CCAGATAGCTCAACAACAACAAC	0.315													4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109864094	109864094	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109864094delC	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						TCACAGTTGACGGACTGGCTG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113655118	113655119	+	IGR	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113655118_113655119insA								IL1B (60762 upstream) : IL1F7 (15429 downstream)																							CAATTAGTTTTGCTCAGCATCT	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119227716	119227717	+	IGR	DEL	AC	-	-	rs35590563		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119227716_119227717delAC								INSIG2 (360120 upstream) : EN1 (372031 downstream)																							CATCGGAAATACACACACACAC	0.391													4	2	---	---	---	---	
GYPC	2995	broad.mit.edu	37	2	127416702	127416703	+	Intron	INS	-	T	T	rs28387090		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127416702_127416703insT	uc002tnq.2	+						GYPC_uc002tnr.2_Intron|GYPC_uc010flv.2_Intron	NM_002101	NP_002092	P04921	GLPC_HUMAN	glycophorin C isoform 1							cortical cytoskeleton|integral to plasma membrane	protein binding			central_nervous_system(1)	1	Colorectal(110;0.0533)			BRCA - Breast invasive adenocarcinoma(221;0.075)		ctcacactgcattttttatctt	0.000													2	7	---	---	---	---	
MAP3K2	10746	broad.mit.edu	37	2	128066283	128066283	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128066283delG	uc002toj.1	-	15	1577	c.1512delC	c.(1510-1512)GCCfs	p.A504fs		NM_006609	NP_006600	Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase	504	Protein kinase.				activation of JUN kinase activity|cellular response to mechanical stimulus	nucleus	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein kinase binding			lung(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)		GCCGTTTGCTGGCCCCAAAAT	0.468													114	78	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	128824754	128824754	+	IGR	DEL	A	-	-	rs113610724		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128824754delA								SAP130 (39121 upstream) : UGGT1 (24000 downstream)																							gactccatctaaaaaaaaaaa	0.174													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129243549	129243550	+	IGR	INS	-	T	T	rs150151109	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129243549_129243550insT								HS6ST1 (167378 upstream) : None (None downstream)																							TCCTGGGAAAGTGAGAGGGCAA	0.446													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130153412	130153413	+	IGR	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130153412_130153413insA								None (None upstream) : LOC389033 (527022 downstream)																							tataatttaagaaaaaaaaatg	0.000													4	2	---	---	---	---	
PTPN18	26469	broad.mit.edu	37	2	131131481	131131482	+	3'UTR	INS	-	AGTC	AGTC	rs138260217	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131131481_131131482insAGTC	uc002trc.2	+	15					PTPN18_uc002trd.2_Intron|PTPN18_uc002trb.2_3'UTR|PTPN18_uc002tre.2_3'UTR	NM_014369	NP_055184	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|nucleus	non-membrane spanning protein tyrosine phosphatase activity			ovary(3)|kidney(1)	4	Colorectal(110;0.1)					CCCCCTAAGTTAGATTACTAGA	0.421													4	3	---	---	---	---	
CCDC74A	90557	broad.mit.edu	37	2	132288576	132288576	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132288576delG	uc002tta.2	+						CCDC74A_uc002ttb.2_Intron	NM_138770	NP_620125	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A											skin(1)	1						AGGGGATTAAGGGGGGGTGGG	0.667													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133066592	133066592	+	Intron	DEL	G	-	-	rs78544491		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133066592delG	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		AAAAGGAAAAGAATGTGCAGG	0.433													2	5	---	---	---	---	
TMEM163	81615	broad.mit.edu	37	2	135523600	135523602	+	Intron	DEL	TGT	-	-	rs72307998		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135523600_135523602delTGT	uc002tty.2	-									Q8TC26	TM163_HUMAN	Homo sapiens DC29 mRNA, complete cds.							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)		AGGAGATGGCtgttgttgttgtt	0.281													4	2	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142089679	142089679	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142089679delT	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		taattgttgattttttttttt	0.090										TSP Lung(27;0.18)			5	5	---	---	---	---	
ARHGAP15	55843	broad.mit.edu	37	2	144203134	144203134	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144203134delT	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)		CCTTCTCCAGTTTTTTTTCAT	0.368													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	156889960	156889960	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156889960delC	uc002tyw.2	-											Homo sapiens cDNA clone IMAGE:5209417.																		ccctttgtcgcccaggctgga	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	157002660	157002661	+	Intron	INS	-	GAAAA	GAAAA	rs145426964	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157002660_157002661insGAAAA	uc002tyw.2	-											Homo sapiens cDNA clone IMAGE:5209417.																		TTGCATTCTTTGAAAAGTCCAG	0.351													3	3	---	---	---	---	
MARCH7	64844	broad.mit.edu	37	2	160604167	160604167	+	Intron	DEL	T	-	-	rs139007980	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160604167delT	uc002uax.2	+						MARCH7_uc010foq.2_Intron|MARCH7_uc010zcn.1_Intron|MARCH7_uc010for.2_Intron|MARCH7_uc002uay.2_5'Flank	NM_022826	NP_073737	Q9H992	MARH7_HUMAN	axotrophin								ligase activity|zinc ion binding				0						TACATTTATGTTTTTTCTATA	0.259													4	2	---	---	---	---	
DPP4	1803	broad.mit.edu	37	2	162879588	162879589	+	Intron	INS	-	CC	CC			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162879588_162879589insCC	uc002ubz.2	-						DPP4_uc010fpb.2_Intron	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	cctctgtcccaccagcctgttc	0.094													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177998841	177998841	+	IGR	DEL	T	-	-	rs112219410		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177998841delT								MIR1246 (533061 upstream) : HNRNPA3 (78581 downstream)																							TAAAATGACATTTTTTTTTTC	0.294													2	4	---	---	---	---	
DYTN	391475	broad.mit.edu	37	2	207555107	207555107	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207555107delG	uc002vbr.1	-							NM_001093730	NP_001087199	A2CJ06	DYTN_HUMAN	dystrotelin							plasma membrane	zinc ion binding			ovary(1)|central_nervous_system(1)	2				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		ccaggctaaaggccactggaa	0.000													4	2	---	---	---	---	
ERBB4	2066	broad.mit.edu	37	2	213307451	213307451	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213307451delC	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		cacactgactccctgactggt	0.000										TSP Lung(8;0.080)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	217716148	217716149	+	IGR	DEL	TG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217716148_217716149delTG								IGFBP5 (155876 upstream) : TNP1 (8035 downstream)																							ACTTTTTGCCtgtgtgtgtgtg	0.302													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	223661903	223661903	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223661903delT								MOGAT1 (87254 upstream) : ACSL3 (63829 downstream)																							AATTTTGGAATTTTTTTCCTA	0.418													4	2	---	---	---	---	
SH3BP4	23677	broad.mit.edu	37	2	235883841	235883842	+	Intron	DEL	TT	-	-	rs5839566		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235883841_235883842delTT	uc002vvp.2	+							NM_014521	NP_055336	Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4						endocytosis	clathrin-coated vesicle|coated pit|nucleus	protein binding			skin(3)|ovary(1)	4		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		AGGGAATTGGTTTCTTGCCTCC	0.545													2	4	---	---	---	---	
GOLGA4	2803	broad.mit.edu	37	3	37360904	37360905	+	Intron	DEL	GA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37360904_37360905delGA	uc003cgv.2	+						GOLGA4_uc010hgr.1_Intron|GOLGA4_uc003cgw.2_Intron|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Intron	NM_002078	NP_002069	Q13439	GOGA4_HUMAN	golgi autoantigen, golgin subfamily a, 4						Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4						ttttttttatgagagagagtct	0.149													4	2	---	---	---	---	
XIRP1	165904	broad.mit.edu	37	3	39227553	39227553	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39227553delG	uc003cjk.1	-	2	3605	c.3384delC	c.(3382-3384)CCCfs	p.P1128fs	XIRP1_uc003cji.2_Intron|XIRP1_uc003cjj.2_Intron	NM_194293	NP_919269	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1128							actin binding			ovary(4)|breast(2)|central_nervous_system(1)|pancreas(1)	8				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GCAGCCCTCTGGGTAGTGCTT	0.597													8	11	---	---	---	---	
BAP1	8314	broad.mit.edu	37	3	52439426	52439426	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52439426delT	uc003ddx.2	-						BAP1_uc003ddw.2_5'Flank|BAP1_uc010hmg.2_5'Flank|BAP1_uc010hmh.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1						monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		AGCCAGCTGGTGCAATGGGAG	0.453			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	53234960	53234961	+	IGR	INS	-	G	G	rs144113410	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53234960_53234961insG								PRKCD (8229 upstream) : TKT (23763 downstream)																							GATGGCATGTTGGGGGCTCTGC	0.505													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	66883131	66883131	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66883131delA								LRIG1 (332286 upstream) : KBTBD8 (165596 downstream)																							GGAAGGCGAGAAAAAAAAAAG	0.418													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75460920	75460920	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75460920delT								CNTN3 (890577 upstream) : FAM86D (9785 downstream)																							tttttctccatttttttggtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75755493	75755493	+	IGR	DEL	C	-	-	rs71277775		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75755493delC								MIR1324 (75484 upstream) : ZNF717 (3301 downstream)																							caggaagacaccaaaagcagc	0.000													4	3	---	---	---	---	
KIAA2018	205717	broad.mit.edu	37	3	113371901	113371901	+	3'UTR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113371901delA	uc003eam.2	-	7					KIAA2018_uc003eal.2_3'UTR	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717						regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3						acagagtctcaaaaaaaaaag	0.289													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116698176	116698177	+	IGR	INS	-	AA	AA			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116698176_116698177insAA								LOC285194 (262291 upstream) : None (None downstream)																							TGCAGCTTCCTGAAGCAGTGGA	0.322													4	2	---	---	---	---	
KBTBD12	166348	broad.mit.edu	37	3	127697300	127697300	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127697300delT	uc010hsr.2	+						KBTBD12_uc003ejy.3_Intron|KBTBD12_uc010hsq.2_Intron|KBTBD12_uc003eka.3_Intron	NM_207335	NP_997218	Q3ZCT8	KBTBC_HUMAN	kelch domain containing 6											ovary(1)	1						aattgtctcatttttttccct	0.000													4	2	---	---	---	---	
FAIM	55179	broad.mit.edu	37	3	138348258	138348259	+	Intron	INS	-	TAGCAAGTAAAATACC	TAGCAAGTAAAATACC	rs144618719	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138348258_138348259insTAGCAAGTAAAATACC	uc003esr.2	+						FAIM_uc003eso.1_3'UTR|FAIM_uc003esp.2_Intron|FAIM_uc003esq.2_Intron|FAIM_uc003ess.2_Intron	NM_001033032	NP_001028204	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule isoform c						apoptosis	cytoplasm					0						AGGCTCCAGCATAGCAAGTAAA	0.446													6	3	---	---	---	---	
SLC9A9	285195	broad.mit.edu	37	3	143465513	143465513	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143465513delT	uc003evn.2	-						SLC9A9_uc011bnk.1_Intron	NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						TACATTTACCTTTTTTTTTAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147484309	147484309	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147484309delA								ZIC1 (349805 upstream) : AGTR1 (931349 downstream)																							TGGAATGCAGAAAAAGATCAT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166509472	166509472	+	IGR	DEL	T	-	-	rs71651536		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166509472delT								BCHE (954219 upstream) : ZBBX (448609 downstream)																							caggatttcctttttttttta	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	167606634	167606634	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167606634delT								SERPINI1 (63278 upstream) : GOLIM4 (121020 downstream)																							TAGAAATTTCTTTTTTTTTTC	0.433													9	5	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173580925	173580925	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173580925delA	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			GATGGCTGATAAAAAAAAAAA	0.234													4	2	---	---	---	---	
MAP3K13	9175	broad.mit.edu	37	3	185175030	185175030	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185175030delA	uc010hyf.2	+						MAP3K13_uc011brt.1_Intron|MAP3K13_uc011bru.1_Intron|MAP3K13_uc003fpi.2_Intron|MAP3K13_uc010hyg.2_Intron	NM_004721	NP_004712	O43283	M3K13_HUMAN	mitogen-activated protein kinase kinase kinase						activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			AATaggaaagaaaaggagagg	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187842457	187842457	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187842457delA								BCL6 (378982 upstream) : LPP (29262 downstream)																							AAAGCCAATTAAAAAGTTCAC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190767652	190767653	+	IGR	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190767652_190767653insA								SNAR-I (171813 upstream) : OSTN (162669 downstream)																							CATGGTTGGGTAAAAAAAACTG	0.332													4	2	---	---	---	---	
IQCG	84223	broad.mit.edu	37	3	197639882	197639882	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197639882delT	uc003fyo.2	-						IQCG_uc003fyn.2_Intron|IQCG_uc003fyp.2_Intron|IQCG_uc003fym.2_5'UTR	NM_001134435	NP_001127907	Q9H095	IQCG_HUMAN	IQ motif containing G												0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		GAAACGGCGCTCCAAGGGCAC	0.602													4	2	---	---	---	---	
CPLX1	10815	broad.mit.edu	37	4	784774	784775	+	Intron	DEL	TC	-	-	rs149307825		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:784774_784775delTC	uc003gbi.2	-						CPLX1_uc003gbj.2_Intron	NM_006651	NP_006642	O14810	CPLX1_HUMAN	complexin 1						glutamate secretion	cytosol					0				Colorectal(103;0.187)		ccctctgtcttctctctgtctc	0.168													4	2	---	---	---	---	
SH3BP2	6452	broad.mit.edu	37	4	2827234	2827235	+	Intron	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2827234_2827235delCA	uc003gfi.3	+						SH3BP2_uc011bvp.1_Intron|SH3BP2_uc003gfj.3_Intron|SH3BP2_uc003gfk.3_Intron|SH3BP2_uc003gfl.3_Intron|SH3BP2_uc003gfm.3_5'Flank	NM_001122681	NP_001116153	P78314	3BP2_HUMAN	SH3-domain binding protein 2 isoform a						signal transduction		SH3 domain binding|SH3/SH2 adaptor activity			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		CGTGGacatgcacacacacaca	0.045									Cherubism				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3051159	3051159	+	IGR	DEL	A	-	-	rs76639666		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3051159delA								GRK4 (8685 upstream) : HTT (25249 downstream)																							tccaaaaaagaaaaaaaaaag	0.000													4	2	---	---	---	---	
HTRA3	94031	broad.mit.edu	37	4	8272955	8272955	+	Intron	DEL	T	-	-	rs67723735		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8272955delT	uc003gla.2	+						HTRA3_uc003gkz.2_Intron	NM_053044	NP_444272	P83110	HTRA3_HUMAN	HtrA serine peptidase 3 precursor						proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity			ovary(1)	1						GGCTTCCTCATTTTTTCTGCG	0.398													4	2	---	---	---	---	
LDB2	9079	broad.mit.edu	37	4	16800818	16800818	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16800818delA	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron	NM_001290	NP_001281	O43679	LDB2_HUMAN	LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0						CGCAGTTAAGAAAAAAAAGAA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	22366612	22366612	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22366612delT								KCNIP4 (416238 upstream) : GPR125 (22387 downstream)																							TTTTATCCTGTTTTTACTTGT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24626014	24626015	+	IGR	INS	-	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24626014_24626015insG								DHX15 (39830 upstream) : SOD3 (171070 downstream)																							aaaaaaaaaaaaaaaaaaGCAA	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	29239916	29239916	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29239916delA								None (None upstream) : None (None downstream)																							tgtgtatcagaaaaaaaaaaG	0.169													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	45139863	45139863	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45139863delT								GNPDA2 (411251 upstream) : GABRG1 (897926 downstream)																							aagagAAACCTGCTGATAGGG	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49160784	49160784	+	IGR	DEL	T	-	-	rs75730677		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49160784delT								CWH43 (96691 upstream) : None (None downstream)																							GACTTTaaactttttcttttc	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49274764	49274764	+	IGR	DEL	A	-	-	rs12152629		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49274764delA								CWH43 (210671 upstream) : None (None downstream)																							actacagaccaatatccttga	0.000													5	3	---	---	---	---	
UGT2B28	54490	broad.mit.edu	37	4	70155971	70155971	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70155971delC	uc003hej.2	+						UGT2B28_uc010ihr.2_Intron	NM_053039	NP_444267	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family,						xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1					Flunitrazepam(DB01544)	GCCTTGCACACCCCACATATC	0.408													4	2	---	---	---	---	
SLC4A4	8671	broad.mit.edu	37	4	72425640	72425641	+	Intron	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72425640_72425641insT	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron|SLC4A4_uc003hgc.3_Intron|SLC4A4_uc010iid.2_Intron	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)			CATGTAGAAAATTATGAGAGTT	0.351													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	85961229	85961229	+	IGR	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85961229delG								C4orf12 (33061 upstream) : ARHGAP24 (435055 downstream)																							tattgaatgtgggagacatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	88332842	88332843	+	IGR	INS	-	GA	GA	rs5860071		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88332842_88332843insGA								HSD17B11 (20387 upstream) : NUDT9 (10892 downstream)																							gggCATTGGTGGtgatctttct	0.040													5	8	---	---	---	---	
GRID2	2895	broad.mit.edu	37	4	93818390	93818391	+	Intron	INS	-	T	T	rs141943922	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93818390_93818391insT	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron|GRID2_uc011cdv.1_Intron	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	tGCCTTCTCTGTTTTCCCCAAA	0.188													3	3	---	---	---	---	
