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
PRDM16	63976	broad.mit.edu	37	1	3350397	3350397	+	3'UTR	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3350397G>T	uc001akf.2	+	17					PRDM16_uc001akc.2_3'UTR|PRDM16_uc001akd.2_3'UTR|PRDM16_uc001ake.2_3'UTR|PRDM16_uc009vlh.2_3'UTR	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GCCGGGGGCCGGTGGCCAGAG	0.687			T	EVI1	MDS|AML								3	5	---	---	---	---	PASS
MTOR	2475	broad.mit.edu	37	1	11184573	11184573	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11184573G>T	uc001asd.2	-	47	6765	c.6644C>A	c.(6643-6645)TCT>TAT	p.S2215Y	MTOR_uc001asc.2_Missense_Mutation_p.S420Y	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	2215	PI3K/PI4K.		S -> Y (in a colorectal adenocarcinoma sample; somatic mutation).		cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity	p.S2215Y(1)		central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						TTTCCGAAGAGATGTTGGGTC	0.438													100	61	---	---	---	---	PASS
KAZ	23254	broad.mit.edu	37	1	15428039	15428039	+	Silent	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15428039C>T	uc001avm.3	+	11	1829	c.1548C>T	c.(1546-1548)AGC>AGT	p.S516S	KAZ_uc001avs.3_5'UTR	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E	516					keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						TCCTCCCCAGCCTGTCCAAAG	0.587													16	2	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16945570	16945570	+	RNA	SNP	A	G	G	rs28552760	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16945570A>G	uc010ocf.1	-	4		c.587T>C			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						TGACAGCGCCATCTTCTCAGA	0.622													4	51	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16976585	16976585	+	RNA	SNP	C	T	T	rs1135350	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16976585C>T	uc010och.1	+	14		c.2306C>T			MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						TACGGGGGCCCACTTGCCTGC	0.567													4	19	---	---	---	---	PASS
TCEA3	6920	broad.mit.edu	37	1	23743879	23743879	+	Silent	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23743879G>A	uc001bgx.1	-	4	378	c.243C>T	c.(241-243)TCC>TCT	p.S81S	TCEA3_uc009vqn.1_Silent_p.S60S|TCEA3_uc010ody.1_Silent_p.S44S	NM_003196	NP_003187	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3	81	TFIIS N-terminal.				regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation, DNA-dependent	nucleus	DNA binding|translation elongation factor activity|zinc ion binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		GGGGTCCAGGGGAGTCTGAAA	0.413													129	49	---	---	---	---	PASS
YTHDF2	51441	broad.mit.edu	37	1	29064082	29064082	+	Intron	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29064082T>C	uc001brc.2	+						YTHDF2_uc001brd.2_Intron|YTHDF2_uc010ofx.1_Intron|YTHDF2_uc001bre.2_5'UTR	NM_016258	NP_057342	Q9Y5A9	YTHD2_HUMAN	high glucose-regulated protein 8						humoral immune response					ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		TCCTTTATTCTCCCTTCGGGC	0.577													5	118	---	---	---	---	PASS
RLF	6018	broad.mit.edu	37	1	40702750	40702750	+	Silent	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40702750A>G	uc001cfc.3	+	8	2407	c.2376A>G	c.(2374-2376)GAA>GAG	p.E792E	RLF_uc001cfd.3_Silent_p.E483E	NM_012421	NP_036553	Q13129	RLF_HUMAN	rearranged L-myc fusion	792	C2H2-type 5.				chromosome organization|DNA integration|DNA mediated transformation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			ovary(2)|pancreas(1)	3	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			ACCACCATGAAGCACAACACT	0.368													5	109	---	---	---	---	PASS
WDR78	79819	broad.mit.edu	37	1	67301400	67301400	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67301400C>T	uc001dcx.2	-	11	1698	c.1642G>A	c.(1642-1644)GCA>ACA	p.A548T	WDR78_uc009waw.2_Missense_Mutation_p.A294T|WDR78_uc009wax.2_Intron	NM_024763	NP_079039	Q5VTH9	WDR78_HUMAN	WD repeat domain 78 isoform 1	548	WD 1.									ovary(2)	2						AGGTTAGGTGCTCCAATTGAA	0.358													16	172	---	---	---	---	PASS
TNNI3K	51086	broad.mit.edu	37	1	75009648	75009648	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75009648C>A	uc001dgf.1	+	25	2541	c.2490C>A	c.(2488-2490)AGC>AGA	p.S830R	TNNI3K_uc001dge.1_Missense_Mutation_p.S931R	NM_015978	NP_057062	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform b	830						cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10						ATAGTAGCAGCTTTGAGGACA	0.458													54	106	---	---	---	---	PASS
LPHN2	23266	broad.mit.edu	37	1	82456186	82456186	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82456186A>C	uc001dit.3	+	21	3750	c.3569A>C	c.(3568-3570)CAA>CCA	p.Q1190P	LPHN2_uc001dis.2_Missense_Mutation_p.Q170P|LPHN2_uc001diu.2_Missense_Mutation_p.Q1190P|LPHN2_uc001div.2_3'UTR|LPHN2_uc009wcd.2_3'UTR|LPHN2_uc001diw.2_Missense_Mutation_p.Q817P	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	1246	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		GACAGCGTGCAAGTTGTGGAC	0.433													55	37	---	---	---	---	PASS
FMO5	2330	broad.mit.edu	37	1	146672930	146672930	+	Silent	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146672930G>A	uc001epi.2	-	7	1376	c.987C>T	c.(985-987)GCC>GCT	p.A329A	FMO5_uc001eph.3_Silent_p.A329A|FMO5_uc001epj.2_Intron	NM_001461	NP_001452	P49326	FMO5_HUMAN	flavin containing monooxygenase 5 isoform 1	329						integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			ovary(3)	3	all_hematologic(923;0.0487)					TATAGCCTGTGGCAAAGATAA	0.438													22	190	---	---	---	---	PASS
IFI16	3428	broad.mit.edu	37	1	159024722	159024722	+	3'UTR	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159024722G>A	uc001ftg.2	+	11					IFI16_uc010pis.1_3'UTR|IFI16_uc001fth.2_3'UTR|IFI16_uc010pit.1_3'UTR	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16						cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)					TAATGTTTATGGAGATAAGGT	0.338													5	328	---	---	---	---	PASS
RABGAP1L	9910	broad.mit.edu	37	1	174190122	174190122	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174190122G>T	uc001gjx.2	+	3	346	c.151G>T	c.(151-153)GGT>TGT	p.G51C	RABGAP1L_uc009wwq.1_Missense_Mutation_p.G51C|RABGAP1L_uc001gjw.2_Missense_Mutation_p.G14C	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A	51					regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						AGTTTCTAATGGTGATGAACA	0.343													5	540	---	---	---	---	PASS
C1orf25	81627	broad.mit.edu	37	1	185125887	185125887	+	5'UTR	SNP	G	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185125887G>C	uc001grf.3	-	1					C1orf26_uc001grg.3_5'Flank|C1orf26_uc001grh.3_5'Flank|C1orf25_uc010pon.1_Intron	NM_030934	NP_112196	Q7Z2T5	TRM1L_HUMAN	N2,N2-dimethylguanosine tRNA							intracellular	RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding				0						ACCCGGAGCGGGGCTCACGGC	0.652													3	3	---	---	---	---	PASS
TPR	7175	broad.mit.edu	37	1	186303510	186303510	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186303510G>C	uc001grv.2	-	36	5426	c.5129C>G	c.(5128-5130)ACT>AGT	p.T1710S		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	1710					carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TGGGGTAGTAGTGGGATTTGT	0.433			T	NTRK1	papillary thyroid								201	311	---	---	---	---	PASS
RBBP5	5929	broad.mit.edu	37	1	205069041	205069041	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205069041C>T	uc001hbu.1	-	8	1034	c.904G>A	c.(904-906)GCT>ACT	p.A302T	RBBP5_uc010prd.1_Missense_Mutation_p.A337T|RBBP5_uc001hbv.1_Missense_Mutation_p.A302T|RBBP5_uc010pre.1_Missense_Mutation_p.A169T	NM_005057	NP_005048	Q15291	RBBP5_HUMAN	retinoblastoma binding protein 5	302	WD 6.				histone H3-K4 methylation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription, DNA-dependent	MLL1 complex|Set1C/COMPASS complex	methylated histone residue binding|transcription regulatory region DNA binding			lung(1)	1	Breast(84;0.0505)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			GTACTCACAGCTACATCCAAG	0.423													4	138	---	---	---	---	PASS
CR1L	1379	broad.mit.edu	37	1	207888661	207888661	+	Intron	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207888661T>C	uc001hga.3	+						CR1L_uc001hfz.2_RNA|CR1L_uc001hgb.1_RNA	NM_175710	NP_783641	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like							cytoplasm|extracellular region|membrane					0						CTTTAGGTTCTGATTAAAAGG	0.413													9	326	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240492737	240492737	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240492737G>A	uc010pyd.1	+	10	4631	c.4406G>A	c.(4405-4407)CGC>CAC	p.R1469H	FMN2_uc010pye.1_Missense_Mutation_p.R1473H|FMN2_uc010pyf.1_Missense_Mutation_p.R115H|FMN2_uc010pyg.1_Missense_Mutation_p.R65H	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1469	FH2.				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)			TCAATTCGTCGCAAACTGGAA	0.408													201	264	---	---	---	---	PASS
TSSC1	7260	broad.mit.edu	37	2	3217939	3217939	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3217939T>C	uc002qxj.2	-	5	690	c.497A>G	c.(496-498)GAA>GGA	p.E166G	TSSC1_uc002qxi.2_RNA	NM_003310	NP_003301	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	166	WD 1.						protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		GCTCGAGCTTTCCTGTAAATC	0.353													72	81	---	---	---	---	PASS
TSSC1	7260	broad.mit.edu	37	2	3217940	3217940	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3217940C>A	uc002qxj.2	-	5	689	c.496G>T	c.(496-498)GAA>TAA	p.E166*	TSSC1_uc002qxi.2_RNA	NM_003310	NP_003301	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	166	WD 1.						protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		CTCGAGCTTTCCTGTAAATCC	0.353													71	81	---	---	---	---	PASS
SMC6	79677	broad.mit.edu	37	2	17898022	17898022	+	Silent	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17898022T>C	uc002rco.2	-	14	1628	c.1332A>G	c.(1330-1332)GAA>GAG	p.E444E	SMC6_uc010exo.2_Silent_p.E444E|SMC6_uc002rcn.2_Silent_p.E444E|SMC6_uc002rcp.1_Silent_p.E470E|SMC6_uc002rcq.2_Silent_p.E470E|SMC6_uc002rcr.1_Silent_p.E444E	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	444	Potential.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTTTGCCATGTTCTTCTTTGT	0.318													8	622	---	---	---	---	PASS
DNAH6	1768	broad.mit.edu	37	2	84880607	84880607	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84880607G>A	uc010fgb.2	+	34	5380	c.5243G>A	c.(5242-5244)GGT>GAT	p.G1748D		NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	1748	AAA 2 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1						GTAAGGCATGGTGTTATGTTA	0.393													33	88	---	---	---	---	PASS
C2orf68	388969	broad.mit.edu	37	2	85835903	85835903	+	3'UTR	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85835903G>A	uc002sqc.2	-	4					USP39_uc002sqb.2_Intron	NM_001013649	NP_001013671	Q2NKX9	CB068_HUMAN	hypothetical protein LOC388969											central_nervous_system(1)	1						AAGAAAGAATGACTGCAAGGC	0.418													5	11	---	---	---	---	PASS
DPP10	57628	broad.mit.edu	37	2	116510751	116510751	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116510751G>T	uc002tla.1	+	11	1409	c.952G>T	c.(952-954)GAA>TAA	p.E318*	DPP10_uc002tlb.1_Nonsense_Mutation_p.E268*|DPP10_uc002tlc.1_Nonsense_Mutation_p.E314*|DPP10_uc002tle.2_Nonsense_Mutation_p.E322*|DPP10_uc002tlf.1_Nonsense_Mutation_p.E311*	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	318	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						CCAAACTAGAGAATACTATAT	0.343													50	137	---	---	---	---	PASS
ZRANB3	84083	broad.mit.edu	37	2	136026630	136026630	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136026630G>A	uc002tum.2	-	11	1405	c.1288C>T	c.(1288-1290)CGA>TGA	p.R430*	ZRANB3_uc002tuk.2_5'UTR|ZRANB3_uc002tul.2_Nonsense_Mutation_p.R430*|ZRANB3_uc002tun.1_3'UTR	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	430	Helicase C-terminal.					intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)		CTGTGAGCTCGGTCTTCTGCT	0.418													7	329	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168103812	168103812	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168103812G>C	uc002udx.2	+	8	5928	c.5910G>C	c.(5908-5910)CAG>CAC	p.Q1970H	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.Q1795H|XIRP2_uc010fpq.2_Missense_Mutation_p.Q1748H|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1795					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						TTGCTGTCCAGAGGAACAAAA	0.453													7	26	---	---	---	---	PASS
TLK1	9874	broad.mit.edu	37	2	171884911	171884911	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171884911T>C	uc002ugn.2	-	12	1646	c.1174A>G	c.(1174-1176)ACT>GCT	p.T392A	TLK1_uc002ugo.2_Missense_Mutation_p.T413A|TLK1_uc002ugp.2_Missense_Mutation_p.T344A|TLK1_uc002ugq.2_RNA|TLK1_uc010zdn.1_Missense_Mutation_p.T296A	NM_012290	NP_036422	Q9UKI8	TLK1_HUMAN	tousled-like kinase 1 isoform 1	392					cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1						TCTGCCAAAGTCAACCTGTCA	0.274													9	587	---	---	---	---	PASS
ALS2CR12	130540	broad.mit.edu	37	2	202172343	202172343	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202172343T>C	uc010ftg.2	-	11	1222	c.778A>G	c.(778-780)AAA>GAA	p.K260E	ALS2CR12_uc002uya.3_Missense_Mutation_p.K260E|ALS2CR12_uc010fth.2_RNA	NM_139163	NP_631902	Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	260					regulation of GTPase activity		protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3						GTCATCTTTTTTTCTGTGGAA	0.363													159	139	---	---	---	---	PASS
ERBB4	2066	broad.mit.edu	37	2	212426720	212426720	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212426720T>A	uc002veg.1	-	20	2493	c.2395A>T	c.(2395-2397)ATG>TTG	p.M799L	ERBB4_uc002veh.1_Missense_Mutation_p.M799L|ERBB4_uc010zji.1_Missense_Mutation_p.M789L|ERBB4_uc010zjj.1_Missense_Mutation_p.M789L|ERBB4_uc010fut.1_Missense_Mutation_p.M799L	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	799	ATP (By similarity).|Protein kinase.|Cytoplasmic (Potential).				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)		CCATGGGGCATAAGTTGAGTA	0.502										TSP Lung(8;0.080)			78	73	---	---	---	---	PASS
ERBB4	2066	broad.mit.edu	37	2	212426721	212426721	+	Silent	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212426721A>T	uc002veg.1	-	20	2492	c.2394T>A	c.(2392-2394)CTT>CTA	p.L798L	ERBB4_uc002veh.1_Silent_p.L798L|ERBB4_uc010zji.1_Silent_p.L788L|ERBB4_uc010zjj.1_Silent_p.L788L|ERBB4_uc010fut.1_Silent_p.L798L	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	798	ATP (By similarity).|Protein kinase.|Cytoplasmic (Potential).				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)		CATGGGGCATAAGTTGAGTAA	0.498										TSP Lung(8;0.080)			80	75	---	---	---	---	PASS
WDR69	164781	broad.mit.edu	37	2	228754578	228754578	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228754578T>A	uc002vpn.1	+	3	199	c.120T>A	c.(118-120)GAT>GAA	p.D40E	WDR69_uc010zlw.1_Missense_Mutation_p.D25E|WDR69_uc002vpo.1_RNA	NM_178821	NP_849143	Q8N136	WDR69_HUMAN	WD repeat domain 69	40										breast(1)	1		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;1.22e-10)|all cancers(144;8.11e-08)|Lung(261;0.011)|LUSC - Lung squamous cell carcinoma(224;0.0148)		TCAGCACTGATGTCAGTGCGT	0.358													47	143	---	---	---	---	PASS
CNTN4	152330	broad.mit.edu	37	3	3084727	3084727	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3084727A>G	uc003bpc.2	+	21	2799	c.2578A>G	c.(2578-2580)ACA>GCA	p.T860A	CNTN4_uc003bpb.1_Missense_Mutation_p.T531A|CNTN4_uc003bpe.2_Missense_Mutation_p.T532A|CNTN4_uc003bpf.2_Missense_Mutation_p.T531A|CNTN4_uc003bpg.2_Missense_Mutation_p.T116A	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	860	Fibronectin type-III 3.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TGGAAATCAGACATCAACAAA	0.383													6	237	---	---	---	---	PASS
RHOA	387	broad.mit.edu	37	3	49397795	49397795	+	Silent	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49397795T>C	uc003cwu.2	-	5	705	c.429A>G	c.(427-429)GAA>GAG	p.E143E	RHOA_uc010hku.2_Silent_p.E62E|GPX1_uc011bcl.1_5'Flank|GPX1_uc011bcm.1_5'Flank	NM_001664	NP_001655	P61586	RHOA_HUMAN	ras homolog gene family, member A precursor	143					axon guidance|interspecies interaction between organisms|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of axonogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of neuron differentiation|positive regulation of NF-kappaB import into nucleus|positive regulation of stress fiber assembly|regulation of cell migration|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|spindle assembly involved in mitosis	cytoskeleton|cytosol|plasma membrane	GTP binding|GTPase activity|myosin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	Atorvastatin(DB01076)|Simvastatin(DB00641)	TATCTCTGCCTTCTTCAGGTT	0.393													8	562	---	---	---	---	PASS
NEK4	6787	broad.mit.edu	37	3	52800372	52800372	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52800372A>G	uc003dfq.3	-	3	569	c.380T>C	c.(379-381)ATC>ACC	p.I127T	NEK4_uc011bej.1_Missense_Mutation_p.I38T|NEK4_uc003dfr.2_Missense_Mutation_p.I127T	NM_003157	NP_003148	P51957	NEK4_HUMAN	NIMA-related kinase 4	127	Protein kinase.				cell division|mitosis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		TCGATGAAGGATGTGTTTTTC	0.333													6	338	---	---	---	---	PASS
ATXN7	6314	broad.mit.edu	37	3	63981575	63981575	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63981575C>A	uc003dlw.3	+	12	2630	c.2077C>A	c.(2077-2079)CAA>AAA	p.Q693K	ATXN7_uc003dlv.2_Missense_Mutation_p.Q693K|ATXN7_uc010hnv.2_Missense_Mutation_p.Q693K|ATXN7_uc011bfn.1_Missense_Mutation_p.Q548K	NM_000333	NP_000324	O15265	ATX7_HUMAN	ataxin 7 isoform a	693	Ser-rich.				cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		CACTAACTGTCAAAATGCCAG	0.413													84	34	---	---	---	---	PASS
RAB43	339122	broad.mit.edu	37	3	128813995	128813995	+	Silent	SNP	C	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128813995C>A	uc003eln.1	-	2	509	c.222G>T	c.(220-222)ACG>ACT	p.T74T	RAB43_uc003elo.1_Missense_Mutation_p.R290L|RAB43_uc010hsy.1_Silent_p.T74T	NM_198490	NP_940892	Q86YS6	RAB43_HUMAN	RAB43 protein	74	GTP (By similarity).				protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			lung(1)	1						CCTGGCCGGCCGTGTCCCAGA	0.592													16	40	---	---	---	---	PASS
COL6A6	131873	broad.mit.edu	37	3	130279260	130279260	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130279260A>G	uc010htl.2	+	1	83	c.52A>G	c.(52-54)AAC>GAC	p.N18D		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	18					axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						TATTTCTGTGAACCAAGATTC	0.284													7	538	---	---	---	---	PASS
TOPBP1	11073	broad.mit.edu	37	3	133377933	133377933	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133377933T>C	uc003eps.2	-	3	278	c.146A>G	c.(145-147)AAG>AGG	p.K49R		NM_007027	NP_008958	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	49					DNA repair|response to ionizing radiation	microtubule organizing center|PML body|spindle pole	DNA binding|protein C-terminus binding			ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1)	7						CTCCTTTATCTTCAATGCCTC	0.328								Other_conserved_DNA_damage_response_genes					7	332	---	---	---	---	PASS
ATR	545	broad.mit.edu	37	3	142169376	142169376	+	Intron	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142169376C>T	uc003eux.3	-						XRN1_uc003eus.2_5'Flank|XRN1_uc003eut.2_5'Flank|XRN1_uc003euu.2_5'Flank|XRN1_uc003euw.2_5'Flank|XRN1_uc011bnh.1_5'Flank|ATR_uc003euy.1_3'UTR	NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein						cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						TCCAGAAAATCAGATCAAGGG	0.388								Other_conserved_DNA_damage_response_genes					69	38	---	---	---	---	PASS
GPR160	26996	broad.mit.edu	37	3	169802072	169802072	+	Silent	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169802072T>C	uc003fgi.2	+	4	902	c.312T>C	c.(310-312)ACT>ACC	p.T104T	GPR160_uc010hwq.2_Silent_p.T104T	NM_014373	NP_055188	Q9UJ42	GP160_HUMAN	G protein-coupled receptor 160	104	Helical; Name=3; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			TTTCCTTTACTTATGGCTTTT	0.294													129	48	---	---	---	---	PASS
DGKG	1608	broad.mit.edu	37	3	185867892	185867892	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185867892C>T	uc003fqa.2	-	25	2900	c.2363G>A	c.(2362-2364)CGT>CAT	p.R788H	DGKG_uc003fqb.2_Missense_Mutation_p.R749H|DGKG_uc003fqc.2_Missense_Mutation_p.R763H|DGKG_uc011brx.1_Missense_Mutation_p.R729H	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1	788					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	GTCTTTTGAACGGCTCTTCCT	0.408													4	157	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506315	195506315	+	Missense_Mutation	SNP	T	C	C	rs62282465		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506315T>C	uc011bto.1	-	3	12212	c.11752A>G	c.(11752-11754)ACC>GCC	p.T3918A	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	818	Ser-rich.				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)		AGAGGGGTGGTGTCACCTGTG	0.587													7	12	---	---	---	---	PASS
SENP5	205564	broad.mit.edu	37	3	196650309	196650309	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196650309C>G	uc003fwz.3	+	7	2158	c.1909C>G	c.(1909-1911)CTG>GTG	p.L637V	SENP5_uc011bty.1_Intron	NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	637	Protease.				cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		AAAGAGTCTTCTGTTGATTCC	0.383													235	110	---	---	---	---	PASS
C4orf48	401115	broad.mit.edu	37	4	2045589	2045589	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2045589C>T	uc003geo.3	+	4	356	c.356C>T	c.(355-357)ACG>ATG	p.T119M	C4orf48_uc003gep.3_Missense_Mutation_p.T75M	NM_001141936	NP_001135408			hypothetical protein LOC401115												0						GCTTTGCAGACGGAGACCCTA	0.657													4	13	---	---	---	---	PASS
GABRA4	2557	broad.mit.edu	37	4	46930501	46930501	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46930501G>A	uc003gxg.2	-	9	1545	c.1406C>T	c.(1405-1407)TCA>TTA	p.S469L		NM_000809	NP_000800	P48169	GBRA4_HUMAN	gamma-aminobutyric acid A receptor, alpha 4	469	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)	4					Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	AGATCCAACTGAAGCCTTTCG	0.468													11	133	---	---	---	---	PASS
EGF	1950	broad.mit.edu	37	4	110862256	110862256	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110862256A>T	uc003hzy.3	+	2	734	c.282A>T	c.(280-282)GAA>GAT	p.E94D	EGF_uc011cfu.1_Missense_Mutation_p.E94D|EGF_uc011cfv.1_Missense_Mutation_p.E94D	NM_001963	NP_001954	P01133	EGF_HUMAN	epidermal growth factor precursor	94	LDL-receptor class B 1.|Extracellular (Potential).				angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)	TGGATTTAGAAAGACAACTTT	0.378													81	113	---	---	---	---	PASS
MAB21L2	10586	broad.mit.edu	37	4	151504561	151504561	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151504561A>T	uc003ilw.2	+	1	1485	c.380A>T	c.(379-381)AAG>ATG	p.K127M	LRBA_uc003ils.3_5'Flank|LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron|LRBA_uc010ipj.2_Intron	NM_006439	NP_006430	Q9Y586	MB212_HUMAN	mab-21-like protein 2	127					nervous system development	nucleus				ovary(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.159)		TCAGCGCGTAAGATCCGCTCG	0.617													10	32	---	---	---	---	PASS
KIAA0922	23240	broad.mit.edu	37	4	154524534	154524534	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154524534A>G	uc003inm.3	+	24	2768	c.2716A>G	c.(2716-2718)AGG>GGG	p.R906G	KIAA0922_uc010ipp.2_Missense_Mutation_p.R907G|KIAA0922_uc010ipq.2_Missense_Mutation_p.R675G	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2	906	Cytoplasmic (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				AACAAGACAGAGGCAAAATGC	0.423													6	300	---	---	---	---	PASS
KIAA0947	23379	broad.mit.edu	37	5	5447953	5447953	+	Splice_Site	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5447953G>T	uc003jdm.3	+	10	770	c.548_splice	c.e10-1	p.E183_splice		NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379											ovary(1)|central_nervous_system(1)	2						CATGCTTTTAGAGTTGAGACA	0.284													23	774	---	---	---	---	PASS
FAM105A	54491	broad.mit.edu	37	5	14610498	14610498	+	3'UTR	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14610498A>G	uc003jfj.2	+	8						NM_019018	NP_061891	Q9NUU6	F105A_HUMAN	hypothetical protein LOC54491											ovary(1)	1	Lung NSC(4;0.00592)					CTCTGAAACCAAAGCTAGCAT	0.463													8	28	---	---	---	---	PASS
DNAJC21	134218	broad.mit.edu	37	5	34933949	34933949	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34933949G>C	uc003jjc.2	+	2	354	c.127G>C	c.(127-129)GCT>CCT	p.A43P	DNAJC21_uc003jjb.2_Missense_Mutation_p.A43P|DNAJC21_uc010iuu.1_5'Flank	NM_001012339	NP_001012339	Q5F1R6	DJC21_HUMAN	DnaJ homology subfamily A member 5 isoform 2	43	J.				protein folding	ribosome	heat shock protein binding|nucleic acid binding|unfolded protein binding|zinc ion binding			breast(1)|skin(1)	2	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			CGCAGAAGCAGCTGAACAATT	0.383													6	353	---	---	---	---	PASS
FBXO4	26272	broad.mit.edu	37	5	41927219	41927219	+	Silent	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41927219G>A	uc003jmq.2	+	2	350	c.294G>A	c.(292-294)CTG>CTA	p.L98L	FBXO4_uc003jmp.2_Silent_p.L98L|FBXO4_uc003jmr.2_Silent_p.L98L	NM_012176	NP_036308	Q9UKT5	FBX4_HUMAN	F-box only protein 4 isoform 1	98	F-box.				positive regulation of protein ubiquitination|protein polyubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|telomere maintenance|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	protein binding|protein homodimerization activity|ubiquitin-protein ligase activity			liver(1)	1		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				ATCCAATTCTGTGGAGATACT	0.368													248	503	---	---	---	---	PASS
MAST4	375449	broad.mit.edu	37	5	66459741	66459741	+	Silent	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66459741G>A	uc003jut.1	+	28	4235	c.4167G>A	c.(4165-4167)CCG>CCA	p.P1389P	MAST4_uc003juw.2_Silent_p.P1317P|MAST4_uc003jux.2_5'Flank	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	1581						cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AAGTCTATCCGAAGGCTGTGG	0.502													27	61	---	---	---	---	PASS
SLC30A5	64924	broad.mit.edu	37	5	68414420	68414420	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68414420A>G	uc003jvh.2	+	12	1735	c.1534A>G	c.(1534-1536)ATT>GTT	p.I512V	SLC30A5_uc003jvj.2_RNA|SLC30A5_uc003jvk.2_Missense_Mutation_p.I241V|SLC30A5_uc003jvi.2_Missense_Mutation_p.I341V	NM_022902	NP_075053	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter),	512	Extracellular (Potential).				cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity			central_nervous_system(1)	1		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		GGCTAGATTGATTGATCCTCC	0.318													165	485	---	---	---	---	PASS
AFF4	27125	broad.mit.edu	37	5	132216688	132216688	+	3'UTR	SNP	T	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132216688T>G	uc003kyd.2	-	21					AFF4_uc011cxk.1_3'UTR	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31						transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTTATGGCAGTTTTCCTTCGT	0.428													14	118	---	---	---	---	PASS
KDM3B	51780	broad.mit.edu	37	5	137771430	137771430	+	3'UTR	SNP	C	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137771430C>A	uc003lcy.1	+	24					KDM3B_uc010jew.1_3'UTR|KDM3B_uc011cys.1_3'UTR	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11						GCAGGTCTTTCACTCACAACA	0.537													71	51	---	---	---	---	PASS
HSPA9	3313	broad.mit.edu	37	5	137895767	137895767	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137895767A>G	uc003ldf.2	-	11	1304	c.1196T>C	c.(1195-1197)GTA>GCA	p.V399A	HSPA9_uc003lde.2_5'Flank|HSPA9_uc011cyw.1_Missense_Mutation_p.V330A	NM_004134	NP_004125	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 precursor	399					anti-apoptosis|protein folding	cell surface|mitochondrial nucleoid	ATP binding|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAGATCCTGTACAGTCTGCTG	0.537													15	44	---	---	---	---	PASS
SPINK13	153218	broad.mit.edu	37	5	147665762	147665762	+	3'UTR	SNP	T	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147665762T>A	uc003lpc.2	+	5					uc003lpb.1_Intron|SPINK13_uc010jgt.2_RNA	NM_001040129	NP_001035218	Q1W4C9	ISK13_HUMAN	serine PI Kazal type 5-like 3 precursor							extracellular region	serine-type endopeptidase inhibitor activity				0						GGAATCAAACTGACAAGAACC	0.294													17	90	---	---	---	---	PASS
KCTD20	222658	broad.mit.edu	37	6	36442785	36442785	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36442785G>A	uc003ome.2	+	3	771	c.380G>A	c.(379-381)CGT>CAT	p.R127H	KCTD20_uc011dtm.1_Intron|KCTD20_uc011dtn.1_Intron|KCTD20_uc010jwk.2_Intron|KCTD20_uc011dto.1_Intron	NM_173562	NP_775833	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerisation domain	127	BTB.					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2						GATGGCACACGTTTTGTTGTG	0.408													45	107	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54806759	54806759	+	Missense_Mutation	SNP	G	A	A	rs146473058		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54806759G>A	uc003pck.2	+	5	3106	c.2990G>A	c.(2989-2991)CGA>CAA	p.R997Q		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	997										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					AACAAGTTTCGAGGATTTATG	0.338													67	32	---	---	---	---	PASS
DOPEY1	23033	broad.mit.edu	37	6	83863722	83863722	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83863722G>C	uc003pjs.1	+	32	6609	c.6349G>C	c.(6349-6351)GAT>CAT	p.D2117H	DOPEY1_uc011dyy.1_Missense_Mutation_p.D2108H|DOPEY1_uc010kbl.1_Missense_Mutation_p.D2108H|DOPEY1_uc003pjt.2_RNA	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	2117					protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CCTCTTTATGGATCCCAGTTT	0.443													9	440	---	---	---	---	PASS
MICAL1	64780	broad.mit.edu	37	6	109771288	109771288	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109771288G>T	uc003ptj.2	-	8	1446	c.1192C>A	c.(1192-1194)CCC>ACC	p.P398T	MICAL1_uc003ptk.2_Missense_Mutation_p.P398T|MICAL1_uc010kdr.2_Missense_Mutation_p.P312T|MICAL1_uc011eaq.1_Missense_Mutation_p.P417T	NM_022765	NP_073602	Q8TDZ2	MICA1_HUMAN	microtubule associated monoxygenase, calponin	398					cytoskeleton organization|signal transduction	cytoplasm|intermediate filament	SH3 domain binding|zinc ion binding			breast(2)|ovary(1)	3		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		GGCCAGAAGGGCTGCAGTGTC	0.617													8	55	---	---	---	---	PASS
FRK	2444	broad.mit.edu	37	6	116288847	116288847	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116288847T>A	uc003pwi.1	-	4	1113	c.666A>T	c.(664-666)AAA>AAT	p.K222N		NM_002031	NP_002022	P42685	FRK_HUMAN	fyn-related kinase	222					negative regulation of cell proliferation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|lung(3)	6		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)		GGTCCACGGTTTTATACGACA	0.383													95	60	---	---	---	---	PASS
C6orf103	79747	broad.mit.edu	37	6	146975333	146975333	+	Silent	SNP	C	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146975333C>G	uc010khx.2	+	4	434	c.393C>G	c.(391-393)CTC>CTG	p.L131L	C6orf103_uc003qlp.2_5'UTR	NM_024694	NP_078970	Q8N7X0	CAN7L_HUMAN	hypothetical protein LOC79747	131	Calpain catalytic.				oxygen transport|proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|heme binding|oxygen binding			central_nervous_system(2)|lung(1)	3		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.04e-08)|GBM - Glioblastoma multiforme(68;0.0113)		AACATTTACTCTGCAGCGAGG	0.348													71	35	---	---	---	---	PASS
C7orf50	84310	broad.mit.edu	37	7	1037413	1037413	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1037413G>T	uc003sju.2	-	5	503	c.433C>A	c.(433-435)CTG>ATG	p.L145M	C7orf50_uc003sjs.2_RNA|C7orf50_uc011jvt.1_Missense_Mutation_p.L145M|C7orf50_uc011jvu.1_Missense_Mutation_p.L145M	NM_032350	NP_115726	Q9BRJ6	CG050_HUMAN	hypothetical protein LOC84310	145							protein binding				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0216)|OV - Ovarian serous cystadenocarcinoma(56;1.3e-15)		AGGTAGGCCAGCAGGGTGGAG	0.672													35	32	---	---	---	---	PASS
IQCE	23288	broad.mit.edu	37	7	2629606	2629606	+	Silent	SNP	C	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2629606C>G	uc003smo.3	+	14	1294	c.1110C>G	c.(1108-1110)GCC>GCG	p.A370A	IQCE_uc010ksm.1_Silent_p.A370A|IQCE_uc003sml.1_Silent_p.A370A|IQCE_uc011jvy.1_Silent_p.A354A|IQCE_uc011jvz.1_Silent_p.A305A|IQCE_uc003smk.3_Silent_p.A354A|IQCE_uc003smn.3_Silent_p.A305A	NM_152558	NP_689771	Q6IPM2	IQCE_HUMAN	IQ motif containing E isoform 1	370											0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		ACCCGCCAGCCTGCCTTGCAT	0.567													19	15	---	---	---	---	PASS
ISPD	729920	broad.mit.edu	37	7	16445697	16445697	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16445697T>C	uc010ktx.2	-	2	523	c.523A>G	c.(523-525)AAG>GAG	p.K175E	ISPD_uc010kty.2_Missense_Mutation_p.K175E	NM_001101426	NP_001094896	A4D126	ISPD_HUMAN	notch1-induced protein isoform a	175					isoprenoid biosynthetic process		nucleotidyltransferase activity			ovary(1)	1						CCGTGTTCCTTAGCAGCTGTG	0.393										Multiple Myeloma(15;0.18)			169	175	---	---	---	---	PASS
ZNF117	51351	broad.mit.edu	37	7	64441811	64441811	+	5'UTR	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64441811T>C	uc003ttr.2	-	3						NM_015852	NP_056936	Q03924	ZN117_HUMAN	zinc finger protein 117							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Lung NSC(55;0.0295)|all_lung(88;0.0691)				TCCAGGGCTCTTTTCCTTGCT	0.398													7	594	---	---	---	---	PASS
POM121C	100101267	broad.mit.edu	37	7	75104426	75104426	+	5'UTR	SNP	A	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75104426A>C	uc003udk.3	-	2					POM121C_uc003udl.1_RNA	NM_001099415	NP_001092885	A8CG34	P121C_HUMAN	POM121 membrane glycoprotein (rat)-like						mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0						GGTGAAATCCACAGCCACATC	0.473													7	10	---	---	---	---	PASS
ASB4	51666	broad.mit.edu	37	7	95157534	95157534	+	Silent	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95157534C>T	uc011kij.1	+	3	897	c.897C>T	c.(895-897)CGC>CGT	p.R299R	ASB4_uc003unx.2_Silent_p.R299R	NM_016116	NP_057200	Q9Y574	ASB4_HUMAN	ankyrin repeat and SOCS box-containing protein 4	299					intracellular signal transduction					central_nervous_system(1)	1	all_cancers(62;2.27e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.218)|all_lung(186;0.246)		STAD - Stomach adenocarcinoma(171;0.0151)			CCTCCGTGCGCCCTGCTGCCC	0.582											OREG0018172	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	24	22	---	---	---	---	PASS
PILRA	29992	broad.mit.edu	37	7	99987688	99987688	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99987688T>G	uc003uuo.1	+	3	844	c.632T>G	c.(631-633)ATT>AGT	p.I211S	PILRA_uc011kjo.1_Intron|PILRA_uc003uup.1_Intron|PILRA_uc003uuq.1_Intron	NM_013439	NP_038467	Q9UKJ1	PILRA_HUMAN	paired immunoglobulin-like type 2 receptor alpha	211	Helical; (Potential).				interspecies interaction between organisms	extracellular region|integral to membrane|plasma membrane	protein binding|receptor activity			skin(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGAATCATGATTTTGGGACTG	0.582													49	147	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100680610	100680610	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100680610T>A	uc003uxp.1	+	3	5966	c.5913T>A	c.(5911-5913)GAT>GAA	p.D1971E	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1971	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|31.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					CAACTGCTGATGGTACCAGCA	0.502													7	307	---	---	---	---	PASS
DNAJC2	27000	broad.mit.edu	37	7	102962991	102962991	+	Silent	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102962991T>C	uc003vbo.2	-	9	1151	c.900A>G	c.(898-900)GAA>GAG	p.E300E	PMPCB_uc011kll.1_Intron|DNAJC2_uc003vbn.2_5'UTR|DNAJC2_uc010lix.2_Silent_p.E300E|DNAJC2_uc003vbp.2_5'UTR	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	300					'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1						tccgtttagcttctgcttttg	0.139													10	825	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142326873	142326873	+	Intron	SNP	C	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142326873C>G	uc011krp.1	+						uc011krr.1_Intron|uc003vzo.2_Missense_Mutation_p.D57E					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																		ACCGACAGGACCCAGGGCAAG	0.478													44	107	---	---	---	---	PASS
OR2A12	346525	broad.mit.edu	37	7	143792898	143792898	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143792898G>T	uc011kty.1	+	1	698	c.698G>T	c.(697-699)CGC>CTC	p.R233L		NM_001004135	NP_001004135	Q8NGT7	O2A12_HUMAN	olfactory receptor, family 2, subfamily A,	233	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	Melanoma(164;0.0783)					GGGGAGGGCCGCAGAAAGGCC	0.592													34	123	---	---	---	---	PASS
SSPO	23145	broad.mit.edu	37	7	149480310	149480310	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149480310A>C	uc010lpk.2	+	16	2192	c.2192A>C	c.(2191-2193)AAG>ACG	p.K731T	SSPO_uc010lpl.1_Missense_Mutation_p.K66T	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	731	VWFD 2.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GTGGCCGGCAAGGGAAGATGC	0.627													32	113	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151945349	151945349	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151945349T>A	uc003wla.2	-	14	2389	c.2170A>T	c.(2170-2172)AAG>TAG	p.K724*		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	724					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)		TTCTGTTCCTTTTCTCCTTGT	0.398			N		medulloblastoma								6	398	---	---	---	---	PASS
DOCK5	80005	broad.mit.edu	37	8	25189787	25189787	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25189787A>T	uc003xeg.2	+	19	2061	c.1924A>T	c.(1924-1926)AAT>TAT	p.N642Y	DOCK5_uc010luf.1_RNA|DOCK5_uc003xeh.1_Missense_Mutation_p.N356Y|DOCK5_uc003xei.2_Missense_Mutation_p.N212Y|DOCK5_uc003xej.2_RNA	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	642	DHR-1.					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		AGGCTTGTTAAATTGGCGTTC	0.373													113	309	---	---	---	---	PASS
ST18	9705	broad.mit.edu	37	8	53124666	53124666	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53124666G>T	uc003xqz.2	-	3	215	c.59C>A	c.(58-60)CCA>CAA	p.P20Q	ST18_uc011ldq.1_5'UTR|ST18_uc011ldr.1_5'UTR|ST18_uc011lds.1_5'UTR|ST18_uc003xra.2_Missense_Mutation_p.P20Q|ST18_uc003xrb.2_Missense_Mutation_p.P20Q|ST18_uc010lyb.2_RNA	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	20						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TGAATCCATTGGCACTGTTGA	0.333													5	260	---	---	---	---	PASS
NSMAF	8439	broad.mit.edu	37	8	59508187	59508187	+	Silent	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59508187T>C	uc003xtt.2	-	22	2038	c.1824A>G	c.(1822-1824)GAA>GAG	p.E608E	NSMAF_uc011lee.1_Silent_p.E639E	NM_003580	NP_003571	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation	608					ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)				GTGTTTTGCTTTCTTCGGTCA	0.403													6	358	---	---	---	---	PASS
CHD7	55636	broad.mit.edu	37	8	61774816	61774816	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61774816G>A	uc003xue.2	+	36	8369	c.7892G>A	c.(7891-7893)CGA>CAA	p.R2631Q		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2631					central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CATAGATGTCGAAACCCTAAT	0.358													11	186	---	---	---	---	PASS
SLCO5A1	81796	broad.mit.edu	37	8	70591818	70591818	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70591818G>A	uc003xyl.2	-	8	2526	c.1819C>T	c.(1819-1821)CGC>TGC	p.R607C	SLCO5A1_uc010lzb.2_Missense_Mutation_p.R552C|SLCO5A1_uc011lfa.1_RNA|SLCO5A1_uc003xyk.2_Missense_Mutation_p.R607C	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	607	Extracellular (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			ATCACTTGGCGACTTTGGACA	0.453													9	123	---	---	---	---	PASS
MTDH	92140	broad.mit.edu	37	8	98703400	98703400	+	Silent	SNP	A	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98703400A>C	uc003yhz.2	+	6	1360	c.1032A>C	c.(1030-1032)TCA>TCC	p.S344S	MTDH_uc010mbf.2_RNA	NM_178812	NP_848927	Q86UE4	LYRIC_HUMAN	metadherin	344	Cytoplasmic (Potential).				lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			GTGACCGTTCAATATTTTCTG	0.338													53	184	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113518989	113518989	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113518989G>A	uc003ynu.2	-	29	4985	c.4826C>T	c.(4825-4827)CCG>CTG	p.P1609L	CSMD3_uc003yns.2_Missense_Mutation_p.P881L|CSMD3_uc003ynt.2_Missense_Mutation_p.P1569L|CSMD3_uc011lhx.1_Missense_Mutation_p.P1505L	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1609	Extracellular (Potential).|CUB 9.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TCTGCTATGCGGATATGGATG	0.383										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			9	319	---	---	---	---	PASS
