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
FAM54B	56181	broad.mit.edu	37	1	26152903	26152903	+	Splice_Site	SNP	G	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26152903G>T	uc001bkq.3	+	4	449	c.239_splice	c.e4+1	p.R80_splice	FAM54B_uc001bkr.3_Splice_Site_p.R80_splice|FAM54B_uc010oet.1_Splice_Site_p.R113_splice|FAM54B_uc009vrz.2_Splice_Site_p.R77_splice|LOC646471_uc010oeu.1_5'Flank|FAM54B_uc001bks.3_Splice_Site_p.R80_splice|FAM54B_uc001bkt.3_Splice_Site_p.R80_splice|FAM54B_uc001bku.3_Splice_Site_p.R77_splice|FAM54B_uc001bkv.3_5'UTR	NM_001099625	NP_001093095	Q9H019	FA54B_HUMAN	hypothetical protein LOC56181 isoform a											pancreas(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.96e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.00095)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0649)		CCCGGGTCAGGTAGTTGAGGC	0.552													24	52	---	---	---	---	PASS
MCOLN3	55283	broad.mit.edu	37	1	85511028	85511028	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85511028C>A	uc001dkp.2	-	2	109	c.16G>T	c.(16-18)GTA>TTA	p.V6L	MCOLN3_uc001dkq.2_Missense_Mutation_p.V6L|MCOLN3_uc001dkr.2_Missense_Mutation_p.V6L|MCOLN3_uc001dks.3_5'UTR	NM_018298	NP_060768	Q8TDD5	MCLN3_HUMAN	mucolipin 3	6						integral to membrane	ion channel activity			skin(1)	1				all cancers(265;0.00957)|Epithelial(280;0.0254)		CTCACAACTACCTCAGGATCT	0.393													14	29	---	---	---	---	PASS
LOC149620	149620	broad.mit.edu	37	1	111824291	111824291	+	RNA	SNP	T	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111824291T>G	uc009wgb.2	+	2		c.149T>G				NR_003928				Homo sapiens CHIA-like pseudogene, mRNA (cDNA clone IMAGE:5176731).												0						TCTACGCCTTTGCTGGAATGC	0.507													4	24	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144220807	144220807	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144220807A>C	uc010oxr.1	+	19	2184	c.2180A>C	c.(2179-2181)GAT>GCT	p.D727A	NBPF9_uc010oxn.1_Missense_Mutation_p.D598A|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Missense_Mutation_p.D515A|NBPF9_uc001ekg.1_Missense_Mutation_p.D27A|NBPF9_uc001ekk.1_Missense_Mutation_p.D271A|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Missense_Mutation_p.D27A|uc010oxz.1_Missense_Mutation_p.D515A	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	700	NBPF 5.					cytoplasm					0						GAGCTGCTGGATGAGAAAGAG	0.483													5	6	---	---	---	---	PASS
RFX5	5993	broad.mit.edu	37	1	151315361	151315361	+	Silent	SNP	G	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151315361G>T	uc001exv.1	-	11	1366	c.1152C>A	c.(1150-1152)ATC>ATA	p.I384I	RFX5_uc001exw.1_Silent_p.I384I|RFX5_uc009wmr.1_Silent_p.I384I|RFX5_uc010pcx.1_Silent_p.I344I	NM_001025603	NP_001020774	P48382	RFX5_HUMAN	regulatory factor X, 5	384						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CAGTTGGTAAGATCATGTTAA	0.612													6	8	---	---	---	---	PASS
SHC1	6464	broad.mit.edu	37	1	154938670	154938670	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154938670C>T	uc001ffv.2	-	9	1441	c.1220G>A	c.(1219-1221)CGC>CAC	p.R407H	SHC1_uc001ffu.2_5'Flank|SHC1_uc001ffz.1_Missense_Mutation_p.R178H|SHC1_uc001ffw.2_Missense_Mutation_p.R407H|SHC1_uc001ffx.2_Missense_Mutation_p.R297H|SHC1_uc001ffy.2_Missense_Mutation_p.R297H	NM_183001	NP_892113	P29353	SHC1_HUMAN	SHC-transforming protein 1 isoform 1	407	CH1.				activation of MAPK activity|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|positive regulation of DNA replication|Ras protein signal transduction|regulation of epidermal growth factor receptor activity|regulation of growth	cytosol|mitochondrial matrix|Shc-EGFR complex	epidermal growth factor receptor binding|insulin receptor binding|insulin-like growth factor receptor binding|phospholipid binding|protein binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(1)|skin(1)	2	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CATCTGTTTGCGGACTTCTGG	0.582													3	34	---	---	---	---	PASS
KIRREL	55243	broad.mit.edu	37	1	158059420	158059420	+	Splice_Site	SNP	T	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158059420T>G	uc001frn.3	+	9	1575	c.1171_splice	c.e9+2	p.G391_splice	KIRREL_uc010pib.1_Splice_Site_p.G291_splice|KIRREL_uc009wsq.2_Splice_Site_p.G227_splice|KIRREL_uc001fro.3_Splice_Site_p.G205_splice	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor							integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)					ATGTGAACGGTGAGTGAGTGG	0.612													4	13	---	---	---	---	PASS