SLC39A8	64116	broad.mit.edu	37	4	103256134	103256134	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103256134delA	uc003hwb.1	-						SLC39A8_uc011ceo.1_Intron|SLC39A8_uc003hwc.2_Intron	NM_022154	NP_071437	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter),							integral to membrane|organelle membrane|plasma membrane	zinc ion transmembrane transporter activity				0		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		aattgttagTAAATATTCTTA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111141108	111141108	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111141108delT								ELOVL6 (21288 upstream) : ENPEP (256121 downstream)																							TTCACATGTCttttttttttc	0.184													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	114691334	114691335	+	IGR	DEL	GT	-	-	rs35829001		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114691334_114691335delGT								CAMK2D (8251 upstream) : ARSJ (130105 downstream)																							CTATAAGTTGgtgtgtgtgtgt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	125390278	125390278	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125390278delT								LOC285419 (538760 upstream) : ANKRD50 (195190 downstream)																							AGACACTTTCTTAAATTTCTC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	126472234	126472234	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126472234delA								MIR2054 (43772 upstream) : None (None downstream)																							GCAGAAGCCCAAAATAATCAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	127636811	127636811	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127636811delT								None (None upstream) : INTU (917309 downstream)																							tgatgaagggtttatttacaa	0.104													4	2	---	---	---	---	
PHF17	79960	broad.mit.edu	37	4	129783527	129783527	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129783527delT	uc003igk.2	+						PHF17_uc003igj.2_3'UTR|PHF17_uc003igl.2_Intron|PHF17_uc011cgy.1_Intron|PHF17_uc003igm.2_3'UTR	NM_199320	NP_955352	Q6IE81	JADE1_HUMAN	PHD finger protein 17 long isoform						apoptosis|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation|negative regulation of cell growth|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	histone acetyltransferase complex|mitochondrion	protein binding|zinc ion binding				0						GTTAAAAATATTTATGGGCTG	0.403													5	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	130965672	130965672	+	IGR	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130965672delG								C4orf33 (931830 upstream) : None (None downstream)																							ctgactacttggatcttggac	0.100													4	2	---	---	---	---	
SCOC	60592	broad.mit.edu	37	4	141217930	141217930	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141217930delA	uc003iib.2	+						uc003iic.1_Intron	NM_032547	NP_115936	Q9UIL1	SCOC_HUMAN	short coiled-coil protein isoform 4							Golgi apparatus|nucleus	protein binding				0	all_hematologic(180;0.162)					TCACGACAAGAAAAAAAAAAA	0.408													4	2	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	143722245	143722245	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143722245delA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					TAAAGTAGTGAAAAAAAAATG	0.294													4	2	---	---	---	---	
KIAA0922	23240	broad.mit.edu	37	4	154505350	154505350	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154505350delT	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron|KIAA0922_uc010ipq.2_Intron|KIAA0922_uc010ips.1_5'Flank	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				GTACATTTAATTTTTTTTTAG	0.423													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	155968400	155968400	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155968400delT								RBM46 (218436 upstream) : NPY2R (161381 downstream)																							tcctatcacatactacactac	0.000													4	2	---	---	---	---	
TLL1	7092	broad.mit.edu	37	4	166998835	166998835	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166998835delA	uc003irh.1	+						TLL1_uc011cjn.1_Intron|TLL1_uc011cjo.1_Intron	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		GATTTATGGTAAATACTTAAT	0.348													4	2	---	---	---	---	
AGA	175	broad.mit.edu	37	4	178361215	178361216	+	Intron	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178361215_178361216insA	uc003iuu.1	-						AGA_uc003iuv.1_5'Flank|AGA_uc003iuw.2_5'Flank	NM_000027	NP_000018	P20933	ASPG_HUMAN	aspartylglucosaminidase precursor						asparagine catabolic process via L-aspartate|protein deglycosylation|protein maturation	endoplasmic reticulum|intermediate filament cytoskeleton|lysosome|microtubule cytoskeleton	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		TCTCCCAGTTCTAAGGGACTAC	0.371													4	2	---	---	---	---	
UFSP2	55325	broad.mit.edu	37	4	186328912	186328912	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186328912delA	uc003ixo.2	-						UFSP2_uc003ixn.2_Intron|UFSP2_uc003ixq.2_Intron|UFSP2_uc003ixp.2_Intron	NM_018359	NP_060829	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2							endoplasmic reticulum|nucleus	small conjugating protein-specific protease activity				0		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;3.4e-25)|Epithelial(43;2.23e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;8.1e-05)|GBM - Glioblastoma multiforme(59;0.000148)|STAD - Stomach adenocarcinoma(60;0.000782)|LUSC - Lung squamous cell carcinoma(40;0.00939)|COAD - Colon adenocarcinoma(29;0.0108)|READ - Rectum adenocarcinoma(43;0.166)		AGAGCCTTCCAAAAAAAAATG	0.244													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190602479	190602488	+	IGR	DEL	TTTTGTTTTG	-	-	rs35344434		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190602479_190602488delTTTTGTTTTG								None (None upstream) : FRG1 (259486 downstream)																							TTCTTTTATTttttgttttgttttgttttg	0.286													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190631243	190631245	+	IGR	DEL	ATT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190631243_190631245delATT								None (None upstream) : FRG1 (230729 downstream)																							TTCAGAACTCATTAATCAGGAAT	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190757583	190757584	+	IGR	INS	-	AC	AC			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190757583_190757584insAC								None (None upstream) : FRG1 (104390 downstream)																							actgcactagtacacacaccat	0.064													5	3	---	---	---	---	
LPCAT1	79888	broad.mit.edu	37	5	1461878	1461878	+	3'UTR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1461878delA	uc003jcm.2	-	14					LPCAT1_uc003jcl.2_3'UTR	NM_024830	NP_079106	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1						phospholipid biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		CATTTCATTCAAAAAACCCTT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1722941	1722941	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1722941delT								LOC728613 (88821 upstream) : MRPL36 (75559 downstream)																							AATTAAGATGTTCTGGGAGTG	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	14569321	14569321	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14569321delT								TRIO (59871 upstream) : FAM105A (12570 downstream)																							TGTGTTGCAATTTTTTTTTCC	0.358													4	2	---	---	---	---	
FAM105A	54491	broad.mit.edu	37	5	14614796	14614797	+	3'UTR	INS	-	CT	CT			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14614796_14614797insCT	uc003jfj.2	+	8						NM_019018	NP_061891	Q9NUU6	F105A_HUMAN	hypothetical protein LOC54491											ovary(1)	1	Lung NSC(4;0.00592)					TGCACTTGAAGCTCATGGAATG	0.510													4	2	---	---	---	---	
FBXL7	23194	broad.mit.edu	37	5	15821704	15821706	+	Intron	DEL	TGG	-	-	rs145146063		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15821704_15821706delTGG	uc003jfn.1	+							NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3						AGGACTTGCTTGGTGGTTATCAG	0.266													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17025163	17025166	+	IGR	DEL	TTAT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17025163_17025166delTTAT								MYO10 (88778 upstream) : LOC285696 (104971 downstream)																							GTTCTAGGCCTTATTTATTCATTC	0.471													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17400791	17400792	+	IGR	DEL	AC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17400791_17400792delAC								BASP1 (123856 upstream) : None (None downstream)																							ATAAAGATGAacacacacacac	0.153													4	2	---	---	---	---	
CDH18	1016	broad.mit.edu	37	5	19653401	19653401	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19653401delT	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					AGCTTGAGTCTTTTTTTTCTC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	29498757	29498759	+	IGR	DEL	TGG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29498757_29498759delTGG								None (None upstream) : None (None downstream)																							tagttcatgctggtggtggtggt	0.000													4	2	---	---	---	---	
PDZD2	23037	broad.mit.edu	37	5	31717225	31717226	+	Intron	DEL	TA	-	-	rs111524312		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31717225_31717226delTA	uc003jhl.2	+							NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						taaagaaaattaaaaaaaagag	0.188													4	2	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33690566	33690566	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33690566delA	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						TAAGCACCTGAAAAAAAAAAA	0.373										HNSCC(64;0.19)			3	3	---	---	---	---	
CAPSL	133690	broad.mit.edu	37	5	35904525	35904525	+	3'UTR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35904525delT	uc003jjt.1	-	5					CAPSL_uc003jju.1_3'UTR	NM_001042625	NP_001036090	Q8WWF8	CAPSL_HUMAN	calcyphosine-like							cytoplasm	calcium ion binding			skin(1)	1	all_lung(31;0.000268)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.167)|Colorectal(62;0.202)			AAATGCAATATTTTGACACAG	0.388													5	3	---	---	---	---	
PTGER4	5734	broad.mit.edu	37	5	40686817	40686817	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40686817delA	uc003jlz.2	+							NM_000958	NP_000949	P35408	PE2R4_HUMAN	prostaglandin E receptor 4, subtype EP4						G-protein signaling, coupled to cAMP nucleotide second messenger|immune response	integral to membrane|plasma membrane	prostaglandin E receptor activity			lung(2)	2						TAATCATCCTAAAAAAAAGTG	0.214													4	2	---	---	---	---	
PLCXD3	345557	broad.mit.edu	37	5	41423879	41423879	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41423879delT	uc003jmm.1	-							NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						GCTCTCATCATTTTTTTTCTC	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	41571018	41571018	+	IGR	DEL	C	-	-	rs75609975		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41571018delC								PLCXD3 (60288 upstream) : OXCT1 (159150 downstream)																							gaaaaaaaaacacaaaacaac	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43853418	43853418	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43853418delA								NNT (147751 upstream) : FGF10 (451679 downstream)																							ATTTATCAGCAAAAAAAAGCA	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56276630	56276630	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56276630delA								MIER3 (9129 upstream) : GPBP1 (193145 downstream)																							CAGACAGGACAAAAAAGGCAG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	65828485	65828486	+	IGR	INS	-	C	C	rs148654515		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65828485_65828486insC								SFRS12 (351773 upstream) : MAST4 (63690 downstream)																							aacattttccaaagagaatttc	0.000													4	2	---	---	---	---	
COL4A3BP	10087	broad.mit.edu	37	5	74793046	74793046	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74793046delT	uc011csu.1	-						COL4A3BP_uc003kds.2_Intron|COL4A3BP_uc003kdt.2_Intron|COL4A3BP_uc003kdu.2_Intron	NM_005713	NP_005704	Q9Y5P4	C43BP_HUMAN	alpha 3 type IV collagen binding protein isoform						ER to Golgi ceramide transport|immune response	cytosol|endoplasmic reticulum membrane|Golgi apparatus	ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity			skin(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		TTTGTCCCCCTTTGATAAAAG	0.373													4	2	---	---	---	---	
SSBP2	23635	broad.mit.edu	37	5	80721428	80721429	+	Intron	INS	-	T	T	rs139983744	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80721428_80721429insT	uc003kho.2	-						RNU5E_uc011cto.1_Intron|SSBP2_uc010jar.2_Intron|SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		ATGAAAAACTATTTTTTTTGAA	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87988469	87988469	+	IGR	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87988469delG								LOC645323 (7849 upstream) : MEF2C (25589 downstream)																							AGCAGAGGTCGGGAAGCTGCT	0.592													4	2	---	---	---	---	
MEF2C	4208	broad.mit.edu	37	5	88018306	88018306	+	3'UTR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88018306delT	uc003kjj.2	-	11					MEF2C_uc003kji.2_3'UTR|MEF2C_uc003kjk.2_3'UTR|MEF2C_uc003kjm.2_3'UTR|MEF2C_uc003kjl.2_3'UTR	NM_002397	NP_002388	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C isoform 1						apoptosis|B cell proliferation|innate immune response|learning or memory|muscle cell differentiation|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|neuron development|positive regulation of muscle cell differentiation|positive regulation of survival gene product expression|positive regulation of transcription from RNA polymerase II promoter|regulation of germinal center formation|regulation of megakaryocyte differentiation|regulation of synaptic activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nuclear speck	activating transcription factor binding|protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			lung(3)|breast(2)|ovary(1)|large_intestine(1)	7		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		AGTACCTGACTTTTTTTTTTT	0.358										HNSCC(66;0.2)			6	3	---	---	---	---	
CHD1	1105	broad.mit.edu	37	5	98199499	98199500	+	Intron	INS	-	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98199499_98199500insC	uc003knf.2	-						CHD1_uc010jbn.2_Intron	NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TTCTGTTATCATTTAAAATCAG	0.302													4	2	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112586885	112586886	+	Intron	INS	-	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112586885_112586886insG	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron|MCC_uc011cwb.1_Intron|MCC_uc010jcd.1_Intron	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CCTTTGCAAATGCCATATGTAC	0.376													4	3	---	---	---	---	
FSTL4	23105	broad.mit.edu	37	5	132792411	132792411	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132792411delA	uc003kyn.1	-							NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			aaaacaaaacaaaaAACCCTG	0.333													4	2	---	---	---	---	
CTNNA1	1495	broad.mit.edu	37	5	138144384	138144385	+	Intron	INS	-	A	A	rs140913171		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138144384_138144385insA	uc003ldh.2	+						CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1						adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GAAAGTGCCTTAAAAAAAAAAA	0.396													4	3	---	---	---	---	
LOC389333	389333	broad.mit.edu	37	5	138728573	138728574	+	Frame_Shift_Del	DEL	AT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138728573_138728574delAT	uc011czc.1	-	1	2312_2313	c.2197_2198delAT	c.(2197-2199)ATCfs	p.I733fs	MGC29506_uc003lei.2_5'Flank|MGC29506_uc010jfd.2_5'Flank|MGC29506_uc010jfe.2_5'Flank|MGC29506_uc003lej.2_5'Flank	NM_001161546	NP_001155018	B4E007	B4E007_HUMAN	hypothetical protein LOC389333	172											0						AGGCAGGCGGATCTCTGTGCGC	0.703													4	2	---	---	---	---	
LOC389333	389333	broad.mit.edu	37	5	138728579	138728579	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138728579delG	uc011czc.1	-	1	2307	c.2192delC	c.(2191-2193)ACAfs	p.T731fs	MGC29506_uc003lei.2_5'Flank|MGC29506_uc010jfd.2_5'Flank|MGC29506_uc010jfe.2_5'Flank|MGC29506_uc003lej.2_5'Flank	NM_001161546	NP_001155018	B4E007	B4E007_HUMAN	hypothetical protein LOC389333	170											0						GCGGATCTCTGTGCGCTTGAA	0.697													4	2	---	---	---	---	
LOC389333	389333	broad.mit.edu	37	5	138728583	138728584	+	Frame_Shift_Ins	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138728583_138728584insT	uc011czc.1	-	1	2302_2303	c.2187_2188insA	c.(2185-2190)AAGCGCfs	p.K729fs	MGC29506_uc003lei.2_5'Flank|MGC29506_uc010jfd.2_5'Flank|MGC29506_uc010jfe.2_5'Flank|MGC29506_uc003lej.2_5'Flank	NM_001161546	NP_001155018	B4E007	B4E007_HUMAN	hypothetical protein LOC389333	168_169											0						ATCTCTGTGCGCTTGAAGGGCT	0.698													4	2	---	---	---	---	
NRG2	9542	broad.mit.edu	37	5	139262700	139262700	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139262700delG	uc003lex.1	-						NRG2_uc003lev.1_Intron|NRG2_uc003lew.1_Intron|NRG2_uc003ley.1_Intron	NM_004883	NP_004874	O14511	NRG2_HUMAN	neuregulin 2 isoform 1						embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTCCAGGTGGAAGCCTGAG	0.627													4	2	---	---	---	---	
NR3C1	2908	broad.mit.edu	37	5	142680488	142680488	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142680488delT	uc003lmz.2	-						NR3C1_uc003lmy.2_Intron|NR3C1_uc003lna.2_Intron|NR3C1_uc003lnb.2_Intron|NR3C1_uc011dbk.1_Intron|NR3C1_uc003lnc.2_Intron|NR3C1_uc003lnd.2_Intron|NR3C1_uc003lne.2_Intron|NR3C1_uc003lnf.2_Intron	NM_000176	NP_000167	P04150	GCR_HUMAN	glucocorticoid receptor isoform alpha						chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter	mitochondrial matrix|nucleoplasm	glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635)	GAGAAAAAACTTTTTTTTTTC	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	144483298	144483298	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144483298delT								KCTD16 (626354 upstream) : PRELID2 (655284 downstream)																							GGAGGGTTTCTTTTTTTTTTA	0.413													4	2	---	---	---	---	
CAMK2A	815	broad.mit.edu	37	5	149623740	149623740	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149623740delG	uc003lru.2	-						CAMK2A_uc003lrs.2_Intron|CAMK2A_uc003lrt.2_Intron|CAMK2A_uc010jhe.2_Intron	NM_171825	NP_741960	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission	cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			gttgtacttaggggaaaattc	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	150375331	150375332	+	IGR	INS	-	CACAAACCGAGAT	CACAAACCGAGAT	rs140754635	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150375331_150375332insCACAAACCGAGAT								LOC134466 (49185 upstream) : GPX3 (24667 downstream)																							aaaaaaaggcacattttgtttt	0.000													4	2	---	---	---	---	
ADAM19	8728	broad.mit.edu	37	5	156915013	156915013	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156915013delG	uc003lwz.2	-						ADAM19_uc003lww.1_Intron|ADAM19_uc003lwy.2_Intron|ADAM19_uc011ddr.1_Intron	NM_033274	NP_150377	Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19 preproprotein						proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			aagttaatatggggtggaagg	0.199													4	2	---	---	---	---	
PWWP2A	114825	broad.mit.edu	37	5	159507969	159507970	+	Intron	INS	-	G	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159507969_159507970insG	uc003lxv.3	-						PWWP2A_uc011dec.1_Intron	NM_052927	NP_443159	Q96N64	PWP2A_HUMAN	PWWP domain containing 2A isoform a												0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTGAGAGCTGTGTAGACACAAC	0.446													6	3	---	---	---	---	
CCNG1	900	broad.mit.edu	37	5	162868696	162868712	+	Intron	DEL	AATCATCTAAAACTCCC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162868696_162868712delAATCATCTAAAACTCCC	uc003lzb.2	+						CCNG1_uc011dek.1_Intron|CCNG1_uc011del.1_Intron|CCNG1_uc003lzc.2_Intron	NM_199246	NP_954854	P51959	CCNG1_HUMAN	cyclin G1						cell division|mitosis|regulation of cyclin-dependent protein kinase activity	nucleus				lung(1)|kidney(1)	2	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)		TTTTGGCCCAAATCATCTAAAACTCCCATATGGTGCC	0.300													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	168987951	168987952	+	IGR	INS	-	GC	GC	rs72532722	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168987951_168987952insGC								SLIT3 (259818 upstream) : CCDC99 (22686 downstream)																							ATAGTGTTTGATAGTGTTTGTT	0.411													3	5	---	---	---	---	
RANBP17	64901	broad.mit.edu	37	5	170585717	170585717	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170585717delC	uc003mba.2	+						RANBP17_uc003max.1_Intron|RANBP17_uc003may.1_Intron|RANBP17_uc003maz.1_Intron|RANBP17_uc010jjr.1_Intron|RANBP17_uc003mbb.2_Intron	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCCCTCTTGGCCCACTTTTCT	0.398			T	TRD@	ALL								4	2	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	2106112	2106113	+	Intron	DEL	TC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2106112_2106113delTC	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		ATACTCCTCTTCTCTGGCAAAC	0.381													4	2	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	2140125	2140126	+	Intron	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2140125_2140126insA	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		GTGAAAGAGGGAGAAAGACTTG	0.460													4	2	---	---	---	---	