SQLE	6713	broad.mit.edu	37	8	126034065	126034065	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126034065T>C	uc011liq.1	+	11	2529	c.1603T>C	c.(1603-1605)TTT>CTT	p.F535L		NM_003129	NP_003120	Q14534	ERG1_HUMAN	squalene epoxidase	535					cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome	flavin adenine dinucleotide binding|squalene monooxygenase activity			ovary(1)|breast(1)	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)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)	GTATTTTTGCTTTAAGTCAGA	0.363													8	607	---	---	---	---	PASS
MURC	347273	broad.mit.edu	37	9	103348313	103348313	+	Silent	SNP	A	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103348313A>C	uc004bba.2	+	2	765	c.675A>C	c.(673-675)ATA>ATC	p.I225I		NM_001018116	NP_001018126	Q5BKX8	MURC_HUMAN	muscle-related coiled-coil protein	225	Potential.				cell differentiation|muscle organ development|transcription, DNA-dependent					ovary(1)	1		Acute lymphoblastic leukemia(62;0.0461)				GAACTAGAATAGTGACCCCGG	0.458													52	19	---	---	---	---	PASS
SLC44A1	23446	broad.mit.edu	37	9	108151473	108151473	+	3'UTR	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108151473C>T	uc004bcn.2	+	16					SLC44A1_uc010mtk.1_Intron|SLC44A1_uc004bco.1_Intron	NM_080546	NP_536856	Q8WWI5	CTL1_HUMAN	CDW92 antigen							integral to membrane|mitochondrial outer membrane|plasma membrane	choline transmembrane transporter activity			breast(3)|ovary(1)	4					Choline(DB00122)	CACACACACACATAAATCAGC	0.219													3	36	---	---	---	---	PASS
FAM129B	64855	broad.mit.edu	37	9	130287413	130287413	+	Silent	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130287413G>A	uc004brh.2	-	4	547	c.345C>T	c.(343-345)GCC>GCT	p.A115A	FAM129B_uc004bri.2_Silent_p.A102A|FAM129B_uc004brj.3_Silent_p.A115A	NM_022833	NP_073744	Q96TA1	NIBL1_HUMAN	hypothetical protein LOC64855 isoform 1	115	PH.						protein binding				0						TGTTGATGACGGCTCGTGGTG	0.587													50	16	---	---	---	---	PASS
TUBBP5	643224	broad.mit.edu	37	9	141069885	141069885	+	5'UTR	SNP	A	C	C	rs62581043		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141069885A>C	uc004com.2	+	2					TUBBP5_uc010ncq.2_Missense_Mutation_p.Q85P					RecName: Full=Putative tubulin beta-4q chain;												0						AGCCACCTGCAGCTGGAGCGC	0.662													5	22	---	---	---	---	PASS
ARMC4	55130	broad.mit.edu	37	10	28233820	28233820	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28233820G>C	uc009xky.2	-	11	1556	c.1458C>G	c.(1456-1458)TGC>TGG	p.C486W	ARMC4_uc010qds.1_Missense_Mutation_p.C11W|ARMC4_uc010qdt.1_Missense_Mutation_p.C178W|ARMC4_uc001itz.2_Missense_Mutation_p.C486W|ARMC4_uc010qdu.1_Missense_Mutation_p.C178W	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	486	ARM 1.						binding			ovary(4)|skin(2)	6						TGGCCAACTGGCAGGTTTCTT	0.453													7	140	---	---	---	---	PASS
ERCC6	2074	broad.mit.edu	37	10	50732744	50732744	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50732744C>A	uc001jhs.3	-	5	886	c.732G>T	c.(730-732)CAG>CAT	p.Q244H	PGBD3_uc001jht.2_5'Flank|PGBD3_uc009xoe.2_Missense_Mutation_p.Q244H|PGBD3_uc001jhu.2_Missense_Mutation_p.Q244H	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	244					base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding			lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1)	16						AAGGTGTCATCTGGCCAGTGC	0.502								Direct_reversal_of_damage|NER					10	53	---	---	---	---	PASS
CTNNA3	29119	broad.mit.edu	37	10	68940123	68940123	+	Silent	SNP	G	A	A	rs146754105		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68940123G>A	uc009xpn.1	-	7	1122	c.999C>T	c.(997-999)AAC>AAT	p.N333N	CTNNA3_uc001jmw.2_Silent_p.N333N|CTNNA3_uc001jmx.3_Silent_p.N333N|CTNNA3_uc009xpo.1_Silent_p.N193N|CTNNA3_uc001jna.2_Silent_p.N345N	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3	333	Potential.				cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						GGCGAATGGCGTTGCATTCTG	0.517													35	109	---	---	---	---	PASS
WDR11	55717	broad.mit.edu	37	10	122624668	122624668	+	Missense_Mutation	SNP	G	C	C	rs145467317		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122624668G>C	uc010qtf.1	+	6	1061	c.823G>C	c.(823-825)GTG>CTG	p.V275L	WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_5'UTR	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2	275						integral to membrane					0						TGACCTTGAGGTGAATCAGAC	0.378													77	284	---	---	---	---	PASS
TRIM22	10346	broad.mit.edu	37	11	5727831	5727831	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5727831T>C	uc001mbr.2	+	5	1035	c.758T>C	c.(757-759)ATT>ACT	p.I253T	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Missense_Mutation_p.I221T|TRIM22_uc009yes.2_Missense_Mutation_p.I249T|TRIM22_uc010qzm.1_Missense_Mutation_p.I81T|TRIM22_uc009yeu.2_Missense_Mutation_p.I64T|OR56B1_uc001mbs.1_5'Flank|OR56B1_uc009yev.1_5'Flank	NM_006074	NP_006065	Q8IYM9	TRI22_HUMAN	tripartite motif-containing 22	253					immune response|interspecies interaction between organisms|protein trimerization|response to virus	Cajal body|Golgi apparatus|nuclear speck	ligase activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		CAGGATGTGATTGACGTCATG	0.254													316	398	---	---	---	---	PASS
C11orf42	160298	broad.mit.edu	37	11	6231300	6231300	+	Missense_Mutation	SNP	G	A	A	rs148934108		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6231300G>A	uc001mcj.2	+	2	341	c.293G>A	c.(292-294)CGG>CAG	p.R98Q		NM_173525	NP_775796	Q8N5U0	CK042_HUMAN	hypothetical protein LOC160298	98										ovary(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.95e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACTGCACTCGGGAATACTCA	0.607													12	49	---	---	---	---	PASS
C11orf42	160298	broad.mit.edu	37	11	6231320	6231320	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6231320C>T	uc001mcj.2	+	2	361	c.313C>T	c.(313-315)CGA>TGA	p.R105*		NM_173525	NP_775796	Q8N5U0	CK042_HUMAN	hypothetical protein LOC160298	105										ovary(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.95e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCAAATGGCCGAGCAGAGAG	0.577													15	52	---	---	---	---	PASS
C11orf42	160298	broad.mit.edu	37	11	6231744	6231744	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6231744C>T	uc001mcj.2	+	2	785	c.737C>T	c.(736-738)ACT>ATT	p.T246I		NM_173525	NP_775796	Q8N5U0	CK042_HUMAN	hypothetical protein LOC160298	246	Pro-rich.									ovary(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.95e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCTGATACAACTGAAGCTGCT	0.612													4	23	---	---	---	---	PASS
SBF2	81846	broad.mit.edu	37	11	9868520	9868520	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9868520T>G	uc001mib.2	-	23	3055	c.2917A>C	c.(2917-2919)ACA>CCA	p.T973P	SBF2_uc001mif.3_Missense_Mutation_p.T729P|uc001mig.2_Intron	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2	973					myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		GATGCTGATGTGATCTGCAGT	0.393													119	269	---	---	---	---	PASS
MICALCL	84953	broad.mit.edu	37	11	12316279	12316279	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12316279A>C	uc001mkg.1	+	3	1592	c.1301A>C	c.(1300-1302)GAA>GCA	p.E434A		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	434					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding			skin(1)	1				Epithelial(150;0.00177)		GTGCTGCCTGAAGATAGTGCG	0.438													11	13	---	---	---	---	PASS
TEAD1	7003	broad.mit.edu	37	11	12958817	12958817	+	3'UTR	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12958817T>C	uc001mkj.3	+	13					TEAD1_uc001mkk.3_3'UTR|TEAD1_uc009ygl.2_3'UTR	NM_021961	NP_068780	P28347	TEAD1_HUMAN	TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		cacacacatatgtgcacacac	0.353													26	37	---	---	---	---	PASS
TNKS1BP1	85456	broad.mit.edu	37	11	57076422	57076422	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57076422C>T	uc001njr.2	-	5	4075	c.3763G>A	c.(3763-3765)GTG>ATG	p.V1255M	TNKS1BP1_uc001njs.2_Missense_Mutation_p.V1255M|TNKS1BP1_uc009ymd.1_Missense_Mutation_p.V706M	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	1255	Gly-rich.|Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				GTCTGCCCCACGCCACTCTCT	0.577													12	40	---	---	---	---	PASS
NPAT	4863	broad.mit.edu	37	11	108032084	108032084	+	Silent	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108032084G>T	uc001pjz.3	-	17	3831	c.3729C>A	c.(3727-3729)ACC>ACA	p.T1243T	NPAT_uc010rvv.1_Silent_p.T299T	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	1243	Required for acceleration of G1 phase.				positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|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)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		ACATTTCTGTGGTAATCAAAG	0.438													4	244	---	---	---	---	PASS
SLC37A2	219855	broad.mit.edu	37	11	124955896	124955896	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124955896C>T	uc001qbn.2	+	17	1723	c.1472C>T	c.(1471-1473)TCC>TTC	p.S491F	SLC37A2_uc010sau.1_Missense_Mutation_p.S491F|SLC37A2_uc010sav.1_Missense_Mutation_p.S116F|SLC37A2_uc001qbp.2_Missense_Mutation_p.S116F	NM_001145290	NP_001138762	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glycerol-3-phosphate	491					carbohydrate transport|transmembrane transport	integral to membrane				ovary(2)	2	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		TGGAAGGTGTCCCTGAGCAGA	0.577													16	65	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	92018	92018	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92018T>C	uc010sdi.1	-	2	320	c.292A>G	c.(292-294)AGT>GGT	p.S98G	uc010sdj.1_RNA					SubName: Full=DEAD/H box polypeptide 11 like 11;																		GACTCCACACTCTCCTGGGTT	0.592													3	10	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	92299	92299	+	Intron	SNP	C	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92299C>G	uc010sdi.1	-						uc010sdj.1_RNA					SubName: Full=DEAD/H box polypeptide 11 like 11;																		GGCTCAGATCCAGGCCAACAG	0.587													9	23	---	---	---	---	PASS
TNFRSF1A	7132	broad.mit.edu	37	12	6443344	6443344	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6443344C>A	uc001qnu.2	-	2	387	c.106G>T	c.(106-108)GAC>TAC	p.D36Y	TNFRSF1A_uc001qnt.2_5'UTR|TNFRSF1A_uc010sey.1_5'UTR|TNFRSF1A_uc010sez.1_Intron|TNFRSF1A_uc009zek.2_Missense_Mutation_p.D36Y|TNFRSF1A_uc010sfa.1_Missense_Mutation_p.D36Y	NM_001065	NP_001056	P19438	TNR1A_HUMAN	tumor necrosis factor receptor 1 precursor	36	Extracellular (Potential).				apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|inflammatory response|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of inflammatory response|positive regulation of transcription from RNA polymerase II promoter|prostaglandin metabolic process	extracellular region|integral to plasma membrane|membrane raft	tumor necrosis factor receptor activity			lung(2)|skin(1)	3						TTCTCCCTGTCCCCTAGGTGA	0.498													6	317	---	---	---	---	PASS
ZNF384	171017	broad.mit.edu	37	12	6776846	6776846	+	3'UTR	SNP	T	A	A	rs142697690	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6776846T>A	uc010sfh.1	-	11					ZNF384_uc001qpz.2_3'UTR|ZNF384_uc001qqa.2_3'UTR|ZNF384_uc001qqb.2_3'UTR|ZNF384_uc001qqc.2_3'UTR|ZNF384_uc001qqd.2_3'UTR|ZNF384_uc001qqe.2_3'UTR	NM_001135734	NP_001129206	Q8TF68	ZN384_HUMAN	nuclear matrix transcription factor 4 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/ZNF384(4)	haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1)	8						CAGGACTACTTCTTCCTCTTC	0.542			T	EWSR1|TAF15 	ALL								34	60	---	---	---	---	PASS
C1S	716	broad.mit.edu	37	12	7177889	7177889	+	Silent	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7177889G>T	uc001qsj.2	+	15	2720	c.2001G>T	c.(1999-2001)CGG>CGT	p.R667R	C1S_uc001qsk.2_Silent_p.R667R|C1S_uc001qsl.2_Silent_p.R667R|C1S_uc009zfr.2_Silent_p.R500R|C1S_uc009zfs.2_RNA	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent	667	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	TCTACACACGGGTAAAGAACT	0.537													40	47	---	---	---	---	PASS
C1R	715	broad.mit.edu	37	12	7242701	7242701	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7242701A>T	uc010sfy.1	-	3	434	c.375T>A	c.(373-375)AAT>AAA	p.N125K	C1R_uc010sfz.1_Missense_Mutation_p.N139K|C1R_uc010sga.1_Missense_Mutation_p.N91K	NM_001733	NP_001724	P00736	C1R_HUMAN	complement component 1, r subcomponent	125	CUB 1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TGATGGTCCCATTCTCCTCGT	0.532													72	123	---	---	---	---	PASS
CCDC91	55297	broad.mit.edu	37	12	28515416	28515416	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28515416G>A	uc001riq.2	+	6	638	c.622G>A	c.(622-624)GAA>AAA	p.E208K	CCDC91_uc001rio.2_Missense_Mutation_p.E178K|CCDC91_uc009zjk.2_RNA|CCDC91_uc001rip.1_Missense_Mutation_p.E208K|CCDC91_uc001rir.2_Missense_Mutation_p.E46K|CCDC91_uc009zjl.2_Missense_Mutation_p.E46K	NM_018318	NP_060788	Q7Z6B0	CCD91_HUMAN	GGA binding partner	208	Potential.				protein transport	Golgi apparatus|membrane				central_nervous_system(1)	1	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					AGCTGGTCACGAAGCCCTCAG	0.323													8	630	---	---	---	---	PASS
ANO6	196527	broad.mit.edu	37	12	45686633	45686633	+	Intron	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45686633A>G	uc001roo.2	+						ANO6_uc010sld.1_Intron|ANO6_uc010sle.1_Intron|ANO6_uc010slf.1_Intron|ANO6_uc010slg.1_5'UTR	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						CACTTAAGGTAGAGGTAGGAG	0.418													7	593	---	---	---	---	PASS
COL2A1	1280	broad.mit.edu	37	12	48386690	48386690	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48386690T>C	uc001rqu.2	-	16	1175	c.994A>G	c.(994-996)AGA>GGA	p.R332G	COL2A1_uc001rqv.2_Missense_Mutation_p.R263G	NM_001844	NP_001835	P02458	CO2A1_HUMAN	collagen, type II, alpha 1 isoform 1 precursor	332	Triple-helical region.				axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	GTCCGTCCTCTTTCACCAGGC	0.458													5	126	---	---	---	---	PASS
ATP2B1	490	broad.mit.edu	37	12	90003742	90003742	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90003742A>T	uc001tbh.2	-	14	2595	c.2414T>A	c.(2413-2415)CTA>CAA	p.L805Q	ATP2B1_uc001tbg.2_Missense_Mutation_p.L805Q|ATP2B1_uc001tbf.2_Missense_Mutation_p.L475Q	NM_001682	NP_001673	P20020	AT2B1_HUMAN	plasma membrane calcium ATPase 1 isoform 1b	805	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						TGCTTTCTTTAGTGCTGGGCC	0.328													169	218	---	---	---	---	PASS
LUM	4060	broad.mit.edu	37	12	91497883	91497883	+	3'UTR	SNP	C	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91497883C>A	uc001tbm.2	-	3					LUM_uc001tbn.2_RNA	NM_002345	NP_002336	P51884	LUM_HUMAN	lumican precursor						collagen fibril organization|visual perception	extracellular space|fibrillar collagen	collagen binding|extracellular matrix structural constituent			central_nervous_system(2)	2						AATATGGATACTATGAAAACT	0.274													10	81	---	---	---	---	PASS
CHPT1	56994	broad.mit.edu	37	12	102120124	102120124	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102120124T>A	uc001tin.2	+	8	1341	c.1118T>A	c.(1117-1119)ATT>AAT	p.I373N	CHPT1_uc001tio.2_RNA|CHPT1_uc001tip.1_Missense_Mutation_p.I373N	NM_020244	NP_064629	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	373					platelet activating factor biosynthetic process|regulation of cell growth	Golgi membrane|integral to membrane|microsome	diacylglycerol binding|diacylglycerol cholinephosphotransferase activity|metal ion binding				0						TGCCTGCAAATTTCAAGACAC	0.333													256	431	---	---	---	---	PASS
SRRM4	84530	broad.mit.edu	37	12	119552153	119552153	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119552153C>T	uc001txa.1	+	3	641	c.349C>T	c.(349-351)CGG>TGG	p.R117W		NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein	117	Lys-rich.				cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						GAAATCCACTCGGAAGAAGAG	0.363													74	273	---	---	---	---	PASS
SBNO1	55206	broad.mit.edu	37	12	123812074	123812074	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123812074A>G	uc010tap.1	-	12	1591	c.1591T>C	c.(1591-1593)TAC>CAC	p.Y531H	SBNO1_uc010tao.1_Missense_Mutation_p.Y530H|SBNO1_uc010taq.1_Intron|SBNO1_uc001uet.2_Missense_Mutation_p.Y531H|SBNO1_uc001ueu.2_Missense_Mutation_p.Y530H|SBNO1_uc001uev.2_Missense_Mutation_p.Y529H|SBNO1_uc009zxy.1_Missense_Mutation_p.Y496H	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	531							ATP binding|DNA binding|hydrolase activity			breast(5)|skin(2)|ovary(1)|kidney(1)	9	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		CGAGCAATGTACATTCCTCTA	0.353													112	135	---	---	---	---	PASS
DHX37	57647	broad.mit.edu	37	12	125435351	125435351	+	Splice_Site	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125435351C>T	uc001ugy.2	-	22	2968	c.2869_splice	c.e22-1	p.T957_splice	DHX37_uc001ugz.1_Splice_Site_p.T44_splice	NM_032656	NP_116045	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		GGAGAGGGGTCTGCAGAGAAT	0.552													132	201	---	---	---	---	PASS
POSTN	10631	broad.mit.edu	37	13	38137276	38137276	+	3'UTR	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38137276G>T	uc001uwo.3	-	23					POSTN_uc010tet.1_3'UTR|POSTN_uc001uwp.3_3'UTR|POSTN_uc001uwr.2_3'UTR|POSTN_uc001uwq.2_3'UTR	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1						cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		CTTTACCACAGGAGGCTAACT	0.318													3	44	---	---	---	---	PASS
SPRY2	10253	broad.mit.edu	37	13	80911818	80911818	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80911818C>T	uc001vli.2	-	2	1001	c.23G>A	c.(22-24)GGC>GAC	p.G8D	SPRY2_uc001vlj.2_Missense_Mutation_p.G8D	NM_005842	NP_005833	O43597	SPY2_HUMAN	sprouty 2	8					epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of ERK1 and ERK2 cascade|positive regulation of gene expression|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein kinase B signaling cascade	cytosol|microtubule|ruffle membrane	protein serine/threonine kinase activator activity			ovary(1)|lung(1)	2	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		CGACCCGTTGCCACTCTGAGC	0.607													3	7	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109707736	109707736	+	Splice_Site	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109707736A>G	uc001vqt.1	+	27	3190	c.3064_splice	c.e27-2	p.K1022_splice	MYO16_uc010agk.1_Splice_Site_p.K1044_splice|MYO16_uc001vqu.1_Splice_Site_p.K822_splice|MYO16_uc010tjh.1_Splice_Site_p.K534_splice	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TTCTCTCCTTAGAAATCACTA	0.343													6	107	---	---	---	---	PASS
NRXN3	9369	broad.mit.edu	37	14	80271498	80271498	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80271498A>T	uc001xun.2	+	16	3340	c.2849A>T	c.(2848-2850)GAT>GTT	p.D950V	NRXN3_uc001xum.1_RNA|NRXN3_uc001xup.2_RNA|NRXN3_uc001xuq.2_Missense_Mutation_p.D318V|NRXN3_uc010asw.2_Missense_Mutation_p.D348V|NRXN3_uc001xur.3_Missense_Mutation_p.D318V	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	1323	Extracellular (Potential).				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TGTTCAAGTGATGATGAAGAC	0.373													5	586	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107062359	107062359	+	RNA	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107062359G>T	uc010tyt.1	-	131		c.6236C>A								Parts of antibodies, mostly variable regions.												0						AGACAGCGCAGATGAGGGACA	0.607													3	36	---	---	---	---	PASS
SECISBP2L	9728	broad.mit.edu	37	15	49301479	49301479	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49301479C>A	uc001zxe.1	-	14	2095	c.1961G>T	c.(1960-1962)AGT>ATT	p.S654I	SECISBP2L_uc001zxd.1_Missense_Mutation_p.S609I|SECISBP2L_uc010bep.1_Missense_Mutation_p.S416I	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	654										breast(1)|skin(1)	2						TATTCCAGAACTAGCAGGAGA	0.413													97	381	---	---	---	---	PASS
RAB11A	8766	broad.mit.edu	37	15	66180126	66180126	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66180126T>C	uc002apk.2	+	5	727	c.599T>C	c.(598-600)GTT>GCT	p.V200A	RAB11A_uc010ujk.1_3'UTR	NM_004663	NP_004654	P62491	RB11A_HUMAN	Ras-related protein Rab-11A	200					cell cycle|cytokinesis|neuron projection development|plasma membrane to endosome transport|protein localization in plasma membrane|small GTPase mediated signal transduction|vesicle-mediated transport	cleavage furrow|plasma membrane|recycling endosome membrane|trans-Golgi network	GTP binding|GTPase activity|syntaxin binding				0						CCTATTCATGTTCCACCAACC	0.438													6	192	---	---	---	---	PASS
HEXA	3073	broad.mit.edu	37	15	72640389	72640389	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72640389G>A	uc002aun.3	-	9	1280	c.1073C>T	c.(1072-1074)ACG>ATG	p.T358M	uc002aug.2_Intron|CELF6_uc002auk.3_Intron|HEXA_uc010ukn.1_Missense_Mutation_p.T369M|HEXA_uc002auo.3_Missense_Mutation_p.T221M|HEXA_uc010bix.2_Missense_Mutation_p.T358M|HEXA_uc010biy.2_Missense_Mutation_p.T221M|HEXA_uc010uko.1_Missense_Mutation_p.T184M|HEXA_uc010biz.1_RNA	NM_000520	NP_000511	P06865	HEXA_HUMAN	hexosaminidase A preproprotein	358					cell death	lysosome	beta-N-acetylhexosaminidase activity|cation binding|protein heterodimerization activity			ovary(3)|upper_aerodigestive_tract(1)	4						CCTTCCTCACGTCTGGATGTA	0.577													16	151	---	---	---	---	PASS
FAM195A	84331	broad.mit.edu	37	16	698116	698116	+	Intron	SNP	A	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:698116A>C	uc002cic.1	+						FAM195A_uc002cid.1_Intron|FAM195A_uc002cie.2_Missense_Mutation_p.T144P|FAM195A_uc002cif.1_Intron|WDR90_uc002cig.1_5'Flank|WDR90_uc002cih.1_5'Flank|WDR90_uc002cii.1_5'Flank|WDR90_uc002cij.1_5'Flank	NM_138418	NP_612427	Q9BUT9	F195A_HUMAN	hypothetical protein LOC84331												0						TTCTCTGCCCACAGACTTTGT	0.642													24	44	---	---	---	---	PASS
LMF1	64788	broad.mit.edu	37	16	920728	920728	+	Splice_Site	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:920728C>T	uc002ckj.2	-	8	1236	c.1232_splice	c.e8+1	p.S411_splice	LMF1_uc010brg.2_5'Flank|LMF1_uc010brh.2_Splice_Site_p.S194_splice|LMF1_uc010bri.2_Splice_Site_p.S174_splice|LMF1_uc002ckk.2_Splice_Site_p.S194_splice	NM_022773	NP_073610	Q96S06	LMF1_HUMAN	lipase maturation factor 1							endoplasmic reticulum membrane|integral to membrane					0		Hepatocellular(780;0.00308)				CAGGCTCATACCTTCCGAAGG	0.602													4	90	---	---	---	---	PASS
A2BP1	54715	broad.mit.edu	37	16	7645620	7645620	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7645620G>A	uc002cys.2	+	8	1526	c.538G>A	c.(538-540)GTG>ATG	p.V180M	A2BP1_uc010buf.1_Missense_Mutation_p.V180M|A2BP1_uc002cyr.1_Missense_Mutation_p.V179M|A2BP1_uc002cyt.2_Missense_Mutation_p.V180M|A2BP1_uc010uxz.1_Missense_Mutation_p.V223M|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Missense_Mutation_p.V180M|A2BP1_uc010uyb.1_Missense_Mutation_p.V180M|A2BP1_uc002cyw.2_Missense_Mutation_p.V200M|A2BP1_uc002cyy.2_Missense_Mutation_p.V200M|A2BP1_uc002cyx.2_Missense_Mutation_p.V200M|A2BP1_uc010uyc.1_Missense_Mutation_p.V200M	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4	180	RRM.				mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		ACACGGCACCGTGGTAGAGGG	0.448													14	174	---	---	---	---	PASS
MKL2	57496	broad.mit.edu	37	16	14334311	14334311	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14334311A>T	uc010uza.1	+	10	1204	c.1049A>T	c.(1048-1050)AAC>ATC	p.N350I	MKL2_uc002dcg.2_Missense_Mutation_p.N350I|MKL2_uc002dch.2_Missense_Mutation_p.N339I|MKL2_uc010uzb.1_Missense_Mutation_p.N299I	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein	339					cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5						CAGCACTACAACTACCAGACC	0.532													30	68	---	---	---	---	PASS
SLC5A11	115584	broad.mit.edu	37	16	24921753	24921753	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24921753G>A	uc002dmu.2	+	15	2009	c.1777G>A	c.(1777-1779)GTC>ATC	p.V593I	SLC5A11_uc002dms.2_Missense_Mutation_p.V529I|SLC5A11_uc010vcd.1_Missense_Mutation_p.V558I|SLC5A11_uc002dmt.2_Missense_Mutation_p.V437I|SLC5A11_uc010vce.1_Missense_Mutation_p.V523I|SLC5A11_uc010bxt.2_Missense_Mutation_p.V529I|SLC5A11_uc002dmv.2_Missense_Mutation_p.V216I	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	593	Cytoplasmic (Potential).				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)		CAGCAGCAGCGTCCAGTTCGA	0.532													10	72	---	---	---	---	PASS
SULT1A1	6817	broad.mit.edu	37	16	28620121	28620121	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28620121G>A	uc002dqi.2	-	1	529	c.56C>T	c.(55-57)CCG>CTG	p.P19L	uc010vct.1_Intron|SULT1A1_uc002dqj.2_Missense_Mutation_p.P19L|SULT1A1_uc002dqk.2_Missense_Mutation_p.P19L|SULT1A1_uc002dql.2_Missense_Mutation_p.P19L|SULT1A1_uc002dqm.2_Intron|SULT1A1_uc002dqn.2_Missense_Mutation_p.P110L|SULT1A1_uc002dqo.2_Missense_Mutation_p.P19L|SULT1A1_uc002dqp.2_Missense_Mutation_p.P19L	NM_177534	NP_803878	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A,	19					3'-phosphoadenosine 5'-phosphosulfate metabolic process|catecholamine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity|flavonol 3-sulfotransferase activity				0						CTTGATGAGCGGGACCCCCTT	0.632													12	57	---	---	---	---	PASS
SRCAP	10847	broad.mit.edu	37	16	30734026	30734026	+	Silent	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30734026C>T	uc002dze.1	+	23	4234	c.3849C>T	c.(3847-3849)ACC>ACT	p.T1283T	SRCAP_uc002dzf.2_Intron|SRCAP_uc002dzg.1_Intron|SRCAP_uc010bzz.1_Silent_p.T853T	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1283	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			CCAGCACCACCCCTGCCCCTA	0.657													5	47	---	---	---	---	PASS
CNGB1	1258	broad.mit.edu	37	16	57991272	57991272	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57991272A>T	uc002emt.2	-	12	912	c.847T>A	c.(847-849)TCC>ACC	p.S283T	CNGB1_uc010cdh.2_Missense_Mutation_p.S277T|CNGB1_uc002emu.2_Missense_Mutation_p.S283T	NM_001297	NP_001288	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1 isoform	283					sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4						ATCCCAGGGGAGTCAGGCTCC	0.453													62	89	---	---	---	---	PASS
LOC283922	283922	broad.mit.edu	37	16	74368798	74368798	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74368798A>G	uc002fcr.2	-	13	2151	c.805T>C	c.(805-807)TTT>CTT	p.F269L	LOC283922_uc010vms.1_RNA					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						ACCTTGCAAAAGAGGCTTGGG	0.448													6	340	---	---	---	---	PASS
CLEC18B	497190	broad.mit.edu	37	16	74445808	74445808	+	Intron	SNP	T	C	C	rs146209466	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74445808T>C	uc002fct.2	-						CLEC18B_uc002fcu.2_Intron|CLEC18B_uc010vmu.1_3'UTR|CLEC18B_uc010vmv.1_Intron	NM_001011880	NP_001011880	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B							extracellular region	sugar binding				0						GGGTcaggagtgagctggtca	0.294													9	127	---	---	---	---	PASS
GP1BA	2811	broad.mit.edu	37	17	4836600	4836600	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4836600G>A	uc010vsq.1	+	2	776	c.701G>A	c.(700-702)CGC>CAC	p.R234H	uc002fzn.1_RNA	NM_000173	NP_000164	P07359	GP1BA_HUMAN	platelet glycoprotein Ib alpha polypeptide	234											0						TATTTTCGTCGCTGGCTGCAG	0.493													22	55	---	---	---	---	PASS
KIF1C	10749	broad.mit.edu	37	17	4923903	4923903	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4923903G>A	uc002gan.1	+	20	2193	c.1867G>A	c.(1867-1869)GAC>AAC	p.D623N		NM_006612	NP_006603	O43896	KIF1C_HUMAN	kinesin family member 1C	623					microtubule-based movement|retrograde vesicle-mediated transport, Golgi to ER	endoplasmic reticulum|Golgi apparatus|microtubule	ATP binding|microtubule motor activity			breast(2)	2						TGAGCCAGTCGACTGGAACTT	0.617													19	12	---	---	---	---	PASS
GAS7	8522	broad.mit.edu	37	17	9873005	9873005	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9873005C>T	uc002gmg.1	-	4	621	c.460G>A	c.(460-462)GGT>AGT	p.G154S	GAS7_uc010vvd.1_Missense_Mutation_p.G106S|GAS7_uc002gmi.2_Missense_Mutation_p.G90S|GAS7_uc002gmj.1_Missense_Mutation_p.G94S|GAS7_uc010coh.1_Missense_Mutation_p.G94S	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c	154					cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						TGGGAATCACCGGTGGATTTT	0.562			T	MLL	AML*								34	104	---	---	---	---	PASS
CCDC144A	9720	broad.mit.edu	37	17	16596346	16596346	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16596346C>T	uc002gqk.1	+	2	474	c.398C>T	c.(397-399)CCT>CTT	p.P133L		NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	133											0						GAAAGTCTTCCTCAAAATAAC	0.303													126	138	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	21731234	21731234	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21731234A>C	uc002gyy.3	+	2	661	c.536A>C	c.(535-537)AAG>ACG	p.K179T						SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																		GAAAATGTGAAGGCCAAGATC	0.532													20	81	---	---	---	---	PASS
MYO18A	399687	broad.mit.edu	37	17	27417116	27417116	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27417116G>C	uc002hdt.1	-	37	5547	c.5389C>G	c.(5389-5391)CTA>GTA	p.L1797V	MYO18A_uc010wbc.1_Missense_Mutation_p.L1330V|MYO18A_uc002hds.2_Missense_Mutation_p.L1339V|MYO18A_uc010csa.1_Missense_Mutation_p.L1760V|MYO18A_uc002hdu.1_Missense_Mutation_p.L1797V	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a	1797	Potential.				anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			AGGGCTTGTAGCTAGAGGTGG	0.577													31	29	---	---	---	---	PASS
RNF135	84282	broad.mit.edu	37	17	29302546	29302546	+	Intron	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29302546A>G	uc002hfz.2	+						RNF135_uc002hga.2_Intron|RNF135_uc010csm.2_Intron|RNF135_uc002hgb.2_Intron|DPRXP4_uc002hgc.2_RNA	NM_032322	NP_115698	Q8IUD6	RN135_HUMAN	ring finger protein 135 isoform 1						innate immune response|negative regulation of type I interferon production|positive regulation of interferon-beta production|regulation of innate immune response	cytosol	protein binding|ribonucleoprotein binding|ubiquitin-protein ligase activity|zinc ion binding	p.?(1)		skin(2)	2		all_cancers(10;8.65e-08)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Myeloproliferative disorder(56;0.0255)				CCTCAGAAATAAATGGCCTCG	0.418													44	116	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	34234138	34234138	+	RNA	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34234138G>A	uc010ctx.1	-	1		c.2816C>T								Homo sapiens cDNA FLJ43944 fis, clone TESTI4014392.																		GTCAGTGTCCGTGGTAGGCTC	0.517													6	12	---	---	---	---	PASS
QRICH2	84074	broad.mit.edu	37	17	74270248	74270248	+	3'UTR	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74270248T>C	uc002jrd.1	-	19					QRICH2_uc010wsz.1_Missense_Mutation_p.T1380A|QRICH2_uc010dgw.1_3'UTR	NM_032134	NP_115510	Q9H0J4	QRIC2_HUMAN	glutamine rich 2								protein binding			ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)|skin(1)	5						CAGCCCCCTGTTTGCCACCGC	0.662													7	26	---	---	---	---	PASS
DNAH17	8632	broad.mit.edu	37	17	76450661	76450661	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76450661C>T	uc010dhp.1	-	9	1519	c.1297G>A	c.(1297-1299)GGC>AGC	p.G433S	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)			TCGGTGTTGCCCAGGATGGTG	0.602													44	109	---	---	---	---	PASS
MYL12A	10627	broad.mit.edu	37	18	3253265	3253265	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3253265A>G	uc002klr.2	+	2	415	c.20A>G	c.(19-21)AAG>AGG	p.K7R	MYL12A_uc002kls.2_Missense_Mutation_p.K13R	NM_006471	NP_006462	P19105	ML12A_HUMAN	myosin, light chain 12A, regulatory,	7						myosin complex	calcium ion binding|protein binding				0						AAAAGAACAAAGACCAAGACC	0.388													5	237	---	---	---	---	PASS
GALR1	2587	broad.mit.edu	37	18	74980933	74980933	+	3'UTR	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74980933T>C	uc002lms.3	+	3						NM_001480	NP_001471	P47211	GALR1_HUMAN	galanin receptor 1						digestion|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity			lung(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		AATGAGCTAGTAAGCGATGCT	0.348													5	10	---	---	---	---	PASS
SHD	56961	broad.mit.edu	37	19	4280225	4280225	+	Silent	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4280225G>A	uc002lzw.2	+	1	1628	c.165G>A	c.(163-165)CCG>CCA	p.P55P	SHD_uc010dtu.2_Silent_p.P55P	NM_020209	NP_064594	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming	55											0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTTGGAGCCGGACCCCGCGG	0.652													6	30	---	---	---	---	PASS
DPP9	91039	broad.mit.edu	37	19	4719861	4719861	+	Splice_Site	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4719861A>T	uc002mba.2	-	3	314	c.56_splice	c.e3+1	p.S19_splice	DPP9_uc002mbb.2_Splice_Site_p.S19_splice|DPP9_uc002mbc.2_Splice_Site_p.S19_splice	NM_139159	NP_631898	Q86TI2	DPP9_HUMAN	dipeptidylpeptidase 9						proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		GGCCAACCTCACCTTCTCCAA	0.592													38	38	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9065043	9065043	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9065043G>A	uc002mkp.2	-	3	22607	c.22403C>T	c.(22402-22404)ACG>ATG	p.T7468M		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	7470	Ser-rich.|Thr-rich.|Extracellular (Potential).				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						AATTTTCTCCGTATCTGTGGT	0.483													7	333	---	---	---	---	PASS
P2RY11	5032	broad.mit.edu	37	19	10222268	10222268	+	5'UTR	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10222268G>A	uc002mnc.2	+	1					PPAN-P2RY11_uc010xla.1_Intron|PPAN-P2RY11_uc002mna.2_Intron	NM_002566	NP_002557	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y11						activation of adenylate cyclase activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|calcium-mediated signaling|cellular response to ATP|defense response|neuronal signal transduction		ATP-activated nucleotide receptor activity|neurotransmitter receptor activity|purinergic nucleotide receptor activity, G-protein coupled			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			GGAAAGGCACGCTGGCCTGCT	0.348													7	14	---	---	---	---	PASS
AKAP8L	26993	broad.mit.edu	37	19	15511221	15511221	+	Intron	SNP	A	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15511221A>T	uc002naw.1	-						AKAP8L_uc002nax.1_Intron|AKAP8L_uc010xoh.1_Intron|AKAP8L_uc002nay.1_Intron|AKAP8L_uc002naz.2_3'UTR	NM_014371	NP_055186	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like							cytoplasm|nuclear matrix	DEAD/H-box RNA helicase binding|DNA binding|zinc ion binding			ovary(1)	1						TTTTTTTTTtaaaagaaacca	0.189													5	154	---	---	---	---	PASS
CPAMD8	27151	broad.mit.edu	37	19	17091401	17091401	+	Silent	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17091401C>T	uc002nfb.2	-	14	1664	c.1632G>A	c.(1630-1632)TCG>TCA	p.S544S		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	497						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						GCTGCTGGCCCGATAGCACAA	0.562													4	74	---	---	---	---	PASS
ETHE1	23474	broad.mit.edu	37	19	44010895	44010895	+	3'UTR	SNP	G	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44010895G>C	uc002owp.2	-	7					PHLDB3_uc002own.3_5'Flank|PHLDB3_uc002owo.2_5'Flank	NM_014297	NP_055112	O95571	ETHE1_HUMAN	ETHE1 protein precursor							mitochondrial matrix|nucleus	hydrolase activity|metal ion binding				0		Prostate(69;0.0153)				GTTTTATTTAGGGAGCTCCAG	0.502													24	14	---	---	---	---	PASS
ZNF226	7769	broad.mit.edu	37	19	44680985	44680985	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44680985G>C	uc002oyp.2	+	6	1714	c.1570G>C	c.(1570-1572)GTC>CTC	p.V524L	ZNF226_uc002oyq.2_Missense_Mutation_p.V407L|ZNF226_uc002oyr.2_Missense_Mutation_p.V407L|ZNF226_uc010ejg.2_3'UTR|ZNF226_uc002oys.2_Missense_Mutation_p.V524L|ZNF226_uc002oyt.2_Missense_Mutation_p.V524L	NM_001032373	NP_001027545	Q9NYT6	ZN226_HUMAN	zinc finger protein 226 isoform a	524	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)|all_neural(266;0.202)				TCATCTAGTGGTCCACACAGG	0.448													19	92	---	---	---	---	PASS
ZNF616	90317	broad.mit.edu	37	19	52619946	52619946	+	Silent	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52619946T>C	uc002pym.2	-	4	754	c.471A>G	c.(469-471)GAA>GAG	p.E157E	ZNF616_uc002pyn.2_RNA	NM_178523	NP_848618	Q08AN1	ZN616_HUMAN	zinc finger protein 616	157					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		AAAGTCTCCCTTCAGTTTGAA	0.363													7	371	---	---	---	---	PASS
ZNF610	162963	broad.mit.edu	37	19	52869427	52869427	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52869427G>A	uc002pyx.3	+	6	1202	c.796G>A	c.(796-798)GAC>AAC	p.D266N	ZNF610_uc002pyy.3_Missense_Mutation_p.D266N|ZNF610_uc002pyz.3_Missense_Mutation_p.D223N|ZNF610_uc002pza.2_Missense_Mutation_p.D266N	NM_001161426	NP_001154898	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610 isoform a	266	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		TAGTGAATGTGACAAGGTGTT	0.398													22	65	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29625905	29625905	+	Missense_Mutation	SNP	T	C	C	rs137871677	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29625905T>C	uc010ztl.1	+	2	91	c.59T>C	c.(58-60)CTT>CCT	p.L20P	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						GGAAAATATCTTGGTATAAAT	0.333													8	208	---	---	---	---	PASS
PPP1R16B	26051	broad.mit.edu	37	20	37534706	37534706	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37534706A>G	uc002xje.2	+	7	980	c.791A>G	c.(790-792)GAG>GGG	p.E264G	PPP1R16B_uc010ggc.2_Intron	NM_015568	NP_056383	Q96T49	PP16B_HUMAN	protein phosphatase 1 regulatory inhibitor	264	ANK 4.				regulation of filopodium assembly|signal transduction	nucleus|plasma membrane	protein phosphatase binding			upper_aerodigestive_tract(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				GATGGCTGGGAGCCCCTGCAT	0.612													8	95	---	---	---	---	PASS
TSHZ2	128553	broad.mit.edu	37	20	51872590	51872590	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51872590T>C	uc002xwo.2	+	2	3549	c.2593T>C	c.(2593-2595)TTC>CTC	p.F865L		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	865	Homeobox; atypical.				multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			CTCGAGCCTCTTCCAGACATC	0.483													5	94	---	---	---	---	PASS
USP25	29761	broad.mit.edu	37	21	17205757	17205757	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17205757G>A	uc002yjy.1	+	17	2301	c.2084G>A	c.(2083-2085)CGA>CAA	p.R695Q	USP25_uc011aby.1_Missense_Mutation_p.R695Q|USP25_uc002yjz.1_Missense_Mutation_p.R695Q|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	695	Potential.				protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		GACAACCAACGATTTGAAAAA	0.408													85	125	---	---	---	---	PASS
KRTAP7-1	337878	broad.mit.edu	37	21	32202006	32202006	+	Nonsense_Mutation	SNP	G	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32202006G>C	uc011adj.1	-	1	46	c.12C>G	c.(10-12)TAC>TAG	p.Y4*		NM_181606	NP_853637	Q8IUC3	KRA71_HUMAN	keratin associated protein 7-1	4						intermediate filament					0						CACAGCAGAAGTAACGAGTCA	0.488													21	76	---	---	---	---	PASS
MTMR3	8897	broad.mit.edu	37	22	30418102	30418102	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30418102G>A	uc003agv.3	+	18	3638	c.3310G>A	c.(3310-3312)GAG>AAG	p.E1104K	MTMR3_uc003agu.3_Intron|MTMR3_uc003agw.3_Intron	NM_021090	NP_066576	Q13615	MTMR3_HUMAN	myotubularin-related protein 3 isoform c	1104					phosphatidylinositol dephosphorylation	cytoplasm|membrane|membrane fraction|nucleus	metal ion binding|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			breast(3)|ovary(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			AGCCAGCTGGGAGCAGGTGGA	0.507													76	73	---	---	---	---	PASS
EIF3L	51386	broad.mit.edu	37	22	38270461	38270461	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38270461G>A	uc003auf.2	+	9	923	c.836G>A	c.(835-837)CGC>CAC	p.R279H	EIF3L_uc003aue.1_Missense_Mutation_p.R279H|EIF3L_uc011ann.1_Missense_Mutation_p.R231H|EIF3L_uc003aug.2_Missense_Mutation_p.R171H|EIF3L_uc003auh.2_Missense_Mutation_p.R12H	NM_016091	NP_057175	Q9Y262	EIF3L_HUMAN	eukaryotic translation initiation factor 3	279						eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1						GGGCTTCTCCGCCTGCACTCC	0.547													29	107	---	---	---	---	PASS