VSIG8	391123	broad.mit.edu	37	1	159832346	159832346	+	5'UTR	SNP	G	C	C			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159832346G>C	uc001fuh.2	-	1						NM_001013661	NP_001013683	Q5VU13	VSIG8_HUMAN	V-set and immunoglobulin domain containing 8							integral to membrane				central_nervous_system(1)	1	all_hematologic(112;0.0597)					GTCTGGGCTGGGTATCCCGTG	0.637													9	17	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176640128	176640128	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176640128C>A	uc001gkz.2	+	4	3178	c.2014C>A	c.(2014-2016)CTG>ATG	p.L672M	PAPPA2_uc001gky.1_Missense_Mutation_p.L672M|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	672	Metalloprotease.				cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						TGTGAAGGAGCTGAAGGAGGC	0.498													9	16	---	---	---	---	PASS
CPSF3	51692	broad.mit.edu	37	2	9563880	9563880	+	5'UTR	SNP	C	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9563880C>A	uc002qzo.1	+	1					CPSF3_uc010ewx.1_5'UTR|CPSF3_uc002qzp.1_5'Flank|ITGB1BP1_uc002qzj.2_5'Flank|ITGB1BP1_uc002qzk.2_5'Flank|ITGB1BP1_uc002qzl.2_5'Flank|ITGB1BP1_uc002qzm.2_5'Flank|ITGB1BP1_uc010yiy.1_5'Flank|ITGB1BP1_uc002qzn.1_5'Flank	NM_016207	NP_057291	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3,						histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		TCCTCACCCCCGCTTCGCCCT	0.557													4	25	---	---	---	---	PASS
ABCG8	64241	broad.mit.edu	37	2	44079623	44079623	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44079623C>T	uc002rtq.2	+	5	782	c.692C>T	c.(691-693)CCA>CTA	p.P231L	ABCG8_uc010yoa.1_Missense_Mutation_p.P231L	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8	231	ABC transporter.|Cytoplasmic (Potential).		P -> T (in STSL).		cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CTGTGGAACCCAGGTGAGGGC	0.682													6	5	---	---	---	---	PASS
C2orf81	388963	broad.mit.edu	37	2	74642858	74642858	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74642858C>G	uc010yrq.1	-	3	764	c.455G>C	c.(454-456)GGC>GCC	p.G152A	uc002sla.2_RNA	NM_001145054	NP_001138526			hypothetical protein LOC388963												0						GTTCTCCAGGCCCTCCGAGGT	0.637													5	11	---	---	---	---	PASS
ITPRIPL1	150771	broad.mit.edu	37	2	96993737	96993737	+	Silent	SNP	C	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96993737C>G	uc002svx.2	+	3	1703	c.1368C>G	c.(1366-1368)CTC>CTG	p.L456L	ITPRIPL1_uc010yuk.1_Silent_p.L448L|ITPRIPL1_uc002svy.2_Silent_p.L464L|ITPRIPL1_uc010yul.1_Silent_p.L448L	NM_001008949	NP_001008949	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-triphosphate receptor interacting	456	Cytoplasmic (Potential).					integral to membrane				central_nervous_system(2)|ovary(1)	3						TCATGCACCTCTTGCTACGGC	0.562													6	27	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152547140	152547140	+	Intron	SNP	G	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152547140G>T	uc010fnx.2	-						NEB_uc010fny.1_3'UTR	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		ATAATATTGGGATGGTAGATG	0.343													10	18	---	---	---	---	PASS
DHX29	54505	broad.mit.edu	37	5	54552206	54552206	+	3'UTR	SNP	G	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54552206G>A	uc003jpx.2	-	27					DHX29_uc010ivw.2_RNA	NM_019030	NP_061903	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29								ATP binding|ATP-dependent helicase activity|translation initiation factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				TTAATGGCTAGTACCAACATT	0.289													9	55	---	---	---	---	PASS
CSF1R	1436	broad.mit.edu	37	5	149449521	149449521	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149449521C>G	uc003lrl.2	-	9	1620	c.1425G>C	c.(1423-1425)GAG>GAC	p.E475D	CSF1R_uc011dcd.1_Missense_Mutation_p.E327D|CSF1R_uc010jhc.2_RNA|CSF1R_uc003lrm.2_Missense_Mutation_p.E475D	NM_005211	NP_005202	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor precursor	475	Ig-like C2-type 5.|Extracellular (Potential).				cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|receptor complex	ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity			haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1)	54			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GCTCTAAGGTCTCAACAGTCA	0.582													10	33	---	---	---	---	PASS