TMEM14B	81853	broad.mit.edu	37	6	10750406	10750407	+	Intron	INS	-	T	T	rs114341199	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10750406_10750407insT	uc003mzk.3	+						SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jor.2_Intron|TMEM14B_uc010jos.1_Intron	NM_030969	NP_112231	Q9NUH8	TM14B_HUMAN	transmembrane protein 14B isoform a							integral to membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)				CTGATCTTCTATTTTTTTTTTA	0.495													4	2	---	---	---	---	
C6orf105	84830	broad.mit.edu	37	6	11770479	11770480	+	Intron	DEL	AA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11770479_11770480delAA	uc003nab.2	-						C6orf105_uc011dip.1_Intron	NM_032744	NP_116133	Q96IZ2	CF105_HUMAN	hypothetical protein LOC84830 isoform 2							integral to membrane					0	Ovarian(93;0.0848)|Breast(50;0.0871)	all_hematologic(90;0.135)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.193)			attctaatgtaatcagtctggg	0.173													4	2	---	---	---	---	
MBOAT1	154141	broad.mit.edu	37	6	20205480	20205480	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20205480delT	uc003ncx.1	-						MBOAT1_uc011dji.1_Intron	NM_001080480	NP_001073949	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain						phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			aaagaagaaatttagggaaag	0.154													4	2	---	---	---	---	
BTN2A2	10385	broad.mit.edu	37	6	26382355	26382356	+	5'Flank	DEL	GT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26382355_26382356delGT	uc003nhq.2	+						BTN2A2_uc011dkf.1_5'Flank|BTN2A2_uc011dkg.1_5'Flank|BTN2A2_uc003nhr.2_5'Flank|BTN2A2_uc011dkh.1_5'Flank|BTN2A2_uc003nhs.2_5'Flank|BTN2A2_uc003nht.2_5'Flank	NM_006995	NP_008926	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2 isoform a						negative regulation of activated T cell proliferation|negative regulation of cellular metabolic process|negative regulation of cytokine secretion	integral to membrane					0						ATGTGTGCTGGTGTGTGTGTGT	0.480													4	2	---	---	---	---	
SRPK1	6732	broad.mit.edu	37	6	35855567	35855567	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35855567delT	uc003olj.2	-						SRPK1_uc011dtg.1_Intron|SRPK1_uc003olh.2_Intron|SRPK1_uc003oli.2_Intron	NM_003137	NP_003128	Q96SB4	SRPK1_HUMAN	SFRS protein kinase 1						cell differentiation|chromosome segregation|interspecies interaction between organisms|intracellular protein kinase cascade|mRNA processing|negative regulation of viral genome replication|positive regulation of viral genome replication|regulation of mRNA processing|RNA splicing	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1						ATTTGAAAGGTTTTTTTTTGG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	41383900	41383900	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41383900delT								NCR2 (65275 upstream) : FOXP4 (130264 downstream)																							AAACCTTGCCTTTTTTTTTTT	0.333													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50233576	50233576	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50233576delT								DEFB112 (217212 upstream) : TFAP2D (447681 downstream)																							TGCTATTCTATTTTTCTTCAC	0.358													4	2	---	---	---	---	
COL21A1	81578	broad.mit.edu	37	6	56003523	56003524	+	Intron	DEL	AG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56003523_56003524delAG	uc003pcs.2	-						COL21A1_uc003pct.1_Intron|COL21A1_uc011dxi.1_Intron|COL21A1_uc003pcu.1_Intron	NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			agagtgggtcagagagagaaat	0.000													4	2	---	---	---	---	
DST	667	broad.mit.edu	37	6	56358577	56358578	+	Intron	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56358577_56358578insT	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pda.3_5'Flank	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GTAACATTTGATCTATATATTT	0.223													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57445293	57445293	+	Intron	DEL	C	-	-	rs7741256		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57445293delC	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TCCATGTTTTCTTTGTCCTTG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57524318	57524318	+	IGR	DEL	C	-	-	rs150905442		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57524318delC								PRIM2 (10943 upstream) : GUSBL2 (721841 downstream)																							gaaagatgatctctctctctc	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57524320	57524320	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57524320delC								PRIM2 (10945 upstream) : GUSBL2 (721839 downstream)																							aagatgatctctctctctcac	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57538773	57538773	+	IGR	DEL	G	-	-	rs10707154		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57538773delG								PRIM2 (25398 upstream) : GUSBL2 (707386 downstream)																							GATTCTCTAAGATTAATTAGC	0.358													3	5	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	66283700	66283700	+	Intron	DEL	A	-	-	rs61328716		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66283700delA	uc011dxu.1	-						EYS_uc003peq.2_Intron|EYS_uc003per.1_Intron|EYS_uc010kaj.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						ACCTGCACACACCTGCATTCC	0.438													4	7	---	---	---	---	
FAM46A	55603	broad.mit.edu	37	6	82461713	82461713	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82461713delC	uc003pjg.2	-	2	464	c.146delG	c.(145-147)GGTfs	p.G49fs	FAM46A_uc003pjf.2_Frame_Shift_Del_p.G68fs|FAM46A_uc003pjh.1_Frame_Shift_Del_p.G49fs	NM_017633	NP_060103	Q96IP4	FA46A_HUMAN	hypothetical protein LOC55603	49											0		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		GCAATGCCCACCGAAgctgcc	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85385707	85385707	+	IGR	DEL	T	-	-	rs67918403		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85385707delT								KIAA1009 (448372 upstream) : TBX18 (11374 downstream)																							GTTCTTTTTCTTTTTTTTttt	0.214													4	2	---	---	---	---	
FUT9	10690	broad.mit.edu	37	6	96599641	96599641	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96599641delT	uc003pop.3	+							NM_006581	NP_006572	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3)						L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			skin(4)|ovary(1)	5		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		TACTTTACCCTTTCTTTTTCT	0.368													4	2	---	---	---	---	
PRDM1	639	broad.mit.edu	37	6	106532415	106532415	+	5'Flank	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106532415delG	uc003prd.2	+							NM_001198	NP_001189	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain isoform						negative regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(54)|ovary(1)|skin(1)	56	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		GTTGCATGATGGTGTATGTGG	0.403			D|N|Mis|F|S		DLBCL								4	2	---	---	---	---	
NR2E1	7101	broad.mit.edu	37	6	108508234	108508234	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108508234delT	uc003psg.2	+							NM_003269	NP_003260	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		CTTAAATTTCTTTTTTTTTCC	0.234													4	2	---	---	---	---	
FIG4	9896	broad.mit.edu	37	6	110024503	110024503	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110024503delT	uc003ptt.2	+						FIG4_uc011eau.1_Intron	NM_014845	NP_055660	Q92562	FIG4_HUMAN	Sac domain-containing inositol phosphatase 3						cell death	endosome membrane	protein binding			ovary(1)	1		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		ttgaagcttgtttttttttct	0.085													5	3	---	---	---	---	
REV3L	5980	broad.mit.edu	37	6	111713848	111713849	+	Intron	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111713848_111713849insA	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta						DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TAACAATATCTACCTTGTATTC	0.248								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					5	3	---	---	---	---	
SLC35F1	222553	broad.mit.edu	37	6	118598985	118598986	+	Intron	INS	-	A	A	rs146987533	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118598985_118598986insA	uc003pxx.3	+						SLC35F1_uc003pxy.1_Intron	NM_001029858	NP_001025029	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)		AACACCAACAGAAAAAAAAAAC	0.381													6	3	---	---	---	---	
PTPRK	5796	broad.mit.edu	37	6	128374972	128374972	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128374972delG	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		TCACTGGTGTGGGTCCTACCA	0.498													4	2	---	---	---	---	
KIAA1244	57221	broad.mit.edu	37	6	138528566	138528567	+	Intron	DEL	AG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138528566_138528567delAG	uc003qhu.2	+							NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		ATCCCAAAAAAGAGACGACAAG	0.347													2	4	---	---	---	---	
SYNE1	23345	broad.mit.edu	37	6	152949720	152949720	+	Intron	DEL	A	-	-	rs74643030		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152949720delA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_5'Flank	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						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)		GGTACAACATAAAAAAAAAAT	0.299										HNSCC(10;0.0054)			4	2	---	---	---	---	
CNKSR3	154043	broad.mit.edu	37	6	154813477	154813478	+	Intron	INS	-	TC	TC	rs150329162	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154813477_154813478insTC	uc003qpy.2	-							NM_173515	NP_775786	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3						negative regulation of ERK1 and ERK2 cascade|negative regulation of peptidyl-serine phosphorylation|positive regulation of sodium ion transport	cytoplasm|membrane				ovary(2)|breast(1)|skin(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		aggtcatccagtctcaaagatt	0.000													3	5	---	---	---	---	
TIAM2	26230	broad.mit.edu	37	6	155574768	155574768	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155574768delC	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron|TIAM2_uc010kjj.2_Intron|TIAM2_uc003qqf.2_Intron|TIAM2_uc011efl.1_Intron|TIAM2_uc003qqg.2_Intron|TIAM2_uc003qqh.2_Intron|uc003qqi.1_RNA	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		ACCTCAAGTACCCCAGCTCCT	0.488													4	2	---	---	---	---	
RPS6KA2	6196	broad.mit.edu	37	6	166916628	166916628	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166916628delG	uc003qvb.1	-						RPS6KA2_uc011ego.1_Intron|RPS6KA2_uc010kkl.1_Intron|RPS6KA2_uc003qvc.1_Intron|RPS6KA2_uc003qvd.1_Intron	NM_021135	NP_066958	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		attttccactggggggtgtcc	0.040													4	2	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945607	945607	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945607delA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						ggagaaagggagaaaggagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	7823030	7823031	+	Intron	INS	-	G	G	rs113076099	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7823030_7823031insG	uc011jxf.1	+											SubName: Full=cDNA FLJ54628; SubName: Full=HCG19535; SubName: Full=Hypothetical gene supported by AK027125;																		AGAAGTTGTTTTTTTTTTTTTT	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17077055	17077055	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17077055delA								AGR3 (155442 upstream) : AHR (261221 downstream)																							GACATGAGGGAAAAAAAATGA	0.209													4	2	---	---	---	---	
DNAH11	8701	broad.mit.edu	37	7	21621246	21621247	+	Intron	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21621246_21621247insT	uc003svc.2	+							NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						GAGCATGTGAGCCAAAGCACTG	0.426									Kartagener_syndrome				4	3	---	---	---	---	
TRA2A	29896	broad.mit.edu	37	7	23544599	23544599	+	3'UTR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23544599delA	uc003swi.2	-	8					TRA2A_uc011jzb.1_RNA|TRA2A_uc011jzc.1_3'UTR|TRA2A_uc011jzd.1_3'UTR	NM_013293	NP_037425	Q13595	TRA2A_HUMAN	transformer-2 alpha						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1						TAACAACAACAAAAAAAATCA	0.284													4	2	---	---	---	---	
OSBPL3	26031	broad.mit.edu	37	7	24996842	24996843	+	Intron	DEL	AA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24996842_24996843delAA	uc003sxf.2	-						OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1						CAGAACAGACAAAAAAAAAAAA	0.356													4	2	---	---	---	---	
CREB5	9586	broad.mit.edu	37	7	28724509	28724509	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28724509delA	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron|CREB5_uc003szs.2_5'Flank|CREB5_uc011jzr.1_5'Flank	NM_182898	NP_878901	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						TGATGGGGTTAAAAAGCCCTG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	40988033	40988035	+	IGR	DEL	ATG	-	-	rs111493363		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40988033_40988035delATG								C7orf10 (87676 upstream) : INHBA (740568 downstream)																							CCTGAAAAACatgatgatgatga	0.202													2	4	---	---	---	---	
HECW1	23072	broad.mit.edu	37	7	43237969	43237970	+	Intron	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43237969_43237970delCA	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.1_Intron	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						cccacgctctcacacacacgtc	0.025													4	2	---	---	---	---	
ABCA13	154664	broad.mit.edu	37	7	48655196	48655197	+	Intron	INS	-	T	T	rs138589769	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48655196_48655197insT	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc010kyt.1_Intron|ABCA13_uc010kyu.1_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						AGACATTTTGCTTTTCTCTTGC	0.446													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54427691	54427691	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54427691delA								HPVC1 (157577 upstream) : VSTM2A (182328 downstream)																							atgtgatgagaAAAAAAAAAA	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57607602	57607602	+	IGR	DEL	C	-	-	rs76455162		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57607602delC								ZNF716 (74337 upstream) : None (None downstream)																							TTCATCTGCTCTTATTTCCTT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57870965	57870968	+	IGR	DEL	ATTG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57870965_57870968delATTG								ZNF716 (337700 upstream) : None (None downstream)																							tctttgttatattgattgattttt	0.113													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65211087	65211090	+	Intron	DEL	ACAC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65211087_65211090delACAC	uc003tud.1	-						uc003tuf.2_Intron					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																		tgacatctctacacacacacacac	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65465783	65465783	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65465783delA								GUSB (18537 upstream) : ASL (74993 downstream)																							ctcaaaaaggaaaaaaaaaga	0.000													3	3	---	---	---	---	
TYW1	55253	broad.mit.edu	37	7	66666295	66666297	+	Intron	DEL	AAC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66666295_66666297delAAC	uc003tvn.2	+						TYW1_uc010lai.2_Intron|TYW1_uc011kef.1_Intron|PMS2L4_uc003tvo.2_Intron	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)				CCATTTCTAAaacaacaacaaca	0.256													6	3	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69424964	69424964	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69424964delT	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		TCTAGGCCTATTTTTTTTTAA	0.423													4	3	---	---	---	---	
GTF2IRD1	9569	broad.mit.edu	37	7	73867555	73867556	+	5'Flank	DEL	GT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73867555_73867556delGT	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_5'Flank|GTF2IRD1_uc003uap.2_5'Flank	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						CGCTGCTGTGGTGTGTGTGTGG	0.490													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78239723	78239723	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78239723delA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				tagaactcttaaagggcatcc	0.189													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78919886	78919886	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78919886delT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				CTTTCCCTCATTTTTTTTTCT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	80876144	80876144	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80876144delA								SEMA3C (324469 upstream) : HGF (455301 downstream)																							aggaatgggcaaaggtttcct	0.000													4	2	---	---	---	---	
ABCB4	5244	broad.mit.edu	37	7	87073977	87073977	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87073977delT	uc003uiv.1	-						ABCB4_uc003uiw.1_Intron|ABCB4_uc003uix.1_Intron	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4						cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					ttatattatctaaagatacat	0.254													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	89568925	89568925	+	IGR	DEL	T	-	-	rs72376257		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89568925delT								ZNF804B (602581 upstream) : DPY19L2P4 (179789 downstream)																							cctagtgtgatttttttcccc	0.080													4	2	---	---	---	---	
AKAP9	10142	broad.mit.edu	37	7	91606990	91606990	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91606990delT	uc003ulg.2	+						AKAP9_uc003uld.3_Intron|AKAP9_uc003ule.2_Intron|AKAP9_uc003ulf.2_Intron	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			tatcctttcctttttttgtac	0.050			T	BRAF	papillary thyroid								4	2	---	---	---	---	
CALCR	799	broad.mit.edu	37	7	93188381	93188381	+	Intron	DEL	A	-	-	rs71815071		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93188381delA	uc003umv.1	-						CALCR_uc003umu.1_Intron|CALCR_uc003umw.2_Intron	NM_001742	NP_001733	P30988	CALCR_HUMAN	calcitonin receptor isoform 2 precursor						activation of adenylate cyclase activity by G-protein signaling pathway|elevation of cytosolic calcium ion concentration|positive regulation of adenylate cyclase activity|response to glucocorticoid stimulus	integral to plasma membrane	calcitonin binding|calcitonin binding|calcitonin receptor activity|calcitonin receptor activity|protein binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Salmon Calcitonin(DB00017)	TAACAACAACAAAAAAAATTC	0.323													4	2	---	---	---	---	
PEG10	23089	broad.mit.edu	37	7	94285913	94285913	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94285913delT	uc011kie.1	+						SGCE_uc003unm.2_5'Flank|SGCE_uc003unl.2_5'Flank|SGCE_uc003unn.2_5'Flank|SGCE_uc011kic.1_5'Flank|SGCE_uc011kid.1_5'Flank	NM_001040152	NP_001035242	Q86TG7	PEG10_HUMAN	paternally expressed 10 isoform RF1						apoptosis|cell differentiation|negative regulation of transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GGTGAGGACGTTTTTTTTTTA	0.572											OREG0018170	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
TRIM4	89122	broad.mit.edu	37	7	99513917	99513917	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99513917delT	uc003usd.2	-						TRIM4_uc003use.2_Intron|TRIM4_uc011kjc.1_Intron|TRIM4_uc003usf.2_Intron	NM_033017	NP_148977	Q9C037	TRIM4_HUMAN	tripartite motif protein TRIM4 isoform alpha						protein trimerization	cytoplasm|plasma membrane	zinc ion binding			ovary(1)|kidney(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				tctttgtgcctttttttactc	0.060													4	2	---	---	---	---	
EMID2	136227	broad.mit.edu	37	7	101039752	101039752	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101039752delT	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)					TAAGCAtttcttttttttttg	0.269													4	2	---	---	---	---	
FBXL13	222235	broad.mit.edu	37	7	102698160	102698161	+	Intron	INS	-	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102698160_102698161insC	uc003vaq.2	-						FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Intron|FBXL13_uc003vav.2_Intron	NM_145032	NP_659469	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13 isoform												0						CCTTATGAGGTCCCCCCAAAAG	0.282													4	2	---	---	---	---	