SREBF2	6721	broad.mit.edu	37	22	42276853	42276853	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42276853G>A	uc003bbi.2	+	10	2064	c.1895G>A	c.(1894-1896)CGC>CAC	p.R632H	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|SREBF2_uc003bbj.2_RNA	NM_004599	NP_004590	Q12772	SRBP2_HUMAN	sterol regulatory element-binding transcription	632	Cytoplasmic (Potential).				cholesterol metabolic process	ER to Golgi transport vesicle membrane|Golgi membrane|nucleus|SREBP-SCAP-Insig complex	protein C-terminus binding			breast(2)|ovary(1)|central_nervous_system(1)	4						CAGAAGCTACGCCTGGTGCGC	0.652													3	5	---	---	---	---	PASS
CXorf30	645090	broad.mit.edu	37	X	36324941	36324941	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36324941G>A	uc011mkc.1	+	9	1123	c.475G>A	c.(475-477)GCA>ACA	p.A159T		NM_001098843	NP_001092313	A6PW82	CX030_HUMAN	hypothetical protein LOC645090	159										lung(2)|breast(1)	3						TTATCCTTCTGCACTTGGAAG	0.363													287	72	---	---	---	---	PASS
TSPYL2	64061	broad.mit.edu	37	X	53115408	53115408	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53115408G>T	uc004drw.2	+	6	1966	c.1834G>T	c.(1834-1836)GAC>TAC	p.D612Y	TSPYL2_uc004drv.2_3'UTR|TSPYL2_uc004drx.1_Missense_Mutation_p.D217Y	NM_022117	NP_071400	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	612	Asp-rich.				cell cycle|chromatin modification|negative regulation of cell cycle|negative regulation of cell growth|negative regulation of DNA replication|nucleosome assembly|regulation of protein kinase activity|regulation of signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|rDNA binding				0						AGTTATTGAAGACTTTGACAA	0.308													132	29	---	---	---	---	PASS
XPNPEP2	7512	broad.mit.edu	37	X	128886138	128886138	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128886138C>A	uc004eut.1	+	10	1078	c.834C>A	c.(832-834)AAC>AAA	p.N278K		NM_003399	NP_003390	O43895	XPP2_HUMAN	X-prolyl aminopeptidase 2, membrane-bound	278					cellular process|proteolysis	anchored to membrane|plasma membrane	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0						TGTTTGCAAACAAGAGTCGCT	0.527													53	13	---	---	---	---	PASS
CD40LG	959	broad.mit.edu	37	X	135730560	135730560	+	Silent	SNP	C	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135730560C>T	uc004faa.2	+	1	225	c.153C>T	c.(151-153)GAC>GAT	p.D51D	CD40LG_uc010nsd.2_Silent_p.D51D|CD40LG_uc010nse.1_5'Flank	NM_000074	NP_000065	P29965	CD40L_HUMAN	CD40 ligand	51	Extracellular (Potential).				anti-apoptosis|B cell proliferation|inflammatory response|isotype switching|leukocyte cell-cell adhesion|platelet activation|positive regulation of endothelial cell apoptosis|positive regulation of interleukin-12 production	extracellular space|integral to plasma membrane|soluble fraction	CD40 receptor binding|cytokine activity|tumor necrosis factor receptor binding			skin(1)	1	Acute lymphoblastic leukemia(192;0.000127)				Atorvastatin(DB01076)	GAAGGTTGGACAAGGTAAGAT	0.358									Immune_Deficiency_with_Hyper-IgM				221	45	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3132	3132	+	5'Flank	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:3132G>A	uc004coq.3	-						uc004cos.3_RNA|uc011mfh.1_5'Flank					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		CTGTACGAAAGGACAAGAGAA	0.433													14	39	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	6578	6578	+	5'UTR	SNP	A	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:6578A>G	uc011mfh.1	+	1					uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		CCCGCCGGAGGAGGAGACCCC	0.478													23	39	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11711	11711	+	RNA	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11711G>A	uc004cov.3	+	1		c.1134G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		TTCTCATAATCGCCCACGGAC	0.483													4	78	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14208	14208	+	RNA	SNP	T	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14208T>C	uc004cox.3	+	1		c.1872T>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.																		TGTTCAACCAGTAACCACTAC	0.428													4	76	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14847	14847	+	Silent	SNP	G	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14847G>A	uc004coy.2	+	1	87	c.12G>A	c.(10-12)CGG>CGA	p.R4R	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		ATGAAACTTCGGCTCACTCCT	0.483													68	23	---	---	---	---	PASS
CDK11B	984	broad.mit.edu	37	1	1600092	1600093	+	Intron	DEL	TG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1600092_1600093delTG	uc001agv.1	-						CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc009vkl.1_Intron|SLC35E2B_uc001ahe.3_Intron|SLC35E2B_uc001ahf.3_Intron|SLC35E2B_uc001ahg.3_Intron|SLC35E2B_uc001ahh.3_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						CTGTTTTTTTTGTTTGTTTGTT	0.317													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	1869932	1869933	+	IGR	INS	-	AT	AT	rs72502756	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1869932_1869933insAT								TMEM52 (19192 upstream) : KIAA1751 (14819 downstream)																							cactgacaaacgcactcacaca	0.069													3	3	---	---	---	---	
KCNAB2	8514	broad.mit.edu	37	1	6157369	6157369	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6157369delG	uc009vlv.1	+	15	1101	c.966delG	c.(964-966)CTGfs	p.L322fs	KCNAB2_uc001alv.1_Frame_Shift_Del_p.L322fs|KCNAB2_uc001alw.1_Frame_Shift_Del_p.L308fs|KCNAB2_uc001alx.1_Frame_Shift_Del_p.L322fs|KCNAB2_uc001aly.1_Frame_Shift_Del_p.L370fs|KCNAB2_uc009vlw.1_Frame_Shift_Del_p.L255fs|KCNAB2_uc001alu.2_Frame_Shift_Del_p.L322fs	NM_003636	NP_003627	Q13303	KCAB2_HUMAN	potassium voltage-gated channel, shaker-related	322						cytoplasm|integral to membrane|juxtaparanode region of axon	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)		CCGTGCTCCTGGGGGCCTCCA	0.652													37	62	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25018774	25018774	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25018774delA								SRRM1 (19003 upstream) : CLIC4 (52986 downstream)																							tcttgaaaacaaaaaaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	39103727	39103727	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39103727delG								POU3F1 (591277 upstream) : RRAGC (201288 downstream)																							ATTTTAAAGAGGAAAAAAAAA	0.383													4	2	---	---	---	---	
MACF1	23499	broad.mit.edu	37	1	39766179	39766180	+	Intron	INS	-	A	A	rs113153873		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39766179_39766180insA	uc010ois.1	+						MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc009vvq.1_Intron|MACF1_uc001cdb.1_Intron	NM_012090	NP_036222	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TCCTATCATTTAAAAAAAAAAA	0.218													7	4	---	---	---	---	
TRIT1	54802	broad.mit.edu	37	1	40307167	40307167	+	3'UTR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40307167delA	uc010oiz.1	-	11					TRIT1_uc001cec.3_RNA|TRIT1_uc001ced.3_3'UTR|TRIT1_uc001cee.3_RNA|TRIT1_uc001cef.3_RNA|TRIT1_uc001ceg.3_3'UTR|TRIT1_uc001ceh.3_3'UTR|TRIT1_uc009vvv.2_3'UTR|TRIT1_uc001cei.3_3'UTR|TRIT1_uc001ceq.2_3'UTR|TRIT1_uc001cek.2_3'UTR|TRIT1_uc009vvx.2_RNA|TRIT1_uc001cel.2_RNA|TRIT1_uc001cem.2_3'UTR|TRIT1_uc001cen.2_3'UTR|TRIT1_uc001ceo.2_3'UTR|TRIT1_uc001cep.2_3'UTR	NM_017646	NP_060116	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1 precursor						tRNA processing	mitochondrion	ATP binding|metal ion binding|tRNA dimethylallyltransferase activity			ovary(1)	1	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AGGTTCAAAGAAAAAAAAAAT	0.378													4	2	---	---	---	---	
ZNF643	65243	broad.mit.edu	37	1	40925453	40925453	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40925453delT	uc001cfn.1	+						ZNF643_uc001cfl.1_Intron|ZNF643_uc001cfm.1_Intron	NM_023070	NP_075558	Q9UJL9	ZN643_HUMAN	zinc finger protein 643						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.25e-18)			CTCTGCTTGCTTTTTAAGCTG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	41966889	41966889	+	IGR	DEL	C	-	-	rs68122649		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41966889delC								EDN2 (16545 upstream) : HIVEP3 (8796 downstream)																							ttaaatgggacccaatacttc	0.169													2	5	---	---	---	---	
RNF220	55182	broad.mit.edu	37	1	44966087	44966087	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44966087delC	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						ctcacatactccccacctggc	0.000													4	2	---	---	---	---	
SCP2	6342	broad.mit.edu	37	1	53403616	53403616	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53403616delG	uc001cur.1	+						SCP2_uc001cus.1_Intron|SCP2_uc010ono.1_Intron|SCP2_uc010onp.1_Intron|SCP2_uc009vzi.1_Intron|SCP2_uc001cuq.1_Intron	NM_002979	NP_002970	P22307	NLTP_HUMAN	sterol carrier protein 2 isoform 1 proprotein						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|lipid transport	mitochondrion|nucleus|peroxisomal matrix	propanoyl-CoA C-acyltransferase activity|propionyl-CoA C2-trimethyltridecanoyltransferase activity|protein binding|sterol binding			breast(1)	1						actgttaaaaggggggtgggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	60935392	60935393	+	IGR	DEL	AC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60935392_60935393delAC								C1orf87 (395966 upstream) : NFIA (607553 downstream)																							tgtgcacacaacacacacacag	0.084													4	2	---	---	---	---	
INADL	10207	broad.mit.edu	37	1	62304772	62304773	+	Intron	INS	-	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62304772_62304773insT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron|INADL_uc001dac.2_Intron	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						ggccccaggtctttttttttct	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	62880998	62880998	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62880998delA								KANK4 (95915 upstream) : USP1 (20977 downstream)																							actctgtctcaaaaaaaaaaa	0.010													4	2	---	---	---	---	
NEGR1	257194	broad.mit.edu	37	1	72401208	72401209	+	Intron	DEL	GT	-	-	rs71688145		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72401208_72401209delGT	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		TAAgtgtgtagtgtgtgtgtgt	0.248													4	2	---	---	---	---	
USP33	23032	broad.mit.edu	37	1	78204691	78204691	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78204691delA	uc001dht.2	-						USP33_uc001dhu.2_Intron|USP33_uc001dhv.2_Intron|USP33_uc001dhw.2_Intron	NM_015017	NP_055832	Q8TEY7	UBP33_HUMAN	ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3						TGAGTCATTTAAAAAAAAAAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120213118	120213118	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120213118delT								ZNF697 (22728 upstream) : PHGDH (41301 downstream)																							TAATGAACTATTATTTCATTA	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142827025	142827026	+	Intron	DEL	AG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142827025_142827026delAG	uc001eiw.1	+						uc001ejb.2_Intron|uc001ejd.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		TTCATCAGAAAGAGGATCATAA	0.366													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144597567	144597568	+	Intron	INS	-	A	A	rs147768495		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144597567_144597568insA	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|NBPF9_uc010oye.1_Intron|uc001elc.2_RNA|NBPF9_uc009wif.1_Intron|uc001ele.2_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						TAAAATCTCTTACAGCTATTAT	0.054													2	5	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144615246	144615247	+	Splice_Site	INS	-	AG	AG			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144615246_144615247insAG	uc009wig.1	+	3	190	c.114_splice	c.e3+2	p.L38_splice	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_5'UTR|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_5'UTR|NBPF9_uc010oyg.1_Frame_Shift_Ins_p.K39fs|NBPF9_uc009wii.1_5'UTR|NBPF9_uc009wif.1_RNA|C1orf152_uc001elf.3_5'Flank	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						GTAAACCTCAAAGAGATGTTTT	0.470													6	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145098702	145098702	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145098702delA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						tagaacaggtactattaaaat	0.015													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145115028	145115028	+	Intron	DEL	T	-	-	rs67870201		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145115028delT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						TTTACTTGCGTTTTTTTTTGT	0.284													3	3	---	---	---	---	
LOC388692	388692	broad.mit.edu	37	1	149280301	149280302	+	RNA	INS	-	A	A	rs145896171	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149280301_149280302insA	uc010pbf.1	+	1		c.826_827insA				NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0						CCAATTTAGTGAAAAAAAACTG	0.411													3	3	---	---	---	---	
IL6R	3570	broad.mit.edu	37	1	154403243	154403244	+	Intron	INS	-	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154403243_154403244insC	uc001fez.1	+						IL6R_uc001ffa.1_Intron	NM_000565	NP_000556	P08887	IL6RA_HUMAN	interleukin 6 receptor isoform 1 precursor						acute-phase response|ciliary neurotrophic factor-mediated signaling pathway|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|endocrine pancreas development|hepatic immune response|negative regulation of collagen biosynthetic process|negative regulation of interleukin-8 production|positive regulation of activation of Janus kinase activity|positive regulation of anti-apoptosis|positive regulation of chemokine production|positive regulation of chemokine production|positive regulation of interleukin-6 production|positive regulation of leukocyte chemotaxis|positive regulation of MAPKKK cascade|positive regulation of osteoblast differentiation|positive regulation of smooth muscle cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of apoptosis	apical plasma membrane|basolateral plasma membrane|extracellular space|interleukin-6 receptor complex	ciliary neurotrophic factor binding|enzyme binding|protein homodimerization activity			ovary(3)|breast(1)	4	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			acatttgactgccccccctgag	0.168													8	4	---	---	---	---	
RAG1AP1	55974	broad.mit.edu	37	1	155273144	155273145	+	Intron	INS	-	CATAG	CATAG			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155273144_155273145insCATAG	uc010pey.1	+						PKLR_uc001fka.3_5'Flank|PKLR_uc001fkb.3_5'Flank|PKLR_uc010pga.1_5'Flank	NM_018845		Q9BRV3	SWET1_HUMAN	recombination activating gene 1 activating						positive regulation of gene expression, epigenetic	Golgi membrane|integral to membrane|plasma membrane	glucoside transmembrane transporter activity				0	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)			ATCATCATCATCATAGCATTCA	0.203													4	2	---	---	---	---	
GON4L	54856	broad.mit.edu	37	1	155822905	155822905	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155822905delA	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					ccgtctcaagaaaaaaaaaaa	0.184													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157899099	157899099	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157899099delT	uc001frl.1	+											Homo sapiens cDNA FLJ32876 fis, clone TESTI2004073.																		CAAGGGCTCCTTTTTAGGTAT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158416254	158416257	+	IGR	DEL	AAAC	-	-	rs72295046		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158416254_158416257delAAAC								OR10K2 (25598 upstream) : OR10K1 (19095 downstream)																							TGATTCAGAAAAACAAACAAAACA	0.225													4	2	---	---	---	---	
PEX19	5824	broad.mit.edu	37	1	160246990	160246990	+	3'UTR	DEL	T	-	-	rs71846573		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160246990delT	uc001fvs.2	-	8					DCAF8_uc010pjc.1_Intron|PEX19_uc010pje.1_RNA|PEX19_uc001fvt.2_3'UTR	NM_002857	NP_002848	P40855	PEX19_HUMAN	peroxisomal biogenesis factor 19 isoform a						peroxisome membrane biogenesis|peroxisome organization|protein targeting to peroxisome|transmembrane transport	brush border membrane|cytosol|integral to membrane|nucleus|peroxisomal membrane	protein binding|protein N-terminus binding				0	all_cancers(52;1.27e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			agtgaacaccttttttttttt	0.134													3	4	---	---	---	---	
NOS1AP	9722	broad.mit.edu	37	1	162100197	162100197	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162100197delG	uc001gbv.2	+						NOS1AP_uc010pkr.1_Intron|NOS1AP_uc010pks.1_Intron|NOS1AP_uc001gbw.2_Intron	NM_014697	NP_055512	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			TGCACCTAGTGGATACTTACT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	162787607	162787608	+	IGR	DEL	CT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162787607_162787608delCT								HSD17B7 (5000 upstream) : C1orf110 (6640 downstream)																							AATTCAGAGACTCTGGATGTTC	0.356													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163235927	163235928	+	IGR	INS	-	CT	CT	rs148816018	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163235927_163235928insCT								RGS5 (63055 upstream) : NUF2 (55795 downstream)																							gggatctgctcctgtttttatt	0.000													8	4	---	---	---	---	
PBX1	5087	broad.mit.edu	37	1	164528905	164528905	+	5'UTR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164528905delT	uc001gct.2	+	1					PBX1_uc010pku.1_5'UTR|PBX1_uc010pkv.1_5'UTR|PBX1_uc001gcs.2_5'UTR	NM_002585	NP_002576	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5						GGCAAAGGGATTTTTTTTTTC	0.413			T	TCF3|EWSR1	pre B-ALL|myoepithelioma								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165907395	165907396	+	IGR	DEL	GA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165907395_165907396delGA								UCK2 (30058 upstream) : FAM78B (122020 downstream)																							GGAGGTCTCTGAGTGGTGCATT	0.307													4	2	---	---	---	---	
SELE	6401	broad.mit.edu	37	1	169699070	169699071	+	Intron	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169699070_169699071insA	uc001ggm.3	-						C1orf112_uc001ggj.2_Intron	NM_000450	NP_000441	P16581	LYAM2_HUMAN	selectin E precursor						actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity			ovary(3)|skin(2)	5	all_hematologic(923;0.208)					GGTAAAAATTTAAAAAAAATAG	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172759640	172759640	+	IGR	DEL	T	-	-	rs34236553		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172759640delT								FASLG (123630 upstream) : TNFSF18 (250720 downstream)																							TCGTGGTCTATGTGTCAGTTA	0.234													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172984828	172984829	+	IGR	INS	-	A	A	rs59657787		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172984828_172984829insA								FASLG (348818 upstream) : TNFSF18 (25531 downstream)																							TGAACTAATTTCCCCTACTCTC	0.342													4	2	---	---	---	---	
RC3H1	149041	broad.mit.edu	37	1	173952329	173952329	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173952329delA	uc001gju.3	-						RC3H1_uc010pms.1_Intron|RC3H1_uc001gjv.2_Intron|RC3H1_uc010pmt.1_Intron	NM_172071	NP_742068	Q5TC82	RC3H1_HUMAN	roquin						cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway	cytoplasmic mRNA processing body|stress granule	mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						TCAAAAAATTAAAAAAAGAAA	0.289													4	2	---	---	---	---	
RABGAP1L	9910	broad.mit.edu	37	1	174535605	174535605	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174535605delT	uc001gjx.2	+							NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						TTTTGTGGCATTTTTTAAGAC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	185506402	185506402	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185506402delT								IVNS1ABP (219941 upstream) : HMCN1 (197281 downstream)																							GCCCAAGTCCTGGGGAAGGGA	0.557													4	2	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	185960837	185960837	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185960837delT	uc001grq.1	+						HMCN1_uc001grr.1_Intron	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						ttgtttattcttttttttaaa	0.000													4	2	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	186008543	186008544	+	Intron	DEL	CA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186008543_186008544delCA	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						TGTTCATGTGcacacacacaca	0.297													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	186483581	186483581	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186483581delG								PDC (53342 upstream) : PTGS2 (157364 downstream)																							TCCTTCTTATGGCCCTCTTTG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	194488701	194488701	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194488701delT								None (None upstream) : None (None downstream)																							AAGAAGAAAGTTTTTTTTTGT	0.199													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	198530687	198530687	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198530687delA								ATP6V1G3 (20612 upstream) : PTPRC (77450 downstream)																							TTTTTGCATTAAAAAAAAGAA	0.343													4	3	---	---	---	---	
CACNA1S	779	broad.mit.edu	37	1	201019881	201019881	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201019881delA	uc001gvv.2	-							NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	TAACCAAAACAAAAAAAAAAA	0.289													3	5	---	---	---	---	
FAIM3	9214	broad.mit.edu	37	1	207077073	207077073	+	3'UTR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207077073delT	uc001hey.2	-	8					FAIM3_uc010prz.1_3'UTR|FAIM3_uc010psa.1_3'UTR|FAIM3_uc010psb.1_3'UTR|IL24_uc001hes.1_3'UTR|IL24_uc001het.1_3'UTR|IL24_uc001heu.1_3'UTR|IL24_uc001hev.1_RNA|IL24_uc001hew.1_3'UTR	NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)					GGTGCCCTCCTTTTTTTTTTA	0.388													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209567357	209567358	+	IGR	INS	-	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209567357_209567358insT								None (None upstream) : LOC642587 (34810 downstream)																							tcctcacatgatttttttttta	0.000													4	2	---	---	---	---	
NENF	29937	broad.mit.edu	37	1	212608314	212608314	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212608314delA	uc001hjd.2	+						NENF_uc010ptf.1_Intron	NM_013349	NP_037481	Q9UMX5	NENF_HUMAN	neuron derived neurotrophic factor precursor							extracellular space	heme binding				0				all cancers(67;0.00967)|OV - Ovarian serous cystadenocarcinoma(81;0.0108)|GBM - Glioblastoma multiforme(131;0.0325)|Epithelial(68;0.132)		CAGAGAGAGGAGGGGAGCGAG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	212717780	212717780	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212717780delA								NENF (98061 upstream) : ATF3 (20917 downstream)																							TTATTCCTGTAAAAGAAAACG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	215413754	215413755	+	IGR	DEL	GT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215413754_215413755delGT								KCNK2 (3319 upstream) : KCTD3 (326980 downstream)																							TTATtgtgtggtgtgtgtgtgt	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222507840	222507840	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222507840delG								DUSP10 (592379 upstream) : HHIPL2 (187762 downstream)																							GGTTTTGCTAGGTCATTGAGA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	225053988	225053989	+	IGR	DEL	AG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225053988_225053989delAG								CNIH3 (125739 upstream) : DNAH14 (63367 downstream)																							taattaatttagagagagagag	0.000													5	4	---	---	---	---	
ACBD3	64746	broad.mit.edu	37	1	226352879	226352879	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226352879delT	uc001hpy.2	-							NM_022735	NP_073572	Q9H3P7	GCP60_HUMAN	acyl-Coenzyme A binding domain containing 3						steroid biosynthetic process|transport	Golgi membrane|integral to membrane|mitochondrion	fatty-acyl-CoA binding|protein binding				0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.121)		ttcttttttcttttttttttt	0.139													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228254475	228254475	+	IGR	DEL	T	-	-	rs58793961		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228254475delT								WNT3A (5514 upstream) : ARF1 (15886 downstream)																							tctctctctctTTTTTTTTTT	0.413													7	5	---	---	---	---	
GNPAT	8443	broad.mit.edu	37	1	231390048	231390048	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231390048delC	uc001hup.3	+						GNPAT_uc009xfo.1_Intron|GNPAT_uc009xfp.2_Intron	NM_014236	NP_055051	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase						ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity			ovary(3)|breast(1)	4	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				cttccatattccccagtaatt	0.040													4	2	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	232171732	232171736	+	Intron	DEL	AAGAA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232171732_232171736delAAGAA	uc001huz.2	+						DISC1_uc001hva.2_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				CCAACAGCTTAAGAAAAGAAAAGAA	0.385													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232428086	232428086	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232428086delC								DISC1 (251070 upstream) : SIPA1L2 (105628 downstream)																							ACTATGGCAGCCCCAGTATGT	0.378													4	2	---	---	---	---	
NID1	4811	broad.mit.edu	37	1	236148505	236148505	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236148505delA	uc001hxo.2	-						NID1_uc009xgd.2_Intron|NID1_uc009xgc.2_Intron	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor						cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	aaaaaaaaagaaaaaaaaaaG	0.164													6	3	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236707832	236707832	+	Intron	DEL	T	-	-	rs72755785		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236707832delT	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TTTTAAAGGGTTTTTTTTTTC	0.408													6	3	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237577337	237577337	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237577337delT	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ttgtttctaatttttttgttt	0.055													4	2	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	241104837	241104837	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241104837delA	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						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)			CAAGAATATTAAAAACCTAAC	0.333													4	2	---	---	---	---	
OPN3	23596	broad.mit.edu	37	1	241767920	241767920	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241767920delG	uc001hza.2	-						OPN3_uc001hzb.2_Intron|OPN3_uc001hzc.2_Intron	NM_014322	NP_055137	Q9H1Y3	OPN3_HUMAN	opsin 3						phototransduction|protein-chromophore linkage|regulation of circadian rhythm|visual perception	integral to plasma membrane	G-protein coupled photoreceptor activity				0	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			GCATGGTGCAGGGGGAAACCG	0.468													18	10	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245440945	245440945	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245440945delA	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			AAAACCACTTAAAAAAAAAGT	0.348													4	2	---	---	---	---	
OR2M7	391196	broad.mit.edu	37	1	248488129	248488132	+	5'Flank	DEL	TACA	-	-	rs61292885		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248488129_248488132delTACA	uc010pzk.1	-							NM_001004691	NP_001004691	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATTGAAAAATTACAATAACAATAT	0.309													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	248570553	248570554	+	IGR	INS	-	T	T	rs146850247	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248570553_248570554insT								OR2T1 (149 upstream) : OR2T2 (45545 downstream)																							ataactccatagttatgatgtt	0.119													13	6	---	---	---	---	
ROCK2	9475	broad.mit.edu	37	2	11398736	11398736	+	Intron	DEL	G	-	-	rs6760802	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11398736delG	uc002rbd.1	-							NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		CCAAGGGGAAGAAAACAAGAC	0.398													4	2	---	---	---	---	
LPIN1	23175	broad.mit.edu	37	2	11890789	11890789	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11890789delC	uc010yjn.1	+						LPIN1_uc010yjm.1_Intron|LPIN1_uc002rbt.2_Intron|LPIN1_uc002rbs.2_Intron|LPIN1_uc010exi.1_Intron	NM_145693	NP_663731	Q14693	LPIN1_HUMAN	lipin 1						fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		ctgatgtcatccctttttata	0.045													4	2	---	---	---	---	
NBAS	51594	broad.mit.edu	37	2	15416818	15416818	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15416818delA	uc002rcc.1	-						NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4						actataagtgaaagagttgga	0.095													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21184938	21184939	+	IGR	INS	-	G	G	rs138795477	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21184938_21184939insG								C2orf43 (162111 upstream) : APOB (39363 downstream)																							TGCCCCATGGCGGGGGGGTTGC	0.520													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21408383	21408383	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21408383delC								APOB (141438 upstream) : None (None downstream)																							GTGAAGTCTTCCCCccactgc	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	22714072	22714072	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22714072delT								None (None upstream) : None (None downstream)																							GCTGTTTACCTGATATCAGTT	0.378													4	2	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29904268	29904268	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29904268delG	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	TACAGATGATGGGCTTATATT	0.313			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
EHD3	30845	broad.mit.edu	37	2	31479721	31479721	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31479721delT	uc002rnu.2	+						EHD3_uc010ymt.1_Intron	NM_014600	NP_055415	Q9NZN3	EHD3_HUMAN	EH-domain containing 3						blood coagulation|endocytic recycling|protein homooligomerization	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding			skin(2)	2	Acute lymphoblastic leukemia(172;0.155)					agttcaggtcttggctctgac	0.239													4	2	---	---	---	---	
LTBP1	4052	broad.mit.edu	37	2	33178996	33178996	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33178996delT	uc002ros.2	+							NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GTCACCACCCTTTTAATACGG	0.478													4	2	---	---	---	---	
FEZ2	9637	broad.mit.edu	37	2	36817798	36817798	+	Intron	DEL	A	-	-	rs146856068		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36817798delA	uc002rph.2	-						FEZ2_uc002rpf.2_Intron|FEZ2_uc002rpg.2_Intron|FEZ2_uc002rpi.2_Intron|FEZ2_uc002rpj.2_Intron	NM_005102	NP_005093	Q9UHY8	FEZ2_HUMAN	zygin 2 isoform 1						axon guidance|signal transduction		protein binding			ovary(1)	1		all_hematologic(82;0.21)				agactccgtcaaaaaaaaaaa	0.199													4	2	---	---	---	---	
DHX57	90957	broad.mit.edu	37	2	39082580	39082591	+	Intron	DEL	CAATCAAAAGGA	-	-	rs72020623		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39082580_39082591delCAATCAAAAGGA	uc002rrf.2	-						DHX57_uc002rrd.3_5'Flank|DHX57_uc002rre.2_Intron|DHX57_uc002rrg.2_Intron	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				ATTTGCACTCCAATCAAAAGGACAATCAAATA	0.311													7	5	---	---	---	---	
DHX57	90957	broad.mit.edu	37	2	39085574	39085575	+	Intron	DEL	TG	-	-	rs144247886		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39085574_39085575delTG	uc002rrf.2	-						DHX57_uc002rre.2_Intron|DHX57_uc002rrg.2_Intron	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				CACATGACTCTGAGACTATTTG	0.327													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43392945	43392945	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43392945delG								HAAO (373194 upstream) : ZFP36L2 (56597 downstream)																							CAACCAGCAAGGGGGGGCGGT	0.478													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46187084	46187084	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46187084delA	uc002rut.2	+							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)			GTCTGGTTTCAAAAAAACTTT	0.343													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46220017	46220019	+	Intron	DEL	CTG	-	-	rs35037187		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46220017_46220019delCTG	uc002rut.2	+							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)			CCAGACAACACTGCTGCTGCTGc	0.399											OREG0014591	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	2	48359145	48359145	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48359145delG								FBXO11 (226331 upstream) : FOXN2 (182650 downstream)																							GGGGCCAGGTGGGGGTGTGCA	0.328													4	2	---	---	---	---	
CCDC88A	55704	broad.mit.edu	37	2	55539478	55539482	+	Intron	DEL	AAAAA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55539478_55539482delAAAAA	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc002ryu.2_Intron|CCDC88A_uc002rys.2_Intron|CCDC88A_uc002ryw.2_Intron|CCDC88A_uc010fby.1_Intron	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						gaaAATCAGTAAAAATTAGCATGAA	0.176													90	43	---	---	---	---	
CCDC85A	114800	broad.mit.edu	37	2	56516700	56516700	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56516700delT	uc002rzn.2	+							NM_001080433	NP_001073902	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A											breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			tttagtatgcttggagcacag	0.030													4	2	---	---	---	---	
VRK2	7444	broad.mit.edu	37	2	58281526	58281527	+	Intron	DEL	TT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58281526_58281527delTT	uc002rzo.2	+						VRK2_uc010fcb.2_Intron|VRK2_uc002rzs.2_Intron|VRK2_uc002rzr.2_Intron|VRK2_uc010fcc.2_Intron|VRK2_uc002rzv.2_Intron|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Intron|VRK2_uc010ypg.1_Intron|VRK2_uc002rzq.2_Intron|VRK2_uc002rzu.2_Intron|VRK2_uc002rzt.2_Intron	NM_001130482	NP_001123954	Q86Y07	VRK2_HUMAN	vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1						GTGGTCAAGGTTTTTTTTTTTT	0.327													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	63904107	63904107	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63904107delT								LOC388955 (53948 upstream) : UGP2 (163991 downstream)																							tttcagtgcattttttgcaac	0.045													4	2	---	---	---	---	
UGP2	7360	broad.mit.edu	37	2	64093558	64093559	+	Intron	INS	-	TT	TT	rs146665999	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64093558_64093559insTT	uc002scm.2	+						UGP2_uc002scl.2_Intron|UGP2_uc010ypx.1_Intron	NM_006759	NP_006750	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2 isoform a						glycogen biosynthetic process|phosphorylation|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	metal ion binding|protein binding|UTP:glucose-1-phosphate uridylyltransferase activity				0						AAATAAGTGGGTTTCTGGTATA	0.198													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67698665	67698666	+	IGR	INS	-	G	G	rs150454445	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67698665_67698666insG								ETAA1 (61132 upstream) : C1D (570667 downstream)																							cttcTTGTTTTTTTTTCCCCCT	0.262													5	4	---	---	---	---	
SNRNP27	11017	broad.mit.edu	37	2	70120910	70120910	+	5'Flank	DEL	A	-	-	rs112156347		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70120910delA	uc002sfw.2	+						SNRNP27_uc002sfv.2_5'Flank|SNRNP27_uc002sfx.2_5'Flank	NM_006857	NP_006848	Q8WVK2	SNR27_HUMAN	small nuclear ribonucleoprotein 27kDa						mRNA processing|RNA splicing	nucleus	nucleic acid binding				0						GGGAAAAATGAAAGCTGTGTT	0.373													3	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	71234133	71234133	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71234133delA								TEX261 (12132 upstream) : OR7E91P (17072 downstream)																							GCAGGAAGGTACCAGACCAAC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	74336840	74336840	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74336840delC								TET3 (1540 upstream) : BOLA3 (25688 downstream)																							caccactactccccaccgtgc	0.020													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	79929585	79929585	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79929585delA	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						ccttttacagaaaaaaaagtg	0.000													4	2	---	---	---	---	
FLJ40330	645784	broad.mit.edu	37	2	89073098	89073099	+	Intron	INS	-	A	A	rs145200928	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89073098_89073099insA	uc002stf.2	+						FLJ40330_uc010fhf.2_Intron|FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						CTTTGGTAGATACAGTGTTTTA	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89882003	89882003	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89882003delA								FLJ40330 (775878 upstream) : None (None downstream)																							GGTCATTTAGAAATGACAATT	0.114													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90452688	90452689	+	Intron	INS	-	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90452688_90452689insC	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		gaagacagagaccttgagactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91739078	91739082	+	IGR	DEL	TCATC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91739078_91739082delTCATC								None (None upstream) : LOC654342 (66110 downstream)																							ttatttcatgtcatctcatctcatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92054678	92054680	+	IGR	DEL	AAG	-	-	rs111503104		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92054678_92054680delAAG								GGT8P (84525 upstream) : FKSG73 (74479 downstream)																							tttaccaagaaagaagatccata	0.000													4	2	---	---	---	---	
ANKRD36B	57730	broad.mit.edu	37	2	98152548	98152548	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98152548delA	uc010yvc.1	-							NM_025190	NP_079466	Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B												0						aaaacaaaacaaaaaaaaaaa	0.090													5	3	---	---	---	---	
AFF3	3899	broad.mit.edu	37	2	100522377	100522377	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100522377delT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						CCATTCAATGTTTTTTTTTTA	0.264													2	4	---	---	---	---	
TBC1D8	11138	broad.mit.edu	37	2	101654343	101654344	+	Intron	INS	-	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101654343_101654344insC	uc010fiv.2	-						TBC1D8_uc010yvw.1_Intron|TBC1D8_uc002tau.3_Intron	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3						GAAGACACAGTCCCACTGCATG	0.589													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102662804	102662804	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102662804delC								IL1R2 (17924 upstream) : IL1R1 (24032 downstream)																							TGGTGTTTATCCCACACCATG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118876064	118876065	+	IGR	DEL	GA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118876064_118876065delGA								INSIG2 (8468 upstream) : EN1 (723683 downstream)																							tcagctgtgggagagagagaac	0.064													4	2	---	---	---	---	