RANBP17	64901	broad.mit.edu	37	5	170380686	170380686	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170380686G>T	uc003mba.2	+	13	1570	c.1554G>T	c.(1552-1554)ATG>ATT	p.M518I	RANBP17_uc003max.1_RNA|RANBP17_uc003may.1_RNA|RANBP17_uc003maz.1_RNA|RANBP17_uc010jjr.1_RNA	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	518					mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ATGATGCTATGGATGGAGAAT	0.333			T	TRD@	ALL								66	134	---	---	---	---	PASS
ATF6B	1388	broad.mit.edu	37	6	32083396	32083396	+	3'UTR	SNP	C	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32083396C>T	uc003nzn.2	-	18					TNXB_uc010jts.1_Intron|ATF6B_uc003nzm.1_Intron|ATF6B_uc003nzo.2_3'UTR	NM_004381	NP_004372	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta isoform						response to unfolded protein|signal transduction	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GCTTAACCCCCACACCTGCTC	0.537													6	19	---	---	---	---	PASS
EYS	346007	broad.mit.edu	37	6	66053998	66053998	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66053998G>A	uc011dxu.1	-	10	2070	c.1532C>T	c.(1531-1533)GCA>GTA	p.A511V	EYS_uc003peq.2_Missense_Mutation_p.A511V|EYS_uc003per.1_Missense_Mutation_p.A511V	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	511					response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						CACATAGGTTGCATCTTCAGT	0.353													4	107	---	---	---	---	PASS
NPY	4852	broad.mit.edu	37	7	24324865	24324865	+	Silent	SNP	A	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24324865A>G	uc003sww.1	+	2	92	c.6A>G	c.(4-6)CTA>CTG	p.L2L		NM_000905	NP_000896	P01303	NPY_HUMAN	neuropeptide Y precursor	2					adult feeding behavior|calcium ion transport|cell proliferation|cellular component movement|central nervous system neuron development|cerebral cortex development|digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|neuron projection development|neuropeptide signaling pathway|positive regulation of appetite|synaptic transmission	cell|extracellular space	calcium channel regulator activity|G-protein coupled receptor activity|neuropeptide hormone activity				0						TGCAGATGCTAGGTAACAAGC	0.677													3	8	---	---	---	---	PASS
GIMAP2	26157	broad.mit.edu	37	7	150389838	150389838	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150389838C>A	uc003who.2	+	3	552	c.464C>A	c.(463-465)TCC>TAC	p.S155Y	GIMAP1_uc003whp.2_Intron	NM_015660	NP_056475	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	155						integral to membrane	GTP binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AATGGTGGCTCCCTGATGGAT	0.522													7	25	---	---	---	---	PASS
MTSS1	9788	broad.mit.edu	37	8	125568483	125568483	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125568483G>A	uc003yrk.2	-	12	1928	c.1394C>T	c.(1393-1395)GCT>GTT	p.A465V	NDUFB9_uc011lim.1_Intron|MTSS1_uc003yrh.2_Missense_Mutation_p.A5V|MTSS1_uc011lin.1_Missense_Mutation_p.A239V|MTSS1_uc011lio.1_Missense_Mutation_p.A355V|MTSS1_uc003yri.2_Missense_Mutation_p.A183V|MTSS1_uc003yrj.2_Missense_Mutation_p.A440V|MTSS1_uc003yrl.2_Missense_Mutation_p.A469V	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1	465					actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CCTGGTGGCAGCCGATACAGT	0.647													9	11	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68414733	68414733	+	RNA	SNP	C	T	T	rs151269495		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68414733C>T	uc004aex.2	+	1		c.1288C>T								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		tcaagaccagcctggccaaaa	0.005													3	8	---	---	---	---	PASS
CBWD3	445571	broad.mit.edu	37	9	70871861	70871861	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70871861T>G	uc004agi.3	+	5	564	c.455T>G	c.(454-456)GTT>GGT	p.V152G	CBWD3_uc011lro.1_Intron|CBWD3_uc004agj.3_Intron|CBWD3_uc011lrp.1_Intron|CBWD3_uc004agl.3_Missense_Mutation_p.V4G	NM_201453	NP_958861	Q5JTY5	CBWD3_HUMAN	COBW domain containing 3	152							ATP binding				0				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		ATGTTTTGGGTTGATGCTGAA	0.239													31	70	---	---	---	---	PASS