LHFPL3	375612	broad.mit.edu	37	7	104160114	104160115	+	Intron	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104160114_104160115insA	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3							integral to membrane					0						TTTCCCATTATAAAAAATCTGC	0.361													4	2	---	---	---	---	
SRPK2	6733	broad.mit.edu	37	7	104777196	104777197	+	Intron	DEL	TC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104777196_104777197delTC	uc003vct.2	-						SRPK2_uc003vcu.2_Intron|SRPK2_uc003vcv.2_Intron|SRPK2_uc003vcw.1_Intron	NM_182691	NP_872633	P78362	SRPK2_HUMAN	serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6						GACAAGAATATCCCCTCTATAT	0.406													4	5	---	---	---	---	
DNAJB9	4189	broad.mit.edu	37	7	108213939	108213939	+	3'UTR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108213939delT	uc003vfn.2	+	3						NM_012328	NP_036460	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9						ER-associated protein catabolic process|protein folding	endoplasmic reticulum|nucleolus	heat shock protein binding|misfolded protein binding|unfolded protein binding				0						TATTTAAGGGTTTTTTTTTTT	0.264													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114521072	114521072	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114521072delT								FOXP2 (189980 upstream) : MDFIC (41137 downstream)																							tttttttttgttttttttgtt	0.000													4	2	---	---	---	---	
CTTNBP2	83992	broad.mit.edu	37	7	117423234	117423235	+	Intron	INS	-	GT	GT	rs145914702	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117423234_117423235insGT	uc003vjf.2	-							NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2											ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		CACTAAGATGCGTGTGTGTGTG	0.426													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	122546716	122546716	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122546716delA								CADPS2 (20162 upstream) : TAS2R16 (88043 downstream)																							AATTGGGAAGAAAAAAAATTA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	122880331	122880331	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122880331delT								SLC13A1 (40306 upstream) : IQUB (211907 downstream)																							TCCCTTGTCCTTAAGGTAAAG	0.478													2	5	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126309416	126309416	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126309416delA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	AGTCAACAAGAAAAaaaaaag	0.020										HNSCC(24;0.065)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	127749037	127749038	+	IGR	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127749037_127749038delCA								SND1 (16379 upstream) : MIR129-1 (98887 downstream)																							catacgcatgcacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128736164	128736164	+	IGR	DEL	T	-	-	rs66837005		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128736164delT								TPI1P2 (38871 upstream) : LOC407835 (30161 downstream)																							GGAATGAATCttttttttttt	0.174													8	5	---	---	---	---	
PODXL	5420	broad.mit.edu	37	7	131208559	131208560	+	Intron	DEL	TT	-	-	rs111266089		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131208559_131208560delTT	uc003vqw.3	-						PODXL_uc003vqx.3_Intron	NM_001018111	NP_001018121	O00592	PODXL_HUMAN	podocalyxin-like isoform 1 precursor						cell adhesion|epithelial tube formation|negative regulation of cell-cell adhesion|positive regulation of cell migration|positive regulation of cell-cell adhesion mediated by integrin|regulation of microvillus assembly	actin cytoskeleton|apical plasma membrane|centrosome|filopodium|integral to plasma membrane|lamellipodium|membrane raft|microvillus membrane|nucleolus|ruffle				breast(2)|pancreas(1)	3	Melanoma(18;0.162)					atctaacaaatttttttttttt	0.000													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	132995636	132995636	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132995636delG	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vri.2_Intron|EXOC4_uc003vrj.2_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				TGCAGTCAGTGGGGATGGACT	0.458													4	2	---	---	---	---	
KEL	3792	broad.mit.edu	37	7	142653538	142653538	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142653538delC	uc003wcb.2	-							NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase						proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)					TTTTTTTTTTCTATTATGTCA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	145810211	145810211	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145810211delT								None (None upstream) : CNTNAP2 (3242 downstream)																							ATTTTGACTCTTTTTTTTCAC	0.289													4	2	---	---	---	---	
ZNF767	79970	broad.mit.edu	37	7	149253684	149253684	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149253684delG	uc003wfy.3	-						ZNF767_uc003wfx.2_Intron|ZNF767_uc011kuq.1_Intron	NR_027789				Homo sapiens cDNA FLJ12700 fis, clone NT2RP1000721.											central_nervous_system(1)	1	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00434)			GTGAGTTTATGGTAAAATCAG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150056559	150056560	+	IGR	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150056559_150056560delCA								RARRES2 (17796 upstream) : REPIN1 (8801 downstream)																							tccaccccaccacacacacaca	0.000													4	3	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151288829	151288829	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151288829delC	uc003wkk.2	-						PRKAG2_uc003wki.2_Intron|PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.2_Intron|PRKAG2_uc003wkl.2_Intron|PRKAG2_uc010lqe.1_Intron	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		ggccttaggacccagcaaggt	0.000													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152104993	152104994	+	Intron	DEL	TC	-	-	rs146856728		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152104993_152104994delTC	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		TTAAAATTTATCTTGTTAGAAT	0.262			N		medulloblastoma								4	3	---	---	---	---	
EN2	2020	broad.mit.edu	37	7	155257198	155257198	+	3'UTR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155257198delT	uc003wmb.2	+	2						NM_001427	NP_001418	P19622	HME2_HUMAN	engrailed homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGTGTAAACCTTTTTAAAAAG	0.348													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157680749	157680750	+	Intron	INS	-	G	G	rs140561510	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157680749_157680750insG	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CACGCTGTCTTGGGGGGTGTGA	0.599													3	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157807776	157807776	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157807776delA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TCCCTCAGATAAAAGTGGGTT	0.428													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157878331	157878334	+	Intron	DEL	CACA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157878331_157878334delCACA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		gacgcccatccacacagataccca	0.000													4	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158298796	158298798	+	Intron	DEL	TGC	-	-	rs35831446		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158298796_158298798delTGC	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		ACAAGGCCGGTGCTGAGACACTG	0.631													4	2	---	---	---	---	
DLC1	10395	broad.mit.edu	37	8	13089861	13089861	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13089861delG	uc003wwm.2	-						DLC1_uc003wwl.1_Intron|DLC1_uc003wwn.2_Intron	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						ttttttttttgagacagaatc	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	33571496	33571496	+	IGR	DEL	T	-	-	rs4733166	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33571496delT								DUSP26 (114057 upstream) : None (None downstream)																							ATGGACCCCCTCCTAAGCCCA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	47206540	47206540	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47206540delT								None (None upstream) : BEYLA (545968 downstream)																							tctaaggatattttttttttc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49665395	49665397	+	IGR	DEL	TCA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49665395_49665397delTCA								EFCAB1 (17525 upstream) : SNAI2 (164842 downstream)																							ATTTGGTTGTTCATCATCTTGCT	0.369													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54441109	54441109	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54441109delC								OPRK1 (276915 upstream) : ATP6V1H (187007 downstream)																							ATTTCATCGGCCCCAAGCCAC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55199286	55199286	+	IGR	DEL	T	-	-	rs34947126		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55199286delT								MRPL15 (138212 upstream) : SOX17 (171209 downstream)																							gtatggctgctgagattggcc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65771083	65771084	+	IGR	INS	-	AG	AG			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65771083_65771084insAG								CYP7B1 (59735 upstream) : ARMC1 (743988 downstream)																							GAGTGAACTGCAGAGTGGCAGA	0.500													4	2	---	---	---	---	
ZNF704	619279	broad.mit.edu	37	8	81750967	81750968	+	Intron	INS	-	GGA	GGA	rs140901931	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81750967_81750968insGGA	uc003yby.1	-							NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			gagcagacactggaggaggagg	0.238													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	84067833	84067833	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84067833delT								None (None upstream) : None (None downstream)																							atttgttttgtttttttgttg	0.318													4	2	---	---	---	---	
FAM92A1	137392	broad.mit.edu	37	8	94719943	94719944	+	Intron	DEL	GA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94719943_94719944delGA	uc010maq.2	+						FAM92A1_uc003yfv.3_Intron|FAM92A1_uc003yfx.3_5'Flank|FAM92A1_uc003yfw.3_5'Flank|FAM92A1_uc010mar.2_5'Flank	NM_145269	NP_660312	A1XBS5	F92A1_HUMAN	hypothetical protein LOC137392												0	Breast(36;2.4e-06)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			AAATGTTTTTGATTCCTGGTTA	0.287													2	5	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100808576	100808576	+	Intron	DEL	T	-	-	rs74377154		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100808576delT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			tgagcatgaattttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125290979	125290979	+	IGR	DEL	T	-	-	rs5894697		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125290979delT								FER1L6 (158678 upstream) : TMEM65 (32182 downstream)																							taatcttggctgtgtctctga	0.060													6	3	---	---	---	---	
MTSS1	9788	broad.mit.edu	37	8	125610979	125610979	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125610979delA	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			AGCAGGCACTAACCCCCTCTC	0.423													4	2	---	---	---	---	
KIAA0196	9897	broad.mit.edu	37	8	126088983	126088984	+	Intron	INS	-	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126088983_126088984insC	uc003yrt.2	-						KIAA0196_uc011lir.1_Intron	NM_014846	NP_055661	Q12768	STRUM_HUMAN	strumpellin						cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			CTAAGTCTTTTCTTAAAAAaaa	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	126779777	126779778	+	IGR	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126779777_126779778insT								TRIB1 (329135 upstream) : FAM84B (784909 downstream)																							AAGATGAGGTCTTTTTTTTGTC	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128259899	128259899	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128259899delA								FAM84B (689433 upstream) : LOC727677 (42163 downstream)																							gaagcagaagaaaaaaaaagt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129323628	129323628	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129323628delA								MIR1208 (161194 upstream) : None (None downstream)																							TATTGCAGGTAGGAGTAGATT	0.373													4	2	---	---	---	---	
JRK	8629	broad.mit.edu	37	8	143750582	143750583	+	Intron	DEL	GT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143750582_143750583delGT	uc003ywo.2	-						JRK_uc003ywp.2_Intron|JRK_uc010mew.1_5'Flank	NM_001077527	NP_001070995			jerky isoform b												0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				CAGGGGCATAgtgtgtgtgtgt	0.436											OREG0019038	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	8	144248169	144248169	+	IGR	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144248169delG								LY6H (6116 upstream) : GPIHBP1 (46899 downstream)																							gaagtggagaggggaaggaag	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	14523441	14523441	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14523441delT								NFIB (209496 upstream) : ZDHHC21 (32040 downstream)																							GAGGTTTCTGTTATTCCTGCG	0.448													4	2	---	---	---	---	
C9orf93	203238	broad.mit.edu	37	9	15900507	15900521	+	Intron	DEL	GACACCCGAGCAGAG	-	-	rs139479264		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15900507_15900521delGACACCCGAGCAGAG	uc003zmd.2	+						C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron	NM_173550	NP_775821	Q6TFL3	CI093_HUMAN	hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)		agcctgctgagacacccgagcagaggaccccacta	0.000													5	3	---	---	---	---	
APTX	54840	broad.mit.edu	37	9	32986220	32986220	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32986220delT	uc003zrm.2	-						APTX_uc010mjm.2_Intron|APTX_uc003zrj.2_Intron|APTX_uc011lns.1_Intron|APTX_uc003zrl.2_Intron|APTX_uc003zrn.2_Intron|APTX_uc003zro.2_Intron|APTX_uc003zrp.2_Intron|APTX_uc003zrq.2_Intron|APTX_uc003zrr.2_Intron|APTX_uc003zrs.2_Intron|APTX_uc003zrt.2_Intron|APTX_uc003zru.2_Intron|APTX_uc003zrv.2_Intron|APTX_uc003zrw.2_Intron|APTX_uc003zrx.2_Intron|APTX_uc003zry.2_Intron|APTX_uc003zrz.2_Intron|APTX_uc003zsa.1_Intron|APTX_uc003zsb.1_Intron|APTX_uc003zsc.1_Intron	NM_175072	NP_778242	Q7Z2E3	APTX_HUMAN	aprataxin isoform c						cell death|double-strand break repair|regulation of protein stability|response to hydrogen peroxide|single strand break repair	chromatin|nucleolus|nucleoplasm	chromatin binding|damaged DNA binding|DNA 5'-adenosine monophosphate hydrolase activity|double-stranded DNA binding|double-stranded RNA binding|phosphoglycolate phosphatase activity|phosphoprotein binding|polynucleotide 3'-phosphatase activity|protein N-terminus binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)		CTATAttctctttttttttga	0.169								Direct_reversal_of_damage|Editing_and_processing_nucleases					6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	35136925	35136925	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35136925delT								KIAA1539 (21032 upstream) : UNC13B (25064 downstream)																							ccaccccccatttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66457193	66457194	+	5'Flank	DEL	AG	-	-	rs3068095		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66457193_66457194delAG	uc010mng.1	-						uc004aeb.2_Frame_Shift_Del_p.L163fs|uc004aec.2_5'Flank					Homo sapiens cDNA, FLJ98602.																		agacagcgatagagagagagag	0.035													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66463853	66463854	+	Intron	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66463853_66463854insT	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		AGAACATGTCATTTTTTCCCAG	0.099													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66481328	66481329	+	IGR	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66481328_66481329insT								FAM74A4 (986942 upstream) : LOC442421 (15141 downstream)																							agattctggtgttttttgtctt	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68407435	68407435	+	5'Flank	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68407435delT	uc004aew.1	+											Homo sapiens cDNA, FLJ98602.																		aatagctgtatttaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68462148	68462148	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68462148delC								FAM27B (667959 upstream) : MIR1299 (540091 downstream)																							ggcatagtttccacaagaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68468837	68468837	+	IGR	DEL	G	-	-	rs112347359		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68468837delG								FAM27B (674648 upstream) : MIR1299 (533402 downstream)																							ttccattttagcattaggagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68490476	68490476	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68490476delA								FAM27B (696287 upstream) : MIR1299 (511763 downstream)																							TGAAAGGTTTAAAAATATAAT	0.209													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91312449	91312449	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91312449delA								LOC286238 (45374 upstream) : C9orf47 (293329 downstream)																							GTGAGGAGTGAGCTCCTCGAG	0.229													2	4	---	---	---	---	
WNK2	65268	broad.mit.edu	37	9	96061681	96061682	+	Intron	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96061681_96061682insA	uc004ati.1	+						WNK2_uc011lud.1_Intron|WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_Intron	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2						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						TTAAAAAGGATAAAAAAAAAAA	0.495													4	2	---	---	---	---	
FBP2	8789	broad.mit.edu	37	9	97334982	97334983	+	Intron	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97334982_97334983delCA	uc004auv.2	-						uc004auu.2_Intron	NM_003837	NP_003828	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2						fructose metabolic process|gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)				GCATTTAATTCACACACACACA	0.074													4	2	---	---	---	---	
TMOD1	7111	broad.mit.edu	37	9	100286805	100286806	+	Intron	DEL	TG	-	-	rs71491755		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100286805_100286806delTG	uc004axk.1	+						TMOD1_uc004axl.1_Intron	NM_003275	NP_003266	P28289	TMOD1_HUMAN	tropomodulin 1						muscle filament sliding	cytosol	actin binding				0		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)		tgtgtgtgtatgtgtgtgtgtg	0.050													6	3	---	---	---	---	
PALM2	114299	broad.mit.edu	37	9	112530120	112530120	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112530120delA	uc004beg.2	+						PALM2_uc004bef.2_Intron	NM_001037293	NP_001032370	Q8IXS6	PALM2_HUMAN	paralemmin 2 isoform b						regulation of cell shape	plasma membrane				ovary(2)	2						TTCTAGGTGGAAAAAAGGCAG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	126985540	126985541	+	IGR	DEL	AC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126985540_126985541delAC								LHX2 (190098 upstream) : NEK6 (34345 downstream)																							acacacacatacacacacacac	0.475													5	3	---	---	---	---	
SPTAN1	6709	broad.mit.edu	37	9	131350898	131350899	+	Intron	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131350898_131350899insT	uc004bvl.3	+						SPTAN1_uc011mbg.1_Intron|SPTAN1_uc011mbh.1_Intron|SPTAN1_uc004bvm.3_Intron|SPTAN1_uc004bvn.3_Intron	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1						actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						ACAAAATGAGATTTTTTTTTTA	0.149													6	3	---	---	---	---	