CLASP1	23332	broad.mit.edu	37	2	122144921	122144921	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122144921delT	uc002tnc.2	-						CLASP1_uc010yyv.1_Intron|CLASP1_uc002tmz.2_Intron|CLASP1_uc002tna.2_Intron|CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tnf.2_Intron	NM_015282	NP_056097	Q7Z460	CLAP1_HUMAN	CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)					CCCAGGATGGTTTTTTTTTTC	0.328													6	3	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	125642754	125642754	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125642754delT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		ttgctgcccctaggtggaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132149808	132149808	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132149808delC								LOC150786 (28077 upstream) : LOC401010 (49926 downstream)																							AAACATCACACCCACATCCCA	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133098548	133098548	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133098548delG								NCRNA00164 (83006 upstream) : GPR39 (75599 downstream)																							taagtgtcatgggggaatctg	0.000													4	2	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	134159932	134159932	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134159932delA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002ttt.1_Intron|NCKAP5_uc002tts.1_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						AGGATTTGGTAACTGATAAAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	140878773	140878773	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140878773delA								None (None upstream) : LRP1B (110223 downstream)																							accagcctgcacctactctgc	0.000													4	2	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	141986474	141986474	+	Intron	DEL	T	-	-	rs300387	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141986474delT	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)		CTCAGTGGAATAAAAAAATCA	0.294										TSP Lung(27;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	148539250	148539250	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148539250delT								None (None upstream) : ACVR2A (62836 downstream)																							CTCTGAATGATTTTTTTAAGT	0.289													4	2	---	---	---	---	
ARL6IP6	151188	broad.mit.edu	37	2	153584994	153584994	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153584994delG	uc002tyn.2	+						ARL6IP6_uc002tym.2_Intron|ARL6IP6_uc002tyo.2_Intron	NM_152522	NP_689735	Q8N6S5	AR6P6_HUMAN	ADP-ribosylation-like factor 6 interacting							integral to membrane					0						CCTCATCCCCGTAAGCTAAAA	0.313													4	2	---	---	---	---	
DPP4	1803	broad.mit.edu	37	2	162879588	162879589	+	Intron	INS	-	CC	CC			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									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													13	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	165343646	165343646	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165343646delA								FIGN (751133 upstream) : GRB14 (5687 downstream)																							taaagggagtaaaaaggaaga	0.000													4	2	---	---	---	---	
ATF2	1386	broad.mit.edu	37	2	175939224	175939224	+	3'UTR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175939224delA	uc002ujl.2	-	14					ATF2_uc010fqv.2_3'UTR|ATF2_uc002ujv.2_3'UTR|ATF2_uc002ujm.2_3'UTR|ATF2_uc002ujn.2_RNA|ATF2_uc002ujo.2_3'UTR|ATF2_uc002ujp.2_RNA|ATF2_uc002ujq.2_3'UTR|ATF2_uc002ujr.2_RNA|ATF2_uc010fqu.2_3'UTR|ATF2_uc002ujs.2_3'UTR|ATF2_uc002ujt.2_RNA|ATF2_uc002uju.2_RNA|uc002ujk.2_5'Flank	NM_001880	NP_001871	P15336	ATF2_HUMAN	activating transcription factor 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor 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	nucleoplasm	protein dimerization activity|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(1)|breast(1)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.125)			AATTTCAAGTAAAAAAAAAAA	0.318													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	176323031	176323031	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176323031delT								ATP5G3 (276541 upstream) : KIAA1715 (467379 downstream)																							TCTGGCAGTCTTTTTTTTTCC	0.408													4	2	---	---	---	---	
NCKAP1	10787	broad.mit.edu	37	2	183888523	183888524	+	Intron	DEL	AG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183888523_183888524delAG	uc002upc.2	-						NCKAP1_uc002upb.2_Intron	NM_013436	NP_038464	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 1						apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			AGAAAAATTTAGATAACTTACA	0.317													355	379	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	191724293	191724293	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191724293delA								NAB1 (166802 upstream) : GLS (21254 downstream)																							TGGTGTGGCCAAAAAAAATGT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	192774949	192774949	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192774949delA								SDPR (62968 upstream) : TMEFF2 (39800 downstream)																							GGCAAACATCACCCACTATCA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	199049067	199049068	+	IGR	INS	-	A	A	rs6706401	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199049067_199049068insA								PLCL1 (34461 upstream) : None (None downstream)																							tactgctgcataaaaaaaactg	0.139													4	2	---	---	---	---	
MYL1	4632	broad.mit.edu	37	2	211166910	211166913	+	Intron	DEL	ATAT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211166910_211166913delATAT	uc002vec.2	-						MYL1_uc002veb.2_Intron	NM_079420	NP_524144	P05976	MYL1_HUMAN	fast skeletal myosin alkali light chain 1						muscle filament sliding|muscle organ development	cytosol|muscle myosin complex|sarcomere	calcium ion binding|structural constituent of muscle			ovary(1)	1				Epithelial(149;0.00573)|Lung(261;0.0422)|LUSC - Lung squamous cell carcinoma(261;0.0444)|all cancers(144;0.057)		TCTTTTTGGGATATATATATATAT	0.255													4	2	---	---	---	---	
BARD1	580	broad.mit.edu	37	2	215677281	215677281	+	5'Flank	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215677281delT	uc002veu.2	-						BARD1_uc010zjm.1_5'Flank	NM_000465	NP_000456	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1						cell cycle arrest|DNA repair|negative regulation of apoptosis|negative regulation of mRNA 3'-end processing|negative regulation of protein export from nucleus|positive regulation of apoptosis|positive regulation of protein catabolic process|protein K6-linked ubiquitination|regulation of phosphorylation|tissue homeostasis	BRCA1-A complex|BRCA1-BARD1 complex|cytoplasm	kinase binding|protein heterodimerization activity|protein homodimerization activity|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AACGAACCAATTTTTTTTTTT	0.294									Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	217267238	217267238	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217267238delG								MARCH4 (30488 upstream) : SMARCAL1 (9899 downstream)																							GCAGGGTAGAGGGACGTGGGG	0.423													4	2	---	---	---	---	
AP1S3	130340	broad.mit.edu	37	2	224700592	224700592	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224700592delG	uc010fwx.1	-						AP1S3_uc002vnn.2_Intron|AP1S3_uc010fww.2_Intron|AP1S3_uc002vno.2_Intron	NM_001039569	NP_001034658	Q96PC3	AP1S3_HUMAN	adaptor-related protein complex 1, sigma 3						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane coat	protein transporter activity				0		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CAGAAACGCAGGGCCTTATTC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	225563207	225563207	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225563207delT								CUL3 (113097 upstream) : DOCK10 (66600 downstream)																							ttcttatgcctttgtgtcctc	0.000													4	2	---	---	---	---	
DOCK10	55619	broad.mit.edu	37	2	225905851	225905851	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225905851delT	uc010fwz.1	-						DOCK10_uc002vod.1_Intron	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GACCTCTGGCTTTAGAGAATA	0.542													4	2	---	---	---	---	
CCL20	6364	broad.mit.edu	37	2	228680515	228680515	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228680515delT	uc002vpl.2	+						CCL20_uc002vpm.2_Intron	NM_004591	NP_004582	P78556	CCL20_HUMAN	chemokine (C-C motif) ligand 20 isoform 1						cell-cell signaling|chemotaxis|defense response to bacterium|immune response|inflammatory response|signal transduction	extracellular space	chemokine activity				0		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;7.3e-11)|all cancers(144;4.13e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		TTTTTAAAAATTTTTTTTGGT	0.303													4	2	---	---	---	---	
SLC4A7	9497	broad.mit.edu	37	3	27478676	27478679	+	Intron	DEL	TACT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27478676_27478679delTACT	uc003cdv.2	-						SLC4A7_uc011awu.1_Intron|SLC4A7_uc011awv.1_Intron|SLC4A7_uc003cdu.3_Intron|SLC4A7_uc011aww.1_Intron|SLC4A7_uc011awx.1_Intron|SLC4A7_uc011awy.1_Intron|SLC4A7_uc011awz.1_Intron|SLC4A7_uc011axa.1_Intron|SLC4A7_uc011axb.1_Intron|SLC4A7_uc010hfm.2_Intron|SLC4A7_uc003cdw.2_Intron	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate							apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5						accccatctctactaaaaatacaa	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	36934344	36934345	+	IGR	DEL	AT	-	-	rs5847939		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36934344_36934345delAT								TRANK1 (31933 upstream) : EPM2AIP1 (93013 downstream)																							aaaacaaaacatatatatatat	0.119													4	2	---	---	---	---	
CCR3	1232	broad.mit.edu	37	3	46271344	46271345	+	Intron	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46271344_46271345insA	uc003cpg.1	+							NM_178329	NP_847899	P51677	CCR3_HUMAN	CC chemokine receptor 3 isoform 1						cell adhesion|cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|inflammatory response|interspecies interaction between organisms|positive regulation of angiogenesis	integral to plasma membrane				ovary(3)|lung(3)|breast(1)|kidney(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		aatgtgctgagaaaaaaaaaca	0.059													4	2	---	---	---	---	
SMARCC1	6599	broad.mit.edu	37	3	47734484	47734484	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47734484delA	uc003crq.2	-						SMARCC1_uc011bbd.1_Intron	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		attccgtcttaaaaaaaaaag	0.000													3	3	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52584643	52584643	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52584643delA	uc003des.2	-	29	4703	c.4691delT	c.(4690-4692)TTGfs	p.L1564fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.L1457fs|PBRM1_uc003der.2_Frame_Shift_Del_p.L1477fs|PBRM1_uc003det.2_Frame_Shift_Del_p.L1472fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.L1527fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.L1509fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.L1484fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.L1457fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1564	Pro-rich.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TGGAGGCCCCAAAACTCCCAC	0.537			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								63	100	---	---	---	---	
SLMAP	7871	broad.mit.edu	37	3	57844109	57844110	+	Intron	INS	-	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57844109_57844110insG	uc003dje.1	+						SLMAP_uc003djc.1_Intron|SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron	NM_007159	NP_009090	Q14BN4	SLMAP_HUMAN	sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		taatatttcttgaaaaaactgg	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105695922	105695922	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105695922delA								CBLB (107656 upstream) : LOC100302640 (859738 downstream)																							AGAGAGGAgcaaaaaaatgtg	0.050													4	2	---	---	---	---	
ARHGAP31	57514	broad.mit.edu	37	3	119082239	119082239	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119082239delC	uc003ecj.3	+							NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2						acccacagcaccccccatcaC	0.239													4	2	---	---	---	---	
GPR156	165829	broad.mit.edu	37	3	119888277	119888277	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119888277delA	uc011bjf.1	-						GPR156_uc011bjg.1_Intron	NM_153002	NP_694547	Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156							integral to membrane|plasma membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.19)		AAAGGAGTGCAAGCATCAGAA	0.114													4	2	---	---	---	---	
KLF15	28999	broad.mit.edu	37	3	126065177	126065178	+	Intron	INS	-	A	A	rs140837225	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126065177_126065178insA	uc011bkk.1	-							NM_014079	NP_054798	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15							nucleus	DNA binding|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(114;0.147)		GAACCAGGATGAGCCAGCCCCA	0.614													1	7	---	---	---	---	
ZBTB38	253461	broad.mit.edu	37	3	141164926	141164926	+	3'UTR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141164926delA	uc003etw.2	+	8					ZBTB38_uc010hun.2_3'UTR|ZBTB38_uc010huo.2_3'UTR|ZBTB38_uc003ety.2_3'UTR|ZBTB38_uc010hup.2_3'UTR	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38						positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						GAGTGAAATTAAAAAAAAAAA	0.264													6	3	---	---	---	---	
PLSCR4	57088	broad.mit.edu	37	3	145912830	145912831	+	Intron	DEL	CT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145912830_145912831delCT	uc010huy.2	-						PLSCR4_uc010huz.2_Intron|PLSCR4_uc003evt.3_Intron|PLSCR4_uc010hva.2_Intron|PLSCR4_uc003evu.3_Intron	NM_001128305	NP_001121777	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4 isoform a						blood coagulation|phospholipid scrambling	integral to membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding				0						ggtttcaaggcttattctttat	0.134													22	36	---	---	---	---	
MED12L	116931	broad.mit.edu	37	3	151075293	151075294	+	Intron	DEL	CT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151075293_151075294delCT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Intron	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,						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)			TTAAAGAACACTCTTGCCAGAA	0.248													13	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	164807703	164807704	+	IGR	DEL	AG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164807703_164807704delAG								SI (11421 upstream) : SLITRK3 (96814 downstream)																							gagagAAACAagagagagagac	0.144													4	2	---	---	---	---	
DCUN1D1	54165	broad.mit.edu	37	3	182683307	182683336	+	Splice_Site	DEL	TCACAAGCAAGCACTCACCTTTGTATCTAT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182683307_182683336delTCACAAGCAAGCACTCACCTTTGTATCTAT	uc003fld.1	-	2	269	c.220_splice	c.e2+1	p.D74_splice	DCUN1D1_uc011bqn.1_Splice_Site	NM_020640	NP_065691	Q96GG9	DCNL1_HUMAN	RP42 homolog							ubiquitin ligase complex	protein binding			ovary(1)	1	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			TTACTTAAAGTCACAAGCAAGCACTCACCTTTGTATCTATTGTACAGCTG	0.343													58	30	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184560716	184560716	+	Intron	DEL	T	-	-	rs68026955		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184560716delT	uc003fpb.1	+						VPS8_uc010hyd.1_Intron	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			AGTTTTCCTCTTTTTTTTTTT	0.269													3	3	---	---	---	---	
FGF12	2257	broad.mit.edu	37	3	192078485	192078485	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192078485delT	uc003fsx.2	-						FGF12_uc003fsy.2_Intron	NM_021032	NP_066360	P61328	FGF12_HUMAN	fibroblast growth factor 12 isoform 1						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		ATATCTATGCTTTTTTTTTTC	0.289													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	196168488	196168489	+	IGR	INS	-	CA	CA	rs140411399	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196168488_196168489insCA								UBXN7 (9143 upstream) : RNF168 (30140 downstream)																							tgggttatctcgttaggggcaa	0.000													2	4	---	---	---	---	
KIAA1530	57654	broad.mit.edu	37	4	1345341	1345341	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1345341delT	uc003gde.3	+							NM_020894	NP_065945	Q2YD98	K1530_HUMAN	hypothetical protein LOC57654												0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)			gcctggctaattttttttttg	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	2435155	2435155	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2435155delG	uc003gfa.1	+											Homo sapiens cDNA FLJ44040 fis, clone TESTI4028983.																		TACACGGGGCGGGGGGGGGAC	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6666787	6666790	+	IGR	DEL	CACT	-	-	rs142180281		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6666787_6666790delCACT								MRFAP1 (22338 upstream) : LOC93622 (9028 downstream)																							gtcatggtcacactcacacatacg	0.000													3	3	---	---	---	---	
PI4K2B	55300	broad.mit.edu	37	4	25262250	25262265	+	Intron	DEL	ATATATATATATATAC	-	-	rs71600578		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25262250_25262265delATATATATATATATAC	uc003grk.2	+						PI4K2B_uc011bxs.1_Intron	NM_018323	NP_060793	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta							cytoplasm|membrane	1-phosphatidylinositol 4-kinase activity|ATP binding			ovary(2)|skin(2)	4		Breast(46;0.173)				atatatatatatatatatatatatacacacacacac	0.148													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	59004310	59004314	+	IGR	DEL	ACACT	-	-	rs112171035		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59004310_59004314delACACT								None (None upstream) : None (None downstream)																							AAAAACATCAACACTACACTACACA	0.356													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	68264381	68264381	+	IGR	DEL	T	-	-	rs138861461		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68264381delT								None (None upstream) : CENPC1 (73608 downstream)																							acttgcagactttacaaagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	78041735	78041736	+	IGR	INS	-	TG	TG	rs145284579	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78041735_78041736insTG								CCNI (44610 upstream) : CCNG2 (36621 downstream)																							GGAATTCACTTTGTTTATCCTA	0.386													1	5	---	---	---	---	
NUDT9	53343	broad.mit.edu	37	4	88351601	88351601	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88351601delT	uc003hqq.2	+						NUDT9_uc003hqr.2_Intron|NUDT9_uc010ikl.2_Intron	NM_024047	NP_076952	Q9BW91	NUDT9_HUMAN	nudix-type motif 9 isoform a							mitochondrion	ADP-ribose diphosphatase activity				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000937)		TGCTTATTTATTTTTTATGTC	0.169													4	2	---	---	---	---	
UGT8	7368	broad.mit.edu	37	4	115563654	115563654	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115563654delT	uc003ibs.2	+						UGT8_uc003ibt.2_Intron|UGT8_uc011cge.1_Intron	NM_001128174	NP_001121646	Q16880	CGT_HUMAN	UDP-galactose-ceramide galactosyltransferase 8						central nervous system development|peripheral nervous system development	integral to membrane	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity			ovary(1)|skin(1)	2		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		AAACCTGATATTTTTTACCAG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	122045069	122045070	+	IGR	DEL	TC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122045069_122045070delTC								C4orf31 (51396 upstream) : TNIP3 (7496 downstream)																							tatttctagttctagatTGGAA	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	132095960	132095961	+	IGR	INS	-	T	T	rs145029796	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132095960_132095961insT								None (None upstream) : None (None downstream)																							TCGGTATTTTCTTGCAGTTTCA	0.391													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	157152060	157152061	+	IGR	DEL	TG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157152060_157152061delTG								CTSO (277012 upstream) : PDGFC (530703 downstream)																							GGAAAATGCCtgtgtgtgtgtg	0.307													4	2	---	---	---	---	
GRIA2	2891	broad.mit.edu	37	4	158254644	158254644	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158254644delT	uc003ipm.3	+						GRIA2_uc011cit.1_Intron|GRIA2_uc003ipl.3_Intron|GRIA2_uc003ipk.3_Intron|GRIA2_uc010iqh.1_Intron	NM_001083619	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2 isoform 2						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|endoplasmic reticulum membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)	TATTTTGAAGTTTTTTTTTCC	0.308													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	165518735	165518735	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165518735delA								MARCH1 (213533 upstream) : TRIM61 (356865 downstream)																							aaaaaaTCAGAAAAAAAAGAC	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190547466	190547466	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190547466delC								None (None upstream) : FRG1 (314508 downstream)																							TAAAGGCTCTCCAGATTCTAC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2147577	2147577	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2147577delT								IRX4 (264697 upstream) : IRX2 (598704 downstream)																							TCTCAATGACttttttttttt	0.279													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3109269	3109269	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3109269delC								C5orf38 (353757 upstream) : IRX1 (486899 downstream)																							GTTGTCTAAGCTTGGGCTGAG	0.463													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5403057	5403057	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5403057delC								ADAMTS16 (82646 upstream) : KIAA0947 (19750 downstream)																							TCAGCACTCTCCAGGAGGGAG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7168324	7168324	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7168324delT								PAPD7 (411163 upstream) : ADCY2 (228019 downstream)																							ATGAAAGTGGTTTTTTTTTCT	0.323													4	2	---	---	---	---	
ADCY2	108	broad.mit.edu	37	5	7407586	7407587	+	Intron	DEL	GA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7407586_7407587delGA	uc003jdz.1	+							NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						atgatggcaggagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	9980353	9980353	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9980353delC								LOC285692 (76417 upstream) : FAM173B (246085 downstream)																							ATTGGGAATGCCCGGCTTTCC	0.443													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13520814	13520814	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13520814delA								None (None upstream) : DNAH5 (169623 downstream)																							caaaaaaaagaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	15492226	15492226	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15492226delA								ANKH (620339 upstream) : FBXL7 (8079 downstream)																							GAGCAAACACAAAAAGAAGTA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	16259559	16259559	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16259559delT								MARCH11 (79662 upstream) : ZNF622 (192070 downstream)																							CCAAATCTACTTTTTTTTCTC	0.239													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	16383470	16383471	+	IGR	DEL	CC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16383470_16383471delCC								MARCH11 (203573 upstream) : ZNF622 (68158 downstream)																							tacgctggttccactttgTGTT	0.124													4	2	---	---	---	---	
MYO10	4651	broad.mit.edu	37	5	16663661	16663662	+	3'UTR	INS	-	AT	AT	rs151153897	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16663661_16663662insAT	uc003jft.3	-	41					MYO10_uc011cnb.1_3'UTR|MYO10_uc011cnc.1_3'UTR|MYO10_uc011cnd.1_3'UTR|MYO10_uc011cne.1_3'UTR|MYO10_uc010itx.2_3'UTR	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						TTTGAAAAAACTTTTTTTGGTG	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20278564	20278564	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20278564delA								CDH18 (290257 upstream) : None (None downstream)																							tttcccagacaaaaaaaagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	25900094	25900095	+	IGR	INS	-	T	T	rs138407898	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25900094_25900095insT								None (None upstream) : CDH9 (980614 downstream)																							ACAGTGTTGGAttttttgtttg	0.307													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27616559	27616559	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27616559delT								CDH9 (577870 upstream) : None (None downstream)																							ttggatggtgtttttgtggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28136737	28136737	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28136737delA								None (None upstream) : None (None downstream)																							TATGCATACTAATCAGAAAAC	0.279													4	2	---	---	---	---	
NPR3	4883	broad.mit.edu	37	5	32781581	32781582	+	Intron	INS	-	T	T	rs142043387	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32781581_32781582insT	uc003jhv.2	+						NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Intron	NM_000908	NP_000899	P17342	ANPRC_HUMAN	natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)	GGCTCCCAGGGCATTGCTCCGG	0.322													5	3	---	---	---	---	
SLC1A3	6507	broad.mit.edu	37	5	36629281	36629281	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36629281delC	uc003jkj.3	+						SLC1A3_uc011cox.1_Intron|SLC1A3_uc010iuy.2_Intron	NM_004172	NP_004163	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity						D-aspartate import|L-glutamate import|neurotransmitter uptake	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		L-Glutamic Acid(DB00142)	ATGAGTTCCACTGCATTCAAG	0.363													4	2	---	---	---	---	
SEPP1	6414	broad.mit.edu	37	5	42807034	42807035	+	RNA	DEL	AA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42807034_42807035delAA	uc011cps.1	-	4		c.567_568delTT			SEPP1_uc011cpt.1_RNA|SEPP1_uc011cpu.1_RNA|SEPP1_uc011cpv.1_RNA|SEPP1_uc003jna.2_RNA			P49908	SEPP1_HUMAN	Homo sapiens cDNA FLJ37321 fis, clone BRAMY2018122.						response to oxidative stress	extracellular region	selenium binding				0						GCTTCCATTTAAAAGAGTCCAG	0.307													378	415	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	45089731	45089731	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45089731delT								MRPS30 (274117 upstream) : HCN1 (169622 downstream)																							ccattagccatcctgtcttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	49565033	49565034	+	IGR	DEL	AC	-	-	rs71612341		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49565033_49565034delAC								None (None upstream) : EMB (126999 downstream)																							ccagttacaaacacacacacac	0.010													4	2	---	---	---	---	
ITGA1	3672	broad.mit.edu	37	5	52127844	52127844	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52127844delC	uc003jou.2	+						ITGA1_uc003jov.2_Intron	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor						axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				CCTCATTCTTCCCCCAGCCAC	0.438													4	2	---	---	---	---	
ARL15	54622	broad.mit.edu	37	5	53583934	53583936	+	Intron	DEL	GAG	-	-	rs72506435		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53583934_53583936delGAG	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)				ACACAAAGCAGAGGAGAATAACA	0.300													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	53947322	53947322	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53947322delA								SNX18 (104907 upstream) : ESM1 (326374 downstream)																							GAGAATTCAGAAAAAGCCCAT	0.408													4	2	---	---	---	---	
ANKRD55	79722	broad.mit.edu	37	5	55523848	55523849	+	Intron	DEL	CA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55523848_55523849delCA	uc003jqu.2	-							NM_024669	NP_078945	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55 isoform 1											skin(1)	1		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				AAAACCGAGTCACAGTGTTGCG	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56739003	56739003	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56739003delT								GPBP1 (179593 upstream) : ACTBL2 (36841 downstream)																							CGCTGCAGGCTTTTTTTTTGA	0.169													4	3	---	---	---	---	
DEPDC1B	55789	broad.mit.edu	37	5	59987437	59987437	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59987437delA	uc003jsh.2	-						DEPDC1B_uc011cqm.1_Intron|DEPDC1B_uc011cqn.1_Intron	NM_018369	NP_060839	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)	1		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				caaacaaaacaaaaaaaatca	0.055													4	2	---	---	---	---	
SFRS12IP1	285672	broad.mit.edu	37	5	64044331	64044331	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64044331delT	uc003jtk.2	-							NM_173829	NP_776190	Q8N9Q2	SR1IP_HUMAN	P18SRP protein						mRNA processing|RNA splicing		nucleic acid binding|zinc ion binding				0		Lung NSC(167;1.66e-05)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.119)		tttaacacaatTTTTTAAAAA	0.060													4	2	---	---	---	---	
SLC30A5	64924	broad.mit.edu	37	5	68409326	68409326	+	Intron	DEL	A	-	-	rs34871242		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68409326delA	uc003jvh.2	+						SLC30A5_uc003jvj.2_5'Flank|SLC30A5_uc003jvk.2_5'Flank|SLC30A5_uc003jvi.2_Intron	NM_022902	NP_075053	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter),						cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity			central_nervous_system(1)	1		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		CTGGTGCTGGAAAAAAAAAAG	0.318													6	4	---	---	---	---	
POLK	51426	broad.mit.edu	37	5	74840919	74840919	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74840919delA	uc003kdw.2	+						POLK_uc003kdx.2_Intron|POLK_uc003kdy.2_Intron|POLK_uc003kdz.2_Intron	NM_016218	NP_057302	Q9UBT6	POLK_HUMAN	DNA-directed DNA polymerase kappa						DNA replication|nucleotide-excision repair, DNA gap filling	nucleus	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			ovary(2)|kidney(2)	4		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		aggtgggcctaatgtgcagca	0.124								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
SERINC5	256987	broad.mit.edu	37	5	79460115	79460115	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79460115delT	uc003kgj.2	-						SERINC5_uc003kgk.2_Intron|SERINC5_uc003kgl.2_Intron|SERINC5_uc003kgm.2_Intron|SERINC5_uc011ctj.1_Intron	NM_178276	NP_840060	Q86VE9	SERC5_HUMAN	developmentally regulated protein TPO1						phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(167;0.00328)|all_lung(232;0.00356)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.93e-46)|Epithelial(54;5.59e-40)|all cancers(79;1.89e-34)		acaaaccaccttttttttgtt	0.000													4	2	---	---	---	---	
SSBP2	23635	broad.mit.edu	37	5	80833277	80833277	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80833277delA	uc003kho.2	-						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)		TTCTGGGATTAAAAAAACCCA	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	81743337	81743338	+	IGR	DEL	AG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81743337_81743338delAG								ATP6AP1L (129191 upstream) : TMEM167A (605329 downstream)																							agagagagacagagagagagag	0.030													4	2	---	---	---	---	
EDIL3	10085	broad.mit.edu	37	5	83551972	83551973	+	Intron	INS	-	CTAC	CTAC			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83551972_83551973insCTAC	uc003kio.1	-						EDIL3_uc003kip.1_Intron	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like						cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		ctatcatctatctatctatcca	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	88406924	88406924	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88406924delA								MEF2C (207055 upstream) : None (None downstream)																							gctttgttctaaaagctctgt	0.065													4	2	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	90211798	90211798	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90211798delA	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron|GPR98_uc003kjx.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTTGGTTTAGAAGGGTATGGG	0.408													4	2	---	---	---	---	
FAM172A	83989	broad.mit.edu	37	5	93072299	93072299	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93072299delA	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron	NM_032042	NP_114431	Q8WUF8	F172A_HUMAN	hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0						GAGTCGGAGGAAAAAAAAAGT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	100621907	100621908	+	IGR	DEL	GT	-	-	rs10563041		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100621907_100621908delGT								ST8SIA4 (382920 upstream) : SLCO4C1 (947786 downstream)																							GTTGTTGGCGGTGTGGTGGTGA	0.426													3	4	---	---	---	---	
SLCO4C1	353189	broad.mit.edu	37	5	101577656	101577656	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101577656delA	uc003knm.2	-							NM_180991	NP_851322	Q6ZQN7	SO4C1_HUMAN	solute carrier organic anion transporter family,						cell differentiation|multicellular organismal development|sodium-independent organic anion transport|spermatogenesis	basolateral plasma membrane|integral to membrane	sodium-independent organic anion transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		tgaagagattaaaaaaaaaca	0.000													4	2	---	---	---	---	
PAM	5066	broad.mit.edu	37	5	102270338	102270338	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102270338delG	uc003knw.2	+						PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase						peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	gcaaatgcttgggggcagatg	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	106038762	106038762	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106038762delA								None (None upstream) : EFNA5 (673829 downstream)																							cttcatttctaaaactgaatc	0.000													4	2	---	---	---	---	
TMEM232	642987	broad.mit.edu	37	5	109763319	109763320	+	Intron	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109763319_109763320insA	uc011cvh.1	-						TMEM232_uc003kov.1_Intron|TMEM232_uc003kow.1_Intron|TMEM232_uc003kox.2_Intron|TMEM232_uc010jbs.2_Intron|TMEM232_uc003koy.3_Intron			C9JQI7	TM232_HUMAN	SubName: Full=cDNA FLJ54480;							integral to membrane					0						agttctggaggaaaaaaaattc	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	111394971	111394971	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111394971delG								C5orf13 (82343 upstream) : EPB41L4A (83167 downstream)																							gatcatcaaagggtaaattat	0.000													4	2	---	---	---	---	
YTHDC2	64848	broad.mit.edu	37	5	112861067	112861067	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112861067delT	uc003kqn.2	+						YTHDC2_uc010jce.1_Intron|YTHDC2_uc010jcf.1_Intron	NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2								ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		TTGAACCAAGttttttttttt	0.144													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	114358549	114358550	+	IGR	INS	-	T	T	rs143269001	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114358549_114358550insT								KCNN2 (526353 upstream) : TRIM36 (101917 downstream)																							GTCCTTCTGCATCACACCCACA	0.455													5	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	114990657	114990657	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114990657delA								TMED7-TICAM2 (28787 upstream) : CDO1 (149775 downstream)																							cgcctatcctaaacctataag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	117153064	117153064	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117153064delG								None (None upstream) : None (None downstream)																							ttgaagttcaggggtacatac	0.124													4	2	---	---	---	---	
TNFAIP8	25816	broad.mit.edu	37	5	118688578	118688578	+	5'Flank	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118688578delC	uc003ksh.2	+						TNFAIP8_uc003ksf.1_Intron|TNFAIP8_uc003ksg.2_Intron|TNFAIP8_uc011cwf.1_Intron	NM_014350	NP_055165	O95379	TFIP8_HUMAN	tumor necrosis factor, alpha-induced protein 8						anti-apoptosis|apoptosis|negative regulation of anti-apoptosis	cytoplasm	caspase inhibitor activity|protein binding			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)		TGTCAATAAGCCCCAGGTGAG	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	121202354	121202354	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121202354delG								FTMT (13833 upstream) : SRFBP1 (95302 downstream)																							GTTTGTGTTTGGGTAGTCATT	0.299													4	2	---	---	---	---	
SNX24	28966	broad.mit.edu	37	5	122317015	122317015	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122317015delG	uc011cwo.1	+						SNX24_uc003ktf.2_Intron|SNX24_uc010jcy.2_Intron	NM_014035	NP_054754	Q9Y343	SNX24_HUMAN	SBBI31 protein						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)		GGCTGACCCAGGAAAAATTTG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123278627	123278627	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123278627delT								CSNK1G3 (326165 upstream) : ZNF608 (693983 downstream)																							ctctctggcatttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124341727	124341727	+	IGR	DEL	T	-	-	rs35688649		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124341727delT								ZNF608 (257227 upstream) : None (None downstream)																							TCAAGCATGATTTTTTTTTAA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	125836365	125836365	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125836365delT								GRAMD3 (6514 upstream) : ALDH7A1 (42553 downstream)																							CATTCTCACATTTTCCTCAAG	0.204													4	2	---	---	---	---	
SLC12A2	6558	broad.mit.edu	37	5	127483600	127483601	+	Intron	INS	-	TTTA	TTTA	rs151080068	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127483600_127483601insTTTA	uc003kus.2	+						SLC12A2_uc010jdf.2_Intron|SLC12A2_uc010jdg.2_Intron	NM_001046	NP_001037	P55011	S12A2_HUMAN	solute carrier family 12						potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	GAATGTGAATGTTTATATAAAT	0.203													5	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	128408890	128408890	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128408890delA								SLC27A6 (39556 upstream) : ISOC1 (21552 downstream)																							TTTCCATCTTAAAAAAAAAAG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	128426637	128426637	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128426637delT								SLC27A6 (57303 upstream) : ISOC1 (3805 downstream)																							gccaactatcttttttttggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129943128	129943128	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129943128delA								CHSY3 (420802 upstream) : HINT1 (551747 downstream)																							AGAAAGGGTTAAAAACAAAAC	0.209													4	2	---	---	---	---	
KDM3B	51780	broad.mit.edu	37	5	137713135	137713136	+	Intron	DEL	AG	-	-	rs34622149		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137713135_137713136delAG	uc003lcy.1	+						KDM3B_uc010jew.1_Intron	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11						cacaagagacagggtcttgttc	0.005													2	4	---	---	---	---	
PPP2R2B	5521	broad.mit.edu	37	5	146132227	146132228	+	Intron	DEL	GT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146132227_146132228delGT	uc003loe.2	-						PPP2R2B_uc010jgm.2_Intron|PPP2R2B_uc003log.3_Intron|PPP2R2B_uc003lof.3_Intron|PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron|PPP2R2B_uc011dbv.1_Intron	NM_004576	NP_004567	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGTTTTTGGGGTGTGTGTGTGT	0.188													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148128311	148128311	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148128311delC	uc003lpp.1	-							NM_024577		Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACTGGCCATCCCCCCTGAAG	0.453													4	2	---	---	---	---	
AFAP1L1	134265	broad.mit.edu	37	5	148658323	148658323	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148658323delT	uc003lqh.2	+						AFAP1L1_uc003lqg.3_Intron|AFAP1L1_uc010jgy.2_Intron	NM_152406	NP_689619	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1								protein binding			breast(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ctaattgttatttcCCATCTT	0.249													5	3	---	---	---	---	
GLRA1	2741	broad.mit.edu	37	5	151228714	151228714	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151228714delT	uc003lut.2	-						GLRA1_uc003lur.2_Intron|GLRA1_uc003lus.2_Intron	NM_001146040	NP_001139512	P23415	GLRA1_HUMAN	glycine receptor, alpha 1 isoform 1 precursor						muscle contraction|negative regulation of transmission of nerve impulse|neuropeptide signaling pathway|positive regulation of acrosome reaction|regulation of membrane potential|startle response	cell junction|chloride channel complex|integral to plasma membrane|intracellular membrane-bounded organelle|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|protein binding|receptor activity|taurine binding|transmitter-gated ion channel activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	tctttctttcttttcttttct	0.040													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	152115628	152115628	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152115628delT	uc003lux.1	-											Homo sapiens cDNA FLJ35529 fis, clone SPLEN2001912.																		atgctgaacatttttttatgt	0.000													4	2	---	---	---	---	