SUPV3L1	6832	broad.mit.edu	37	10	70954975	70954975	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70954975G>A	uc001jpe.1	+	7	940	c.885G>A	c.(883-885)ATG>ATA	p.M295I	SUPV3L1_uc010qjd.1_Missense_Mutation_p.M164I	NM_003171	NP_003162	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 precursor	295	Helicase ATP-binding.				DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2						AAATTCAAATGATTAGAGATC	0.383													26	78	---	---	---	---	PASS
KIF20B	9585	broad.mit.edu	37	10	91497461	91497461	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91497461C>A	uc001kgs.1	+	20	2935	c.2863C>A	c.(2863-2865)CAA>AAA	p.Q955K	KIF20B_uc001kgr.1_Missense_Mutation_p.Q915K|KIF20B_uc001kgt.1_Missense_Mutation_p.Q166K|KIF20B_uc009xtw.1_RNA	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	955					cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						AAGTAAAAATCAAGAACAGGA	0.284													23	62	---	---	---	---	PASS
PAX6	5080	broad.mit.edu	37	11	31816305	31816305	+	Silent	SNP	C	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31816305C>T	uc001mtd.3	-	7	1445	c.555G>A	c.(553-555)GAG>GAA	p.E185E	PAX6_uc001mte.3_Silent_p.E185E|PAX6_uc001mtg.3_Silent_p.E199E|PAX6_uc001mtf.3_Silent_p.E185E|PAX6_uc001mth.3_Silent_p.E185E|PAX6_uc009yjr.2_Silent_p.E185E	NM_001127612	NP_001121084	P26367	PAX6_HUMAN	paired box gene 6 isoform a	185	Gln/Gly-rich.				blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	9	Lung SC(675;0.225)					AGTTGGTATTCTCTCCCCCTC	0.473									Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				18	53	---	---	---	---	PASS
PTPRJ	5795	broad.mit.edu	37	11	48153229	48153229	+	Intron	SNP	G	C	C			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48153229G>C	uc001ngp.3	+						PTPRJ_uc001ngo.3_3'UTR	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8						tttggtgctagaattgagtag	0.020													3	8	---	---	---	---	PASS
OR4C6	219432	broad.mit.edu	37	11	55433031	55433031	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55433031A>G	uc001nht.3	+	3	654	c.389A>G	c.(388-390)TAC>TGC	p.Y130C	OR4C6_uc010rik.1_Missense_Mutation_p.Y130C	NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C,	130	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						CCCCTGCACTACACGATCATC	0.522													20	32	---	---	---	---	PASS
ODZ4	26011	broad.mit.edu	37	11	78516425	78516425	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78516425T>G	uc001ozl.3	-	15	2554	c.2091A>C	c.(2089-2091)TTA>TTC	p.L697F		NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	697	Extracellular (Potential).|EGF-like 5.				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						AACACTGGTCTAAGCATGTGG	0.612													19	30	---	---	---	---	PASS
GLB1L3	112937	broad.mit.edu	37	11	134188869	134188869	+	3'UTR	SNP	G	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134188869G>T	uc009zdf.2	+	20					GLB1L3_uc001qho.3_RNA	NM_001080407	NP_001073876	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		ttttttttgagatggagtctc	0.174													4	7	---	---	---	---	PASS
ERGIC2	51290	broad.mit.edu	37	12	29509405	29509405	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29509405T>G	uc001riv.2	-	8	615	c.482A>C	c.(481-483)GAT>GCT	p.D161A	ERGIC2_uc001riw.2_RNA	NM_016570	NP_057654	Q96RQ1	ERGI2_HUMAN	PTX1 protein	161	Lumenal (Potential).				vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi apparatus|integral to membrane|nucleus				ovary(1)	1	Lung NSC(12;2.02e-08)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)|Lung SC(9;0.184)				Arsenic trioxide(DB01169)	TGATGAATCATCTTCTCTGTT	0.308													42	58	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32138193	32138193	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32138193C>T	uc001rks.2	+	4	4718	c.4304C>T	c.(4303-4305)GCG>GTG	p.A1435V	C12orf35_uc001rkt.2_5'Flank	NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	1435										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			GACACGAAAGCGAGTTCATCT	0.353													13	24	---	---	---	---	PASS
PAN2	9924	broad.mit.edu	37	12	56720186	56720186	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56720186G>C	uc001skx.2	-	8	1643	c.1270C>G	c.(1270-1272)CCA>GCA	p.P424A	PAN2_uc001skw.2_5'Flank|PAN2_uc001skz.2_Missense_Mutation_p.P424A|PAN2_uc001sky.2_Missense_Mutation_p.P424A	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	424					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						TCCACGGGTGGTGCTCGCCTA	0.527													5	10	---	---	---	---	PASS