RAPGEF1	2889	broad.mit.edu	37	9	134488641	134488641	+	Intron	DEL	G	-	-	rs67145993		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134488641delG	uc004cbc.2	-						RAPGEF1_uc004cbb.2_Intron|RAPGEF1_uc010mzm.2_Intron|RAPGEF1_uc010mzn.2_Intron|RAPGEF1_uc004cbd.2_Intron|RAPGEF1_uc010mzs.1_Intron|RAPGEF1_uc010mzl.1_Intron|RAPGEF1_uc010mzo.1_Intron|RAPGEF1_uc010mzp.1_Intron|RAPGEF1_uc010mzq.1_Intron|RAPGEF1_uc010mzr.1_Intron	NM_005312	NP_005303	Q13905	RPGF1_HUMAN	guanine nucleotide-releasing factor 2 isoform a						activation of MAPKK activity|nerve growth factor receptor signaling pathway|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome	guanyl-nucleotide exchange factor activity|SH3 domain binding			lung(3)|ovary(2)|breast(1)|skin(1)	7		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		AAAACACGGTGGGGGAGAAGA	0.313													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137333559	137333559	+	IGR	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137333559delG								RXRA (1128 upstream) : COL5A1 (200093 downstream)																							TCTTGGGTGCGGGGCTGAGCC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137484365	137484365	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137484365delC								RXRA (151934 upstream) : COL5A1 (49287 downstream)																							TCTCCTGCCTCCGTGGACAAG	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	140012446	140012446	+	IGR	DEL	T	-	-	rs113173716		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140012446delT								DPP7 (3251 upstream) : GRIN1 (21163 downstream)																							CAttttgtccttttttttttt	0.010													3	3	---	---	---	---	
PNPLA7	375775	broad.mit.edu	37	9	140384938	140384938	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140384938delC	uc004cnf.2	-						C9orf167_uc011mew.1_Intron|PNPLA7_uc004cnd.1_5'Flank|PNPLA7_uc004cne.1_5'Flank|PNPLA7_uc011mfa.1_Intron|PNPLA7_uc010ncj.1_Intron	NM_152286	NP_689499	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7						lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity			skin(1)	1	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		gcaacagaggccatgaggaag	0.000													4	2	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1692699	1692700	+	Intron	INS	-	G	G	rs144570707	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1692699_1692700insG	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		ACCACAGCGCAGGGAAACGCAC	0.530													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2833502	2833502	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2833502delA								None (None upstream) : PFKP (276250 downstream)																							GGTCGGATTTAAAAAAAAAGA	0.493													4	2	---	---	---	---	
DNAJC1	64215	broad.mit.edu	37	10	22193512	22193512	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22193512delT	uc001irc.2	-	7	1046	c.759delA	c.(757-759)AAAfs	p.K253fs	DNAJC1_uc001ird.2_Frame_Shift_Del_p.K139fs	NM_022365	NP_071760	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	253	Cytoplasmic (By similarity).				negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				ATCTTGTTTCTTTATATTTAG	0.279													527	229	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30839927	30839928	+	IGR	INS	-	TGAG	TGAG			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30839927_30839928insTGAG								MAP3K8 (89166 upstream) : LYZL2 (60781 downstream)																							tcagaggcctatgagtgtgttt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42641671	42641673	+	IGR	DEL	TCA	-	-	rs112369070	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42641671_42641673delTCA								None (None upstream) : LOC441666 (185642 downstream)																							tttcttcatttcatcatttcatc	0.000													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42676291	42676292	+	IGR	DEL	AG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42676291_42676292delAG								None (None upstream) : LOC441666 (151023 downstream)																							acacagagacagagattgcagt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	47009062	47009062	+	IGR	DEL	A	-	-	rs4129920	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47009062delA								GPRIN2 (3419 upstream) : ANXA8 (2691 downstream)																							TCTTGGGGAGAGGGTCAAGGA	0.353													4	2	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53566621	53566621	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53566621delT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTCCCTGTGCTTTTTCACAGC	0.478													4	2	---	---	---	---	
HKDC1	80201	broad.mit.edu	37	10	71007489	71007489	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71007489delT	uc001jpf.3	+						HKDC1_uc010qje.1_Intron	NM_025130	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1						glycolysis	mitochondrion|nucleus	ATP binding|hexokinase activity			ovary(4)|skin(1)	5						AGGGAAAAGGTGAATCCAGGG	0.483													4	2	---	---	---	---	
HK1	3098	broad.mit.edu	37	10	71132308	71132308	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71132308delT	uc001jpl.3	+						HK1_uc001jpg.3_Intron|HK1_uc001jph.3_Intron|HK1_uc001jpi.3_Intron|HK1_uc001jpj.3_Intron|HK1_uc001jpk.3_Intron|HK1_uc009xqd.2_Intron	NM_000188	NP_000179	P19367	HXK1_HUMAN	hexokinase 1 isoform HKI						glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1						ATTATGGCCCTAGAATAGGAC	0.448													4	2	---	---	---	---	
ZMIZ1	57178	broad.mit.edu	37	10	80894933	80894933	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80894933delA	uc001kaf.2	+							NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17						transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			TACAGTACCTAATAAGGTGGG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	83279433	83279433	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83279433delC								SH2D4B (873117 upstream) : NRG3 (355637 downstream)																							gagccatggtcacagagtagc	0.000													4	2	---	---	---	---	
NOC3L	64318	broad.mit.edu	37	10	96097334	96097334	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96097334delA	uc001kjq.1	-							NM_022451	NP_071896	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog							nuclear speck|nucleolus	binding			ovary(1)	1		Colorectal(252;0.0897)				ACAGAAGAAGAAAAAAAATGT	0.204													4	2	---	---	---	---	
SORBS1	10580	broad.mit.edu	37	10	97163900	97163900	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97163900delT	uc001kkp.2	-						SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		AGGAGCCACCTTTTTTTTTCA	0.478													4	2	---	---	---	---	
C10orf26	54838	broad.mit.edu	37	10	104570748	104570749	+	Intron	DEL	TC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104570748_104570749delTC	uc001kwe.3	+						C10orf26_uc001kwf.3_Intron|C10orf26_uc009xxg.1_Intron	NM_017787	NP_060257	Q9NX94	OPA1L_HUMAN	hypothetical protein LOC54838 isoform 2							integral to membrane				central_nervous_system(1)	1		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;6.14e-09)|all cancers(201;1.66e-07)|BRCA - Breast invasive adenocarcinoma(275;0.224)		cATTCATCCATCTCTCTCTCTC	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122067332	122067332	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122067332delA								SEC23IP (366087 upstream) : PPAPDC1A (149134 downstream)																							GTTAGCACCTATGGCTGTGTG	0.483													4	2	---	---	---	---	
FGFR2	2263	broad.mit.edu	37	10	123309140	123309141	+	Intron	DEL	CT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123309140_123309141delCT	uc010qtk.1	-						FGFR2_uc010qtg.1_Intron|FGFR2_uc010qth.1_Intron|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Intron|FGFR2_uc010qtl.1_Intron|FGFR2_uc010qtm.1_Intron|FGFR2_uc001lfl.3_Intron|FGFR2_uc001lfm.2_Intron|FGFR2_uc001lfn.3_Intron|FGFR2_uc010qtn.1_Intron|FGFR2_uc010qto.1_Intron|FGFR2_uc001lfo.1_Intron|FGFR2_uc010qtp.1_Intron|FGFR2_uc010qtq.1_Intron	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1						angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)	tgcgatcctgctctctctctct	0.000		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	124483974	124483974	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124483974delC								C10orf120 (24636 upstream) : FLJ46361 (32236 downstream)																							CCTTTTCTCACCCCCACAGAC	0.557													4	2	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127615446	127615447	+	Intron	INS	-	T	T	rs148348150		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127615446_127615447insT	uc001ljh.3	+						FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				CTCATACTTAATTTtttttatt	0.050													4	2	---	---	---	---	
RASSF7	8045	broad.mit.edu	37	11	562893	562893	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:562893delC	uc001lqc.2	+						C11orf35_uc001lpx.2_5'Flank|RASSF7_uc001lqa.2_Intron|RASSF7_uc001lqb.2_Intron|RASSF7_uc001lqd.2_Intron	NM_003475	NP_003466	Q02833	RASF7_HUMAN	Ras association (RalGDS/AF-6) domain family						regulation of transcription, DNA-dependent|signal transduction	nucleus	DNA binding|protein binding			skin(1)	1		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCCTGTCACTCCCCCACCCCT	0.672													4	2	---	---	---	---	
IGF2	3481	broad.mit.edu	37	11	2163758	2163758	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2163758delC	uc001lvh.2	-						IGF2_uc009ydf.2_5'Flank|INS-IGF2_uc001lvi.2_Intron|IGF2AS_uc001lvk.1_Intron|IGF2AS_uc010qxi.1_Intron|IGF2AS_uc001lvl.1_Intron	NM_001007139	NP_001007140	P01344	IGF2_HUMAN	insulin-like growth factor 2 isoform 1						glucose metabolic process|ossification|phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling|positive regulation of activated T cell proliferation|positive regulation of cell division|positive regulation of glycogen (starch) synthase activity|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|skeletal system development	extracellular space	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|protein serine/threonine kinase activator activity|receptor activator activity			central_nervous_system(1)	1		all_epithelial(84;5.04e-06)|Breast(177;0.000777)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.0179)|COAD - Colon adenocarcinoma(6;0.029)	BRCA - Breast invasive adenocarcinoma(625;1.09e-05)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		TCAGTGCTGTCCTGTGATCCG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	3094334	3094334	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3094334delC								CARS (15663 upstream) : OSBPL5 (14012 downstream)																							AAGCAGGCAGCCCAGAGAGCT	0.463													4	2	---	---	---	---	
LOC650368	650368	broad.mit.edu	37	11	3425129	3425129	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3425129delT	uc010qxs.1	+						LOC650368_uc001lxx.2_Intron|LOC650368_uc001lxy.2_Intron	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						TCCAAGCATCTTTTTTTTGTT	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	4561358	4561359	+	IGR	INS	-	TG	TG	rs148899386	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4561358_4561359insTG								OR52K1 (50283 upstream) : OR52M1 (5062 downstream)																							ACAGAATAGACAGATACTAAGT	0.337													3	3	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16205031	16205031	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16205031delA	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						TTTTTCTCATAATTGGTCCAA	0.199													4	2	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16600355	16600355	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16600355delA	uc001mmi.3	-						SOX6_uc001mmh.1_Intron|SOX6_uc001mmj.2_Intron			P35712	SOX6_HUMAN	Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						GAGAGATCCTAAGCAGTGAGG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	17584118	17584118	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17584118delA								USH1C (18155 upstream) : MYOD1 (156992 downstream)																							CCCATTTTACAAAAAAAAAAT	0.313													4	2	---	---	---	---	
PTPN5	84867	broad.mit.edu	37	11	18776462	18776462	+	Intron	DEL	C	-	-	rs71050630		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18776462delC	uc001mpd.2	-						PTPN5_uc001mpb.2_Intron|PTPN5_uc001mpc.2_Intron|PTPN5_uc001mpe.2_Intron|PTPN5_uc010rdj.1_Intron|PTPN5_uc001mpf.2_Intron|PTPN5_uc010rdk.1_Intron	NM_006906	NP_008837	P54829	PTN5_HUMAN	protein-tyrosine-phosphatase non-receptor 5							integral to membrane	phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(2)	2						aggtggccctcagtgaaccct	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	38636304	38636304	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38636304delA								None (None upstream) : None (None downstream)																							cattatatctaaaaaaagtac	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	38976860	38976860	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38976860delA								None (None upstream) : None (None downstream)																							CCAAAGTCAGAAGGCAAATGA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59848440	59848443	+	IGR	DEL	ATAC	-	-	rs72094307		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59848440_59848443delATAC								MS4A3 (9853 upstream) : MS4A2 (7694 downstream)																							gaacagactaatacaTAAGGTATG	0.020													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	61515171	61515171	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61515171delC								DAGLA (699 upstream) : C11orf9 (4950 downstream)																							AATGCAGGGGCCACTAGAAGT	0.607											OREG0021011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70444661	70444661	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70444661delC	uc001oqc.2	-						SHANK2_uc010rqn.1_Intron|SHANK2_uc001opz.2_Intron|uc009ysn.1_Intron|SHANK2_uc010rqp.1_Intron	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			agagaacactccccagcttct	0.000													4	2	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70550736	70550736	+	Intron	DEL	T	-	-	rs35772412		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70550736delT	uc001oqc.2	-							NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			AGAGATGCGATGGAAGGACAC	0.512													4	2	---	---	---	---	
ARHGEF17	9828	broad.mit.edu	37	11	73036596	73036597	+	Intron	DEL	CT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73036596_73036597delCT	uc001otu.2	+							NM_014786	NP_055601	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0						TACACACACACTCTCTCTCTCT	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	75265132	75265132	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75265132delT								GDPD5 (28533 upstream) : SERPINH1 (8038 downstream)																							gctagctcccttTCTCCTGTG	0.274													4	2	---	---	---	---	
GRIA4	2893	broad.mit.edu	37	11	105624097	105624097	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105624097delA	uc001pix.2	+						GRIA4_uc001piu.1_Intron|GRIA4_uc001piw.2_Intron|GRIA4_uc001piv.2_Intron|GRIA4_uc009yxk.1_Intron	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	GACTCTGGGGAAAAATTTCTA	0.299													4	2	---	---	---	---	
NCAM1	4684	broad.mit.edu	37	11	113061118	113061118	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113061118delA	uc009yyq.1	+						NCAM1_uc001pno.2_Intron	NM_001076682	NP_001070150	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		GATGCATCATAATGTTGCCAG	0.488													4	2	---	---	---	---	
FAM55B	120406	broad.mit.edu	37	11	114549970	114549971	+	Intron	DEL	GT	-	-	rs35145055		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114549970_114549971delGT	uc009yyy.2	+							NM_182495	NP_872301	Q96DL1	FA55B_HUMAN	hypothetical protein LOC120406							integral to membrane				ovary(1)	1						Atgtgtgtgcgtgtgtgtgtgt	0.322													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114834437	114834438	+	IGR	DEL	GC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114834437_114834438delGC								FAM55B (256785 upstream) : CADM1 (205515 downstream)																							actggcagaggcctcctggtgt	0.193													3	4	---	---	---	---	
DSCAML1	57453	broad.mit.edu	37	11	117414537	117414537	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117414537delT	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GTTTGTTTTGTTTTTTTTAAA	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	118746668	118746670	+	IGR	DEL	TGC	-	-	rs139637756	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118746668_118746670delTGC								DDX6 (84696 upstream) : CXCR5 (7871 downstream)																							gctgtgttgttgctgtgggttgt	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	120078263	120078263	+	IGR	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120078263delG								TRIM29 (69400 upstream) : OAF (3484 downstream)																							ACATGTGGCAGGGGGTGAGAG	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124453578	124453578	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124453578delA								OR8A1 (12634 upstream) : PANX3 (27875 downstream)																							agacaacatgaaaaaaaagat	0.035													3	4	---	---	---	---	
NINJ2	4815	broad.mit.edu	37	12	753283	753283	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:753283delA	uc001qil.2	-						NINJ2_uc010sdr.1_5'Flank|NINJ2_uc010sds.1_Intron|uc001qim.1_RNA|uc009zdl.1_RNA	NM_016533	NP_057617	Q9NZG7	NINJ2_HUMAN	ninjurin 2						nervous system development|neuron cell-cell adhesion|tissue regeneration	integral to plasma membrane				ovary(2)	2	all_cancers(10;0.0101)|all_epithelial(11;0.0174)|Ovarian(42;0.0512)|all_lung(10;0.103)|Lung NSC(10;0.185)		OV - Ovarian serous cystadenocarcinoma(31;3.26e-05)|BRCA - Breast invasive adenocarcinoma(9;0.0508)			GGCAAGAAGGAAAACCGGAAA	0.373													4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2651080	2651083	+	Intron	DEL	TCAG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2651080_2651083delTCAG	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron|CACNA1C_uc009zdy.1_Intron|CACNA1C_uc001qkv.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	CTGGTGCCACTCAGTCAGTCATGA	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	5514656	5514657	+	IGR	INS	-	G	G	rs147836366	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5514656_5514657insG								KCNA5 (358708 upstream) : NTF3 (26623 downstream)																							ACTGGATCAGAGGGGGCTTCTC	0.490													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	5619325	5619325	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5619325delT								NTF3 (14862 upstream) : ANO2 (52492 downstream)																							TTGGCagtggttaagagtgtg	0.294													4	2	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	5726123	5726123	+	Intron	DEL	A	-	-	rs143669468		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5726123delA	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						agatcacaccataacacactc	0.109													3	4	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	6024630	6024633	+	Intron	DEL	CAAA	-	-	rs78083110		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6024630_6024633delCAAA	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						ATCTGCTATTCAAACAGAGTTCAG	0.402													4	3	---	---	---	---	
FAM66C	440078	broad.mit.edu	37	12	8356595	8356598	+	Intron	DEL	TCTT	-	-	rs149662213	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8356595_8356598delTCTT	uc009zgc.2	+						FAM66C_uc001qug.3_Intron					Homo sapiens cDNA FLJ38982 fis, clone NT2RI2005239.												0						tttctctttctctttctttctttc	0.054													4	2	---	---	---	---	
RIMKLB	57494	broad.mit.edu	37	12	8862498	8862498	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8862498delC	uc001quu.2	+						RIMKLB_uc009zgf.1_Intron|RIMKLB_uc001qux.2_Intron|RIMKLB_uc010sgl.1_Intron|RIMKLB_uc001quw.2_Intron	NM_020734	NP_065785	Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0						tttcaggcatccactgggggt	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	22915916	22915916	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22915916delT								ETNK1 (72309 upstream) : SOX5 (769316 downstream)																							gtttgtggtattttttttttg	0.040													3	3	---	---	---	---	
SOX5	6660	broad.mit.edu	37	12	24422111	24422111	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24422111delA	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						TGACTGAGGGAAAAAAGTGAT	0.313													4	2	---	---	---	---	
TMTC1	83857	broad.mit.edu	37	12	29791804	29791804	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29791804delT	uc001rjb.2	-						TMTC1_uc001riz.2_Intron|TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					CTGCTGCCTGTTTTCATCCTC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	43280405	43280405	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43280405delT								PRICKLE1 (296833 upstream) : ADAMTS20 (467608 downstream)																							gttttctccattttttttctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	44019539	44019540	+	IGR	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44019539_44019540delCA								ADAMTS20 (73815 upstream) : PUS7L (102874 downstream)																							ttcctgtccccacacacacaca	0.020													4	2	---	---	---	---	