GEMIN5	25929	broad.mit.edu	37	5	154305780	154305780	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154305780delA	uc003lvx.3	-						GEMIN5_uc011ddk.1_Intron	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5						ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CACTGCTAAGAAAAAAAAAAT	0.234													8	5	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155723020	155723021	+	Intron	DEL	AG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155723020_155723021delAG	uc003lwa.1	+							NM_172244	NP_758447	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 2						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			gtaggaagcaagagagagagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	158826873	158826874	+	IGR	INS	-	T	T	rs145409078	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158826873_158826874insT								IL12B (69392 upstream) : LOC285627 (48690 downstream)																							TCCTTACCTAGTTTATTAGGTA	0.485													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163967628	163967628	+	Intron	DEL	C	-	-	rs78146852	byFrequency	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163967628delC	uc003lzn.2	+											Homo sapiens, clone IMAGE:4479080, mRNA, partial cds.																		TTGGTTTTGGCCAGGTAGGTG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165025350	165025351	+	IGR	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165025350_165025351insA								None (None upstream) : None (None downstream)																							taatccaaattaaaaaaaaaac	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166474746	166474746	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166474746delG								None (None upstream) : ODZ2 (237097 downstream)																							TTTTCAGGCTGGTGACTGTTA	0.363													4	2	---	---	---	---	
GABRP	2568	broad.mit.edu	37	5	170215352	170215352	+	Intron	DEL	A	-	-	rs5873237		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170215352delA	uc003mau.2	+						GABRP_uc011dev.1_Intron	NM_014211	NP_055026	O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi							cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			breast(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ggccctgtttaaaaaaaataa	0.164													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170733147	170733147	+	RNA	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170733147delA	uc003mbe.1	-	1		c.2613delT								Homo sapiens cDNA FLJ33675 fis, clone BRAWH2002060.																		ccaacaaaataacaaaccttt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172253020	172253020	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172253020delG								DUSP1 (54817 upstream) : ERGIC1 (8203 downstream)																							agaggagtcagggatgatggt	0.114													4	2	---	---	---	---	
C5orf41	153222	broad.mit.edu	37	5	172552305	172552306	+	Intron	INS	-	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172552305_172552306insT	uc003mch.2	+						C5orf41_uc011dfd.1_Intron	NM_153607	NP_705835	Q8IUR6	CE041_HUMAN	luman-recruiting factor								protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			actttcaggaattttcccctgt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173590415	173590416	+	IGR	DEL	GT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173590415_173590416delGT								HMP19 (54234 upstream) : MSX2 (561159 downstream)																							ctgagacccagtgtgtgtgtgt	0.000													4	2	---	---	---	---	
UNC5A	90249	broad.mit.edu	37	5	176250825	176250825	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176250825delT	uc003mey.2	+						UNC5A_uc003mex.1_Intron	NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTTCTTACCCTTTGAGAACTG	0.522													4	2	---	---	---	---	
GFPT2	9945	broad.mit.edu	37	5	179774857	179774857	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179774857delG	uc003mlw.1	-							NM_005110	NP_005101	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	CCTGGGGGATGGGGAAGACAC	0.572													4	2	---	---	---	---	
BTNL8	79908	broad.mit.edu	37	5	180335488	180335500	+	Intron	DEL	GGAGCTGTAGACC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180335488_180335500delGGAGCTGTAGACC	uc003mmp.2	+						BTNL8_uc003mmq.2_Intron|BTNL8_uc011dhg.1_Intron|BTNL8_uc010jll.2_Intron|BTNL8_uc010jlm.2_Intron|BTNL8_uc011dhh.1_5'Flank	NM_001040462	NP_001035552	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8 isoform 2 precursor							integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			gctcactctgggagctgtagaccggagctgttc	0.127													5	6	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	1796508	1796508	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1796508delA	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)		GACATGTAGGAAAAAAAATCT	0.388													4	2	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5312969	5312969	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5312969delA	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	GGACTCAAATAAGAATttgag	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26698284	26698284	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26698284delG								ZNF322A (38321 upstream) : GUSBL1 (140982 downstream)																							GGTAGGTGACgagtgagcgca	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27374680	27374681	+	IGR	INS	-	CT	CT	rs146317047	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27374680_27374681insCT								ZNF391 (5453 upstream) : ZNF184 (43841 downstream)																							catccatctgactggcggtaaa	0.000													0	6	---	---	---	---	
HIST1H2AL	8332	broad.mit.edu	37	6	27830845	27830846	+	5'Flank	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27830845_27830846insA	uc003njw.2	+							NM_003511	NP_003502	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al						nucleosome assembly	nucleosome|nucleus	DNA binding|enzyme binding				0						CCTTATTACAGAAAAAAACAGT	0.356													4	2	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32551868	32551869	+	Intron	INS	-	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32551868_32551869insC	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obo.1_Intron|HLA-DRB1_uc003obp.3_Intron|HLA-DRB1_uc011dqb.1_5'Flank|HLA-DRB1_uc011dqc.1_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						CTCAGGCCCCGCCCGCGGCCAT	0.446													6	3	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32551874	32551874	+	Intron	DEL	G	-	-	rs41285654	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32551874delG	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obo.1_Intron|HLA-DRB1_uc003obp.3_Intron|HLA-DRB1_uc011dqb.1_5'Flank|HLA-DRB1_uc011dqc.1_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						CCCCGCCCGCGGCCATGCTCA	0.463													5	5	---	---	---	---	
HLA-DQB1	3119	broad.mit.edu	37	6	32629013	32629014	+	Intron	INS	-	TCCACTTCCAG	TCCACTTCCAG	rs9282082		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32629013_32629014insTCCACTTCCAG	uc003obw.2	-						HLA-DQB1_uc010juc.1_Intron|HLA-DQB1_uc003obv.2_Intron|HLA-DQB1_uc011dqd.1_Intron	NM_002123	NP_002114	P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TCCTGTCTCCTCGCACTTCTTC	0.520									Melanoma_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia|T-cell_Lymphoma_(Cutaneous)__Familial_Clustering_of|Sj_gren_syndrome				4	3	---	---	---	---	
HLA-DQB1	3119	broad.mit.edu	37	6	32629017	32629018	+	Intron	INS	-	GCTTT	GCTTT	rs140684436	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32629017_32629018insGCTTT	uc003obw.2	-						HLA-DQB1_uc010juc.1_Intron|HLA-DQB1_uc003obv.2_Intron|HLA-DQB1_uc011dqd.1_Intron	NM_002123	NP_002114	P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	GTCTCCTCGCACTTCTTCTCAG	0.520									Melanoma_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia|T-cell_Lymphoma_(Cutaneous)__Familial_Clustering_of|Sj_gren_syndrome				5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	47313827	47313828	+	IGR	DEL	CT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47313827_47313828delCT								TNFRSF21 (36147 upstream) : CD2AP (131697 downstream)																							ATATTCACCACTCTCTCTCTCC	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	49172255	49172255	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49172255delA								None (None upstream) : MUT (226739 downstream)																							TCTTTCTCACAAAAAAATGAC	0.358													4	2	---	---	---	---	
FAM135A	57579	broad.mit.edu	37	6	71242635	71242635	+	Intron	DEL	A	-	-	rs76625823		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71242635delA	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfl.2_Intron|FAM135A_uc003pfn.2_Intron|FAM135A_uc003pfo.1_Intron|FAM135A_uc010kan.1_Intron	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1						actccatctcaaaaaaaaaaa	0.114													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	77063844	77063845	+	IGR	DEL	AC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77063844_77063845delAC								IMPG1 (281509 upstream) : None (None downstream)																							TCATTTATGAacacacacacac	0.317													4	2	---	---	---	---	
RARS2	57038	broad.mit.edu	37	6	88228194	88228194	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88228194delT	uc003pme.2	-						RARS2_uc003pmb.2_Intron|RARS2_uc003pmc.2_Intron|RARS2_uc003pmd.2_Intron|RARS2_uc003pmf.2_Intron	NM_020320	NP_064716	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial						arginyl-tRNA aminoacylation	mitochondrial matrix	arginine-tRNA ligase activity|ATP binding|protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		gctcaataaatTTTTTTTTTT	0.209													8	6	---	---	---	---	
ASCC3	10973	broad.mit.edu	37	6	101205118	101205119	+	Intron	INS	-	T	T	rs140978278	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101205118_101205119insT	uc003pqk.2	-						ASCC3_uc011eai.1_Intron|ASCC3_uc003pql.2_Intron	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		agatacagatatacacacacaa	0.000													0	6	---	---	---	---	
MAN1A1	4121	broad.mit.edu	37	6	119672901	119672901	+	5'Flank	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119672901delT	uc003pym.1	-						MAN1A1_uc010kei.1_5'Flank	NM_005907	NP_005898	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		GATTTTTTTCTTATTTTCCGT	0.274													4	2	---	---	---	---	
PTPRK	5796	broad.mit.edu	37	6	128368120	128368120	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128368120delA	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)		CTGCACAGAGAAAAGGGCACC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	140126999	140126999	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140126999delT	uc003qir.2	+											Homo sapiens, clone IMAGE:5557975, mRNA.																		AGCACACTAGTTTTTTTTCCC	0.179													4	2	---	---	---	---	
PLEKHG1	57480	broad.mit.edu	37	6	150998630	150998634	+	Intron	DEL	ATGTC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150998630_150998634delATGTC	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		ctcaattcatatgtcatcccttcta	0.176													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156980117	156980117	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156980117delC								MIR1202 (712104 upstream) : ARID1B (118969 downstream)																							CCCCCAATAACCCAGGAAACA	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	157691609	157691610	+	IGR	INS	-	CAC	CAC			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157691609_157691610insCAC								ARID1B (161208 upstream) : C6orf35 (18445 downstream)																							actatcactgtcaccaccacca	0.015													2	4	---	---	---	---	
PRKAR1B	5575	broad.mit.edu	37	7	693705	693706	+	Intron	INS	-	ATCA	ATCA			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:693705_693706insATCA	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		tcaccatcttcatcaccatcac	0.000													1	7	---	---	---	---	
C7orf50	84310	broad.mit.edu	37	7	1111187	1111202	+	Intron	DEL	GGAGAGGGAGGAAAGG	-	-	rs72055182		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1111187_1111202delGGAGAGGGAGGAAAGG	uc003sju.2	-						C7orf50_uc011jvt.1_Intron|C7orf50_uc011jvu.1_Intron	NM_032350	NP_115726	Q9BRJ6	CG050_HUMAN	hypothetical protein LOC84310								protein binding				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0216)|OV - Ovarian serous cystadenocarcinoma(56;1.3e-15)		AAAGCAGGCAGGAGAGGGAGGAAAGGGGAGAGGGAG	0.565													3	4	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	1888764	1888765	+	Intron	INS	-	CA	CA	rs148740106	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1888764_1888765insCA	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc003sld.1_Intron|uc003slj.1_RNA	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		acacagacatgcacacacacgt	0.243													7	5	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	1927298	1927301	+	Intron	DEL	TGTG	-	-	rs140023600		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1927298_1927301delTGTG	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc003sld.1_Intron	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		tgcctgtgcatgtgtgtgtgAGCA	0.172													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	7132150	7132150	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7132150delA								C7orf28B (266289 upstream) : C1GALT1 (90096 downstream)																							TTTTCACTATAAAAAAAATGA	0.299													4	2	---	---	---	---	
NXPH1	30010	broad.mit.edu	37	7	8584899	8584900	+	Intron	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8584899_8584900insA	uc003srv.2	+						NXPH1_uc011jxh.1_Intron	NM_152745	NP_689958	P58417	NXPH1_HUMAN	neurexophilin 1 precursor							extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		ctactcttgggatcatttttat	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	12328839	12328840	+	IGR	INS	-	AAAG	AAAG	rs146889948	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12328839_12328840insAAAG								TMEM106B (51950 upstream) : VWDE (41669 downstream)																							tgaaagaaagaaaagaaagaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	14140344	14140344	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14140344delT								ETV1 (109294 upstream) : DGKB (44331 downstream)																							agcaattttatttttagctga	0.000													4	2	---	---	---	---	
ISPD	729920	broad.mit.edu	37	7	16139621	16139621	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16139621delT	uc010ktx.2	-						ISPD_uc010kty.2_Intron	NM_001101426	NP_001094896	A4D126	ISPD_HUMAN	notch1-induced protein isoform a						isoprenoid biosynthetic process		nucleotidyltransferase activity			ovary(1)	1						CTTCTGTCTGTTTTTGGCTAC	0.443										Multiple Myeloma(15;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	19195245	19195245	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19195245delT								FERD3L (10201 upstream) : TWISTNB (539840 downstream)																							atgaaggacatttttagccat	0.000													4	2	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23792945	23792945	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23792945delA	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						cacttaggtgaattggtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	26028790	26028791	+	IGR	DEL	TC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26028790_26028791delTC								MIR148A (39184 upstream) : NFE2L3 (163056 downstream)																							TAAACTACCAtctctctctctc	0.228													4	2	---	---	---	---	
WIPF3	644150	broad.mit.edu	37	7	29944372	29944372	+	3'UTR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29944372delT	uc003taj.1	+	7						NM_001080529	NP_001073998	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3											ovary(1)	1						ACACTTGGAGTTTTTTTTTCC	0.343													4	2	---	---	---	---	
ZNRF2	223082	broad.mit.edu	37	7	30337351	30337351	+	Intron	DEL	T	-	-	rs113985448		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30337351delT	uc003tat.2	+							NM_147128	NP_667339	Q8NHG8	ZNRF2_HUMAN	zinc finger/RING finger 2							cell junction|endosome membrane|lysosomal membrane|presynaptic membrane	ligase activity|zinc ion binding				0						CTTTCTGTGATTTTTTTTTTT	0.169													2	4	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	33060476	33060476	+	Intron	DEL	G	-	-	rs143102323		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33060476delG	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						tgatctgcctggaacactgca	0.000													5	4	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33282289	33282289	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33282289delT	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc011kan.1_Intron|BBS9_uc011kao.1_Intron	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			TTTGATTTTATTTACATTTGC	0.279									Bardet-Biedl_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35617029	35617029	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35617029delC								TBX20 (323787 upstream) : HERPUD2 (55243 downstream)																							TCAATGGTCTCTGCTCCTGTA	0.577													4	2	---	---	---	---	
SEPT7	989	broad.mit.edu	37	7	35925791	35925792	+	Intron	INS	-	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35925791_35925792insC	uc010kxc.2	+						SEPT7_uc011kat.1_Intron|SEPT7_uc011kau.1_Intron|SEPT7_uc011kav.1_Intron|SEPT7_uc003tey.2_Intron	NM_001788	NP_001779	Q16181	SEPT7_HUMAN	cell division cycle 10 isoform 1						cilium morphogenesis|cytokinesis|mitosis|protein heterooligomerization|regulation of embryonic cell shape	cilium axoneme|cleavage furrow|condensed chromosome kinetochore|midbody|nucleus|septin complex|spindle|stress fiber	GTP binding|protein binding|structural molecule activity				0						CTTTTTTCTTAATGTGAAAACC	0.337													5	3	---	---	---	---	
KIAA0895	23366	broad.mit.edu	37	7	36373192	36373192	+	Intron	DEL	G	-	-	rs197315	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36373192delG	uc003tfd.2	-						KIAA0895_uc003tfc.2_Intron|KIAA0895_uc011kaw.1_Intron|KIAA0895_uc003tfb.2_Intron|KIAA0895_uc011kax.1_Intron	NM_001100425	NP_001093895	Q8NCT3	K0895_HUMAN	hypothetical protein LOC23366 isoform 1												0						agcaaaaaaagaaatgttaac	0.010													4	2	---	---	---	---	
TARP	445347	broad.mit.edu	37	7	38314849	38314849	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38314849delA	uc003tge.1	-						uc003tfz.1_Intron|TARP_uc003tgb.2_5'Flank|TARP_uc003tgc.1_5'Flank|TARP_uc003tgd.1_Intron|TARP_uc010kxi.1_Intron|TARP_uc003tgf.1_Intron|TARP_uc003tgj.1_Intron|TARP_uc003tgh.1_Intron|TARP_uc003tgi.1_Intron|TARP_uc003tgg.1_Intron			A2JGV3	A2JGV3_HUMAN	Homo sapiens TCRgamma alternate reading frame protein (TCRg) mRNA, complete cds.												0						TTTTCTCCTTAAAAGGACAAT	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41079033	41079034	+	IGR	DEL	TG	-	-	rs57495174		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41079033_41079034delTG								C7orf10 (178676 upstream) : INHBA (649569 downstream)																							CAGTGTGGGCtgtgtgtgtgtg	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41576069	41576070	+	IGR	INS	-	T	T	rs138105012	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41576069_41576070insT								C7orf10 (675712 upstream) : INHBA (152533 downstream)																							TGTCAAAGGCGTAAGTGAGAAG	0.441													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	42394460	42394461	+	IGR	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42394460_42394461insA								GLI3 (117842 upstream) : C7orf25 (554413 downstream)																							ctaaaactgctaaaaaaaaaaa	0.178													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46194492	46194493	+	IGR	DEL	TT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46194492_46194493delTT								IGFBP3 (233621 upstream) : None (None downstream)																							CCTGATTGTATTTTTTTTTTCC	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46290552	46290552	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46290552delA								IGFBP3 (329681 upstream) : None (None downstream)																							GAAGGTGTTGAAGATAAAAGG	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46450543	46450543	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46450543delT								IGFBP3 (489672 upstream) : TNS3 (864210 downstream)																							gttatttttctttccTTACTG	0.035													4	2	---	---	---	---	
SUN3	256979	broad.mit.edu	37	7	48031991	48031991	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48031991delA	uc003tof.2	-						SUN3_uc010kyq.2_Intron|SUN3_uc003tog.2_Intron|SUN3_uc011kcf.1_Intron	NM_152782	NP_689995	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 1							integral to membrane				central_nervous_system(1)	1						ttcataaaagaaaaaaatata	0.000													4	2	---	---	---	---	
ABCA13	154664	broad.mit.edu	37	7	48352044	48352044	+	Intron	DEL	A	-	-	rs143168215		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48352044delA	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc003tos.1_5'Flank	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						tgagaatatgaaaaaaaaaaa	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54896309	54896310	+	IGR	DEL	CA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54896309_54896310delCA								SEC61G (69370 upstream) : EGFR (190415 downstream)																							CTGGCTTGTTcattagtagttc	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56231403	56231403	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56231403delA								PSPH (47313 upstream) : DKFZp434L192 (332513 downstream)																							TGCTGCTGCGAAAAAAAAAAA	0.244													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57279021	57279022	+	IGR	INS	-	GAC	GAC	rs141827506	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57279021_57279022insGAC								ZNF479 (71450 upstream) : ZNF716 (230861 downstream)																							CCTTGCTGGCTATTTCCCTGCT	0.550													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57730973	57730974	+	IGR	INS	-	T	T	rs111771815		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57730973_57730974insT								ZNF716 (197708 upstream) : None (None downstream)																							CCTGTCTTGAATTGCACCGAGA	0.277													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57825701	57825702	+	IGR	INS	-	A	A	rs145053031	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57825701_57825702insA								ZNF716 (292436 upstream) : None (None downstream)																							attttgtttctagtttttgtca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61763059	61763059	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61763059delC								None (None upstream) : LOC643955 (988613 downstream)																							GAAAAAAAAACAGTATGCCAT	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61765778	61765778	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61765778delA								None (None upstream) : LOC643955 (985894 downstream)																							atcaaaatttaaaaaaaaaag	0.000													4	2	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69720651	69720651	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69720651delT	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)		AGAATATGACTTTTTTTTTTC	0.308													4	2	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	70981224	70981225	+	Intron	INS	-	A	A	rs77658884		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70981224_70981225insA	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ttccatttaggaaaaaaaaagg	0.045													4	2	---	---	---	---	
TRIM50	135892	broad.mit.edu	37	7	72727667	72727670	+	Intron	DEL	TGAA	-	-	rs72391257		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72727667_72727670delTGAA	uc010lbd.1	-						FKBP6_uc003twz.2_Intron|TRIM50_uc003txy.1_Intron|TRIM50_uc003txz.1_Intron	NM_178125	NP_835226	Q86XT4	TRI50_HUMAN	tripartite motif protein 50A							cytoplasm|intracellular membrane-bounded organelle	ligase activity|zinc ion binding			skin(1)	1						GGCTGCTCCCtgaatgaatgaatg	0.230													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	73062848	73062849	+	IGR	DEL	CT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73062848_73062849delCT								MLXIPL (23978 upstream) : VPS37D (19325 downstream)																							ctctctttccctctctctctcc	0.000													4	2	---	---	---	---	
WBSCR28	135886	broad.mit.edu	37	7	73278760	73278761	+	Intron	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73278760_73278761insA	uc003tzk.2	+						RFC2_uc011kfa.1_Intron|WBSCR28_uc003tzl.2_Intron	NM_182504	NP_872310	Q6UE05	WBS28_HUMAN	hypothetical protein LOC135886							integral to membrane				breast(1)	1		Lung NSC(55;0.159)				tcctgtttcttaaaaaaaaaTA	0.188													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	76450715	76450715	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76450715delA								POMZP3 (194095 upstream) : PMS2L11 (159424 downstream)																							TCAAAAGCAGAAAAAAAAATG	0.308													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78774893	78774893	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78774893delA	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)				TACAAGTTAGAAAAAAAAAAG	0.358													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78899703	78899703	+	Intron	DEL	C	-	-	rs34520749		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78899703delC	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)				attacaTATTCACCTTGTTTA	0.179													0	6	---	---	---	---	
PCLO	27445	broad.mit.edu	37	7	82449347	82449347	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82449347delA	uc003uhx.2	-							NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1						cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						TTCTTGGGGGAAAATTCTAGC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84415405	84415405	+	IGR	DEL	A	-	-	rs11309956		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84415405delA								SEMA3A (591188 upstream) : SEMA3D (209469 downstream)																							cagagataggaaaaaaaaaga	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	86151328	86151328	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86151328delA								None (None upstream) : GRM3 (121902 downstream)																							gagaaggcctaggagactgag	0.000													4	2	---	---	---	---	
ABCB1	5243	broad.mit.edu	37	7	87267661	87267662	+	Intron	INS	-	TGTG	TGTG	rs150303267	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87267661_87267662insTGTG	uc003uiz.1	-						ABCB1_uc003uja.1_Intron|ABCB1_uc010lei.1_Intron|RUNDC3B_uc011khd.1_Intron|RUNDC3B_uc003ujb.2_Intron|RUNDC3B_uc011khe.1_Intron|RUNDC3B_uc003ujc.2_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	aagtatgtgtttgtgtgtgtgt	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	88352814	88352815	+	IGR	INS	-	A	A	rs145403253	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88352814_88352815insA								STEAP4 (416605 upstream) : ZNF804B (35938 downstream)																							ACAATGTGCATAAAGAAGGCTG	0.267													0	8	---	---	---	---	
ZNF804B	219578	broad.mit.edu	37	7	88679649	88679650	+	Intron	DEL	AG	-	-	rs72567397		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88679649_88679650delAG	uc011khi.1	+							NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GCATGGGATCAGAGTCTTAAAA	0.337										HNSCC(36;0.09)			3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	89741691	89741691	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89741691delT								ZNF804B (775347 upstream) : DPY19L2P4 (7023 downstream)																							AACTCGATGGTTTTTCTACTA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	92038077	92038077	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92038077delT								ANKIB1 (7379 upstream) : GATAD1 (38688 downstream)																							ACCAATGCCCTTTTTCTTTCA	0.438													4	2	---	---	---	---	
CCDC132	55610	broad.mit.edu	37	7	92891202	92891203	+	Intron	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92891202_92891203insA	uc003umo.2	+						CCDC132_uc003umq.2_Intron|CCDC132_uc003ump.2_Intron|CCDC132_uc003umr.2_Intron|CCDC132_uc011khz.1_Intron|CCDC132_uc003umn.2_Intron	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a												0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			agttaccaagcaaaatgaagac	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	93040213	93040213	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93040213delA								CCDC132 (51876 upstream) : CALCR (13586 downstream)																							ctaaagggggaaaaggtttta	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	93759402	93759402	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93759402delA								BET1 (125712 upstream) : COL1A2 (264471 downstream)																							TGCTTTGGGTAAGAGACCCTG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	95097241	95097241	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95097241delT								PON2 (32857 upstream) : ASB4 (18043 downstream)																							gccacatacatttttttttga	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	96903465	96903465	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96903465delC								ACN9 (92392 upstream) : TAC1 (457806 downstream)																							tggcagtattccactaagctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	97352561	97352561	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97352561delC								ACN9 (541488 upstream) : TAC1 (8710 downstream)																							TATTCTAGGACCCCCCCCCAT	0.338													4	2	---	---	---	---	
SMURF1	57154	broad.mit.edu	37	7	98730323	98730326	+	Intron	DEL	ACAC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98730323_98730326delACAC	uc003upu.1	-						SMURF1_uc003upv.1_Intron|SMURF1_uc003upt.2_Intron	NM_020429	NP_065162	Q9HCE7	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 isoform						BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			agacacacggacacacacacacac	0.000													4	2	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103192386	103192387	+	Intron	DEL	GT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103192386_103192387delGT	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		gtgtgtgtgggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103396356	103396356	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103396356delA	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ATAAAGTGTTAAAAAGAAAAG	0.264													4	2	---	---	---	---	
LHFPL3	375612	broad.mit.edu	37	7	104035156	104035156	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104035156delT	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3							integral to membrane					0						CGTCAttttcttttttttttt	0.124													4	2	---	---	---	---	
ATXN7L1	222255	broad.mit.edu	37	7	105375083	105375083	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105375083delT	uc003vde.2	-							NM_020725	NP_065776	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1 isoform 1												0						TCCTTTCATGTTTTTTTTTTT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	105708576	105708577	+	IGR	INS	-	A	A	rs142515024	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105708576_105708577insA								CDHR3 (31700 upstream) : SYPL1 (22376 downstream)																							gatgtgcgctcaaaattgtgca	0.114													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	106552480	106552480	+	IGR	DEL	A	-	-	rs75868597		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106552480delA								PIK3CG (4895 upstream) : PRKAR2B (132698 downstream)																							acaaaaacagaaaaaaaaaAC	0.443													6	3	---	---	---	---	
LAMB4	22798	broad.mit.edu	37	7	107744731	107744732	+	Intron	INS	-	A	A	rs142737442	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107744731_107744732insA	uc010ljo.1	-						LAMB4_uc003vey.2_Intron	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor						cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						GTTTCATTTTTAAAGTTAAACT	0.431													4	6	---	---	---	---	
NRCAM	4897	broad.mit.edu	37	7	107804992	107804993	+	Intron	INS	-	CAGCGGGAG	CAGCGGGAG	rs145160841	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107804992_107804993insCAGCGGGAG	uc003vfb.2	-						NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron|NRCAM_uc011kmj.1_Intron	NM_001037132	NP_001032209	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule isoform A						angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5						ACCGCGGAACCgagaggagagg	0.406													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109267566	109267568	+	IGR	DEL	CTG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109267566_109267568delCTG								C7orf66 (742929 upstream) : EIF3IP1 (331716 downstream)																							GCCTGAATTTCTGCTGCTGCTGC	0.414													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109376449	109376450	+	IGR	DEL	AC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109376449_109376450delAC								C7orf66 (851812 upstream) : EIF3IP1 (222834 downstream)																							cacacacaagacacacacacac	0.267													4	2	---	---	---	---	
DOCK4	9732	broad.mit.edu	37	7	111367415	111367415	+	3'UTR	DEL	T	-	-	rs113170416		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111367415delT	uc003vfx.2	-	52					DOCK4_uc011kml.1_3'UTR|DOCK4_uc011kmm.1_3'UTR|DOCK4_uc003vfw.2_3'UTR|DOCK4_uc003vfy.2_3'UTR|DOCK4_uc003vfv.2_3'UTR	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)				TTTCACTAAGTTTTTTTTTTC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	113447301	113447301	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113447301delT								LOC401397 (688664 upstream) : PPP1R3A (69581 downstream)																							TTTCATTTTATTTTTTTTCAT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114378629	114378629	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114378629delA								FOXP2 (47537 upstream) : MDFIC (183580 downstream)																							CTGTGGACTTAAAAAAAAAAT	0.343													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114963458	114963458	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114963458delT								MDFIC (304195 upstream) : TFEC (611744 downstream)																							gcccaccatattatagagggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	115098952	115098952	+	IGR	DEL	T	-	-	rs11357430		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115098952delT								MDFIC (439689 upstream) : TFEC (476250 downstream)																							TAAAAAAAAATATCATAGTTT	0.294													0	8	---	---	---	---	
CTTNBP2	83992	broad.mit.edu	37	7	117385674	117385675	+	Intron	INS	-	ATAACAAAAG	ATAACAAAAG	rs149512543	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117385674_117385675insATAACAAAAG	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)		ATTAATGATTAATAACAAAAAG	0.361													9	6	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	121970088	121970088	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121970088delA	uc010lkp.2	-						CADPS2_uc011knx.1_Intron|CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						TTCTCCAGCTATGCTTGTCTC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	127181729	127181729	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127181729delC								ZNF800 (148962 upstream) : GCC1 (38954 downstream)																							TCACCCTTCTCCCCGCGATTG	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	127812896	127812896	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127812896delG								SND1 (80238 upstream) : MIR129-1 (35029 downstream)																							CGGATGCCCTGGAAGTTCTCT	0.418													4	2	---	---	---	---	
MKLN1	4289	broad.mit.edu	37	7	131047967	131047967	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131047967delT	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_Intron|MKLN1_uc003vqs.2_Intron	NM_013255	NP_037387	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)					CATTTGTGAATTTTTTTTTTA	0.373													4	2	---	---	---	---	
CHCHD3	54927	broad.mit.edu	37	7	132563120	132563121	+	Intron	DEL	CA	-	-	rs147866061		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132563120_132563121delCA	uc003vre.2	-						CHCHD3_uc010lmi.2_Intron|CHCHD3_uc003vrf.2_Intron|CHCHD3_uc010lmj.2_Intron	NM_017812	NP_060282	Q9NX63	CHCH3_HUMAN	coiled-coil-helix-coiled-coil-helix domain						inner mitochondrial membrane organization|mitochondrial fusion	mitochondrial inner membrane	protein complex scaffold				0						AAGAAGAAGTCACACACAATCA	0.351													0	7	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133238404	133238404	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133238404delT	uc003vrk.2	+						EXOC4_uc011kpo.1_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)				tgtccCTTAATTTTTTTTCCT	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	136148166	136148166	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136148166delC								LUZP6 (485962 upstream) : CHRM2 (405233 downstream)																							GTTTTTTTTTCCCCACACAAT	0.254													4	2	---	---	---	---	
ATP6V0A4	50617	broad.mit.edu	37	7	138473974	138473975	+	Intron	INS	-	G	G	rs149298565	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138473974_138473975insG	uc003vug.2	-						ATP6V0A4_uc003vuh.2_Intron	NM_020632	NP_065683	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit						cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1						GGGGTTTTTTTTTGTTGttgtt	0.223													4	2	---	---	---	---	
HIPK2	28996	broad.mit.edu	37	7	139437583	139437583	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139437583delA	uc003vvf.3	-						HIPK2_uc003vvd.3_Intron	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)					AAGTGATTAGAAAAAAGAAAA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141188625	141188625	+	IGR	DEL	A	-	-	rs76790246		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141188625delA								MRPS33 (473844 upstream) : AGK (62453 downstream)																							GTCATTTTAGAAAAAAAAAAA	0.289													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141969146	141969147	+	RNA	DEL	TT	-	-	rs150680725		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141969146_141969147delTT	uc003vxd.2	-	3		c.1009_1010delAA								Homo sapiens similar to trypsin X5, mRNA (cDNA clone MGC:44510 IMAGE:5298751), complete cds.																		TCATACTGTCTTTGTGCACGAG	0.431													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149731732	149731732	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149731732delC								ATP6V0E2 (153946 upstream) : ACTR3C (212570 downstream)																							tgccttcggacccgtcggatc	0.030													4	2	---	---	---	---	
ATG9B	285973	broad.mit.edu	37	7	150719079	150719079	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150719079delT	uc011kvc.1	-						ATG9B_uc003wig.3_Intron	NM_173681	NP_775952	Q674R7	ATG9B_HUMAN	ATG9 autophagy related 9 homolog B						autophagic vacuole assembly	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane				ovary(1)	1	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AAtttccttcttttttttttt	0.065													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152396816	152396816	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152396816delT								XRCC2 (23566 upstream) : ACTR3B (60035 downstream)																							TGGAAGGAGCTTGGTGAGACA	0.562													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153941215	153941215	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153941215delA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			aatctaacccaaagagaaaac	0.000													2	5	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157832758	157832759	+	Intron	DEL	AG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157832758_157832759delAG	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)		caaaaagcaaagagagagagag	0.000													3	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157864356	157864358	+	Intron	DEL	GTG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157864356_157864358delGTG	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron|uc003wnt.1_5'Flank	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)		ggaggtgctcgtggtggtggagg	0.000													5	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158008595	158008595	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158008595delA	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)		agagaaatataaaaaaaggaa	0.000													4	2	---	---	---	---	