LEMD3	23592	broad.mit.edu	37	12	65564430	65564430	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65564430A>T	uc001ssl.1	+	1	1060	c.1054A>T	c.(1054-1056)AGC>TGC	p.S352C	LEMD3_uc009zqo.1_Missense_Mutation_p.S352C	NM_014319	NP_055134	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	352					negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway	integral to nuclear inner membrane|membrane fraction	DNA binding|nucleotide binding|protein binding			central_nervous_system(3)|ovary(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		AGTGGACTCCAGCCCCGTTCC	0.607													8	24	---	---	---	---	PASS
RIMBP2	23504	broad.mit.edu	37	12	130926444	130926444	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130926444C>T	uc001uil.2	-	8	1566	c.1402G>A	c.(1402-1404)GAG>AAG	p.E468K	RIMBP2_uc001uim.2_Missense_Mutation_p.E376K|RIMBP2_uc001uin.1_Missense_Mutation_p.E127K	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2	468						cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		TCCCTTTGCTCCAGCGGGAGC	0.587													4	8	---	---	---	---	PASS
ATP11A	23250	broad.mit.edu	37	13	113481084	113481084	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113481084C>A	uc001vsi.3	+	12	1188	c.1100C>A	c.(1099-1101)ACG>AAG	p.T367K	ATP11A_uc001vsj.3_Missense_Mutation_p.T367K|ATP11A_uc001vsm.1_Missense_Mutation_p.T243K	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a	367	Helical; (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				ATGTACGTCACGGTCGAGATG	0.547													14	31	---	---	---	---	PASS
ARID4A	5926	broad.mit.edu	37	14	58830901	58830901	+	Silent	SNP	T	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58830901T>A	uc001xdp.2	+	20	2348	c.2094T>A	c.(2092-2094)TCT>TCA	p.S698S	ARID4A_uc001xdo.2_Silent_p.S698S|ARID4A_uc001xdq.2_Silent_p.S698S|ARID4A_uc010apg.1_Silent_p.S376S	NM_002892	NP_002883	P29374	ARI4A_HUMAN	retinoblastoma-binding protein 1 isoform I	698					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	transcriptional repressor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|lung(1)	6						CTTGTTCATCTGATAGTGAAA	0.229													3	6	---	---	---	---	PASS
CXADRP2	646243	broad.mit.edu	37	15	22016431	22016431	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22016431T>G	uc010tzk.1	-	1	448	c.286A>C	c.(286-288)AAA>CAA	p.K96Q		NR_024387				RecName: Full=Coxsackievirus and adenovirus receptor; AltName: Full=Coxsackievirus B-adenovirus receptor; AltName: Full=HCVADR;          Short=hCAR; AltName: Full=CVB3-binding protein; Flags: Precursor;												0						GGAGCTCTTTTCACTTTGCAC	0.393													20	110	---	---	---	---	PASS
HERC2	8924	broad.mit.edu	37	15	28473477	28473477	+	Missense_Mutation	SNP	C	A	A	rs149550128		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28473477C>A	uc001zbj.2	-	35	5457	c.5351G>T	c.(5350-5352)CGC>CTC	p.R1784L		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	1784					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CAGGAGGAAGCGGGCTTGCGG	0.602													12	33	---	---	---	---	PASS
CDAN1	146059	broad.mit.edu	37	15	43026473	43026473	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43026473G>T	uc001zql.2	-	7	1325	c.1208C>A	c.(1207-1209)CCA>CAA	p.P403Q	CDAN1_uc001zqk.2_5'UTR|CDAN1_uc010bcx.1_Intron	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	403						integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		TTGCAGAGCTGGTGAGAAGCA	0.567													3	12	---	---	---	---	PASS
MVP	9961	broad.mit.edu	37	16	29858602	29858602	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29858602G>A	uc002dui.2	+	14	2434	c.2350G>A	c.(2350-2352)GCT>ACT	p.A784T	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MVP_uc002duj.2_Missense_Mutation_p.A784T|MVP_uc010vea.1_Missense_Mutation_p.A378T	NM_005115	NP_005106	Q14764	MVP_HUMAN	major vault protein	784					mRNA transport|protein transport|response to drug|transmembrane transport	cytoplasm|nuclear pore|ribonucleoprotein complex	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4						GGTGAGCAAGGCTCAGCAGCT	0.597													8	15	---	---	---	---	PASS