ANO6	196527	broad.mit.edu	37	12	45708802	45708802	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45708802delA	uc001roo.2	+						ANO6_uc010sld.1_Intron|ANO6_uc010sle.1_Intron|ANO6_uc010slf.1_Intron|ANO6_uc010slg.1_Intron	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a						activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2						AGGATGTTGGAAAGATAATGT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	46518789	46518789	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46518789delT								SFRS2IP (132886 upstream) : SLC38A1 (58054 downstream)																							CTCTTGTTCCTTTTTTTTTTA	0.328													4	3	---	---	---	---	
FAIM2	23017	broad.mit.edu	37	12	50276929	50276929	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50276929delA	uc001rvj.1	-						FAIM2_uc001rvi.1_Intron|FAIM2_uc001rvk.1_Intron	NM_012306	NP_036438	Q9BWQ8	FAIM2_HUMAN	Fas apoptotic inhibitory molecule 2						anti-apoptosis|apoptosis	cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|ovary(1)|skin(1)	3						gggagtggggaggtcagagag	0.000													4	2	---	---	---	---	
KRT8	3856	broad.mit.edu	37	12	53291008	53291008	+	3'UTR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53291008delA	uc001sbd.2	-	8					KRT8_uc009zmj.2_3'UTR|KRT8_uc009zmk.1_3'UTR|KRT8_uc009zml.1_3'UTR|KRT8_uc009zmm.1_3'UTR	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8						cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	ATTTTGGACCAAAAAAAAAAA	0.532													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82395133	82395133	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82395133delT								PPFIA2 (242024 upstream) : CCDC59 (350957 downstream)																							GTCAGTGCACTTTTTTTttca	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82691079	82691079	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82691079delT								PPFIA2 (537970 upstream) : CCDC59 (55011 downstream)																							cattactccatttggtattgt	0.109													4	2	---	---	---	---	
CRADD	8738	broad.mit.edu	37	12	94256317	94256317	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94256317delT	uc010sur.1	+						CRADD_uc010sus.1_Intron	NM_003805	NP_003796	P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1						GTGAAGATGGTTAGGATGCCT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106184507	106184508	+	IGR	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106184507_106184508delCA								C12orf75 (419212 upstream) : NUAK1 (272617 downstream)																							AACTGATCATCACCATGCACTC	0.396													4	2	---	---	---	---	
PRKAB1	5564	broad.mit.edu	37	12	120117511	120117512	+	Intron	DEL	AC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120117511_120117512delAC	uc009zwu.2	+						PRKAB1_uc001txg.2_Intron	NM_006253	NP_006244	Q9Y478	AAKB1_HUMAN	AMP-activated protein kinase beta 1						cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol					0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.166)	Adenosine monophosphate(DB00131)|Metformin(DB00331)	CTGGCCAGAGACACACACCGAT	0.584													4	2	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124952858	124952859	+	Intron	INS	-	TCC	TCC			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124952858_124952859insTCC	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		caccctcatcatcctcatcacc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127282104	127282104	+	IGR	DEL	C	-	-	rs67048831		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127282104delC								LOC100128554 (324774 upstream) : None (None downstream)																							AATTAATTCACCAGAGTTGAG	0.408													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131887437	131887437	+	IGR	DEL	A	-	-	rs60425958		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131887437delA								LOC116437 (189962 upstream) : SFRS8 (308198 downstream)																							GGAGACTCATAGGGCAAGGCT	0.602													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131991400	131991400	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131991400delC								LOC116437 (293925 upstream) : SFRS8 (204235 downstream)																							tgagctccagcccccacactg	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	23039498	23039498	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23039498delT								FGF9 (760858 upstream) : SGCG (715562 downstream)																							ATATACCTGCTTTTTTTTTTT	0.388													4	3	---	---	---	---	
EEF1DP3	196549	broad.mit.edu	37	13	32504568	32504569	+	Intron	DEL	TG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32504568_32504569delTG	uc001utu.2	+						EEF1DP3_uc010tdv.1_Intron					Homo sapiens similar to hypothetical protein FLJ20897, mRNA (cDNA clone IMAGE:5267252).												0						CATTTGGTCCTGAACTCTTACT	0.342													4	2	---	---	---	---	
TRPC4	7223	broad.mit.edu	37	13	38357629	38357629	+	Intron	DEL	T	-	-	rs7339215	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38357629delT	uc001uws.2	-						TRPC4_uc010abv.2_5'Flank|TRPC4_uc001uwt.2_Intron|TRPC4_uc010tey.1_Intron|TRPC4_uc010abw.2_Intron|TRPC4_uc010abx.2_Intron|TRPC4_uc010aby.2_Intron	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,						axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		AGAGTTAAGGTTTTTTTTTTT	0.229													6	3	---	---	---	---	
CCDC122	160857	broad.mit.edu	37	13	44452038	44452038	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44452038delT	uc010acf.2	-						CCDC122_uc010tfn.1_5'Flank|C13orf31_uc010acg.2_5'Flank|C13orf31_uc001uzf.3_5'Flank	NM_144974	NP_659411	Q5T0U0	CC122_HUMAN	coiled-coil domain containing 122												0		Lung NSC(96;7.5e-06)|Breast(139;0.00765)|Hepatocellular(98;0.00826)|Prostate(109;0.0143)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000767)|BRCA - Breast invasive adenocarcinoma(63;0.128)		acattaattattttttttttc	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	44847727	44847727	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44847727delC								LOC121838 (243129 upstream) : SERP2 (100251 downstream)																							TCCAAAGCCACCAGAGCATGT	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	53944992	53944992	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53944992delT								OLFM4 (318806 upstream) : MIR1297 (941115 downstream)																							AGTTGCAGTGTTTATGTGGCT	0.358													4	2	---	---	---	---	
DIAPH3	81624	broad.mit.edu	37	13	60255738	60255738	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60255738delT	uc001vht.2	-						DIAPH3_uc001vhs.2_Intron	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		GTTTTAAGTGTTTTTTTTTTC	0.174													4	2	---	---	---	---	
TDRD3	81550	broad.mit.edu	37	13	61058253	61058253	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61058253delT	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		TGGGAGAGGGTTTTTTTTTGA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	61171856	61171856	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61171856delA								TDRD3 (23844 upstream) : PCDH20 (811965 downstream)																							tctgtattacaaaaaaaagga	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63621302	63621303	+	IGR	INS	-	C	C	rs112606463		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63621302_63621303insC								None (None upstream) : OR7E156P (690265 downstream)																							AGAATTTATTGCTTTTTTATGA	0.342													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63625822	63625823	+	IGR	DEL	GG	-	-	rs66850611	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63625822_63625823delGG								None (None upstream) : OR7E156P (685745 downstream)																							gaagacaagaggttcagacaga	0.015													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	82474554	82474555	+	IGR	INS	-	A	A	rs139839723	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82474554_82474555insA								None (None upstream) : None (None downstream)																							TGACCAAAAACAAAAAACAAGA	0.361													1	5	---	---	---	---	
CLDN10	9071	broad.mit.edu	37	13	96127068	96127068	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96127068delA	uc001vmg.2	+						CLDN10_uc010tii.1_Intron	NM_182848	NP_878268	P78369	CLD10_HUMAN	claudin 10 isoform a						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)			AGCTCATTCCAGGGGGTAGGG	0.572													4	2	---	---	---	---	
CLYBL	171425	broad.mit.edu	37	13	100273093	100273096	+	Intron	DEL	AAAG	-	-	rs67220471		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100273093_100273096delAAAG	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron	NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					aaagaaagaaaaagaaagaaagaa	0.167													8	5	---	---	---	---	
CDC16	8881	broad.mit.edu	37	13	115028568	115028568	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115028568delA	uc001vuk.1	+						CDC16_uc001vul.1_Intron|CDC16_uc001vum.1_Intron|CDC16_uc001vun.1_Intron|CDC16_uc001vuo.1_Intron	NM_003903	NP_003894	Q13042	CDC16_HUMAN	anaphase-promoting complex, subunit 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cell proliferation|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	binding				0	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			TTTTCTAGGTAATATTGACTT	0.308													25	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19041617	19041617	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19041617delA								None (None upstream) : OR11H12 (335977 downstream)																							ggcaaacatcacaaagaagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20292351	20292351	+	IGR	DEL	T	-	-	rs79595296		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20292351delT								OR4M1 (42929 upstream) : OR4N2 (3257 downstream)																							CATATATGGATTTTTTTTTTG	0.358													4	2	---	---	---	---	
NDRG2	57447	broad.mit.edu	37	14	21506205	21506206	+	Intron	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21506205_21506206insA	uc010tll.1	-							NM_201541	NP_963835	Q9UN36	NDRG2_HUMAN	N-myc downstream-regulated gene 2 isoform b						cell differentiation|nervous system development	centrosome|cytosol|Golgi apparatus|nucleus|perinuclear region of cytoplasm				ovary(1)|breast(1)	2	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		TCAAACAATATACTGTGTCATG	0.465													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	27386322	27386322	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27386322delC								NOVA1 (319362 upstream) : None (None downstream)																							ACAAAATGAACATTTAAAAAA	0.343													4	2	---	---	---	---	
SNX6	58533	broad.mit.edu	37	14	35051043	35051043	+	Intron	DEL	T	-	-	rs33966364		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35051043delT	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419	Q9UNH7	SNX6_HUMAN	sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		TTGAtttttgtttttttttgc	0.144													4	2	---	---	---	---	
SLC25A21	89874	broad.mit.edu	37	14	37574608	37574608	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37574608delA	uc001wtz.1	-							NM_030631	NP_085134	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial						lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		GAGGGCTAAGAAAATGTGGTG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	41457558	41457559	+	IGR	DEL	TG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41457558_41457559delTG								None (None upstream) : LRFN5 (619205 downstream)																							aattttcttttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
SYT16	83851	broad.mit.edu	37	14	62496499	62496499	+	Intron	DEL	A	-	-	rs35272199		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62496499delA	uc001xfu.1	+						SYT16_uc010tsd.1_Intron	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like											central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GTCTAGTTGGAAAAAAAAAAA	0.343													2	4	---	---	---	---	
SPTB	6710	broad.mit.edu	37	14	65252070	65252070	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65252070delA	uc001xht.2	-						SPTB_uc001xhr.2_Intron|SPTB_uc001xhs.2_Intron|SPTB_uc001xhu.2_Intron|SPTB_uc010aqi.2_5'Flank	NM_000347	NP_000338	P11277	SPTB1_HUMAN	spectrin beta isoform b						actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		TTCAGATTTGAAAAAAAAAAA	0.299													4	3	---	---	---	---	
FUT8	2530	broad.mit.edu	37	14	66015210	66015210	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66015210delT	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron	NM_178155	NP_835368	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a						in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		gccatcttgattttttttttg	0.000													3	3	---	---	---	---	
GPHN	10243	broad.mit.edu	37	14	67470663	67470664	+	Intron	INS	-	T	T	rs143277840	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67470663_67470664insT	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		gggtctgtgtcgatttaatcag	0.074			T	MLL	AL								5	5	---	---	---	---	
RGS6	9628	broad.mit.edu	37	14	73015955	73015955	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73015955delT	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron|RGS6_uc010ttp.1_Intron|RGS6_uc001xmz.1_Intron	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		CTGTTTTTTGTTTTTTTTTTT	0.483													4	2	---	---	---	---	
ESRRB	2103	broad.mit.edu	37	14	76843927	76843927	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76843927delT	uc001xsr.2	+						ESRRB_uc001xso.2_Intron	NM_004452	NP_004443	A2VDJ2	A2VDJ2_HUMAN	estrogen-related receptor beta							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.0213)		CGTCTTCCTCTTTTTTTTCTG	0.458													5	3	---	---	---	---	
AHSA1	10598	broad.mit.edu	37	14	77932171	77932171	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77932171delT	uc001xtw.2	+						AHSA1_uc010tvk.1_Intron	NM_012111	NP_036243	O95433	AHSA1_HUMAN	activator of heat shock 90kDa protein ATPase						protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		CTCTAttctcttttttttttt	0.224													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82605306	82605307	+	IGR	INS	-	C	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82605306_82605307insC								SEL1L (605101 upstream) : None (None downstream)																							AATTAATTTTTCCTCAGTGTTG	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	84713896	84713896	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84713896delC								None (None upstream) : None (None downstream)																							agactcctcaccccatcatag	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	84799678	84799679	+	IGR	DEL	AG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84799678_84799679delAG								None (None upstream) : None (None downstream)																							agcgggaggaagagagagagtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	85321065	85321065	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85321065delC								None (None upstream) : FLRT2 (675423 downstream)																							TTTGGTGATGCCCCACTCTCT	0.448													4	2	---	---	---	---	
EML5	161436	broad.mit.edu	37	14	89236828	89236829	+	Intron	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89236828_89236829insA	uc001xxg.2	-							NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like							cytoplasm|microtubule				ovary(3)	3						tcagtacagagaaaaaatgctg	0.005													4	2	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	89647258	89647259	+	Intron	INS	-	AACAT	AACAT	rs140257053	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89647258_89647259insAACAT	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						gagagacagagggcagagacag	0.173													4	2	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	90081654	90081654	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90081654delT	uc001xxo.3	-						FOXN3_uc010atk.2_Intron|FOXN3_uc001xxp.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						GGCATAGCCATCCAAAAACAG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98984635	98984635	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98984635delT								C14orf64 (540174 upstream) : C14orf177 (193315 downstream)																							AATTCTCCCATTTTTAAAAAG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99353824	99353825	+	IGR	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99353824_99353825insA								C14orf177 (169727 upstream) : BCL11B (281802 downstream)																							ATCTGCCACTTAAAAAAAATAA	0.450													4	2	---	---	---	---	
AMN	81693	broad.mit.edu	37	14	103391246	103391246	+	Intron	DEL	A	-	-	rs35919524		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103391246delA	uc001ymg.3	+						AMN_uc001ymh.3_Intron	NM_030943	NP_112205	Q9BXJ7	AMNLS_HUMAN	amnionless protein precursor						lipid metabolic process|lipoprotein metabolic process|multicellular organismal development	integral to membrane|plasma membrane					0				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	atcgttggggaaaaaaagaac	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20452825	20452826	+	IGR	INS	-	AGAA	AGAA	rs148892008	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20452825_20452826insAGAA								None (None upstream) : GOLGA6L6 (284268 downstream)																							ATGGGGAGgagagaaagagaga	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26144586	26144586	+	IGR	DEL	T	-	-	rs141426701		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26144586delT								ATP10A (34269 upstream) : GABRB3 (644109 downstream)																							tgtgtcttcattttttttttt	0.000													6	3	---	---	---	---	
MEIS2	4212	broad.mit.edu	37	15	37329741	37329742	+	Intron	DEL	AA	-	-	rs67575355		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37329741_37329742delAA	uc001zjr.2	-						MEIS2_uc001zjl.2_Intron|MEIS2_uc010ucj.1_Intron|MEIS2_uc001zjm.2_Intron|MEIS2_uc001zjn.2_Intron|MEIS2_uc001zjo.2_Intron|MEIS2_uc001zjp.2_Intron|MEIS2_uc001zjs.2_Intron|MEIS2_uc001zju.2_Intron|MEIS2_uc001zjt.2_Intron	NM_170675	NP_733775	O14770	MEIS2_HUMAN	Meis homeobox 2 isoform c						negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)	2		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		CATTATCATGAAAAAAAAAAAG	0.391													4	2	---	---	---	---	
ZSCAN29	146050	broad.mit.edu	37	15	43661549	43661549	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43661549delA	uc001zrk.1	-						ZSCAN29_uc001zrj.1_5'Flank|ZSCAN29_uc010bdf.1_Intron|ZSCAN29_uc001zrl.1_Intron|ZSCAN29_uc010bdg.1_Intron|ZSCAN29_uc001zrm.2_Intron|TUBGCP4_uc001zrn.2_5'Flank|TUBGCP4_uc001zro.2_5'Flank	NM_152455	NP_689668	Q8IWY8	ZSC29_HUMAN	zinc finger protein 690						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		CTTCAGGCTGAAAAAAAAAAA	0.408													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	47122019	47122020	+	IGR	DEL	AG	-	-	rs34446655		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47122019_47122020delAG								None (None upstream) : SEMA6D (354383 downstream)																							ATCAAAGCAAagagagagagag	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	48123068	48123069	+	IGR	INS	-	AC	AC	rs144809286	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48123068_48123069insAC								SEMA6D (56649 upstream) : SLC24A5 (290100 downstream)																							TATCTACATAGacacacacaca	0.124													6	4	---	---	---	---	
SHC4	399694	broad.mit.edu	37	15	49176726	49176727	+	Intron	INS	-	T	T	rs146399374	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49176726_49176727insT	uc001zxb.1	-							NM_203349	NP_976224	Q6S5L8	SHC4_HUMAN	rai-like protein						intracellular signal transduction	cell junction|postsynaptic membrane				ovary(3)|pancreas(2)	5		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		attaaataaacttttttttaaa	0.312													6	10	---	---	---	---	
TCF12	6938	broad.mit.edu	37	15	57484134	57484134	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57484134delA	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		tccatctcagaaaaaaaaaag	0.174			T	TEC	extraskeletal myxoid chondrosarcoma								4	3	---	---	---	---	
NARG2	79664	broad.mit.edu	37	15	60728185	60728185	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60728185delA	uc002agp.2	-						NARG2_uc002ago.2_Intron	NM_024611	NP_078887	Q659A1	NARG2_HUMAN	NMDA receptor regulated 2 isoform a							nucleus				ovary(1)|lung(1)	2						cacaaagaacaaaaaaaaaga	0.104													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63380307	63380308	+	IGR	INS	-	A	A	rs150860625	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63380307_63380308insA								TPM1 (16196 upstream) : LACTB (33724 downstream)																							gaaaaggaaagaaaaaaaaaga	0.218													6	4	---	---	---	---	