VIPR2	7434	broad.mit.edu	37	7	158834871	158834871	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158834871delC	uc003woh.2	-						VIPR2_uc010lqx.2_Intron|VIPR2_uc010lqy.2_Intron	NM_003382	NP_003373	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2						cell-cell signaling	integral to plasma membrane				lung(1)|central_nervous_system(1)	2	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		AGCAACTGTGCCAGCAGAGGG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	7347247	7347247	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7347247delT								DEFB105A (175 upstream) : DEFB107A (6121 downstream)																							ACtttttttcttttttttttt	0.075													7	5	---	---	---	---	
SGK223	157285	broad.mit.edu	37	8	8195005	8195006	+	Intron	DEL	AG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8195005_8195006delAG	uc003wsh.3	-							NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin								ATP binding|non-membrane spanning protein tyrosine kinase activity				0						agagagagaaagagagagagag	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	11802976	11802976	+	IGR	DEL	A	-	-	rs34446502		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11802976delA								CTSB (77330 upstream) : DEFB136 (28472 downstream)																							acaaacaaacaaaaaaaaaCA	0.229													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	26289363	26289363	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26289363delC								BNIP3L (18719 upstream) : PNMA2 (72833 downstream)																							atatgttgtacccaccaacta	0.000													4	2	---	---	---	---	
HMBOX1	79618	broad.mit.edu	37	8	28908874	28908875	+	3'UTR	INS	-	AACC	AACC	rs147395804	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28908874_28908875insAACC	uc003xhd.3	+	10					HMBOX1_uc003xhc.3_Intron|HMBOX1_uc010lve.2_RNA|HMBOX1_uc003xhe.2_3'UTR|HMBOX1_uc011lay.1_3'UTR|HMBOX1_uc003xhf.2_3'UTR|HMBOX1_uc003xhg.2_3'UTR	NM_001135726	NP_001129198	Q6NT76	HMBX1_HUMAN	homeobox containing 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)		CAGTAAATAATAACCAACCAAC	0.455													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	31179792	31179792	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31179792delA								WRN (148516 upstream) : NRG1 (317476 downstream)																							GTTGCTTCTCAAGGCCTCCAA	0.458													4	2	---	---	---	---	
AP3M2	10947	broad.mit.edu	37	8	42015152	42015153	+	Intron	INS	-	AT	AT	rs138724039	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42015152_42015153insAT	uc003xop.2	+						AP3M2_uc003xoo.2_Intron|AP3M2_uc010lxe.2_Intron|AP3M2_uc003xoq.1_Intron|AP3M2_uc003xor.1_Intron	NM_001134296	NP_001127768	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus					0	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)			TTGATAAGCACATAATCAAGAT	0.282													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	57148101	57148101	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57148101delG								CHCHD7 (16927 upstream) : SDR16C5 (64469 downstream)																							ctgtagatcaggggtcctcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	57405108	57405108	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57405108delG	uc003xtb.1	+											Homo sapiens cDNA FLJ34244 fis, clone FCBBF3028794.																		tatatctcttgggtaaacacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61833440	61833440	+	IGR	DEL	A	-	-	rs11321147		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61833440delA								CHD7 (53977 upstream) : CLVS1 (367085 downstream)																							acaaacaaacaaaaaaaacaa	0.284													4	3	---	---	---	---	
CLVS1	157807	broad.mit.edu	37	8	62329478	62329478	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62329478delG	uc003xuh.2	+						CLVS1_uc003xui.2_Intron|CLVS1_uc010lyp.2_Intron	NM_173519	NP_775790	Q8IUQ0	CLVS1_HUMAN	retinaldehyde binding protein 1-like 1						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5						TTGAGAGGGTGGAAGAGGGAT	0.438													4	2	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	69002479	69002480	+	Intron	INS	-	TTA	TTA			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69002479_69002480insTTA	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						TATGTTTCTGGTCTTCTCATTT	0.287													5	5	---	---	---	---	
EYA1	2138	broad.mit.edu	37	8	72257556	72257556	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72257556delA	uc003xys.3	-						EYA1_uc003xyr.3_Intron|EYA1_uc003xyt.3_Intron|EYA1_uc010lzf.2_Intron|EYA1_uc003xyu.2_Intron|EYA1_uc011lfe.1_Intron|EYA1_uc003xyv.2_Intron	NM_172058	NP_742055	Q99502	EYA1_HUMAN	eyes absent 1 isoform b						double-strand break repair|histone dephosphorylation|positive regulation of DNA repair|protein sumoylation|regulation of transcription, DNA-dependent|response to ionizing radiation|sensory perception of sound|transcription, DNA-dependent	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	5	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			actctgttctaagcactttac	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	73075833	73075833	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73075833delA								TRPA1 (88014 upstream) : KCNB2 (373793 downstream)																							CAGGCGTCAGAAGCATCAACA	0.299													4	2	---	---	---	---	
CA1	759	broad.mit.edu	37	8	86250894	86250895	+	Intron	DEL	TT	-	-	rs68187707		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86250894_86250895delTT	uc003ydh.2	-						CA13_uc003ydf.1_Intron|CA1_uc010mae.1_Intron|CA1_uc003ydi.2_Intron	NM_001738	NP_001729	P00915	CAH1_HUMAN	carbonic anhydrase I						one-carbon metabolic process	Golgi apparatus	carbonate dehydratase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dichlorphenamide(DB01144)|Ethinamate(DB01031)|Ethoxzolamide(DB00311)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Levetiracetam(DB01202)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Verapamil(DB00661)|Zonisamide(DB00909)	tctttctttctttctttctttc	0.064													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	92590538	92590539	+	IGR	DEL	TA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92590538_92590539delTA								SLC26A7 (180158 upstream) : RUNX1T1 (380613 downstream)																							aggttataagtatatgtgacta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	117459103	117459103	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117459103delA								TRPS1 (777875 upstream) : EIF3H (197953 downstream)																							ACCCTTCGGTAAAAAAAAGAA	0.413													4	2	---	---	---	---	
EXT1	2131	broad.mit.edu	37	8	118929804	118929804	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118929804delT	uc003yok.1	-							NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			CTCACCAGCATTTTTGAGGTG	0.348			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127486599	127486599	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127486599delA								None (None upstream) : FAM84B (78088 downstream)																							TGTGCTTGGGAATCCCAGGAC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130599383	130599383	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130599383delC								None (None upstream) : GSDMC (161060 downstream)																							CCCACAGTGACCCAAGGACTA	0.488													4	2	---	---	---	---	
EFR3A	23167	broad.mit.edu	37	8	132996928	132996929	+	Intron	DEL	GT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132996928_132996929delGT	uc003yte.2	+							NM_015137	NP_055952	Q14156	EFR3A_HUMAN	EFR3 homolog A							plasma membrane	binding			ovary(3)|breast(1)|central_nervous_system(1)	5	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			ATGCATGTCCGTGTGTGTGTGT	0.327													3	3	---	---	---	---	
TG	7038	broad.mit.edu	37	8	133941865	133941866	+	Intron	INS	-	AA	AA	rs146719721	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133941865_133941866insAA	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		aagacaaaaatagttttaagag	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136195533	136195534	+	IGR	INS	-	A	A	rs71693278		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136195533_136195534insA								MIR30D (378345 upstream) : LOC286094 (50840 downstream)																							GAACTAGGGGTAAAAAAAAAAA	0.332													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143537883	143537884	+	IGR	DEL	CA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143537883_143537884delCA								TSNARE1 (53340 upstream) : BAI1 (7493 downstream)																							CCcactcgctcacacacacaca	0.327													4	2	---	---	---	---	
GPT	2875	broad.mit.edu	37	8	145731528	145731528	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145731528delA	uc011lli.1	+						GPT_uc011llj.1_Frame_Shift_Del_p.E346fs|GPT_uc003zdh.3_Intron	NM_005309	NP_005300	P24298	ALAT1_HUMAN	glutamic pyruvate transaminase						gluconeogenesis	cytosol	1-aminocyclopropane-1-carboxylate synthase activity|L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|central_nervous_system(1)	2	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)		L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	CGTGCGTACGAGGCGGGTGGG	0.721													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16055331	16055332	+	IGR	INS	-	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16055331_16055332insG								C9orf93 (83436 upstream) : BNC2 (354170 downstream)																							gagagaagtttggggtcctctt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	29415814	29415814	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29415814delT								MIR873 (526861 upstream) : None (None downstream)																							TGTTTGTTCCTTTTTAGTCAT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69348132	69348132	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69348132delA								CBWD6 (85539 upstream) : ANKRD20A4 (33849 downstream)																							ACATTGCTGCAAAAATGTCTG	0.368													4	2	---	---	---	---	
VPS13A	23230	broad.mit.edu	37	9	79895392	79895392	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79895392delT	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10						TGGAGTTTGATTTTTTTTTTC	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	83086091	83086091	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83086091delA								TLE4 (744434 upstream) : None (None downstream)																							ACTAAGTGGTAAATTGCATTT	0.249													4	2	---	---	---	---	
TLE1	7088	broad.mit.edu	37	9	84237357	84237357	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84237357delT	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2						TAATGTCTTGTTTTTTTTTGT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85122678	85122678	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85122678delA								FLJ46321 (512508 upstream) : RASEF (474639 downstream)																							tcagtggaagaaaaaaaaaaa	0.000													5	3	---	---	---	---	
SPIN1	10927	broad.mit.edu	37	9	91093032	91093032	+	3'UTR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91093032delA	uc010mqj.2	+	6					SPIN1_uc004apy.2_3'UTR|SPIN1_uc004apz.2_3'UTR|SPIN1_uc010mqk.2_3'UTR	NM_006717	NP_006708	Q9Y657	SPIN1_HUMAN	spindlin						cell cycle|gamete generation|multicellular organismal development	nucleus	methylated histone residue binding				0						TTCCAGTTGTAAATGTCATGC	0.343													4	2	---	---	---	---	
ECM2	1842	broad.mit.edu	37	9	95266306	95266307	+	Intron	DEL	GA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95266306_95266307delGA	uc004ash.2	-						CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ECM2_uc004asf.3_Intron|ECM2_uc011lty.1_Intron|ECM2_uc004asg.2_Intron|ECM2_uc010mqz.1_Intron	NM_001393	NP_001384	O94769	ECM2_HUMAN	extracellular matrix protein 2 precursor						cell-matrix adhesion		integrin binding			ovary(1)|skin(1)	2						GATCCCTCTGGAGAGAGAGAAG	0.465													4	2	---	---	---	---	
HIATL1	84641	broad.mit.edu	37	9	97221855	97221855	+	3'UTR	DEL	T	-	-	rs34087557		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97221855delT	uc004aur.2	+	12					HIATL1_uc011luh.1_3'UTR	NM_032558	NP_115947	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1						transmembrane transport	integral to membrane|plasma membrane	protein binding|transporter activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)				CCTCCTCCTGTTTTTTTTTTT	0.403													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	109228482	109228483	+	Intron	DEL	TG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109228482_109228483delTG	uc004bcx.2	+											Homo sapiens, clone IMAGE:4246712, mRNA.																		CTTTCTCCTTtgtgtgtgtgtg	0.139													4	2	---	---	---	---	
STRBP	55342	broad.mit.edu	37	9	125958117	125958117	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125958117delA	uc004bns.2	-						STRBP_uc004bnt.2_Intron|STRBP_uc004bnu.2_Intron|STRBP_uc004bnv.2_Intron	NM_018387	NP_060857	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein						multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2						acagaaatagaaaaaaataaa	0.000													4	2	---	---	---	---	
COL5A1	1289	broad.mit.edu	37	9	137720965	137720966	+	Intron	INS	-	TCAT	TCAT	rs139866702	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137720965_137720966insTCAT	uc004cfe.2	+						uc004cff.2_Intron	NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCCTTGGTCCAtcattcattca	0.520													3	3	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1768000	1768000	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1768000delA	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)		CTATCCTGGGAAACACTAAGG	0.493													4	2	---	---	---	---	
KLF6	1316	broad.mit.edu	37	10	3828621	3828621	+	5'Flank	DEL	A	-	-	rs35966983		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3828621delA	uc001iha.2	-						KLF6_uc010qaj.1_5'Flank|KLF6_uc010qak.1_5'Flank|KLF6_uc010qal.1_5'Flank|KLF6_uc001ihb.2_5'Flank	NM_001300	NP_001291	Q99612	KLF6_HUMAN	Kruppel-like factor 6 isoform A						B cell differentiation	nucleus	zinc ion binding			central_nervous_system(3)|lung(1)	4				Colorectal(1;0.238)		TGGACTATGTAAAAAAAAATT	0.328													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	13873146	13873147	+	Intron	DEL	CA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13873146_13873147delCA	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						GACAAAGAGGCACACACACACA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	20775890	20775891	+	IGR	INS	-	A	A	rs138294604	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20775890_20775891insA								PLXDC2 (206775 upstream) : NEBL (293014 downstream)																							AGCCAGGAGCTGGGGAGGGAGC	0.535													4	2	---	---	---	---	
APBB1IP	54518	broad.mit.edu	37	10	26776141	26776142	+	Intron	DEL	CT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26776141_26776142delCT	uc001iss.2	+						APBB1IP_uc001isr.2_Intron|APBB1IP_uc009xks.1_Intron	NM_019043	NP_061916	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding,						blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7						TTTTTTTTTCctctctctctct	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29080850	29080851	+	RNA	DEL	AA	-	-	rs1775947	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29080850_29080851delAA	uc001iuk.1	-	2		c.1224_1225delTT								Homo sapiens mRNA; cDNA DKFZp434F083 (from clone DKFZp434F083).																		ACACACACACAAAAAAGACAAG	0.540													4	2	---	---	---	---	
KIAA1462	57608	broad.mit.edu	37	10	30326107	30326107	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30326107delT	uc001iux.2	-						KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Intron|KIAA1462_uc009xle.1_Intron	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608											ovary(4)	4						CTCAGCCATGTTCCGCTCCAG	0.502													4	2	---	---	---	---	
KIAA1462	57608	broad.mit.edu	37	10	30349040	30349041	+	Intron	DEL	AC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30349040_30349041delAC	uc001iuz.2	-						KIAA1462_uc001iuy.2_5'Flank|KIAA1462_uc009xle.1_5'Flank			Q9P266	K1462_HUMAN	RecName: Full=Uncharacterized protein KIAA1462;											ovary(4)	4						GTATGGCTATacacacacacac	0.233													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	34110321	34110322	+	IGR	DEL	CA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34110321_34110322delCA								NRP1 (486315 upstream) : PARD3 (289776 downstream)																							aacacacacgcacacacacaca	0.223													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	36592051	36592051	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36592051delC								FZD8 (661689 upstream) : ANKRD30A (822734 downstream)																							GTGCCTAACTCCCATCTCTGG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42660861	42660862	+	IGR	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42660861_42660862insA								None (None upstream) : LOC441666 (166453 downstream)																							attgaaatctgaaaaaatgaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42941685	42941686	+	Intron	INS	-	A	A	rs146072577	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42941685_42941686insA	uc001izx.2	-											Homo sapiens cyclin Y-like 2, mRNA (cDNA clone IMAGE:4704933), with apparent retained intron.																		TCACTTCTGATAAAAATACCAT	0.248													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44019634	44019641	+	IGR	DEL	CATAATAG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44019634_44019641delCATAATAG								ZNF487 (41627 upstream) : ZNF239 (32154 downstream)																							TATCATAGTACATAATAGGATATACACA	0.409													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44620763	44620763	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44620763delA								HNRNPA3P1 (334898 upstream) : CXCL12 (244844 downstream)																							tgtatccagtaaaattatcct	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46977496	46977496	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46977496delA								SYT15 (6895 upstream) : GPRIN2 (16050 downstream)																							TCACTTCCATAAAAAAATCAG	0.433													4	2	---	---	---	---	
GPRIN2	9721	broad.mit.edu	37	10	46998220	46998221	+	Intron	DEL	CA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46998220_46998221delCA	uc001jec.2	+						GPRIN2_uc010qfq.1_5'Flank	NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth												0						CAGGGAACCCCAGAGACATGCC	0.545													7	6	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47065849	47065849	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47065849delA	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						aactggcgggaaaaaaaaaag	0.015													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47109455	47109456	+	Intron	INS	-	C	C	rs71868789		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47109455_47109456insC	uc001jed.3	-						uc001jef.2_Intron			P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						tagagcaTCCTCCCCCCCCATC	0.292													4	4	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47127718	47127719	+	Intron	DEL	AC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47127718_47127719delAC	uc001jed.3	-						uc001jef.2_Intron			P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						Tcacacacttacacacacacac	0.178													4	3	---	---	---	---	
C10orf53	282966	broad.mit.edu	37	10	50887761	50887761	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50887761delG	uc001jib.2	+	1	78	c.18delG	c.(16-18)GTGfs	p.V6fs	CHAT_uc010qgs.1_Intron|C10orf53_uc001jic.1_Frame_Shift_Del_p.V6fs|C10orf53_uc001jid.1_Frame_Shift_Del_p.V6fs	NM_001042427	NP_001035892	Q8N6V4	CJ053_HUMAN	chromosome 10 open reading frame 53 isoform b	6											0		all_neural(218;0.107)				AGAACGCAGTGGTCATCCTGC	0.697													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	59074415	59074415	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59074415delA								ZWINT (953381 upstream) : IPMK (881203 downstream)																							ATAATAATGCAAAAAAAAGTA	0.333													4	2	---	---	---	---	
CCDC6	8030	broad.mit.edu	37	10	61640988	61640988	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61640988delG	uc001jks.3	-							NM_005436	NP_005427	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6							cytoplasm|cytoskeleton	SH3 domain binding|structural constituent of cytoskeleton			ovary(3)|breast(1)	4				Kidney(211;0.0597)		CTGGGCCCCTGATACTGACAG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	67580242	67580243	+	IGR	INS	-	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67580242_67580243insT								ANXA2P3 (993608 upstream) : CTNNA3 (99482 downstream)																							tatttcttgagtttttttttta	0.000													4	2	---	---	---	---	
SGPL1	8879	broad.mit.edu	37	10	72611211	72611212	+	Intron	INS	-	C	C	rs3842238		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72611211_72611212insC	uc001jrm.2	+							NM_003901	NP_003892	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1						apoptosis|carboxylic acid metabolic process|ceramide metabolic process|sphingolipid catabolic process	integral to endoplasmic reticulum membrane	carboxy-lyase activity|pyridoxal phosphate binding|sphinganine-1-phosphate aldolase activity				0					Pyridoxal Phosphate(DB00114)	gtacagggcagcccccccccac	0.064													3	3	---	---	---	---	
ADK	132	broad.mit.edu	37	10	76080050	76080050	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76080050delT	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron	NM_006721	NP_006712	P55263	ADK_HUMAN	adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)	aactcactgctttttggccta	0.000													4	2	---	---	---	---	
PTEN	5728	broad.mit.edu	37	10	89723933	89723933	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89723933delT	uc001kfb.2	+							NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.R55fs*1(4)|p.Y27fs*1(2)|p.N212fs*1(2)|p.G165_*404del(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TTAGGTAAAGTTTTTAGGGCT	0.239		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			4	2	---	---	---	---	
LOC100188947	100188947	broad.mit.edu	37	10	93278596	93278596	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93278596delT	uc010qnl.1	-							NR_024467				Homo sapiens, clone IMAGE:6063621, mRNA.												0						tgtttttttgttttttttttt	0.174													4	2	---	---	---	---	
C10orf12	26148	broad.mit.edu	37	10	98685924	98685924	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98685924delT	uc009xvg.1	+						LCOR_uc001kmr.2_Intron|LCOR_uc001kms.1_Intron|LCOR_uc001kmt.1_Intron|LCOR_uc001kmu.1_Intron	NM_015652	NP_056467	Q8N655	CJ012_HUMAN	hypothetical protein LOC26148											skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		ACATACCCCCTTTTTtgccca	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	101244968	101244968	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101244968delC								GOT1 (54438 upstream) : NKX2-3 (47722 downstream)																							ACTCCAGAGTCCACACATGCA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	111503129	111503129	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111503129delG								None (None upstream) : XPNPEP1 (121395 downstream)																							ACTCAGGCCTGGGCTGTTTCA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	112883023	112883023	+	IGR	DEL	G	-	-	rs72022283		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112883023delG								ADRA2A (42363 upstream) : None (None downstream)																							TATTGGAGGTGGGGGGGGTCT	0.473													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	120586055	120586056	+	IGR	DEL	TG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120586055_120586056delTG								C10orf46 (71297 upstream) : NANOS1 (203172 downstream)																							CTAAAATGGCTGTAGGCACCAA	0.441													4	2	---	---	---	---	
DMBT1	1755	broad.mit.edu	37	10	124321183	124321184	+	Intron	DEL	TC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124321183_124321184delTC	uc001lgk.1	+						DMBT1_uc001lgl.1_Intron|DMBT1_uc001lgm.1_Intron|DMBT1_uc009xzz.1_Intron|DMBT1_uc010qtx.1_Intron	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b						epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				tgtctgtgtttctctctctctc	0.114													4	2	---	---	---	---	
CHST15	51363	broad.mit.edu	37	10	125802620	125802621	+	Intron	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125802620_125802621insA	uc001lhl.2	-						CHST15_uc001lhm.2_Intron|CHST15_uc001lhn.2_Intron|CHST15_uc010que.1_Intron|CHST15_uc001lho.2_Intron	NM_015892	NP_056976	Q7LFX5	CHSTF_HUMAN	B cell RAG associated protein						hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity			ovary(1)	1						TGCAAACATTTAAAAATCCACT	0.406													4	2	---	---	---	---	
PTPRE	5791	broad.mit.edu	37	10	129746488	129746488	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129746488delT	uc001lkb.2	+						PTPRE_uc009yat.2_Intron	NM_006504	NP_006495	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway|protein phosphorylation	cytoplasm|integral to membrane|intermediate filament cytoskeleton|nucleus|plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(1)	1		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)				CACCCCCTCCTTTTTTTTTGt	0.308													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132502154	132502154	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132502154delG								GLRX3 (519370 upstream) : TCERG1L (388502 downstream)																							AGACATAGTTGGGGGCTGCCC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132839382	132839383	+	IGR	INS	-	ATTT	ATTT			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132839382_132839383insATTT								GLRX3 (856598 upstream) : TCERG1L (51273 downstream)																							gagacgattcaatttatgtttg	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133152776	133152776	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133152776delG								TCERG1L (42792 upstream) : PPP2R2D (595184 downstream)																							CAACTTGGGTGGGGCTCACGT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133606841	133606841	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133606841delA								TCERG1L (496857 upstream) : PPP2R2D (141119 downstream)																							ACTTTCCTTGAAAAAAATATT	0.433													4	2	---	---	---	---	
PSMD13	5719	broad.mit.edu	37	11	252816	252816	+	3'UTR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:252816delG	uc001lol.2	+	13					PSMD13_uc010qvr.1_RNA|PSMD13_uc001loo.2_3'UTR|PSMD13_uc001lon.2_3'UTR|PSMD13_uc001lom.2_3'UTR|PSMD13_uc001lop.2_3'UTR	NM_002817	NP_002808	Q9UNM6	PSD13_HUMAN	proteasome 26S non-ATPase subunit 13 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding			ovary(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		TGCAGAGGGTGGGGGTCTCAG	0.567													4	2	---	---	---	---	
STIM1	6786	broad.mit.edu	37	11	4053501	4053501	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4053501delG	uc001lyv.2	+						STIM1_uc009yef.2_Intron	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor						activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		cttgagcccaggagttggagt	0.000													4	2	---	---	---	---	
ANO3	63982	broad.mit.edu	37	11	26321089	26321089	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26321089delT	uc010rdr.1	+							NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C							chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						agagattgccttttttttttc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	28565720	28565720	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28565720delC								METT5D1 (210666 upstream) : None (None downstream)																							GGCACTCCTACCCCACAGGTA	0.423													4	2	---	---	---	---	
QSER1	79832	broad.mit.edu	37	11	32998331	32998332	+	3'UTR	INS	-	T	T	rs79855050		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32998331_32998332insT	uc001mty.2	+	13					QSER1_uc001mtz.1_Intron	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1											ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					ACTAAGTATAATTTTTTTTTAT	0.312													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	34402566	34402566	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34402566delG								ABTB2 (23764 upstream) : CAT (57912 downstream)																							TGAAAGGTCAGGGGCCAAGGG	0.433													4	2	---	---	---	---	
EHF	26298	broad.mit.edu	37	11	34664616	34664617	+	Intron	DEL	TG	-	-	rs59989036		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34664616_34664617delTG	uc001mvr.1	+						EHF_uc009yke.1_Intron|EHF_uc009ykf.1_Intron	NM_012153	NP_036285	Q9NZC4	EHF_HUMAN	ets homologous factor						cell proliferation|epithelial cell differentiation|multicellular organismal development|positive regulation of transcription, DNA-dependent		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			AGAAAGGgtatgtgtgtgtgtg	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37110750	37110750	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37110750delT								C11orf74 (414360 upstream) : None (None downstream)																							TAAGGTTGAATAAGCAGGATG	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37522024	37522025	+	IGR	DEL	AC	-	-	rs72176350	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37522024_37522025delAC								C11orf74 (825634 upstream) : None (None downstream)																							gtgtatatatacacacacacac	0.035													4	2	---	---	---	---	
PHF21A	51317	broad.mit.edu	37	11	46140824	46140824	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46140824delG	uc001ncc.3	-						PHF21A_uc001ncb.3_Intron|PHF21A_uc009ykx.2_Intron|PHF21A_uc001nce.2_Intron	NM_001101802	NP_001095272	Q96BD5	PF21A_HUMAN	BRAF35/HDAC2 complex isoform a						blood coagulation|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|transcription, DNA-dependent	histone deacetylase complex	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2						CCCCAGCTATGGGGCAAATCT	0.448													4	2	---	---	---	---	
PACSIN3	29763	broad.mit.edu	37	11	47205906	47205907	+	Intron	DEL	CT	-	-	rs112564612		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47205906_47205907delCT	uc001ndw.2	-						PACSIN3_uc001ndx.2_Intron|PACSIN3_uc001ndy.2_Intron|PACSIN3_uc001ndz.2_Intron|PACSIN3_uc001nea.2_Intron	NM_016223	NP_057307	Q9UKS6	PACN3_HUMAN	protein kinase C and casein kinase substrate in						endocytosis|negative regulation of endocytosis|positive regulation of membrane protein ectodomain proteolysis	cytoplasm|plasma membrane	cytoskeletal protein binding				0						GTCACTTCCCCTGTTTCTCTGT	0.550													2	4	---	---	---	---	
FNBP4	23360	broad.mit.edu	37	11	47755698	47755698	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47755698delA	uc009ylv.2	-						FNBP4_uc001ngj.2_Intron|FNBP4_uc001ngl.2_Intron	NM_015308	NP_056123	Q8N3X1	FNBP4_HUMAN	formin binding protein 4											ovary(1)	1						TGCAAAAAAGAAAAAAAGTAA	0.318													235	173	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50184569	50184569	+	IGR	DEL	A	-	-	rs34225305		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50184569delA								OR4C12 (180532 upstream) : LOC441601 (54431 downstream)																							ATATTTTCTCaaaaaaaaaaa	0.149													4	4	---	---	---	---	
MS4A1	931	broad.mit.edu	37	11	60236247	60236247	+	3'UTR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60236247delT	uc001npp.2	+	8					MS4A1_uc001npq.2_3'UTR|MS4A1_uc009yna.2_3'UTR|MS4A1_uc009ymz.2_3'UTR|MS4A1_uc010rlc.1_3'UTR	NM_152866	NP_690605	P11836	CD20_HUMAN	membrane-spanning 4-domains, subfamily A, member						B cell activation|immune response	integral to plasma membrane				ovary(3)|lung(2)	5					Ibritumomab(DB00078)|Rituximab(DB00073)|Tositumomab(DB00081)	TAGTATAGTATTTTTTTTTGT	0.348													3	3	---	---	---	---	
PLA2G16	11145	broad.mit.edu	37	11	63378076	63378076	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63378076delT	uc001nxh.2	-						PLA2G16_uc001nxi.2_Intron|PLA2G16_uc009you.1_Intron	NM_007069	NP_009000	P53816	PAG16_HUMAN	HRAS-like suppressor 3						lipid catabolic process	integral to membrane|perinuclear region of cytoplasm	hydrolase activity|protein binding			ovary(1)	1						TCCTCTTCTCTTCTTCTCTCC	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	75249958	75249958	+	IGR	DEL	T	-	-	rs33928158		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75249958delT								GDPD5 (13359 upstream) : SERPINH1 (23212 downstream)																							aggaccactcttttttttttt	0.000													4	2	---	---	---	---	
CTSC	1075	broad.mit.edu	37	11	88055042	88055042	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88055042delC	uc001pck.3	-						CTSC_uc001pcl.3_Intron|CTSC_uc001pcm.3_3'UTR|CTSC_uc001pcn.3_3'UTR	NM_001814	NP_001805	P53634	CATC_HUMAN	cathepsin C isoform a preproprotein						immune response	lysosome	cysteine-type endopeptidase activity				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				agttgacattcccaccaacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	90095449	90095451	+	IGR	DEL	TTC	-	-	rs140613889		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90095449_90095451delTTC								CHORDC1 (138917 upstream) : MIR1261 (506838 downstream)																							CATTCCCTTGTTCTTCTGTGCTG	0.433													2	4	---	---	---	---	
MRE11A	4361	broad.mit.edu	37	11	94183426	94183426	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94183426delG	uc001peu.2	-						MRE11A_uc001pev.2_Intron|MRE11A_uc009ywj.2_Intron	NM_005591	NP_005582	P49959	MRE11_HUMAN	meiotic recombination 11 homolog A isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase	Mre11 complex|nucleoplasm	3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity			breast(4)|lung(1)	5		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				atttcccctaggagcaatgat	0.030								Homologous_recombination	Ataxia-Telangiectasia-Like_Disorder				4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	95976200	95976201	+	Intron	DEL	AC	-	-	rs34648958		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95976200_95976201delAC	uc001pfw.1	-							NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				CAGTTCAGGGacacacacacac	0.327			T	MECT1|CRTC3	salivary gland mucoepidermoid								4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	100213146	100213146	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100213146delA	uc001pga.2	+						CNTN5_uc001pgb.2_Intron|CNTN5_uc010ruk.1_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TATGATGAACAATATCCCAAA	0.383													4	2	---	---	---	---	
MMP20	9313	broad.mit.edu	37	11	102449531	102449532	+	Intron	INS	-	AAAC	AAAC	rs144316355	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102449531_102449532insAAAC	uc001phc.2	-							NM_004771	NP_004762	O60882	MMP20_HUMAN	matrix metalloproteinase 20 preproprotein						proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)		cacaaaaacaaaaacaaacaaa	0.124													14	12	---	---	---	---	
GRIA4	2893	broad.mit.edu	37	11	105728017	105728018	+	Intron	INS	-	AC	AC			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105728017_105728018insAC	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)	GACACACACAGACACACACACC	0.416													4	2	---	---	---	---	
ZC3H12C	85463	broad.mit.edu	37	11	109984932	109984932	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109984932delT	uc009yxw.2	+						ZC3H12C_uc010rwc.1_Intron	NM_033390	NP_203748	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C								endonuclease activity|nucleic acid binding|zinc ion binding				0		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GCAACAATCCTTTTTTTTCTT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	110668513	110668513	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110668513delT								ARHGAP20 (84601 upstream) : C11orf53 (458194 downstream)																							ctggtgggaatttcagttgtg	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112527870	112527871	+	IGR	DEL	CT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112527870_112527871delCT								PTS (387193 upstream) : NCAM1 (304124 downstream)																							CTCCCCTCTCCTCTCTCTCTCT	0.525													3	3	---	---	---	---	
FAM55D	54827	broad.mit.edu	37	11	114465968	114465968	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114465968delT	uc001ppc.2	-						FAM55D_uc001ppd.2_Intron	NM_001077639	NP_001071107	Q6UWF7	FA55D_HUMAN	hypothetical protein LOC54827 isoform 1							extracellular region				ovary(2)|skin(2)	4		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.82e-06)|Epithelial(105;0.000129)|all cancers(92;0.000938)		TCCTTTTCTGTTTTAGCAGGC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115622000	115622001	+	IGR	DEL	TG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115622000_115622001delTG								CADM1 (246759 upstream) : BUD13 (996887 downstream)																							CCCACTGAGCTGTGTGGTGGCC	0.574													4	2	---	---	---	---	
MLL	4297	broad.mit.edu	37	11	118328355	118328355	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118328355delT	uc001pta.2	+						MLL_uc001ptb.2_Intron|MLL_uc001psz.1_Intron	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		tccagaactatttttaatttc	0.005			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								4	2	---	---	---	---	
TMEM136	219902	broad.mit.edu	37	11	120199714	120199715	+	Intron	DEL	GT	-	-	rs111952858	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120199714_120199715delGT	uc001pxh.1	+						TMEM136_uc001pxg.2_Intron|TMEM136_uc010rzm.1_Intron|TMEM136_uc001pxj.2_Intron|TMEM136_uc009zas.1_Intron|TMEM136_uc001pxi.1_Intron	NM_174926	NP_777586	Q6ZRR5	TM136_HUMAN	transmembrane protein 136							integral to membrane				ovary(1)	1		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Hepatocellular(160;0.206)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.07e-06)		aacagtcatagtgTGTGTGTGT	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	121594533	121594533	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121594533delA								SORL1 (90062 upstream) : LOC399959 (365278 downstream)																							caaagtgctcaaaaaaagcat	0.030													4	2	---	---	---	---	
FOXRED1	55572	broad.mit.edu	37	11	126146772	126146772	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126146772delA	uc001qdi.2	+						FOXRED1_uc010sbn.1_Intron|FOXRED1_uc010sbo.1_Intron|FOXRED1_uc010sbp.1_Intron|FOXRED1_uc010sbq.1_Intron|FOXRED1_uc001qdj.2_Intron|FOXRED1_uc010sbr.1_Intron|FOXRED1_uc001qdk.2_Intron	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing							integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		actccatctcaaaaaaaaaaa	0.184													4	3	---	---	---	---	
DCPS	28960	broad.mit.edu	37	11	126176268	126176268	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126176268delA	uc001qdp.2	+							NM_014026	NP_054745	Q96C86	DCPS_HUMAN	mRNA decapping enzyme						deadenylation-dependent decapping of nuclear-transcribed mRNA|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	exoribonuclease activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		actccatctcaaaaaaaaaaa	0.209													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127469977	127469977	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127469977delC								KIRREL3 (596622 upstream) : ETS1 (858679 downstream)																							atgtaaagggcccaggtggca	0.000													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132741467	132741467	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132741467delC	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		tggaaccaatccccatggatg	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4139622	4139622	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4139622delG								PARP11 (157014 upstream) : CCND2 (243280 downstream)																							cattcagattggggcacaggg	0.000													4	2	---	---	---	---	
A2ML1	144568	broad.mit.edu	37	12	9020244	9020244	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9020244delA	uc001quz.3	+						A2ML1_uc001qva.1_Intron|A2ML1_uc010sgm.1_Intron|A2ML1_uc001qvb.1_5'Flank	NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor							extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3						actccatctgaaaaaaaaaaa	0.194													8	5	---	---	---	---	