ARHGAP23	57636	broad.mit.edu	37	17	36622485	36622485	+	Silent	SNP	G	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36622485G>T	uc010wdp.1	+	7	941	c.279G>T	c.(277-279)CCG>CCT	p.P93P	ARHGAP23_uc002hqc.2_5'UTR	NM_020876	NP_065927	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	187	Pro-rich.				signal transduction	intracellular	GTPase activator activity			lung(1)	1						AGCCACCGCCGATCTGCTACC	0.662													6	3	---	---	---	---	PASS
KIAA0802	23255	broad.mit.edu	37	18	8793068	8793068	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8793068G>C	uc002knr.2	+	8	2102	c.1960G>C	c.(1960-1962)GCC>CCC	p.A654P	KIAA0802_uc002knq.2_Intron|KIAA0802_uc002kns.2_Intron	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment											0						CGTGCAGGCGGCCAGACTGCA	0.512													10	27	---	---	---	---	PASS
TYK2	7297	broad.mit.edu	37	19	10473019	10473019	+	Silent	SNP	C	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10473019C>A	uc002moc.3	-	11	1968	c.1590G>T	c.(1588-1590)GGG>GGT	p.G530G	TYK2_uc010dxe.2_Silent_p.G345G|TYK2_uc002mod.2_Silent_p.G530G	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	530					intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			GCAAGGCAGCCCCAAGTTCCC	0.652													4	6	---	---	---	---	PASS
U2AF1L4	199746	broad.mit.edu	37	19	36233771	36233771	+	Intron	SNP	G	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36233771G>T	uc002obg.2	-						TMEM149_uc002obb.2_5'Flank|TMEM149_uc002obc.2_5'Flank|TMEM149_uc002obd.3_5'Flank|TMEM149_uc010xsy.1_5'Flank|TMEM149_uc010eej.2_Intron|U2AF1L4_uc002obh.1_3'UTR|U2AF1L4_uc002obe.2_Intron|U2AF1L4_uc002obf.2_Intron|PSENEN_uc002obi.1_5'Flank|PSENEN_uc002obj.1_5'Flank|PSENEN_uc002obk.1_5'Flank			Q8WU68	U2AF4_HUMAN	Homo sapiens cDNA FLJ35525 fis, clone SPLEN2001650.						mRNA processing|RNA splicing	nuclear speck|spliceosomal complex	nucleotide binding|RNA binding|zinc ion binding				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTGCAGGCCTGCCTCTCTGCT	0.557													2	0	---	---	---	---	PASS
BCAM	4059	broad.mit.edu	37	19	45317871	45317871	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45317871A>G	uc002ozu.2	+	8	976	c.932A>G	c.(931-933)GAG>GGG	p.E311G	BCAM_uc002ozt.1_Missense_Mutation_p.E311G	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1	311	Extracellular (Potential).|Interaction with laminin alpha5.|Ig-like C2-type 1.				cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GATGAGCAGGAGGAAGTGCTG	0.612													4	37	---	---	---	---	PASS
MED25	81857	broad.mit.edu	37	19	50338353	50338353	+	Silent	SNP	C	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50338353C>T	uc002ppw.1	+	14	1646	c.1593C>T	c.(1591-1593)AGC>AGT	p.S531S	MED25_uc010ybe.1_Silent_p.S318S|MED25_uc002ppx.1_Silent_p.S312S	NM_030973	NP_112235	Q71SY5	MED25_HUMAN	mediator complex subunit 25	531	Interaction with VP16.|Interaction with CREBBP.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm				ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		ACGACCAGAGCGGCTTCGTCA	0.607													6	14	---	---	---	---	PASS
CLTCL1	8218	broad.mit.edu	37	22	19175075	19175075	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19175075A>T	uc002zpb.2	-	30	4675	c.4600T>A	c.(4600-4602)TAC>AAC	p.Y1534N	CLTCL1_uc011agv.1_Intron|CLTCL1_uc011agw.1_Missense_Mutation_p.Y1513N|CLTCL1_uc011agt.1_Missense_Mutation_p.Y325N|CLTCL1_uc011agu.1_Intron	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1 isoform 1	1534	Proximal segment.|Heavy chain arm.				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)					CCAACCTTGTAGAGATGATCC	0.557			T	?	ALCL								13	22	---	---	---	---	PASS
GGT5	2687	broad.mit.edu	37	22	24627459	24627459	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24627459G>A	uc002zzo.3	-	6	1211	c.794C>T	c.(793-795)CCC>CTC	p.P265L	GGT5_uc002zzp.3_Missense_Mutation_p.P265L|GGT5_uc002zzr.3_Missense_Mutation_p.P233L|GGT5_uc002zzq.3_Missense_Mutation_p.P233L|GGT5_uc011ajm.1_Missense_Mutation_p.P188L|GGT5_uc011ajn.1_RNA	NM_004121	NP_004112	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5 isoform b	265	Extracellular (Potential).				glutathione biosynthetic process|hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	integral to membrane|plasma membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(2)|skin(1)	3						CACCACCTCGGGCTGGAACTT	0.622													5	10	---	---	---	---	PASS