DENND4A	10260	broad.mit.edu	37	15	65992745	65992746	+	Intron	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65992745_65992746delCA	uc002aph.2	-						DENND4A_uc002api.2_Intron|DENND4A_uc002apj.3_Intron	NM_005848	NP_005839	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						aatctaatatcaaataaaatac	0.163													4	2	---	---	---	---	
MAP2K5	5607	broad.mit.edu	37	15	67841455	67841455	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67841455delG	uc002aqu.2	+						MAP2K5_uc002aqt.1_Intron|MAP2K5_uc002aqv.2_Intron|MAP2K5_uc010ujw.1_5'UTR	NM_145160	NP_660143	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5						nerve growth factor receptor signaling pathway		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)	2						CAGCCTGGGAGGGACACTGTG	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70006924	70006928	+	IGR	DEL	GCTTC	-	-	rs144913472		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70006924_70006928delGCTTC								LOC145837 (143145 upstream) : C15orf50 (120645 downstream)																							gggaagagGGGCTTCTTGCGGTTGC	0.220													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84033236	84033237	+	IGR	DEL	AC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84033236_84033237delAC								BNC1 (79768 upstream) : SH3GL3 (82854 downstream)																							GCTATCAGCTacacacacacac	0.262													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	85121557	85121557	+	RNA	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85121557delA	uc002bko.1	+	3		c.757delA								Homo sapiens cDNA: FLJ22824 fis, clone KAIA3991.																		TTCTTGCCTTAAAAAAAAAAA	0.279													4	2	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	87417868	87417868	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87417868delG	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						CCCTCTATGTGGAGTAAGGCA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93891672	93891673	+	Intron	DEL	TG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93891672_93891673delTG	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																		ATGTCTAGGAtgtgtgtgtgtg	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96933471	96933471	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96933471delT								NR2F2 (49981 upstream) : SPATA8 (393208 downstream)																							CACAACTATGTTTAGCATGGG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98246831	98246832	+	IGR	INS	-	C	C	rs71743721		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98246831_98246832insC								SPATA8 (917987 upstream) : LOC91948 (39014 downstream)																							taaatacacctccccccccaca	0.050													6	3	---	---	---	---	
CRAMP1L	57585	broad.mit.edu	37	16	1706867	1706867	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1706867delG	uc010uvh.1	+	9	2109	c.2109delG	c.(2107-2109)CTGfs	p.L703fs	CRAMP1L_uc002cmf.2_RNA	NM_020825	NP_065876	Q96RY5	CRML_HUMAN	Crm, cramped-like	703						nucleus	DNA binding				0						AGCTGCAGCTGGAGTACGACT	0.677													4	2	---	---	---	---	
PKD1	5310	broad.mit.edu	37	16	2180134	2180134	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2180134delA	uc002cos.1	-						PKD1_uc002cot.1_Intron	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor						calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3						TCTAATAAAGAAACTACCGTT	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20268540	20268540	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20268540delC								GPR139 (183440 upstream) : GP2 (53272 downstream)																							CACTGCCCTACCCCAGAAGGA	0.517													4	2	---	---	---	---	
VWA3A	146177	broad.mit.edu	37	16	22151203	22151204	+	Intron	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22151203_22151204delCA	uc010vbq.1	+						VWA3A_uc010bxd.2_Intron	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		ACTCTCATCTcacacacacaca	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	24463693	24463693	+	IGR	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24463693delG								CACNG3 (89957 upstream) : RBBP6 (85321 downstream)																							GCTGACTTTTGGGGGCATCCA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32848034	32848034	+	IGR	DEL	A	-	-	rs75274373		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32848034delA								TP53TG3B (159156 upstream) : SLC6A10P (40763 downstream)																							tatttctttcattaaaaaatt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33535747	33535748	+	IGR	DEL	AC	-	-	rs142655542		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33535747_33535748delAC								SLC6A10P (639284 upstream) : MIR1826 (429760 downstream)																							gGAAAAAAAAACACAATAGAAT	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33944572	33944572	+	IGR	DEL	T	-	-	rs111472633		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33944572delT								None (None upstream) : MIR1826 (20936 downstream)																							atgattaagcttactgaagat	0.030													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33981776	33981776	+	IGR	DEL	A	-	-	rs112170917		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33981776delA								MIR1826 (16184 upstream) : UBE2MP1 (422026 downstream)																							gcttatggtgaaaaaggaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33987872	33987872	+	IGR	DEL	G	-	-	rs112544542		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33987872delG								MIR1826 (22280 upstream) : UBE2MP1 (415930 downstream)																							ttctcagaaagcttctatctt	0.000													6	3	---	---	---	---	
NUP93	9688	broad.mit.edu	37	16	56869732	56869732	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56869732delT	uc002eka.2	+						NUP93_uc002ekb.2_Intron|NUP93_uc010vhi.1_Intron	NM_014669	NP_055484	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(1)|lung(1)	2						GTGATGGTGATTTTTTTTTAA	0.289													4	2	---	---	---	---	
CCDC102A	92922	broad.mit.edu	37	16	57552045	57552047	+	In_Frame_Del	DEL	GCC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57552045_57552047delGCC	uc002elw.2	-	6	1394_1396	c.1181_1183delGGC	c.(1180-1185)CGGCAA>CAA	p.R394del		NM_033212	NP_149989	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	394	Potential.									ovary(1)	1						CTGGCTGTTTGCCGCCGCCGCCG	0.680													4	2	---	---	---	---	
CCDC135	84229	broad.mit.edu	37	16	57739718	57739725	+	Intron	DEL	TTCTCCTC	-	-	rs138801901	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57739718_57739725delTTCTCCTC	uc002emi.2	+						CCDC135_uc002emj.2_Intron|CCDC135_uc002emk.2_Intron	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135							cytoplasm				central_nervous_system(1)	1						atcctcccatttctcctcccatccatcc	0.000													3	3	---	---	---	---	
CDH8	1006	broad.mit.edu	37	16	62055486	62055486	+	5'UTR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62055486delT	uc002eog.1	-	2						NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		ATCCATTGGCTTTTCTTTTCA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65800985	65800985	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65800985delT								LOC283867 (190782 upstream) : CDH5 (599540 downstream)																							TCATTTGCCATTTTGTTGGGT	0.294													4	2	---	---	---	---	
CMTM3	123920	broad.mit.edu	37	16	66641739	66641739	+	Intron	DEL	T	-	-	rs165206	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66641739delT	uc002epu.2	+						CMTM3_uc002epv.2_Intron|CMTM3_uc002epw.2_Intron|CMTM3_uc002epx.2_Intron|CMTM3_uc002epy.2_Intron	NM_001048251	NP_001041716	Q96MX0	CKLF3_HUMAN	chemokine-like factor superfamily 3						chemotaxis	extracellular space|integral to membrane	cytokine activity			central_nervous_system(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0671)|Epithelial(162;0.164)		CCATGCTGGGttttttttttt	0.323													5	3	---	---	---	---	
NFATC3	4775	broad.mit.edu	37	16	68160480	68160480	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68160480delA	uc002evo.1	+	3	1578	c.1368delA	c.(1366-1368)GTAfs	p.V456fs	NFATC3_uc010vkl.1_5'UTR|NFATC3_uc010vkm.1_5'UTR|NFATC3_uc010vkn.1_5'UTR|NFATC3_uc010vko.1_5'UTR|NFATC3_uc010vkp.1_5'UTR|NFATC3_uc010vkq.1_5'UTR|NFATC3_uc002evl.2_Intron|NFATC3_uc002evk.2_Frame_Shift_Del_p.V456fs|NFATC3_uc002evm.1_Frame_Shift_Del_p.V456fs|NFATC3_uc002evn.1_Frame_Shift_Del_p.V456fs|NFATC3_uc010vkr.1_5'UTR|NFATC3_uc010vks.1_5'UTR|NFATC3_uc010vkt.1_5'UTR|NFATC3_uc010vku.1_5'UTR|NFATC3_uc010vkv.1_5'UTR|NFATC3_uc010vkw.1_5'UTR|NFATC3_uc010vkx.1_5'UTR|NFATC3_uc010vky.1_5'UTR|NFATC3_uc010vkz.1_5'UTR|NFATC3_uc010vla.1_5'UTR|NFATC3_uc010vlb.1_5'UTR|NFATC3_uc010vlc.1_5'UTR	NM_173165	NP_775188	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells,	456	RHD.				inflammatory response|transcription from RNA polymerase II promoter	nucleolus|plasma membrane	DNA binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		GAGGGGCAGTAAAAGCATCTA	0.423													142	69	---	---	---	---	
NFAT5	10725	broad.mit.edu	37	16	69729377	69729378	+	Intron	DEL	AT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69729377_69729378delAT	uc002exm.1	+						NFAT5_uc002exi.2_3'UTR|NFAT5_uc002exj.1_Intron|NFAT5_uc002exk.1_Intron|NFAT5_uc002exl.1_Intron|NFAT5_uc002exn.1_Intron|NFAT5_uc002exo.1_Intron	NM_006599	NP_006590	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5 isoform c						excretion|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0						ATCTTTTAAAATGTGGCTTTCT	0.257													36	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87597482	87597483	+	IGR	DEL	GT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87597482_87597483delGT								ZCCHC14 (72022 upstream) : JPH3 (37958 downstream)																							gtgtgtgcgcgtgtgtgttggg	0.020													3	4	---	---	---	---	
RNF166	115992	broad.mit.edu	37	16	88767462	88767462	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88767462delC	uc002flk.2	-						RNF166_uc002fll.2_Intron	NM_178841	NP_849163	Q96A37	RN166_HUMAN	ring finger protein 166							intracellular	zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0476)		ACCGGGCTGGCCCCCCCGTCA	0.682													6	3	---	---	---	---	
ANKRD11	29123	broad.mit.edu	37	16	89489288	89489288	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89489288delT	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		CACTTTTTTCTTTTTTTCTTT	0.353													4	2	---	---	---	---	
RPL13	6137	broad.mit.edu	37	16	89629119	89629119	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89629119delT	uc002fnm.1	+						RPL13_uc010vpj.1_Intron|RPL13_uc002fnn.1_Intron|RPL13_uc002fno.1_Intron	NM_000977	NP_000968	P26373	RL13_HUMAN	ribosomal protein L13						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic ribosome	protein binding|RNA binding|structural constituent of ribosome				0		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)		AGGGTTTTTCTTTTTTTTTTT	0.478													3	3	---	---	---	---	
C17orf85	55421	broad.mit.edu	37	17	3714929	3714929	+	3'UTR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3714929delC	uc010ckl.1	-	13					uc010vry.1_5'Flank|C17orf85_uc002fwr.2_3'UTR|C17orf85_uc002fwq.2_3'UTR	NM_001114118	NP_001107590	Q53F19	CQ085_HUMAN	ELG protein isoform a								nucleotide binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (3;0.0725)		ATTAGCTCCGCCACAAGTAAA	0.453													4	2	---	---	---	---	
MYOCD	93649	broad.mit.edu	37	17	12586794	12586794	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12586794delT	uc002gnn.2	+						MYOCD_uc002gno.2_Intron	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin isoform 2						cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		tctctctctctcccgctcctt	0.294													4	2	---	---	---	---	
MYOCD	93649	broad.mit.edu	37	17	12586798	12586798	+	Intron	DEL	G	-	-	rs1519256	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12586798delG	uc002gnn.2	+						MYOCD_uc002gno.2_Intron	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin isoform 2						cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		tctctctcccgctccttctct	0.284													4	2	---	---	---	---	
TEKT3	64518	broad.mit.edu	37	17	15234151	15234151	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15234151delA	uc002gon.2	-							NM_031898	NP_114104	Q9BXF9	TEKT3_HUMAN	tektin 3						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		TAATGCATTTAAAAAAAAAAT	0.323													3	3	---	---	---	---	
TNFRSF13B	23495	broad.mit.edu	37	17	16839798	16839799	+	Intron	DEL	AT	-	-	rs66615973		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16839798_16839799delAT	uc010vwt.1	-						uc002gqr.1_5'Flank			O14836	TR13B_HUMAN	Homo sapiens transmembrane activator and CAML interactor (TACI) mRNA, complete cds.						cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding|receptor activity			kidney(2)	2						acacacacacatatatatatat	0.045									IgA_Deficiency_Selective				6	3	---	---	---	---	
CCDC144B	284047	broad.mit.edu	37	17	18445505	18445505	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18445505delA	uc002gua.3	-						LOC220594_uc002gty.2_5'Flank					Homo sapiens cDNA FLJ36492 fis, clone THYMU2018455.											ovary(1)|skin(1)	2						GTAGCAGCTGAAAAAAAAAAG	0.199													5	3	---	---	---	---	
ALDH3A1	218	broad.mit.edu	37	17	19643966	19643966	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19643966delT	uc010cqu.2	-						ALDH3A1_uc010vzd.1_Intron|ALDH3A1_uc002gwj.2_Intron|ALDH3A1_uc010cqv.2_Intron|ALDH3A1_uc002gwk.2_Intron|ALDH3A1_uc002gwl.1_Intron	NM_001135168	NP_001128640	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3A1						cellular aldehyde metabolic process	cytosol|endoplasmic reticulum	alcohol dehydrogenase (NADP+) activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(1)|pancreas(1)	2	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)	NADH(DB00157)	gtgcattatcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	32966412	32966413	+	IGR	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32966412_32966413delCA								TMEM132E (76 upstream) : CCT6B (288527 downstream)																							tgcacacatgcacacacacaca	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35112239	35112239	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35112239delC								MRM1 (146833 upstream) : LHX1 (182260 downstream)																							caatctgcagccccacccagc	0.000													4	2	---	---	---	---	
NAGLU	4669	broad.mit.edu	37	17	40686233	40686233	+	5'Flank	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40686233delA	uc002hzv.2	+							NM_000263	NP_000254	P54802	ANAG_HUMAN	alpha-N-acetylglucosaminidase precursor							lysosome	alpha-N-acetylglucosaminidase activity				0		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	AATGTTTAAGAAAAAAAaaga	0.154													4	2	---	---	---	---	
RND2	8153	broad.mit.edu	37	17	41182409	41182412	+	3'UTR	DEL	TCAT	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41182409_41182412delTCAT	uc002icn.2	+	5						NM_005440	NP_005431	P52198	RND2_HUMAN	Rho family GTPase 2 precursor						small GTPase mediated signal transduction	acrosomal membrane	GTP binding|GTPase activity				0		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CATTCCTCCCTCattcattcattc	0.270													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	42008316	42008316	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42008316delC								C17orf88 (12961 upstream) : PPY (9857 downstream)																							CCAGGGAGGTCCAGTTTCTGA	0.527													4	2	---	---	---	---	
ANKFN1	162282	broad.mit.edu	37	17	54248944	54248944	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54248944delG	uc002iun.1	+							NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2						GTGAACAGAAGGGGAAAAAAA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	54854633	54854633	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54854633delT								NOG (181682 upstream) : C17orf67 (14642 downstream)																							acaagaggcattttttagatg	0.000													4	2	---	---	---	---	
MED13	9969	broad.mit.edu	37	17	60029840	60029840	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60029840delA	uc002izo.2	-							NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						CAAAAACTACAAAAAAATGAC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	69983399	69983400	+	IGR	INS	-	A	A	rs138154412	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69983399_69983400insA								None (None upstream) : SOX9 (133761 downstream)																							TTCAAGACAGTAAAAAAATCAA	0.361													4	3	---	---	---	---	
SLC38A10	124565	broad.mit.edu	37	17	79242147	79242147	+	Intron	DEL	A	-	-	rs35900115		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79242147delA	uc002jzz.1	-						SLC38A10_uc002jzy.1_Intron|SLC38A10_uc002kab.2_Intron	NM_001037984	NP_001033073	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10 isoform a						amino acid transport|sodium ion transport	integral to membrane				pancreas(1)|skin(1)	2	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			accccaggacaaaaaaacaag	0.020													6	3	---	---	---	---	
ASPSCR1	79058	broad.mit.edu	37	17	79941739	79941739	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79941739delT	uc002kcx.2	+						ASPSCR1_uc002kcw.1_Intron|ASPSCR1_uc002kcy.2_Intron|ASPSCR1_uc002kcz.2_Intron|ASPSCR1_uc002kda.2_Intron|ASPSCR1_uc002kdb.1_Intron	NM_024083	NP_076988	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region,								protein binding		ASPSCR1/TFE3(161)	soft_tissue(118)|kidney(43)|breast(1)	162	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GCATCTCATGttttttttttt	0.244			T	TFE3	alveolar soft part sarcoma								4	2	---	---	---	---	
METRNL	284207	broad.mit.edu	37	17	81051140	81051140	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:81051140delC	uc002kgh.2	+						METRNL_uc002kgi.2_Intron	NM_001004431	NP_001004431	Q641Q3	METRL_HUMAN	meteorin, glial cell differentiation							extracellular region					0	Breast(20;0.000443)|all_neural(118;0.0779)		BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			CCTCCACCAGCCCTGGGGACA	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	6729191	6729191	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6729191delA								L3MBTL4 (314281 upstream) : ARHGAP28 (59302 downstream)																							TGAGAAAAGGAAAAAAAAAGA	0.512													4	2	---	---	---	---	
VAPA	9218	broad.mit.edu	37	18	9936725	9936726	+	Intron	INS	-	AAAA	AAAA			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9936725_9936726insAAAA	uc002kok.2	+						VAPA_uc002koj.2_Intron	NM_194434	NP_919415	Q9P0L0	VAPA_HUMAN	vesicle-associated membrane protein-associated						cell death|cellular membrane fusion|neuron projection development|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein localization in endoplasmic reticulum|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane|vesicle	protein heterodimerization activity|signal transducer activity|structural molecule activity				0						tggaaaaaaagaaagaaaTGCT	0.153													4	2	---	---	---	---	
CHST9	83539	broad.mit.edu	37	18	24528356	24528356	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24528356delA	uc002kwd.2	-						C18orf16_uc010xbm.1_Intron|CHST9_uc002kwc.2_Intron|CHST9_uc002kwe.2_Intron	NM_031422	NP_113610	Q7L1S5	CHST9_HUMAN	GalNAc-4-sulfotransferase 2						carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)					acttaaagttaaaaaaaaaaT	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	29187485	29187486	+	IGR	INS	-	T	T	rs147787088	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29187485_29187486insT								TTR (8501 upstream) : B4GALT6 (14724 downstream)																							ATAATAAATGAATGGAGTCATG	0.505													4	2	---	---	---	---	
CELF4	56853	broad.mit.edu	37	18	35146711	35146711	+	5'Flank	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35146711delT	uc002lae.2	-						CELF4_uc010dnd.1_5'Flank|CELF4_uc002lag.2_5'Flank|CELF4_uc002laf.2_5'Flank|CELF4_uc002lai.2_5'Flank	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						tctttctctgtttttttttcc	0.353													4	3	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	51031600	51031603	+	Intron	DEL	GTCT	-	-	rs147550177		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51031600_51031603delGTCT	uc002lfe.1	+						DCC_uc010dpf.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CACCTGTCCAGTCTGTCTGTCGAG	0.471													4	5	---	---	---	---	