CLEC7A	64581	broad.mit.edu	37	12	10279513	10279514	+	Intron	INS	-	A	A	rs35532667		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10279513_10279514insA	uc001qxg.2	-						CLEC7A_uc001qxe.3_Intron|CLEC7A_uc001qxf.2_Intron|CLEC7A_uc001qxh.2_Intron|CLEC7A_uc001qxi.2_Intron|CLEC7A_uc001qxj.2_Intron|CLEC7A_uc009zhg.1_Intron|CLEC7A_uc001qxk.1_Intron|CLEC7A_uc001qxl.1_Intron|CLEC7A_uc010sgy.1_Intron|CLEC7A_uc001qxm.1_Intron	NM_197947	NP_922938	Q9BXN2	CLC7A_HUMAN	dendritic cell-associated C-type lectin 1						carbohydrate mediated signaling|defense response to protozoan|inflammatory response|innate immune response|phagocytosis, recognition|T cell activation	cytoplasm|integral to membrane	metal ion binding|MHC protein binding|sugar binding			central_nervous_system(1)	1						GGAGGTATAGTaaaaaaaaaaa	0.297													12	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	11596746	11596746	+	IGR	DEL	A	-	-	rs35092836		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11596746delA								PRB2 (48248 upstream) : ETV6 (206042 downstream)																							CACAGGTGGCAAAAAAAAAAG	0.393													8	5	---	---	---	---	
BCL2L14	79370	broad.mit.edu	37	12	12231338	12231338	+	Intron	DEL	A	-	-	rs10716109		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12231338delA	uc001rac.2	+						ETV6_uc001raa.1_Intron|BCL2L14_uc001raf.1_5'Flank|BCL2L14_uc001rad.2_Intron|BCL2L14_uc001rae.2_Intron	NM_138723	NP_620049	Q9BZR8	B2L14_HUMAN	BCL2-like 14 isoform 1						apoptosis|regulation of apoptosis	cytosol|endomembrane system|intracellular organelle|membrane	protein binding			skin(1)	1		Prostate(47;0.0872)		BRCA - Breast invasive adenocarcinoma(232;0.154)		CAAGACCTTTAACTCCACAGT	0.403													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	13078668	13078668	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13078668delA								MIR614 (9816 upstream) : GPRC5D (15043 downstream)																							AAAACAAAACAAAAAAAACCC	0.328													4	2	---	---	---	---	
RERG	85004	broad.mit.edu	37	12	15273317	15273317	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15273317delA	uc001rcs.2	-						RERG_uc001rct.2_Intron|RERG_uc010shu.1_Intron	NM_032918	NP_116307	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor						negative regulation of cell growth|negative regulation of cell proliferation|response to hormone stimulus|small GTPase mediated signal transduction	cytosol|membrane|nucleus	estrogen receptor binding|GDP binding|GTP binding|GTPase activity			lung(1)	1						tgacacacagaaggcgcttga	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30311396	30311396	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30311396delA								TMTC1 (373704 upstream) : IPO8 (470527 downstream)																							GCAAATGGACAAAAAAAAGTA	0.413													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	44830059	44830060	+	IGR	DEL	TA	-	-	rs7961768	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44830059_44830060delTA								TMEM117 (46519 upstream) : NELL2 (71998 downstream)																							CTAGAAATTTTAAAAAAAAAAG	0.371													4	2	---	---	---	---	
SPATS2	65244	broad.mit.edu	37	12	49912475	49912475	+	Intron	DEL	C	-	-	rs35298057		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49912475delC	uc001rud.2	+						SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron|SPATS2_uc001rug.2_Intron	NM_023071	NP_075559	Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1						ACAGTCGTTTCCCCTGGAGAG	0.274													4	2	---	---	---	---	
SMARCD1	6602	broad.mit.edu	37	12	50482953	50482954	+	Intron	INS	-	G	G			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50482953_50482954insG	uc001rvx.3	+						SMARCD1_uc010smo.1_3'UTR|SMARCD1_uc001rvy.3_Intron|SMARCD1_uc009zlp.2_Intron	NM_003076	NP_003067	Q96GM5	SMRD1_HUMAN	SWI/SNF-related matrix-associated						chromatin-mediated maintenance of transcription|nervous system development|regulation of transcription from RNA polymerase II promoter	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	protein complex scaffold|transcription coactivator activity			ovary(1)	1						CAGTATTCTTTGGGAAACAGGC	0.441													4	2	---	---	---	---	
FAM186A	121006	broad.mit.edu	37	12	50730244	50730244	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50730244delG	uc001rwl.2	-						FAM186A_uc010smt.1_Intron	NM_001145475	NP_001138947	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A												0						TGGGGTAGACGGGTGgggtgc	0.164													4	2	---	---	---	---	
KRT6A	3853	broad.mit.edu	37	12	52882489	52882489	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52882489delT	uc001sam.2	-							NM_005554	NP_005545	P02538	K2C6A_HUMAN	keratin 6A						cell differentiation|ectoderm development|positive regulation of cell proliferation	keratin filament	protein binding|structural constituent of cytoskeleton			ovary(4)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.189)		TATTTTGCAGTTTTTGTCCAG	0.413													11	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	56058439	56058439	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56058439delC								OR10P1 (26823 upstream) : METTL7B (16891 downstream)																							CACAGTGCTGCCCTCTGGTAA	0.493													4	2	---	---	---	---	
PAN2	9924	broad.mit.edu	37	12	56726546	56726546	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56726546delG	uc001skx.2	-						PAN2_uc001skz.2_Intron|PAN2_uc001sky.2_Intron	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process	cytosol|nucleus	nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity			ovary(2)|skin(2)|large_intestine(1)|breast(1)	6						GTTAAGACCAGATAAAGACCT	0.507													40	22	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	60242837	60242838	+	IGR	DEL	CT	-	-	rs35806710		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60242837_60242838delCT								SLC16A7 (67430 upstream) : None (None downstream)																							cccttccccactctctctctct	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	63015063	63015064	+	IGR	INS	-	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63015063_63015064insT								MIRLET7I (17514 upstream) : PPM1H (22699 downstream)																							GTTAGAGgctctcgtaacacct	0.243													10	11	---	---	---	---	
HMGA2	8091	broad.mit.edu	37	12	66265679	66265679	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66265679delC	uc001ssw.1	+						HMGA2_uc001ssx.2_Intron|HMGA2_uc001sss.1_Intron|HMGA2_uc001sst.1_Intron|HMGA2_uc001ssu.1_Intron|HMGA2_uc001ssv.2_Intron|uc001ssz.1_Intron|uc001sta.1_Intron	NM_003483	NP_003474	P52926	HMGA2_HUMAN	high mobility group AT-hook 2 isoform a						cell division|chromatin organization|mitosis|multicellular organismal development|regulation of growth|transcription, DNA-dependent	chromatin	AT DNA binding		HMGA2/LPP(161)|HMGA2/WIF1_ENST00000286574(14)|HMGA2/RAD51B(11)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/CCNB1IP1(2)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/COX6C(2)	soft_tissue(159)|bone(27)|salivary_gland(22)	208	all_cancers(1;5.78e-46)		GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)		TAGGCTGATGCCGCAGAAAAT	0.388			T	 LHFP|RAD51L1|LPP|HEI10|COX6C|CMKOR1|NFIB|ALDH2|CCNB1IP1|EBF1|WIF1|FHIT	lipoma|leiomyoma|pleiomorphic salivary gland adenoma								4	2	---	---	---	---	
CPSF6	11052	broad.mit.edu	37	12	69638714	69638714	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69638714delA	uc001sut.3	+						CPSF6_uc001suu.3_Intron	NM_007007	NP_008938	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6,						mRNA polyadenylation|protein tetramerization	mRNA cleavage factor complex|paraspeckles|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			ttgaagtaggaagagtacact	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80146921	80146921	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80146921delA								PAWR (62131 upstream) : PPP1R12A (20423 downstream)																							acacacacacaaaaaaaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80434265	80434266	+	IGR	DEL	AG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80434265_80434266delAG								PPP1R12A (105030 upstream) : PTPRQ (403860 downstream)																							agagagaaacagagagagagaG	0.198													4	3	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	82115232	82115233	+	Intron	DEL	AC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82115232_82115233delAC	uc001szo.1	-						PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6						acacacataaacacacacacac	0.252													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93397419	93397419	+	IGR	DEL	G	-	-	rs73211422	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93397419delG								EEA1 (74312 upstream) : NUDT4 (374282 downstream)																							GTGCAGGGGAGGGGGGGAGGA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	94043973	94043974	+	IGR	INS	-	TC	TC	rs138969016	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94043973_94043974insTC								SOCS2 (73995 upstream) : CRADD (27177 downstream)																							cctgctccttttctctctctct	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	94065426	94065426	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94065426delG								SOCS2 (95448 upstream) : CRADD (5725 downstream)																							acgagaaaatggcagtttatt	0.000													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99480571	99480571	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99480571delT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc001tgi.2_Intron|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.1_Intron|ANKS1B_uc001tgm.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		CAGATCACTATTTTTTTTGAC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108181340	108181341	+	IGR	INS	-	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108181340_108181341insC								ASCL4 (10920 upstream) : WSCD2 (342170 downstream)																							caccacacacacacacacacac	0.104													4	2	---	---	---	---	
SSH1	54434	broad.mit.edu	37	12	109197141	109197141	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109197141delA	uc001tnm.2	-						SSH1_uc001tnl.2_Intron|SSH1_uc010sxg.1_Intron|SSH1_uc001tnn.3_Intron	NM_018984	NP_061857	Q8WYL5	SSH1_HUMAN	slingshot 1 isoform 1						actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(4)	4						GGAACGGGGGAAAAAAAAAAA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	111232979	111232979	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111232979delC								PPP1CC (52222 upstream) : CCDC63 (51832 downstream)																							GGGGCAGTTGCCAGGCAGTCA	0.413													4	2	---	---	---	---	
C12orf51	283450	broad.mit.edu	37	12	112608460	112608473	+	Intron	DEL	AAACAATGCAAACA	-	-	rs79313730	byFrequency	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112608460_112608473delAAACAATGCAAACA	uc009zwc.2	-							NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						CAATTTCTAGAAACAATGCAAACAAACTAGAGTT	0.425											OREG0022132	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114726924	114726924	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114726924delG								RBM19 (322748 upstream) : TBX5 (64812 downstream)																							GCAGGAGGcaggggggaatga	0.114													4	2	---	---	---	---	
ATP6V0A2	23545	broad.mit.edu	37	12	124218114	124218114	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124218114delA	uc001ufr.2	+						ATP6V0A2_uc001ufq.1_Intron	NM_012463	NP_036595	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|immune response|insulin receptor signaling pathway|transferrin transport	endosome membrane|integral to membrane|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		tgaaatcaccaaaaaaagcac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125080888	125080889	+	IGR	DEL	CA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125080888_125080889delCA								NCOR2 (28878 upstream) : SCARB1 (181286 downstream)																							aaatacacaccacacacacaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128768074	128768075	+	IGR	DEL	TC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128768074_128768075delTC								None (None upstream) : TMEM132C (131216 downstream)																							TATCTAGGCAtctctctctctc	0.257													4	2	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129767182	129767182	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129767182delT	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGAGTTTGGATTTTGGATCAT	0.264													4	2	---	---	---	---	
EP400	57634	broad.mit.edu	37	12	132518618	132518618	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132518618delT	uc001ujn.2	+						EP400_uc001ujl.2_Intron|EP400_uc001ujm.2_Intron	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400						histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		TTTTGTAAACTTTTTTTTTCT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	29574499	29574499	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29574499delT								SLC46A3 (281349 upstream) : MTUS2 (24249 downstream)																							tgttttttccttttttttctt	0.000													4	2	---	---	---	---	
PDS5B	23047	broad.mit.edu	37	13	33270686	33270686	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33270686delA	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		TTTCAGCTCTAAAAAAAAAAA	0.393													9	4	---	---	---	---	
TRPC4	7223	broad.mit.edu	37	13	38357629	38357629	+	Intron	DEL	T	-	-	rs7339215	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									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	4	---	---	---	---	
PHF11	51131	broad.mit.edu	37	13	50094900	50094900	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50094900delA	uc001vdb.2	+						PHF11_uc001vdc.2_Intron|PHF11_uc001vdd.2_Intron	NM_001040443	NP_001035533	Q9UIL8	PHF11_HUMAN	PHD finger protein 11 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding				0		Lung NSC(96;2.1e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.38e-09)		ACAGGGCTTCAAAAAAAAAAA	0.343													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63633384	63633385	+	IGR	DEL	TT	-	-	rs72302550		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63633384_63633385delTT								None (None upstream) : OR7E156P (678183 downstream)																							TGCTGAACTCTTTGTGCATAAA	0.287													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	70841449	70841449	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70841449delA								ATXN8OS (127564 upstream) : None (None downstream)																							ACTGCAAAAGAAAAGGTCAGA	0.373													4	2	---	---	---	---	
COMMD6	170622	broad.mit.edu	37	13	76102187	76102187	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76102187delT	uc001vjo.1	-						COMMD6_uc001vjn.1_Intron|COMMD6_uc010aet.1_Intron|COMMD6_uc001vjp.1_Intron	NM_203495	NP_987091	Q7Z4G1	COMD6_HUMAN	COMM domain containing 6 isoform b							cytoplasm|nucleus	protein binding				0		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)		acacactctctccaaaaaaaa	0.000													4	2	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	92100400	92100400	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92100400delA	uc010tif.1	+							NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				TTGTACAACTAAAAAGTGCTT	0.383													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	107890766	107890766	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107890766delG	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						AGTCAGGCAAGGAGTCAGGTC	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	114992891	114992891	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114992891delT								RASA3 (94796 upstream) : CDC16 (7471 downstream)																							TTTCCCAATATTTTCATCAAA	0.343											OREG0022541	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	14	20996880	20996881	+	IGR	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20996880_20996881insA								RNASE10 (17566 upstream) : RNASE9 (27372 downstream)																							GACGTCTTCTGAAAAAATGGTT	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26085171	26085171	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26085171delT								STXBP6 (566000 upstream) : NOVA1 (829919 downstream)																							cttacattccttggattgggt	0.020													4	2	---	---	---	---	
CTAGE5	4253	broad.mit.edu	37	14	39762428	39762440	+	Intron	DEL	ATGAAAAATTCTT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39762428_39762440delATGAAAAATTCTT	uc001wvg.3	+						CTAGE5_uc010tqe.1_Intron|CTAGE5_uc001wuz.3_Intron|CTAGE5_uc001wuy.3_Intron|CTAGE5_uc001wvb.3_Intron|CTAGE5_uc001wvc.3_Intron|CTAGE5_uc001wva.3_Intron|CTAGE5_uc001wve.1_Intron|CTAGE5_uc001wvh.3_Intron|CTAGE5_uc001wvf.3_Intron|CTAGE5_uc001wvi.3_Intron|CTAGE5_uc010amz.2_Intron|CTAGE5_uc001wvj.3_Intron	NM_005930	NP_005921	O15320	CTGE5_HUMAN	CTAGE family, member 5 isoform 1								enzyme activator activity|protein binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		GATTTCCCTAATGAAAAATTCTTATATCTGTTT	0.282													36	19	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66374154	66374155	+	IGR	DEL	TG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66374154_66374155delTG								FUT8 (164193 upstream) : C14orf53 (578954 downstream)																							tgtgcgtgtctgtgtgtgtgtg	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66384147	66384147	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66384147delT								FUT8 (174186 upstream) : C14orf53 (568962 downstream)																							TTTCCTTCTCTTTTTTTTTTT	0.423													3	3	---	---	---	---	
GALNTL1	57452	broad.mit.edu	37	14	69759795	69759796	+	Intron	INS	-	T	T	rs140746104	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69759795_69759796insT	uc010aqu.1	+						GALNTL1_uc001xla.1_Intron|GALNTL1_uc001xlb.1_Intron	NM_020692	NP_065743	Q8N428	GLTL1_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)	2				all cancers(60;0.00793)|BRCA - Breast invasive adenocarcinoma(234;0.0174)|OV - Ovarian serous cystadenocarcinoma(108;0.0656)		ctccaagcaggtttttttttcc	0.030													4	3	---	---	---	---	
ERH	2079	broad.mit.edu	37	14	69861328	69861329	+	Intron	INS	-	AAAC	AAAC	rs138016178	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69861328_69861329insAAAC	uc001xlc.2	-							NM_004450	NP_004441	P84090	ERH_HUMAN	enhancer of rudimentary homolog						cell cycle|pyrimidine nucleoside metabolic process	midbody	protein binding				0				all cancers(60;0.00365)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0507)		aatacataaataaacaaacaaa	0.134													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	70320563	70320564	+	IGR	INS	-	A	A	rs148883162	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70320563_70320564insA								SLC10A1 (56557 upstream) : SMOC1 (25579 downstream)																							TGGAAGGTGACGGGGGCGTGTG	0.535													4	3	---	---	---	---	
DPF3	8110	broad.mit.edu	37	14	73225105	73225105	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73225105delC	uc001xnc.2	-						DPF3_uc001xnf.2_Intron|DPF3_uc010ari.1_Intron|DPF3_uc010ttq.1_Intron	NM_012074	NP_036206	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3						chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		caggtggagacctgcagattc	0.000													4	2	---	---	---	---	
YLPM1	56252	broad.mit.edu	37	14	75284384	75284384	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75284384delT	uc001xqj.3	+						YLPM1_uc001xql.3_Intron|YLPM1_uc001xqm.1_Intron	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		GTTTATCTCCTTTTTTTTTCA	0.244													4	2	---	---	---	---	
ADCK1	57143	broad.mit.edu	37	14	78353262	78353272	+	Intron	DEL	CACACACACAC	-	-	rs35621906	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78353262_78353272delCACACACACAC	uc001xui.2	+						ADCK1_uc010tvo.1_Intron|ADCK1_uc001xuj.2_Intron|ADCK1_uc001xuk.1_Intron	NM_020421	NP_065154	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1 isoform a							extracellular region	ATP binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		cacacacacacacacacacacacacacacac	0.180													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82797102	82797102	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82797102delA								SEL1L (796897 upstream) : None (None downstream)																							GCTGGTAAAGAAAAAAAAAAG	0.219													1	5	---	---	---	---	
TTC8	123016	broad.mit.edu	37	14	89343511	89343511	+	Intron	DEL	A	-	-	rs34301947		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89343511delA	uc010ath.2	+						TTC8_uc001xxl.2_Intron|TTC8_uc010ati.2_Intron|TTC8_uc001xxm.2_Intron|TTC8_uc010atj.2_Intron|TTC8_uc001xxi.2_Intron|TTC8_uc001xxj.2_Intron|TTC8_uc001xxk.2_Intron	NM_198309	NP_938051	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8 isoform B						cilium assembly|establishment of anatomical structure orientation|sensory processing	BBSome|centrosome|cilium membrane|microtubule basal body	protein binding				0						TGGGTTTGTTAAAAAAAAAAG	0.279									Bardet-Biedl_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95342068	95342069	+	IGR	INS	-	GTTT	GTTT	rs142104641	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95342068_95342069insGTTT								GSC (105569 upstream) : DICER1 (210496 downstream)																							tcctttgtggggtttgtttgtt	0.020													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95345844	95345844	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95345844delA								GSC (109345 upstream) : DICER1 (206721 downstream)																							actgggtcccaaaaaaggata	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	96216845	96216845	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96216845delT	uc001yfd.1	+											human full-length cDNA clone CS0DG006YJ19 of B cells (Ramos cell line) of Homo sapiens (human).																		ATACTAGACATTATGACTTCA	0.423													4	2	---	---	---	---	
TRAF3	7187	broad.mit.edu	37	14	103270524	103270524	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103270524delA	uc001ymc.1	+						TRAF3_uc001yme.1_Intron|TRAF3_uc001ymd.1_Intron|TRAF3_uc010txy.1_Intron	NM_145725	NP_663777	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3 isoform 1						apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion	signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		gagactgtttaaaaaaaaaaa	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20114406	20114406	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20114406delC								None (None upstream) : GOLGA6L6 (622688 downstream)																							agaacactcactaaacacatg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20406932	20406932	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20406932delG								None (None upstream) : GOLGA6L6 (330162 downstream)																							ATTTTCCATAGGGACTTGAGG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21101924	21101925	+	IGR	INS	-	C	C	rs111888019		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21101924_21101925insC								POTEB (29947 upstream) : NF1P1 (20096 downstream)																							tctcaaaaaaaaTcaaaacatg	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21894540	21894540	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21894540delT								NF1P1 (759915 upstream) : LOC646214 (37974 downstream)																							ATATCAATGATTTTTTTTACT	0.284													4	2	---	---	---	---	
CYFIP1	23191	broad.mit.edu	37	15	22952525	22952525	+	Intron	DEL	A	-	-	rs74844639		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22952525delA	uc001yus.2	+						CYFIP1_uc001yut.2_Intron|CYFIP1_uc010aya.1_Intron	NM_014608	NP_055423	Q7L576	CYFP1_HUMAN	cytoplasmic FMR1 interacting protein 1 isoform						axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		GAAAAGCACCAAAATCATATA	0.348													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24197257	24197257	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24197257delT								NDN (264807 upstream) : PWRN2 (212669 downstream)																							atttccgtgattttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24556113	24556113	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24556113delA								PWRN2 (141018 upstream) : PWRN1 (222726 downstream)																							ccaggctgtcaaaaaaaaata	0.020													3	4	---	---	---	---	
ATP10A	57194	broad.mit.edu	37	15	25928848	25928850	+	Intron	DEL	AAG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25928848_25928850delAAG	uc010ayu.2	-							NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		tccctTAAGAAAGAAGAACTGGC	0.365													5	9	---	---	---	---	
GABRG3	2567	broad.mit.edu	37	15	27285087	27285087	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27285087delC	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		ATTTCATCTTCCCAGGAAGTT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	28913367	28913367	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28913367delT	uc010azc.2	+						uc010uao.1_Intron					Homo sapiens I.M.A.G.E. clone 321824, mRNA sequence.																		TGAGTTCTCCTTTTTTTTTTT	0.308													14	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	28952506	28952507	+	5'Flank	DEL	AC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28952506_28952507delAC	uc001zce.1	+						uc001zcg.2_5'Flank					DQ588687																		catagtatgtacacacacacac	0.203													4	2	---	---	---	---	
AQR	9716	broad.mit.edu	37	15	35152611	35152611	+	Intron	DEL	A	-	-	rs35242788		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35152611delA	uc001ziv.2	-							NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius							catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		GACTCCCATTAAAAAAAAAAA	0.353													4	3	---	---	---	---	
ATPBD4	89978	broad.mit.edu	37	15	35674335	35674335	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35674335delA	uc001zja.2	-						ATPBD4_uc001ziz.2_Intron	NM_080650	NP_542381	Q7L8W6	ATBD4_HUMAN	ATP binding domain 4 isoform 1												0		all_epithelial(112;2.11e-09)|Lung NSC(122;2.38e-08)|all_lung(180;3.65e-07)		all cancers(64;9.9e-19)|GBM - Glioblastoma multiforme(113;2.01e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)		CAAAACTCTTAAAAAAAAATA	0.164													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37542579	37542579	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37542579delA								MEIS2 (149079 upstream) : TMCO5A (684248 downstream)																							CAAAGACTGGAAGGGGATGAT	0.323													4	2	---	---	---	---	
MGA	23269	broad.mit.edu	37	15	41913120	41913120	+	5'Flank	DEL	T	-	-	rs74794783		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41913120delT	uc001zog.1	+							NM_001080541	NP_001074010	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 2							MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)		ACCCTTGCTGTTTTTTTTTTT	0.368													4	2	---	---	---	---	
PPIP5K1	9677	broad.mit.edu	37	15	43831398	43831398	+	Intron	DEL	A	-	-	rs67877426		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43831398delA	uc001zrw.2	-						PPIP5K1_uc001zrx.1_Intron|PPIP5K1_uc001zru.2_Intron|PPIP5K1_uc001zry.3_Intron|PPIP5K1_uc001zrv.2_Intron	NM_001130858	NP_001124330	Q6PFW1	VIP1_HUMAN	histidine acid phosphatase domain containing 2A						inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity				0						tctgtctctcaaaaaaaaaaa	0.154													4	2	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	48002078	48002078	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48002078delA	uc001zvw.2	+							NM_020858	NP_065909	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AAAAACTGGCAAAAAAAAAAA	0.328													4	3	---	---	---	---	
CCPG1	9236	broad.mit.edu	37	15	55657286	55657287	+	Intron	INS	-	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55657286_55657287insT	uc002acv.1	-						CCPG1_uc002acy.2_Intron|CCPG1_uc002acu.1_Intron|CCPG1_uc002acw.1_Intron|CCPG1_uc002acx.2_Intron|CCPG1_uc010bfk.1_Intron|CCPG1_uc002acz.1_Intron	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)		gatcagcattattactGATTTA	0.124													22	21	---	---	---	---	
PRTG	283659	broad.mit.edu	37	15	55919524	55919525	+	Intron	INS	-	T	T	rs35771809		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55919524_55919525insT	uc002adg.2	-							NM_173814	NP_776175	Q2VWP7	PRTG_HUMAN	protogenin precursor						multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		CAATATTAAAGttttttttttt	0.163													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	57647326	57647327	+	IGR	INS	-	CAAT	CAAT	rs146787191	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57647326_57647327insCAAT								LOC283663 (47361 upstream) : CGNL1 (21378 downstream)																							GACCCCCACTGCAATCCTTCAC	0.624													2	5	---	---	---	---	
LIPC	3990	broad.mit.edu	37	15	58716073	58716074	+	Intron	INS	-	GG	GG			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58716073_58716074insGG	uc010bga.1	+						LIPC_uc010bfz.1_Intron	NM_000236	NP_000227	P11150	LIPC_HUMAN	lipase C precursor						cholesterol homeostasis|chylomicron remnant clearance|fatty acid biosynthetic process|high-density lipoprotein particle remodeling|intermediate-density lipoprotein particle remodeling|low-density lipoprotein particle remodeling|phosphatidylcholine catabolic process|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle	apolipoprotein binding|heparin binding|low-density lipoprotein particle binding|phospholipase activity|triglyceride lipase activity			ovary(1)	1		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		atggagattctggcactgtgca	0.193													8	7	---	---	---	---	
LIPC	3990	broad.mit.edu	37	15	58854747	58854747	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58854747delT	uc010bga.1	+						LIPC_uc010bfz.1_Intron|LIPC_uc002afa.1_Intron|LIPC_uc010bgb.1_Intron|LIPC_uc010ugy.1_Intron	NM_000236	NP_000227	P11150	LIPC_HUMAN	lipase C precursor						cholesterol homeostasis|chylomicron remnant clearance|fatty acid biosynthetic process|high-density lipoprotein particle remodeling|intermediate-density lipoprotein particle remodeling|low-density lipoprotein particle remodeling|phosphatidylcholine catabolic process|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle	apolipoprotein binding|heparin binding|low-density lipoprotein particle binding|phospholipase activity|triglyceride lipase activity			ovary(1)	1		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		GCATGGACTCTCCCTGGAAAG	0.567													3	3	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62148198	62148198	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62148198delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						ATATGAAGTTAAAAAAAAAAC	0.294													5	4	---	---	---	---	
MAP2K5	5607	broad.mit.edu	37	15	67892634	67892635	+	Intron	DEL	GT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67892634_67892635delGT	uc002aqu.2	+						MAP2K5_uc002aqt.1_Intron|MAP2K5_uc002aqv.2_Intron|MAP2K5_uc002aqw.2_Intron|MAP2K5_uc010ujw.1_Intron	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						AGATTACTGAGTGTGTGTGTGT	0.347													4	2	---	---	---	---	
UACA	55075	broad.mit.edu	37	15	70964602	70964602	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70964602delA	uc002asr.2	-						UACA_uc010uke.1_Intron|UACA_uc002asq.2_Intron|UACA_uc010bin.1_Intron	NM_018003	NP_060473	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and							cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4						TGCTCAAAAGAAAAAAAAAAG	0.348													4	2	---	---	---	---	
THSD4	79875	broad.mit.edu	37	15	71641438	71641439	+	Intron	INS	-	C	C	rs144550519	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71641438_71641439insC	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2						gaaaaccaggacaggagcaagc	0.149													1	5	---	---	---	---	
HIGD2B	123346	broad.mit.edu	37	15	72968749	72968749	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72968749delT	uc002ava.2	-							NR_002780				Homo sapiens HIG1 domain family, member 2B pseudogene, mRNA (cDNA clone IMAGE:5742106).												0						AAATCCtttgttttttttttt	0.279													5	3	---	---	---	---	
TBC1D2B	23102	broad.mit.edu	37	15	78322651	78322651	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78322651delT	uc002bcy.3	-						TBC1D2B_uc010bla.2_Intron	NM_144572	NP_653173	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B isoform a							intracellular	protein binding|Rab GTPase activator activity			ovary(1)|large_intestine(1)|breast(1)	3						ggggattcccttttttttttt	0.000													8	4	---	---	---	---	
ARNT2	9915	broad.mit.edu	37	15	80852856	80852856	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80852856delC	uc002bfr.2	+						ARNT2_uc010unm.1_Intron|ARNT2_uc002bfs.2_Intron	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator						central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)			GCTTCCCTTTCCCCAGCTCCT	0.418													4	2	---	---	---	---	
AKAP13	11214	broad.mit.edu	37	15	86148356	86148356	+	Intron	DEL	G	-	-	rs11320127		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86148356delG	uc002blv.1	+						AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron|AKAP13_uc010bne.1_Intron	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2						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|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						GCGCTTTGCAGGGCTTCTGAG	0.388													4	2	---	---	---	---	
PCSK6	5046	broad.mit.edu	37	15	101996452	101996453	+	Intron	INS	-	CACTAAGACTG	CACTAAGACTG	rs142437422	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101996452_101996453insCACTAAGACTG	uc002bwy.2	-						PCSK6_uc010bpe.2_Intron|PCSK6_uc002bxa.2_Intron|PCSK6_uc002bxb.2_Intron|PCSK6_uc002bxc.1_Intron|PCSK6_uc002bxd.1_Intron|PCSK6_uc002bxe.2_Intron|PCSK6_uc002bxg.1_Intron	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4						glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ACGTGCTGATTCACGTAACAGC	0.500													3	4	---	---	---	---	
CREBBP	1387	broad.mit.edu	37	16	3864166	3864167	+	Intron	DEL	GT	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3864166_3864167delGT	uc002cvv.2	-						CREBBP_uc002cvw.2_Intron	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a						cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		ATGTTGTTTAgtgtgtgtgtgt	0.233			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				4	2	---	---	---	---	
C16orf5	29965	broad.mit.edu	37	16	4568156	4568157	+	Intron	DEL	CA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4568156_4568157delCA	uc002cwv.2	-						C16orf5_uc002cww.2_Intron|C16orf5_uc010uxl.1_Intron|C16orf5_uc010uxm.1_Intron|C16orf5_uc010btu.2_Intron	NM_013399	NP_037531	Q9H305	LITFL_HUMAN	cell death inducing protein						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|tumor necrosis factor-mediated signaling pathway	nucleus				ovary(1)	1		Ovarian(90;0.17)				TTGCAGGGAGCACACACACACA	0.525											OREG0023584	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7121813	7121814	+	Intron	DEL	AC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7121813_7121814delAC	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		tgtgtcttctacacacacacac	0.000													3	3	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7759450	7759450	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7759450delT	uc002cys.2	+						A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc010uyb.1_Intron|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		AATGCAGAACTTTTTTTTTTC	0.408													2	5	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12274038	12274038	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12274038delA	uc002dby.3	+						SNX29_uc010uyx.1_Intron	NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						ttctttttctAAAAAAAACAA	0.149													4	2	---	---	---	---	
MYH11	4629	broad.mit.edu	37	16	15857442	15857442	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15857442delT	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002dea.1_Intron	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						ATTAGGTTTGTTTTTTTTTAA	0.229			T	CBFB	AML								4	2	---	---	---	---	
XYLT1	64131	broad.mit.edu	37	16	17435526	17435526	+	Intron	DEL	A	-	-	rs79153757		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17435526delA	uc002dfa.2	-							NM_022166	NP_071449	Q86Y38	XYLT1_HUMAN	xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4						AAGTAGTAGCAAAAAAAAAAT	0.204													4	2	---	---	---	---	
TMC5	79838	broad.mit.edu	37	16	19439183	19439184	+	Intron	DEL	TC	-	-	rs141091340		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19439183_19439184delTC	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1						CCACTCTCTTTCTTAAATAGAA	0.287													3	5	---	---	---	---	
C16orf62	57020	broad.mit.edu	37	16	19602874	19602875	+	Intron	INS	-	A	A	rs35875567		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19602874_19602875insA	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron|C16orf62_uc010vas.1_Intron|C16orf62_uc002dgm.1_Intron	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020							integral to membrane				ovary(1)	1						cccatctctacaaaaaaaaaaa	0.114													3	4	---	---	---	---	
DCUN1D3	123879	broad.mit.edu	37	16	20870873	20870874	+	3'UTR	INS	-	C	C	rs1858901		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20870873_20870874insC	uc002dhz.2	-	3					ERI2_uc002dht.3_Intron	NM_173475	NP_775746	Q8IWE4	DCNL3_HUMAN	DCN1, defective in cullin neddylation 1, domain						negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|positive regulation of apoptosis|response to gamma radiation|response to UV-C	perinuclear region of cytoplasm				ovary(2)	2				GBM - Glioblastoma multiforme(48;0.249)		aaaaaaaaaaaaaaaaaaacaa	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	23185352	23185353	+	IGR	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23185352_23185353insA								USP31 (24761 upstream) : SCNN1G (8687 downstream)																							TAAAGAAAACTAAAAAAAAACC	0.139													4	2	---	---	---	---	
PRKCB	5579	broad.mit.edu	37	16	23850950	23850950	+	Intron	DEL	A	-	-	rs11356603		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23850950delA	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	CCCCACCAagaggcagcgtag	0.124													4	2	---	---	---	---	
LOC440354	440354	broad.mit.edu	37	16	30278845	30278845	+	RNA	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30278845delA	uc010vep.1	-	2		c.2382delT								Homo sapiens mRNA; cDNA DKFZp686H21113 (from clone DKFZp686H21113).												0						TTTCTCTTACAAAAAAAAAAA	0.219													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32847247	32847247	+	IGR	DEL	T	-	-	rs112612876		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32847247delT								TP53TG3B (158369 upstream) : SLC6A10P (41550 downstream)																							ctgcttaaccttttttgattt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33491209	33491211	+	IGR	DEL	GAG	-	-	rs147067680		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33491209_33491211delGAG								SLC6A10P (594746 upstream) : MIR1826 (474297 downstream)																							atggaactatgaggtctcaacag	0.256													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33507254	33507254	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33507254delA								SLC6A10P (610791 upstream) : MIR1826 (458254 downstream)																							tcaagtgcttaaaaaaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33531101	33531102	+	IGR	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33531101_33531102insA								SLC6A10P (634638 upstream) : MIR1826 (434406 downstream)																							GCAGCATGTGCAAAAAAATAAA	0.391													4	5	---	---	---	---	
GNAO1	2775	broad.mit.edu	37	16	56358842	56358842	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56358842delG	uc002eit.3	+						GNAO1_uc002eiu.3_Intron	NM_138736	NP_620073	P09471	GNAO_HUMAN	guanine nucleotide binding protein, alpha						dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			lung(1)|breast(1)	2		all_neural(199;0.159)				CACTTTAGCTGGACAGCTCAA	0.488													4	2	---	---	---	---	
SLC12A3	6559	broad.mit.edu	37	16	56921123	56921123	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56921123delT	uc010ccm.2	+						SLC12A3_uc002ekd.3_Intron|SLC12A3_uc010ccn.2_Intron	NM_001126108	NP_001119580	P55017	S12A3_HUMAN	solute carrier family 12, member 3 isoform 3						sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	GAGCCCCAACttttttttttt	0.289													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	63314537	63314537	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63314537delA								None (None upstream) : None (None downstream)																							aaaaacaaacaaaaaaaatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64247133	64247133	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64247133delG								None (None upstream) : CDH11 (733552 downstream)																							AGAAAGTGCAGGAACAGCAGA	0.413													4	2	---	---	---	---	