MOSPD2	158747	broad.mit.edu	37	X	14891810	14891810	+	Splice_Site	SNP	G	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14891810G>A	uc004cwi.2	+	2	98	c.10_splice	c.e2-1	p.N4_splice	FANCB_uc004cwg.1_5'Flank|FANCB_uc004cwh.1_5'Flank	NM_152581	NP_689794	Q8NHP6	MSPD2_HUMAN	motile sperm domain containing 2							integral to membrane	structural molecule activity			lung(1)	1	Hepatocellular(33;0.183)					CTCCCATCCAGAATCACGCCC	0.557													27	73	---	---	---	---	PASS
PDHA1	5160	broad.mit.edu	37	X	19373319	19373319	+	Intron	SNP	T	C	C			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19373319T>C	uc004czg.3	+						PDHA1_uc004czh.3_Intron|PDHA1_uc011mjc.1_Intron|PDHA1_uc011mjd.1_Intron|PDHA1_uc010nfk.2_Intron|PDHA1_uc010nfl.2_5'UTR	NM_000284	NP_000275	P08559	ODPA_HUMAN	pyruvate dehydrogenase E1 alpha 1 precursor						glycolysis|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	protein binding|pyruvate dehydrogenase (acetyl-transferring) activity			ovary(1)	1	Hepatocellular(33;0.183)				NADH(DB00157)	CCACCCCGCTTTCCCTCACCA	0.498													3	14	---	---	---	---	PASS
MAGEB3	4114	broad.mit.edu	37	X	30254277	30254277	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30254277A>T	uc004dca.1	+	5	973	c.236A>T	c.(235-237)TAC>TTC	p.Y79F		NM_002365	NP_002356	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	79											0						GATGTTTCTTACAAAAAGTCA	0.463													9	16	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	8103784	8103784	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8103784delG								ERRFI1 (17391 upstream) : SLC45A1 (280606 downstream)																							taggctttgtgggccatatgg	0.065													4	2	---	---	---	---	
ALPL	249	broad.mit.edu	37	1	21868227	21868227	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21868227delG	uc001bet.2	+						ALPL_uc010odn.1_Intron|ALPL_uc010odo.1_Intron|ALPL_uc010odp.1_Intron	NM_000478	NP_000469	P05186	PPBT_HUMAN	tissue-nonspecific alkaline phosphatase						response to vitamin D|skeletal system development	anchored to membrane|cytoplasm|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)	GGCAGGGGGAGGGATTCATTG	0.587													4	2	---	---	---	---	
SEPN1	57190	broad.mit.edu	37	1	26139056	26139057	+	Intron	DEL	AC	-	-	rs66781270		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26139056_26139057delAC	uc010oer.1	+						SEPN1_uc010oes.1_Intron	NM_020451	NP_065184	Q9NZV5	SELN_HUMAN	selenoprotein N, 1 isoform 1 precursor							endoplasmic reticulum membrane|extracellular region	protein binding			ovary(2)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0421)|OV - Ovarian serous cystadenocarcinoma(117;1.26e-25)|Colorectal(126;3.01e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0143)|READ - Rectum adenocarcinoma(331;0.0649)		ctacacacaaacacacacacac	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	28023222	28023223	+	IGR	INS	-	T	T	rs141607341	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28023222_28023223insT								IFI6 (24498 upstream) : FAM76A (29267 downstream)																							gcctccttttgtttttttttat	0.000													4	2	---	---	---	---	
BMP8B	656	broad.mit.edu	37	1	40229212	40229212	+	Intron	DEL	A	-	-	rs113575841		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40229212delA	uc001cdz.1	-						PPIE_uc001cdv.2_Intron|PPIE_uc001cdw.2_Intron	NM_001720	NP_001711	P34820	BMP8B_HUMAN	bone morphogenetic protein 8B preproprotein						cartilage development|cell differentiation|growth|ossification	extracellular space	cytokine activity|growth factor activity				0	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-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;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AAAACTGAACAAAAAAAAAAC	0.338													4	2	---	---	---	---	
ZSWIM5	57643	broad.mit.edu	37	1	45617913	45617913	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45617913delA	uc001cnd.2	-							NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM domain containing 5								zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)					agatctgaccaaaaaaaaagt	0.090													4	2	---	---	---	---	