POLI	11201	broad.mit.edu	37	18	51823584	51823584	+	3'UTR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51823584delC	uc002lfj.3	+	10					POLI_uc010xds.1_3'UTR|POLI_uc002lfk.3_3'UTR|POLI_uc010dpg.2_3'UTR	NM_007195	NP_009126	Q9UNA4	POLI_HUMAN	DNA polymerase iota						DNA repair|DNA replication	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding|protein binding			ovary(2)|kidney(1)	3				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		CAGGGATAAACCCCATCTTTC	0.338								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65511378	65511380	+	IGR	DEL	ATT	-	-	rs148889550		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65511378_65511380delATT								DSEL (327411 upstream) : TMX3 (829547 downstream)																							ATTGTTTATAATTGTTtctacca	0.227													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73533648	73533648	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73533648delC								C18orf62 (394059 upstream) : ZNF516 (537971 downstream)																							CAACACAGGGCCACAAAAAGA	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75213268	75213268	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75213268delA								GALR1 (231174 upstream) : None (None downstream)																							TCTGTGCCTCAAGAACTCTGA	0.353													4	2	---	---	---	---	
PALM	5064	broad.mit.edu	37	19	746066	746066	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:746066delT	uc002lpm.1	+						PALM_uc002lpn.1_Intron|PALM_uc010xfu.1_Intron	NM_002579	NP_002570	O75781	PALM_HUMAN	paralemmin isoform 1						cellular component movement|negative regulation of adenylate cyclase activity|negative regulation of dopamine receptor signaling pathway|positive regulation of filopodium assembly|regulation of cell shape	cytoplasmic membrane-bounded vesicle|filopodium membrane|integral to plasma membrane					0		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)		tcaaaaaaaaTTTTTTTTCCT	0.224													4	2	---	---	---	---	
PIP5K1C	23396	broad.mit.edu	37	19	3673392	3673392	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3673392delC	uc002lyj.1	-						PIP5K1C_uc010xhq.1_Intron|PIP5K1C_uc010xhr.1_Intron	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type						axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		ctgttgtcatccccacaacaG	0.289													4	2	---	---	---	---	
SAFB2	9667	broad.mit.edu	37	19	5599608	5599608	+	Intron	DEL	T	-	-	rs3080631		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5599608delT	uc002mcd.2	-							NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		AGTTGGCTTATTTTTTTTTGC	0.398													3	4	---	---	---	---	
EPS15L1	58513	broad.mit.edu	37	19	16512290	16512290	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16512290delG	uc002ndz.1	-						EPS15L1_uc002ndx.2_Intron|EPS15L1_uc002ndy.2_Intron|EPS15L1_uc010xpe.1_Intron|EPS15L1_uc010xpf.1_Intron|EPS15L1_uc002nea.1_Intron|EPS15L1_uc010eah.1_Intron|EPS15L1_uc002neb.1_3'UTR|EPS15L1_uc002nec.1_3'UTR	NM_021235	NP_067058	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway						endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|nucleus|plasma membrane	calcium ion binding			ovary(3)|skin(2)	5						GTGGCAGCACGGAGAGAGCTG	0.612													4	2	---	---	---	---	
CHERP	10523	broad.mit.edu	37	19	16643105	16643105	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16643105delC	uc002nei.1	-						MED26_uc002nee.2_Intron|CHERP_uc002nej.2_3'UTR	NM_006387	NP_006378	Q8IWX8	CHERP_HUMAN	calcium homeostasis endoplasmic reticulum						cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing	endoplasmic reticulum|perinuclear region of cytoplasm	RNA binding			ovary(2)	2						CAAGAAGCTGCCCCATGAGAG	0.622													4	2	---	---	---	---	
TMEM161A	54929	broad.mit.edu	37	19	19247860	19247860	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19247860delC	uc002nlg.2	-						TMEM161A_uc010eca.2_Intron|TMEM161A_uc002nlh.2_Intron|TMEM161A_uc002nli.2_Intron|TMEM161A_uc002nlj.2_Intron	NM_017814	NP_060284	Q9NX61	T161A_HUMAN	transmembrane protein 161A precursor						cellular response to oxidative stress|cellular response to UV|negative regulation of apoptosis|positive regulation of DNA repair|response to retinoic acid	integral to membrane				breast(2)	2			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)			CACGGTGACACCTCCAGCCCA	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29053799	29053800	+	Intron	INS	-	T	T	rs144876403	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29053799_29053800insT	uc002nsa.1	-											Homo sapiens cDNA clone IMAGE:5297319, with apparent retained intron.																		TCAGAGCCCTGTTTTTTGTGGG	0.490													4	3	---	---	---	---	
C19orf46	163183	broad.mit.edu	37	19	36498925	36498925	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36498925delA	uc002ocq.1	-						C19orf46_uc002ocr.1_Intron|C19orf46_uc002ocs.1_Intron|C19orf46_uc010een.1_Intron	NM_001039876	NP_001034965	Q8N205	SYNE4_HUMAN	hypothetical protein LOC163183						establishment of epithelial cell apical/basal polarity	integral to nuclear outer membrane	actin binding			ovary(1)	1	all_lung(56;1.35e-06)|Lung NSC(56;2.15e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			actccatctcaaaaaaaaaaa	0.194													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	37784743	37784744	+	IGR	INS	-	AC	AC			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37784743_37784744insAC								ZNF383 (50169 upstream) : HKR1 (18995 downstream)																							gcatccccccaacacacacaca	0.054													6	3	---	---	---	---	
ACTN4	81	broad.mit.edu	37	19	39208409	39208409	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39208409delG	uc002oja.1	+						ACTN4_uc010egc.1_Intron	NM_004924	NP_004915	O43707	ACTN4_HUMAN	actinin, alpha 4						platelet activation|platelet degranulation|positive regulation of cellular component movement|positive regulation of sodium:hydrogen antiporter activity|protein transport|regulation of apoptosis	extracellular region|nucleolus|perinuclear region of cytoplasm|platelet alpha granule lumen|protein complex|pseudopodium|ribonucleoprotein complex	actin filament binding|calcium ion binding|integrin binding|nucleoside binding|protein homodimerization activity				0	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			gctgagtgctggggggccctg	0.239													4	2	---	---	---	---	
APOC1P1	342	broad.mit.edu	37	19	45431268	45431268	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45431268delA	uc010eju.2	+											Homo sapiens clone DKFZp781C1677 mRNA sequence.												0						GAACAGATTGAAAAAAAAAAC	0.527													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	51719031	51719031	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51719031delC								SIGLECP3 (42257 upstream) : CD33 (9304 downstream)																							CCACTCTTGTCCCTCTTTCTC	0.547													4	2	---	---	---	---	
ZNF766	90321	broad.mit.edu	37	19	52780712	52780712	+	Intron	DEL	A	-	-	rs79554348		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52780712delA	uc002pyr.1	+						ZNF766_uc002pys.1_Intron|ZNF766_uc002pyt.1_5'UTR	NM_001010851	NP_001010851	Q5HY98	ZN766_HUMAN	zinc finger protein 766						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00236)|OV - Ovarian serous cystadenocarcinoma(262;0.00871)		actccgtctcaaaaaaaaaca	0.194													3	3	---	---	---	---	
EPS8L1	54869	broad.mit.edu	37	19	55598015	55598016	+	Intron	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55598015_55598016insA	uc002qis.3	+						EPS8L1_uc010yfr.1_Intron|EPS8L1_uc002qiu.2_Intron|EPS8L1_uc002qiv.2_Intron|EPS8L1_uc002qiw.2_Intron	NM_133180	NP_573441	Q8TE68	ES8L1_HUMAN	epidermal growth factor receptor pathway							cytoplasm					0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CCCCCCGCCCCGCCCTCTGGCC	0.480													4	2	---	---	---	---	
FERMT1	55612	broad.mit.edu	37	20	6068752	6068753	+	Intron	INS	-	AAATC	AAATC	rs143362093	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6068752_6068753insAAATC	uc002wmr.2	-						FERMT1_uc002wmq.2_Intron|FERMT1_uc010gbt.2_Intron|FERMT1_uc002wms.2_Intron	NM_017671	NP_060141	Q9BQL6	FERM1_HUMAN	kindlin-1						cell adhesion|establishment of epithelial cell polarity|keratinocyte migration|keratinocyte proliferation	cytosol|focal adhesion|ruffle membrane	binding			ovary(1)|pancreas(1)|skin(1)	3						ACAGTTTTCTTAAAAAGTCAAT	0.267													4	4	---	---	---	---	
ESF1	51575	broad.mit.edu	37	20	13765461	13765462	+	Intron	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13765461_13765462delCA	uc002woj.2	-						ESF1_uc002wok.1_Intron|C20orf7_uc002wol.1_5'Flank|C20orf7_uc002wom.2_5'Flank|C20orf7_uc002won.2_5'Flank|C20orf7_uc002woo.2_5'Flank	NM_016649	NP_057733	Q9H501	ESF1_HUMAN	ABT1-associated protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1						TTCCCCGCGCCACACACACACA	0.554													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22455305	22455305	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22455305delC								LOC284788 (54024 upstream) : C20orf56 (85889 downstream)																							TCAAAATCTACCCAGTAGGAA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	24665215	24665216	+	IGR	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24665215_24665216insT								TMEM90B (18048 upstream) : CST7 (264650 downstream)																							AGAAAACAGGGTTTTTTTAACT	0.401													4	2	---	---	---	---	
NINL	22981	broad.mit.edu	37	20	25436620	25436620	+	Intron	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25436620delT	uc002wux.1	-						NINL_uc010gdn.1_Intron|NINL_uc002wuw.1_Intron	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like						G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						taatcccagctacttgggagg	0.000													4	2	---	---	---	---	
NINL	22981	broad.mit.edu	37	20	25436622	25436623	+	Intron	INS	-	T	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25436622_25436623insT	uc002wux.1	-						NINL_uc010gdn.1_Intron|NINL_uc002wuw.1_Intron	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like						G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						atcccagctacttgggaggctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25912775	25912775	+	IGR	DEL	T	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25912775delT								FAM182B (63989 upstream) : LOC100134868 (77660 downstream)																							TAATTATGGATTTTAATGTGA	0.284													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29653081	29653082	+	3'UTR	INS	-	G	G	rs138979932		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29653081_29653082insG	uc010ztl.1	+	4					FRG1B_uc010ztj.1_RNA|FRG1B_uc010ztk.1_3'UTR					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						tgatgtaaaaacaaacctgccc	0.000													4	2	---	---	---	---	
CHD6	84181	broad.mit.edu	37	20	40188526	40188527	+	Intron	DEL	AC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40188526_40188527delAC	uc002xka.1	-						CHD6_uc002xkd.2_Intron|CHD6_uc002xkc.2_Intron	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				acgcacacatacacacacacac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46972601	46972603	+	IGR	DEL	AGA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46972601_46972603delAGA								SULF2 (557241 upstream) : LOC284749 (16051 downstream)																							aggaaaaaggagaaggaggcaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55463531	55463532	+	IGR	DEL	AC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55463531_55463532delAC								TFAP2C (249195 upstream) : BMP7 (280277 downstream)																							CAAAAACAAAACACACACACAC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9856378	9856380	+	IGR	DEL	CTC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9856378_9856380delCTC								None (None upstream) : None (None downstream)																							CCTCTGCCTTCTCCTCCAGGGCA	0.581													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9863060	9863060	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9863060delA								None (None upstream) : None (None downstream)																							acagggacacacgggtgaggt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10704482	10704483	+	IGR	INS	-	A	A	rs141719157		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10704482_10704483insA								None (None upstream) : TPTE (202260 downstream)																							aatatcttcacaaaaaaagtag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10756589	10756589	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10756589delA								None (None upstream) : TPTE (150154 downstream)																							gagtgtttccaaactgctcaa	0.000													4	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11088497	11088497	+	Intron	DEL	G	-	-	rs56256692	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11088497delG	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tgttgttgttgttttttttga	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14361863	14361864	+	IGR	INS	-	C	C	rs146825566		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14361863_14361864insC								None (None upstream) : C21orf99 (48623 downstream)																							ctccatccaaaaaaagttcaac	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	24771292	24771292	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24771292delA								None (None upstream) : None (None downstream)																							gtctggctccaacattctccc	0.000													4	2	---	---	---	---	
GABPA	2551	broad.mit.edu	37	21	27121629	27121629	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27121629delA	uc002ylx.3	+						GABPA_uc002yly.3_Intron	NM_002040	NP_002031	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha						positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2						gttcaatcataaaaggatata	0.095													4	2	---	---	---	---	
SETD4	54093	broad.mit.edu	37	21	37435605	37435605	+	Intron	DEL	T	-	-	rs150031730	by1000genomes	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37435605delT	uc002yuv.2	-						SETD4_uc002yux.1_5'Flank|SETD4_uc002yuu.2_5'Flank|SETD4_uc002yuy.2_5'Flank|SETD4_uc002yuz.2_5'Flank|SETD4_uc002yva.2_Intron	NM_017438	NP_059134	Q9NVD3	SETD4_HUMAN	SET domain containing 4 isoform a											large_intestine(1)|ovary(1)	2						ggccgggtgctgggggcagag	0.000													4	2	---	---	---	---	
DYRK1A	1859	broad.mit.edu	37	21	38796770	38796770	+	Intron	DEL	T	-	-	rs111346005		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38796770delT	uc002ywk.2	+						DYRK1A_uc002ywg.1_Intron|DYRK1A_uc010gno.1_Intron|DYRK1A_uc002ywh.1_Intron|DYRK1A_uc002ywi.2_Intron|DYRK1A_uc002ywj.2_Intron|DYRK1A_uc002ywl.2_Intron|DYRK1A_uc002ywm.2_Intron	NM_001396	NP_001387	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation						nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4						TTTCATGCCATTTTTTTAACT	0.333													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	43092855	43092856	+	IGR	DEL	CA	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43092855_43092856delCA								TMPRSS2 (189812 upstream) : NCRNA00111 (6606 downstream)																							ATACATATGCcacacacacaca	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44070628	44070628	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44070628delC	uc002zbl.3	-											Homo sapiens, clone IMAGE:5459012, mRNA.																		CAAATGAAGACCCCACAACCT	0.403													4	2	---	---	---	---	
PCBP3	54039	broad.mit.edu	37	21	47126444	47126445	+	Intron	DEL	TC	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47126444_47126445delTC	uc010gqb.2	+							NM_020528	NP_065389	P57721	PCBP3_HUMAN	poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		tatctctatttctctctctccc	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16423014	16423015	+	IGR	DEL	TG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16423014_16423015delTG								POTEH (135077 upstream) : OR11H1 (25811 downstream)																							tgtgtgtgtatgtgtgtgtgtg	0.272													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20270734	20270735	+	IGR	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20270734_20270735insA								RTN4R (14918 upstream) : DGCR6L (31067 downstream)																							TGTCATTTGCTAGACAGGCGCT	0.604													4	2	---	---	---	---	
MAPK1	5594	broad.mit.edu	37	22	22173360	22173361	+	Intron	INS	-	A	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22173360_22173361insA	uc002zvn.2	-						MAPK1_uc002zvo.2_Intron|MAPK1_uc010gtk.1_Intron	NM_002745	NP_002736	P28482	MK01_HUMAN	mitogen-activated protein kinase 1						activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|epidermal growth factor receptor signaling pathway|ERK1 and ERK2 cascade|induction of apoptosis|innate immune response|insulin receptor signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription, DNA-dependent	cytosol|nucleoplasm	ATP binding|DNA binding|MAP kinase activity|phosphatase binding|RNA polymerase II carboxy-terminal domain kinase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)	CCTGGGGCGACAGAGTGCCTGC	0.554													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	30103568	30103568	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30103568delA								NF2 (8985 upstream) : CABP7 (12776 downstream)																							AGCAGCTTCTAAAAAGGCCTC	0.577													4	2	---	---	---	---	
ASCC2	84164	broad.mit.edu	37	22	30203075	30203075	+	Intron	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30203075delA	uc003agr.2	-						ASCC2_uc003ags.2_Intron|ASCC2_uc003agt.2_Intron|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580	Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			caaaaaatacaaaaaattagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	34454143	34454143	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34454143delC								LARGE (135559 upstream) : None (None downstream)																							cttgagtgatccagtccaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	39955015	39955016	+	IGR	DEL	AG	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39955015_39955016delAG								RPS19BP1 (26155 upstream) : CACNA1I (11742 downstream)																							tgAGAGAGACAGAGAGAGAGAA	0.490													4	2	---	---	---	---	
SCUBE1	80274	broad.mit.edu	37	22	43695559	43695559	+	Intron	DEL	G	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43695559delG	uc003bdt.1	-						SCUBE1_uc003bdu.1_Intron	NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1						adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)				ctgtgcacatggtctgCTTGG	0.179													4	2	---	---	---	---	
ODF3B	440836	broad.mit.edu	37	22	50971640	50971640	+	5'Flank	DEL	A	-	-	rs35548253		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50971640delA	uc003bmh.2	-						ODF3B_uc003bmg.2_5'Flank	NM_001014440	NP_001014440	A8MYP8	ODF3B_HUMAN	outer dense fiber of sperm tails 3B												0						ttaaaaaaagaaaaaaaaagg	0.119													4	2	---	---	---	---	
FRMPD4	9758	broad.mit.edu	37	X	12450359	12450359	+	Intron	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12450359delC	uc004cuz.1	+						FRMPD4_uc011mij.1_Intron	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4						positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13						cacttcccctccagcacctgc	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	113247513	113247513	+	IGR	DEL	C	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113247513delC								None (None upstream) : HTR2C (571038 downstream)																							TTCTTCTCCACCCCTTCCAGC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	134732234	134732234	+	IGR	DEL	A	-	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134732234delA								DDX26B (15775 upstream) : CT45A1 (114951 downstream)																							ACACATAGTTAGCTATGAGGA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59011712	59011715	+	IGR	DEL	CAAT	-	-	rs71268707		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59011712_59011715delCAAT								None (None upstream) : None (None downstream)																							CTGCCAAAAACAATCACTTGCACT	0.314													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59012233	59012234	+	IGR	DEL	TA	-	-	rs57027995		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59012233_59012234delTA								None (None upstream) : None (None downstream)																							CTTTGAACTGTAAGGAATTAAT	0.391													4	7	---	---	---	---	