GLG1	2734	broad.mit.edu	37	16	74513892	74513892	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74513892delA	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						TTTGGGAATTAAAAAAAAAAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77065753	77065754	+	IGR	INS	-	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77065753_77065754insC								CNTNAP4 (472618 upstream) : MON1B (159082 downstream)																							ACCAGAATTTTCCCAAGGCTTA	0.257													4	2	---	---	---	---	
ADAMTS18	170692	broad.mit.edu	37	16	77359576	77359576	+	Intron	DEL	A	-	-	rs36036462		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77359576delA	uc002ffc.3	-						ADAMTS18_uc010chc.1_Intron|ADAMTS18_uc002ffe.1_Intron	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						TTATAGGGGGAAAAAAAAAAA	0.378													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80070774	80070774	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80070774delA								MAF (436152 upstream) : DYNLRB2 (504080 downstream)																							TAAGCATCAGAAAAATGCTGA	0.383													4	2	---	---	---	---	
ANKRD11	29123	broad.mit.edu	37	16	89532757	89532757	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89532757delG	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)		aaagggggaagggggacaagg	0.000													4	2	---	---	---	---	
ZNF276	92822	broad.mit.edu	37	16	89800163	89800164	+	Intron	INS	-	G	G	rs147083892	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89800163_89800164insG	uc002fos.3	+						ZNF276_uc010ciq.2_Intron|ZNF276_uc002fop.2_Intron|ZNF276_uc002foq.3_Intron|ZNF276_uc010cir.2_Intron|ZNF276_uc002for.3_Intron|ZNF276_uc010cis.2_Intron|ZNF276_uc002fot.3_Intron|ZNF276_uc010vpm.1_Intron|ZNF276_uc010cit.1_Intron	NM_001113525	NP_001106997	Q8N554	ZN276_HUMAN	zinc finger protein 276 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		AGACACCCCCCGGGGGGTCTAG	0.564													5	4	---	---	---	---	
SMG6	23293	broad.mit.edu	37	17	2173906	2173906	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2173906delA	uc002fub.1	-							NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4						tgtctcaaggaaaaaaaaaaT	0.174													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	4830800	4830801	+	IGR	DEL	GG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4830800_4830801delGG								CHRNE (24431 upstream) : GP1BA (4791 downstream)																							actctaggccgggtgtgatggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5395548	5395549	+	IGR	DEL	AA	-	-	rs71898590		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5395548_5395549delAA								MIS12 (1420 upstream) : LOC728392 (7199 downstream)																							ATGTAAATGCAAAAAAAAAAAA	0.188													4	3	---	---	---	---	
CCDC42	146849	broad.mit.edu	37	17	8643213	8643214	+	Intron	INS	-	C	C	rs149149374	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8643213_8643214insC	uc002gln.2	-						CCDC42_uc002glo.2_Intron	NM_144681	NP_653282	Q96M95	CCD42_HUMAN	coiled-coil domain containing 42 isoform 1											ovary(1)	1						CTTACTTCCTGCCCCCCCAACA	0.342													2	4	---	---	---	---	
MYH13	8735	broad.mit.edu	37	17	10236041	10236041	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10236041delT	uc002gmk.1	-							NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle						muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						aggggtgtggtttgctaccac	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13669626	13669626	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13669626delT								HS3ST3A1 (164382 upstream) : CDRT15P (258189 downstream)																							TATAGAAGCCTTTTTTTTTCT	0.363													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	16502679	16502679	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16502679delG								ZNF287 (30159 upstream) : ZNF624 (21369 downstream)																							gtgggtgaatggattaatggg	0.000													4	2	---	---	---	---	
COPS3	8533	broad.mit.edu	37	17	17179758	17179759	+	Intron	INS	-	AT	AT	rs72535825	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17179758_17179759insAT	uc002grd.2	-						COPS3_uc010vwv.1_Intron|COPS3_uc010vww.1_Intron	NM_003653	NP_003644	Q9UNS2	CSN3_HUMAN	COP9 constitutive photomorphogenic homolog						cullin deneddylation|response to light stimulus|signal transduction	cytoplasm|signalosome	protein binding			skin(1)	1						CAGAAATGCACGTTACTATTAA	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20679710	20679710	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20679710delA								LGALS9B (308862 upstream) : CCDC144NL (87000 downstream)																							actccgtctcaaaaaaaaaaa	0.095													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20895278	20895278	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20895278delT								CCDC144NL (95825 upstream) : USP22 (7630 downstream)																							CCAGGGAGACTTTTTTTTGAT	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21236359	21236360	+	IGR	INS	-	G	G	rs138211082	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21236359_21236360insG								MAP2K3 (17810 upstream) : KCNJ12 (43339 downstream)																							TCTATTCTTTTCGGCTTGTCTT	0.347													4	2	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21306688	21306690	+	Intron	DEL	ACA	-	-	rs144651249	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21306688_21306690delACA	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	attggttttgacaacatcataca	0.039										Prostate(3;0.18)			1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22252629	22252630	+	IGR	INS	-	A	A	rs112679765		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22252629_22252630insA								FLJ36000 (339559 upstream) : None (None downstream)																							tgtttgggcctctttgaagatt	0.000													4	2	---	---	---	---	
NF1	4763	broad.mit.edu	37	17	29521347	29521348	+	Intron	DEL	AA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29521347_29521348delAA	uc002hgg.2	+						NF1_uc002hge.1_Intron|NF1_uc002hgf.1_Intron|NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		tgtggaagctaaaaaaaagttg	0.000			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			4	2	---	---	---	---	
NF1	4763	broad.mit.edu	37	17	29575850	29575850	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29575850delT	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron|NF1_uc002hgi.1_Intron	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CAAAGTTGTCTTTTTTTTTTT	0.174			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			12	6	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31843427	31843428	+	Intron	DEL	GT	-	-	rs113344287		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31843427_31843428delGT	uc002hhu.2	-							NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	gtgagtgtgagtgtgtgtgtgt	0.144													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	32859244	32859244	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32859244delA								CCL1 (168992 upstream) : C17orf102 (41898 downstream)																							TTTTCAAATGAAAAAAAAAAC	0.323													4	2	---	---	---	---	
JUP	3728	broad.mit.edu	37	17	39808563	39808564	+	Intron	DEL	AC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39808563_39808564delAC	uc010wfs.1	-							NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		acatgcacatacacacacacaA	0.312													6	3	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44244639	44244639	+	Intron	DEL	A	-	-	rs117299592	byFrequency	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44244639delA	uc002ikb.2	-						KIAA1267_uc002ikc.2_Intron|KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				AATTGCAGGGAAAAAAAAACA	0.313													4	2	---	---	---	---	
NPEPPS	9520	broad.mit.edu	37	17	45679340	45679340	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45679340delA	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010wkv.1_Intron|NPEPPS_uc002ils.1_5'Flank	NM_006310	NP_006301	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0						GGAGGAGAAGAAAAAAAAAAA	0.373													3	3	---	---	---	---	
STXBP4	252983	broad.mit.edu	37	17	53076447	53076448	+	Intron	INS	-	G	G	rs142505374	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53076447_53076448insG	uc002iuf.1	+						STXBP4_uc010dcc.1_Intron|STXBP4_uc010dcd.1_Intron	NM_178509	NP_848604	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4							cytoplasm	calcium ion binding			ovary(1)	1						TACTGGCCTATGTCCTACCTAC	0.376													2	8	---	---	---	---	
HEATR6	63897	broad.mit.edu	37	17	58120625	58120625	+	3'UTR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58120625delT	uc002iyk.1	-	20					HEATR6_uc010ddk.1_3'UTR|HEATR6_uc010wos.1_3'UTR	NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6								binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			TCCTTCTACATTTTTTTTTTC	0.398													4	3	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	58938591	58938591	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58938591delG	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			agtattcctagggattgtatt	0.000													4	2	---	---	---	---	
FTSJ3	117246	broad.mit.edu	37	17	61898063	61898064	+	Intron	INS	-	GCTTGAACCTGGAAGACGG	GCTTGAACCTGGAAGACGG	rs142835534	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61898063_61898064insGCTTGAACCTGGAAGACGG	uc002jbz.2	-						FTSJ3_uc002jca.2_Intron	NM_017647	NP_060117	Q8IY81	RRMJ3_HUMAN	FtsJ homolog 3						RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1						caaggagaatcaggctgcagtg	0.059													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66701391	66701392	+	IGR	DEL	TC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66701391_66701392delTC								FAM20A (104296 upstream) : ABCA8 (162041 downstream)																							TGTGAATCTTTCTCTCTCTCTC	0.356													4	2	---	---	---	---	
SLC39A11	201266	broad.mit.edu	37	17	70860449	70860451	+	Intron	DEL	TTT	-	-	rs36113238		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70860449_70860451delTTT	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						AAGCATCGGCTTTTTTTTTTTTT	0.424													4	2	---	---	---	---	
TNRC6C	57690	broad.mit.edu	37	17	76044235	76044235	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76044235delT	uc002jud.2	+						TNRC6C_uc002juf.2_Intron|TNRC6C_uc002jue.2_5'Flank	NM_018996	NP_061869	Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C isoform 2						gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GAGCTACAGATTTTTTTTTTT	0.328													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	78432979	78432979	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78432979delC								FLJ35220 (21098 upstream) : NPTX1 (7654 downstream)																							CCTCCTCTCTCCCAGGATGTC	0.498													4	2	---	---	---	---	
AZI1	22994	broad.mit.edu	37	17	79180013	79180013	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79180013delA	uc002jzp.1	-						AZI1_uc002jzn.1_Intron|AZI1_uc002jzo.1_Intron|AZI1_uc010wum.1_Intron	NM_014984	NP_055799	Q9UPN4	AZI1_HUMAN	5-azacytidine induced 1 isoform a						cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centrosome|cytosol|intracellular membrane-bounded organelle				central_nervous_system(2)|large_intestine(1)|ovary(1)	4	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			actccatctcaaaaaaaaaaa	0.214													4	2	---	---	---	---	
C17orf56	146705	broad.mit.edu	37	17	79204128	79204134	+	Intron	DEL	TGAGTGC	-	-	rs150422103		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79204128_79204134delTGAGTGC	uc002jzu.1	-						C17orf56_uc002jzr.1_Intron|C17orf56_uc002jzs.1_Intron|C17orf56_uc002jzt.1_Intron|C17orf56_uc002jzv.1_Intron|uc002jzw.1_RNA	NM_144679	NP_653280	Q96N21	CQ056_HUMAN	hypothetical protein LOC146705							integral to membrane					0	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			cagtgtaCTGTGAGTGCTGCAGAGTTT	0.338											OREG0024811	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10134	10135	+	IGR	INS	-	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10134_10135insT								None (None upstream) : USP14 (148348 downstream)																							aaccctaaccctaaccctaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	4831173	4831173	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4831173delA								DLGAP1 (375907 upstream) : LOC642597 (312499 downstream)																							ATAGATAGGGAAATGAAAAAT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	6641635	6641635	+	IGR	DEL	T	-	-	rs7235523	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6641635delT								L3MBTL4 (226725 upstream) : ARHGAP28 (146858 downstream)																							cacattcacctgctgacacac	0.000													4	2	---	---	---	---	
SEH1L	81929	broad.mit.edu	37	18	12979075	12979076	+	Intron	INS	-	T	T	rs71370922		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12979075_12979076insT	uc002krr.2	+						SEH1L_uc002krq.2_Intron	NM_031216	NP_112493	Q96EE3	SEH1_HUMAN	sec13-like protein isoform 2						attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|carbohydrate metabolic process|cell division|glucose transport|mitotic metaphase plate congression|mitotic prometaphase|mRNA transport|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex					0						TTttttctttcttttttttttt	0.104													7	5	---	---	---	---	
KCTD1	284252	broad.mit.edu	37	18	24099901	24099901	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24099901delT	uc002kvw.2	-						KCTD1_uc010xbj.1_Intron|KCTD1_uc010xbk.1_Intron	NM_001136205	NP_001129677	Q719H9	KCTD1_HUMAN	potassium channel tetramerisation domain						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|voltage-gated potassium channel complex	transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity			ovary(1)	1	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			TCAAAATCAATTCGGTTCAGT	0.388													4	2	---	---	---	---	
KIAA1328	57536	broad.mit.edu	37	18	34419205	34419205	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34419205delT	uc002kzz.2	+							NM_020776	NP_065827	Q86T90	K1328_HUMAN	hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)		tctgttcatatttttttcatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	45297556	45297556	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45297556delC								IER3IP1 (594811 upstream) : SMAD2 (61911 downstream)																							AAAGGCCTTTCCCCCCAGGAT	0.413													4	2	---	---	---	---	
GNA11	2767	broad.mit.edu	37	19	3096280	3096280	+	Intron	DEL	G	-	-	rs5826792		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3096280delG	uc002lxd.2	+							NM_002067	NP_002058	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein),						activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			eye(70)|skin(16)	86		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		CATCTTTCCAGGGGGCCGCGG	0.547			Mis		uveal melanoma								0	6	---	---	---	---	
HNRNPM	4670	broad.mit.edu	37	19	8538344	8538344	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8538344delA	uc010dwe.2	+						HNRNPM_uc010dwc.1_Intron|HNRNPM_uc010xke.1_Intron|HNRNPM_uc010dwd.2_Intron|HNRNPM_uc002mka.2_Intron	NM_005968	NP_005959	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0						tactgtgtttaaaaaaaaaaa	0.119													5	5	---	---	---	---	
C19orf39	126074	broad.mit.edu	37	19	11486488	11486489	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11486488_11486489delTC	uc002mrg.1	+	2	523_524	c.486_487delTC	c.(484-489)TTTCCTfs	p.F162fs		NM_175871	NP_787067	Q6NVH7	CS039_HUMAN	hypothetical protein LOC126074	162_163											0						AGCGGTATTTTCCTGCCCAGTG	0.668													29	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13635109	13635110	+	IGR	DEL	AG	-	-	rs112516659		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13635109_13635110delAG								CACNA1A (17835 upstream) : CCDC130 (207464 downstream)																							agaaaagaaaagagagaaagaa	0.000													3	5	---	---	---	---	
PALM3	342979	broad.mit.edu	37	19	14166128	14166128	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14166128delT	uc010xnk.1	-							NM_001145028	NP_001138500	A6NDB9	PALM3_HUMAN	hypothetical protein LOC342979						negative regulation of cytokine-mediated signaling pathway|response to lipopolysaccharide|Toll signaling pathway	cytoplasm|plasma membrane	ATP binding|protein binding			pancreas(1)	1						TCCCCTTGAGTCACCCTCTCA	0.582													26	31	---	---	---	---	
CPAMD8	27151	broad.mit.edu	37	19	17023564	17023564	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17023564delA	uc002nfb.2	-							NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						cagtgagctgaaaAAAAAAAG	0.274													6	3	---	---	---	---	
ZNF100	163227	broad.mit.edu	37	19	21910934	21910934	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21910934delA	uc002nqi.2	-						ZNF100_uc002nqh.2_Intron	NM_173531	NP_775802	Q8IYN0	ZN100_HUMAN	zinc finger protein 100						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ATATAAATGTAAAAAAAAAAA	0.313													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	22688165	22688165	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22688165delC								ZNF98 (83017 upstream) : ZNF492 (128961 downstream)																							GCCCCCTTCTCCTCCCCACCC	0.572													4	2	---	---	---	---	
ZNF99	7652	broad.mit.edu	37	19	22951832	22951832	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22951832delA	uc010xrh.1	-							NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				actctgtttcaaaaaaaaaaa	0.134													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	23126165	23126165	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23126165delA								ZNF99 (173381 upstream) : ZNF91 (395254 downstream)																							AATTTATCATAAAAGCATGTA	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31113855	31113855	+	IGR	DEL	T	-	-	rs72332201		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31113855delT								ZNF536 (64890 upstream) : DKFZp566F0947 (526928 downstream)																							cctcctagagttttttttttt	0.239													4	2	---	---	---	---	
UPK1A	11045	broad.mit.edu	37	19	36167074	36167081	+	Intron	DEL	TTTCTTTC	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36167074_36167081delTTTCTTTC	uc002oaw.2	+						UPK1A_uc010eeh.2_Intron|uc002oax.1_5'Flank	NM_007000	NP_008931	O00322	UPK1A_HUMAN	uroplakin 1A						epithelial cell differentiation|protein oligomerization	endoplasmic reticulum|integral to membrane	monosaccharide binding|protein homodimerization activity				0	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ttgttttctttttctttctttctttctt	0.000													3	3	---	---	---	---	
SHKBP1	92799	broad.mit.edu	37	19	41083855	41083860	+	Intron	DEL	ACACAC	-	-	rs71962226		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41083855_41083860delACACAC	uc002oob.2	+						SHKBP1_uc002ooc.2_Intron|SHKBP1_uc002ood.2_Intron|SHKBP1_uc010xvl.1_Intron|SHKBP1_uc002ooe.2_Intron|SHKBP1_uc002oof.2_Intron|SHKBP1_uc010xvm.1_5'Flank|SHKBP1_uc010xvn.1_5'Flank	NM_138392	NP_612401	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|pancreas(1)	2			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			ATTTCTCCCTacacacacacacacac	0.214													6	3	---	---	---	---	
APOC4	346	broad.mit.edu	37	19	45448708	45448708	+	3'UTR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45448708delA	uc002pag.1	+	3					APOC2_uc002pah.2_5'Flank	NM_001646	NP_001637	P55056	APOC4_HUMAN	apolipoprotein C-IV precursor						lipid metabolic process|positive regulation of sequestering of triglyceride|triglyceride homeostasis	high-density lipoprotein particle|very-low-density lipoprotein particle	lipid transporter activity			breast(1)	1	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00334)|Epithelial(262;0.178)		aaacaaaaagaaaaaAAAAAG	0.224													5	3	---	---	---	---	
MKKS	8195	broad.mit.edu	37	20	10412651	10412651	+	5'Flank	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10412651delC	uc002wnt.1	-						MKKS_uc002wnu.1_Intron|MKKS_uc010zrd.1_Intron	NM_018848	NP_061336	Q9NPJ1	MKKS_HUMAN	McKusick-Kaufman syndrome protein						brain morphogenesis|cerebral cortex development|convergent extension involved in gastrulation|detection of mechanical stimulus involved in sensory perception of sound|fat cell differentiation|flagellum assembly|gonad development|heart looping|hippocampus development|intracellular transport|melanosome transport|photoreceptor cell maintenance|pigment granule aggregation in cell center|protein folding|regulation of cilium beat frequency involved in ciliary motility|sensory perception of smell|social behavior|spermatid development|striatum development	cytosol|microtubule organizing center|motile cilium	ATP binding|unfolded protein binding				0						gccaccctgacccccctaagg	0.070									Bardet-Biedl_syndrome				4	2	---	---	---	---	
KIF16B	55614	broad.mit.edu	37	20	16349299	16349299	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16349299delT	uc002wpg.1	-						KIF16B_uc002wpe.1_Intron|KIF16B_uc002wpf.1_Intron|KIF16B_uc010gch.1_Intron|KIF16B_uc010gci.1_Intron	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23						cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						GATGAGCTCATTTTTTTAGCA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16998398	16998398	+	IGR	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16998398delT								OTOR (265590 upstream) : PCSK2 (208354 downstream)																							TTTCCAGGCCTTTTTTTTTCA	0.363													3	3	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17210926	17210926	+	Intron	DEL	A	-	-	rs34406447		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17210926delA	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TTATTTATTCATCCATATGAA	0.323													3	4	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19243677	19243678	+	Intron	INS	-	TG	TG	rs150091274	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19243677_19243678insTG	uc002wrl.2	+						LOC100130264_uc010zsd.1_Intron	NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						ACTCCAGCCTTtgtgtgtgtgt	0.401													4	3	---	---	---	---	
C20orf26	26074	broad.mit.edu	37	20	20132950	20132951	+	Intron	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20132950_20132951insA	uc002wru.2	+						C20orf26_uc010gcw.1_Intron|C20orf26_uc010zse.1_Intron|C20orf26_uc010zsf.1_Intron	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		ataacacaatgaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22305566	22305566	+	IGR	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22305566delC								PAX1 (608946 upstream) : LOC284788 (75405 downstream)																							AACCTTGATGCCCCAGAAATT	0.453													4	2	---	---	---	---	
GZF1	64412	broad.mit.edu	37	20	23350716	23350716	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23350716delT	uc010gdb.2	+						GZF1_uc002wsy.2_Intron|GZF1_uc010zsq.1_Intron|GZF1_uc010zsr.1_Intron|GZF1_uc002wsz.2_Intron	NM_022482	NP_071927	Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1						transcription, DNA-dependent	nucleolus|nucleoplasm	sequence-specific DNA binding|zinc ion binding			kidney(1)	1	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					TTGTTTTGTGTTTAACTTATA	0.393													47	29	---	---	---	---	
C20orf3	57136	broad.mit.edu	37	20	24954586	24954586	+	Intron	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24954586delG	uc002wty.2	-						C20orf3_uc002wtz.2_Intron|C20orf3_uc010zsw.1_Intron	NM_020531	NP_065392	Q9HDC9	APMAP_HUMAN	chromosome 20 open reading frame 3						biosynthetic process	cell surface|integral to membrane	arylesterase activity|strictosidine synthase activity			ovary(1)	1						AGCAGCCTGTGGGCATGAACC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29597737	29597738	+	IGR	INS	-	TT	TT			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29597737_29597738insTT								None (None upstream) : FRG1B (14141 downstream)																							cacttaccttatgcaagtctca	0.114													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29609373	29609373	+	5'Flank	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29609373delT	uc002wvm.1	+						FRG1B_uc010ztj.1_5'Flank|FRG1B_uc010gdr.1_5'Flank	NR_003579				Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						CATCTTTAACTGTAAATATGA	0.313													2	4	---	---	---	---	
TM9SF4	9777	broad.mit.edu	37	20	30721276	30721276	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30721276delT	uc002wxj.2	+						TM9SF4_uc010ztr.1_Intron|TM9SF4_uc010zts.1_Intron|TM9SF4_uc002wxk.2_Intron	NM_014742	NP_055557	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4							integral to membrane				central_nervous_system(1)|pancreas(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TCTGCCTCCCTTTCTCACCTG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31776104	31776104	+	IGR	DEL	T	-	-	rs67745079		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31776104delT								C20orf70 (6881 upstream) : BASE (5307 downstream)																							TATAAGTGGGTTtttttttgt	0.209													5	3	---	---	---	---	
ITCH	83737	broad.mit.edu	37	20	33036397	33036397	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33036397delT	uc010geu.1	+						ITCH_uc002xak.2_Intron|ITCH_uc010zuj.1_Intron	NM_031483	NP_113671	Q96J02	ITCH_HUMAN	itchy homolog E3 ubiquitin protein ligase						apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity			breast(4)|lung(1)|central_nervous_system(1)	6						GTTTTACTTGTTTTTTTTTTC	0.219													4	2	---	---	---	---	
TRPC4AP	26133	broad.mit.edu	37	20	33647700	33647714	+	Intron	DEL	GAAGAAGACGAAGAC	-	-	rs67999415		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33647700_33647714delGAAGAAGACGAAGAC	uc002xbk.2	-						TRPC4AP_uc002xbl.2_Intron|TRPC4AP_uc010zur.1_Intron|TRPC4AP_uc002xbm.1_Intron	NM_015638	NP_056453	Q8TEL6	TP4AP_HUMAN	TRPC4-associated protein isoform a						protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)			agatgaagatgaagaagacgaagacgaagaagaca	0.000													4	2	---	---	---	---	
DHX35	60625	broad.mit.edu	37	20	37612319	37612319	+	Intron	DEL	C	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37612319delC	uc002xjh.2	+						DHX35_uc010zwa.1_Intron|DHX35_uc010zwb.1_Intron|DHX35_uc010zwc.1_Intron	NM_021931	NP_068750	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35							catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				CATATGTATACTTAGATGTGA	0.453													292	206	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37966806	37966807	+	IGR	INS	-	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37966806_37966807insC								LOC339568 (113415 upstream) : None (None downstream)																							gttcaacacatcatctcctcta	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	39524772	39524772	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39524772delA								MAFB (206896 upstream) : TOP1 (132690 downstream)																							ACAGATGTCCAAaagggagac	0.249													4	2	---	---	---	---	
DPM1	8813	broad.mit.edu	37	20	49562303	49562304	+	Intron	DEL	AA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49562303_49562304delAA	uc002xvw.1	-						DPM1_uc002xvv.1_Intron|DPM1_uc002xvx.1_Intron	NM_003859	NP_003850	O60762	DPM1_HUMAN	dolichyl-phosphate mannosyltransferase 1						C-terminal protein lipidation|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|protein N-linked glycosylation via asparagine|protein O-linked mannosylation	dolichol-phosphate-mannose synthase complex|endoplasmic reticulum membrane|membrane fraction	dolichyl-phosphate beta-D-mannosyltransferase activity|dolichyl-phosphate-mannose-protein mannosyltransferase activity|protein binding			ovary(1)	1						ATTTTGGCTGAAATTTGAAAAG	0.302													263	167	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49974621	49974622	+	IGR	INS	-	TGGA	TGGA			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49974621_49974622insTGGA								KCNG1 (334946 upstream) : NFATC2 (33144 downstream)																							ggatgaatgggtggatggatgg	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53440426	53440426	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53440426delA								DOK5 (172717 upstream) : None (None downstream)																							CCCCACTCCCAAAAAAATCTC	0.363													4	2	---	---	---	---	
PMEPA1	56937	broad.mit.edu	37	20	56234228	56234229	+	Intron	INS	-	CTC	CTC	rs143496846	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56234228_56234229insCTC	uc002xyq.2	-						PMEPA1_uc002xyr.2_Intron|PMEPA1_uc002xys.2_Intron|PMEPA1_uc002xyt.2_Intron	NM_020182	NP_064567	Q969W9	PMEPA_HUMAN	transmembrane prostate androgen-induced protein						androgen receptor signaling pathway	integral to membrane|plasma membrane	WW domain binding			pancreas(1)	1						CCACTGGGCgtctcatctccct	0.327													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58138214	58138216	+	IGR	DEL	AGG	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58138214_58138216delAGG								EDN3 (237168 upstream) : PHACTR3 (14348 downstream)																							GAAGATGAACAGGAGGAGGAGAG	0.320													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58144529	58144530	+	IGR	INS	-	ATGG	ATGG	rs144949742	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58144529_58144530insATGG								EDN3 (243483 upstream) : PHACTR3 (8034 downstream)																							cagatggatgaatggatggatg	0.000													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60147880	60147881	+	Intron	INS	-	ATGG	ATGG	rs150075946	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60147880_60147881insATGG	uc002ybn.1	+						CDH4_uc002ybo.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			TTCAGAACACTatggatggatg	0.238													6	7	---	---	---	---	
DNAJC5	80331	broad.mit.edu	37	20	62555565	62555565	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62555565delA	uc002yhf.2	+						DNAJC5_uc002yhg.1_Intron|DNAJC5_uc002yhh.2_Intron	NM_025219	NP_079495	Q9H3Z4	DNJC5_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5						neurotransmitter secretion|protein folding	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|melanosome|plasma membrane	heat shock protein binding|unfolded protein binding			pancreas(1)	1	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					cagtttctgcaaaaaaaaatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10735736	10735736	+	IGR	DEL	C	-	-	rs111875771		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10735736delC								None (None upstream) : TPTE (171007 downstream)																							tctcagattgcttctgtctgg	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14853606	14853607	+	IGR	INS	-	TG	TG	rs76336513	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14853606_14853607insTG								C21orf99 (363037 upstream) : POTED (128891 downstream)																							gtgtctgtgtctgtgtgtgtgt	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	15449232	15449235	+	Intron	DEL	AGAC	-	-	rs111767328		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15449232_15449235delAGAC	uc002yjk.2	+						uc002yjl.2_Intron					Homo sapiens, clone IMAGE:4102980, mRNA.																		ATCCAGACAAAGACAGACAgagga	0.255													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	20296656	20296657	+	IGR	INS	-	A	A			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20296656_20296657insA								TMPRSS15 (520686 upstream) : None (None downstream)																							gggagtgtaacagggaatcatt	0.000													1	5	---	---	---	---	
MRPL39	54148	broad.mit.edu	37	21	26977847	26977847	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26977847delA	uc002ylo.2	-						MRPL39_uc002yln.2_Intron	NM_017446	NP_059142	Q9NYK5	RM39_HUMAN	mitochondrial ribosomal protein L39 isoform a							mitochondrial ribosome	nucleotide binding				0						AAAAGGCGGCAAAAAAAAGCT	0.438													4	3	---	---	---	---	
GRIK1	2897	broad.mit.edu	37	21	31176765	31176765	+	Intron	DEL	A	-	-	rs460401	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31176765delA	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)	AACTCCAATTAAAAAAAAAAA	0.313													1	5	---	---	---	---	
TIAM1	7074	broad.mit.edu	37	21	32526388	32526388	+	Intron	DEL	A	-	-	rs113677415		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32526388delA	uc002yow.1	-						TIAM1_uc011adk.1_Intron|TIAM1_uc011adl.1_Intron	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10						ttaaaaaaacaaaaaaaaCAA	0.169													6	3	---	---	---	---	
URB1	9875	broad.mit.edu	37	21	33724346	33724346	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33724346delA	uc002ypn.2	-							NM_014825	NP_055640	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog							nucleolus	protein binding				0						gtatgcctccaaaaaacacac	0.119													4	2	---	---	---	---	
C21orf59	56683	broad.mit.edu	37	21	33957940	33957940	+	Intron	DEL	T	-	-	rs148817899		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33957940delT	uc002ypy.1	-						TCP10L_uc002ypw.3_5'Flank|C21orf59_uc002ypx.1_Intron|C21orf59_uc002ypz.1_Intron	NM_021254	NP_067077	P57076	CU059_HUMAN	hypothetical protein LOC56683							cytosol|nucleus					0						CCTGCAATTCTTAATATAGAA	0.413											OREG0003581	type=REGULATORY REGION|Gene=TCP10L|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	8	8	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36341697	36341697	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36341697delA	uc010gmu.2	-						RUNX1_uc002yut.1_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron	NM_001754	NP_001745	Q01196	RUNX1_HUMAN	runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						GCCAACagagaaaaaaaaaac	0.274			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				5	3	---	---	---	---	
ERG	2078	broad.mit.edu	37	21	40008651	40008651	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40008651delA	uc010gnw.2	-						ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gnz.2_Intron	NM_001136155	NP_001129627	P11308	ERG_HUMAN	ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)				GATGTCACCCAAAAAGCTCCG	0.562													4	2	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45815583	45815584	+	Intron	INS	-	G	G	rs67276218		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45815583_45815584insG	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						agggctgtggaggatgtggagg	0.218													2	7	---	---	---	---	
RTN4R	65078	broad.mit.edu	37	22	20239600	20239602	+	Intron	DEL	TCA	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20239600_20239602delTCA	uc002zrv.2	-						MIR1286_hsa-mir-1286|MI0006348_5'Flank	NM_023004	NP_075380	Q9BZR6	RTN4R_HUMAN	reticulon 4 receptor precursor						axonogenesis|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	anchored to membrane|cell surface|endoplasmic reticulum|plasma membrane	protein binding|receptor activity				0	Colorectal(54;0.0993)					atcaccatcctcatcatcaccat	0.000													2	5	---	---	---	---	
SEZ6L	23544	broad.mit.edu	37	22	26684194	26684194	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26684194delA	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6						AGGCACTTGGAAGACAAAACA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27117003	27117004	+	IGR	INS	-	G	G	rs150988863	by1000genomes	TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27117003_27117004insG								MIAT (2054 upstream) : None (None downstream)																							GTGGGGGTTGCGGGGAGCACCA	0.282													2	5	---	---	---	---	
TCN2	6948	broad.mit.edu	37	22	31012013	31012016	+	Intron	DEL	TGGA	-	-	rs145631512		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31012013_31012016delTGGA	uc003aip.1	+						TCN2_uc003aiq.1_Intron|TCN2_uc003air.1_Intron	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor						cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAGAAATGTTtggatggatggatg	0.333													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	33616496	33616496	+	IGR	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33616496delA								SYN3 (162119 upstream) : LARGE (52567 downstream)																							GTGAAAGGGGAAAAAAATAGA	0.403													4	2	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	34217443	34217444	+	Intron	INS	-	C	C			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34217443_34217444insC	uc003and.3	-						LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				tctcattctttccccaccatgc	0.089													4	2	---	---	---	---	
APOBEC3F	200316	broad.mit.edu	37	22	39440506	39440506	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39440506delT	uc003aww.2	+						APOBEC3F_uc011aog.1_Intron	NM_145298	NP_660341	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic						base conversion or substitution editing|DNA cytosine deamination|innate immune response|interspecies interaction between organisms|negative regulation of retroviral genome replication|negative regulation of transposition|positive regulation of defense response to virus by host|response to virus|viral reproduction	apolipoprotein B mRNA editing enzyme complex|cytosol|mitochondrion	cytidine deaminase activity|dCTP deaminase activity|protein homodimerization activity|RNA binding|zinc ion binding				0	Melanoma(58;0.04)					cacgtgggggTAAAGGTTGTT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	44878571	44878571	+	IGR	DEL	G	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44878571delG								KIAA1644 (169840 upstream) : LDOC1L (9879 downstream)																							ggctgaatatgggatactgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	1367247	1367248	+	IGR	INS	-	AAGAG	AAGAG			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1367247_1367248insAAGAG								CRLF2 (35717 upstream) : CSF2RA (20445 downstream)																							GAAGAAAAGAAAAGAGAAGAGG	0.193													12	6	---	---	---	---	
FAM9B	171483	broad.mit.edu	37	X	9042997	9042997	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9042997delA	uc011mhv.1	-									Q8IZU0	FAM9B_HUMAN	Homo sapiens family with sequence similarity 9, member B (FAM9B) mRNA, complete cds.							nucleus					0		Hepatocellular(5;0.219)				TCAAAAGGCCAAACATGGAAG	0.507													4	2	---	---	---	---	
SYAP1	94056	broad.mit.edu	37	X	16772851	16772851	+	Intron	DEL	A	-	-	rs34569073		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16772851delA	uc004cxp.2	+						SYAP1_uc004cxo.2_Intron|SYAP1_uc011miv.1_Intron	NM_032796	NP_116185	Q96A49	SYAP1_HUMAN	SYAP1 protein											skin(1)	1	Hepatocellular(33;0.0997)					actccgtgtcaaaaaaaaaaa	0.189													4	2	---	---	---	---	
GK	2710	broad.mit.edu	37	X	30714806	30714809	+	Intron	DEL	AAAC	-	-	rs12844258		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30714806_30714809delAAAC	uc004dch.3	+						GK_uc010ngj.2_Intron|GK_uc004dci.3_Intron|GK_uc011mjz.1_Intron|GK_uc011mka.1_Intron|GK_uc010ngk.2_Intron	NM_203391	NP_976325	P32189	GLPK_HUMAN	glycerol kinase isoform a						glycerol-3-phosphate metabolic process|triglyceride biosynthetic process	cytosol|mitochondrial outer membrane	ATP binding|glycerol kinase activity			central_nervous_system(1)	1						TAATGGTAAAaaacaaacaaacaa	0.206													90	157	---	---	---	---	
SYTL5	94122	broad.mit.edu	37	X	37935825	37935825	+	Frame_Shift_Del	DEL	T	-	-	rs144659697		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37935825delT	uc004ddu.2	+	7	1094	c.560delT	c.(559-561)CTTfs	p.L187fs	SYTL5_uc004ddv.2_Frame_Shift_Del_p.L187fs|SYTL5_uc004ddx.2_Frame_Shift_Del_p.L187fs	NM_001163335	NP_001156807	Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5 isoform 1	187					intracellular protein transport	membrane	metal ion binding|Rab GTPase binding			skin(1)	1						TTCAGATTTCTTCTTAGCAAG	0.313													20	88	---	---	---	---	
ZNF673	55634	broad.mit.edu	37	X	46310141	46310141	+	Intron	DEL	T	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46310141delT	uc004dgn.3	+						ZNF673_uc004dgp.3_Intron|ZNF673_uc010nhl.2_Intron|ZNF673_uc004dgm.3_Intron	NM_001129898	NP_001123370	Q5JUW0	ZN673_HUMAN	zinc finger family member 673 isoform 1						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding				0						tttctttctcttttttttttt	0.119													5	3	---	---	---	---	
LOC550643	550643	broad.mit.edu	37	X	56811707	56811707	+	Intron	DEL	A	-	-			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56811707delA	uc004dut.3	+							NR_015367				Homo sapiens hypothetical protein LOC550643, mRNA (cDNA clone IMAGE:5285100).												0						TCCTAGGGACAAAGGGAGAAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	3720505	3720506	+	IGR	INS	-	T	T			TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:3720505_3720506insT								TGIF2LY (272425 upstream) : None (None downstream)																							CCATTTTTCTCTTTTTTTCCCA	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59024711	59024714	+	IGR	DEL	TAAT	-	-	rs140947617		TCGA-CJ-5679-01A-11D-1534-10	TCGA-CJ-5679-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59024711_59024714delTAAT								None (None upstream) : None (None downstream)																							TGTGCCTAACTAATTaggcacaag	0.039													2	5	---	---	---	---	