MYSM1	114803	broad.mit.edu	37	1	59158900	59158901	+	Intron	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59158900_59158901insA	uc009wab.1	-						MYSM1_uc001czc.2_5'Flank|MYSM1_uc001czd.2_Intron	NM_001085487	NP_001078956	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1						histone deubiquitination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin remodeling complex	DNA binding|histone binding|metal ion binding|metallopeptidase activity|transcription coactivator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(1)	1	all_cancers(7;9.36e-06)					ATTCAAAAAAGGAATCATTTGT	0.272													4	2	---	---	---	---	
NEGR1	257194	broad.mit.edu	37	1	72126622	72126622	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72126622delG	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)		ttatgaatgagaacatgcagt	0.000													4	2	---	---	---	---	
TTLL7	79739	broad.mit.edu	37	1	84356392	84356392	+	Intron	DEL	G	-	-	rs66679189		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84356392delG	uc001djc.2	-						TTLL7_uc001djb.2_Intron|TTLL7_uc001djd.2_Intron|TTLL7_uc001dje.2_Intron|TTLL7_uc001djf.2_Intron|TTLL7_uc001djg.2_Intron	NM_024686	NP_078962	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7						cell differentiation|nervous system development|protein modification process	cilium|dendrite|microtubule basal body|perikaryon	tubulin-tyrosine ligase activity			ovary(1)	1				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		aagtagtcaaggatgcagtaa	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	89515850	89515850	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89515850delA								GBP3 (27301 upstream) : GBP1 (2137 downstream)																							gagacacctcagggcttaatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96933365	96933365	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96933365delT								None (None upstream) : PTBP2 (253810 downstream)																							CTCATATGCATTTTTCAGTCC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	102175218	102175218	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102175218delG								S1PR1 (468142 upstream) : OLFM3 (92909 downstream)																							GGACCACTATGGCAGAATCCT	0.353													4	2	---	---	---	---	
VAV3	10451	broad.mit.edu	37	1	108493267	108493267	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108493267delC	uc001dvk.1	-						VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		GCAAGGGCAGCAAAGCCTGAG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	111929883	111929883	+	IGR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111929883delC								C1orf88 (34244 upstream) : OVGP1 (27055 downstream)																							ACTGGAAGGACTTTGGCCTTT	0.488													4	2	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120580260	120580261	+	Intron	DEL	TC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120580260_120580261delTC	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGGAGAAACATCTGTCTTCCTC	0.312			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145006106	145006106	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145006106delA	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CAAAACAAACAAAAAAGAAGA	0.239			T	PDGFRB	MPD								4	2	---	---	---	---	
VPS45	11311	broad.mit.edu	37	1	150116661	150116661	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150116661delA	uc001etp.2	+						VPS45_uc010pbq.1_Intron|VPS45_uc010pbs.1_Intron|VPS45_uc001etq.2_Intron	NM_007259	NP_009190	Q9NRW7	VPS45_HUMAN	vacuolar protein sorting 45A						blood coagulation|intracellular protein transport|vesicle docking involved in exocytosis	endosome membrane|Golgi membrane|integral to membrane of membrane fraction				central_nervous_system(1)|skin(1)	2	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			ATTTAATTCTAAAAAAAAAAA	0.348													5	3	---	---	---	---	
EFNA3	1944	broad.mit.edu	37	1	155044536	155044536	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155044536delT	uc010pew.1	+							NM_004952	NP_004943	P52797	EFNA3_HUMAN	ephrin A3 precursor						cell-cell signaling	anchored to membrane|integral to plasma membrane	ephrin receptor binding|transmembrane-ephrin receptor activity				0	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		all cancers(21;5.67e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000284)|LUSC - Lung squamous cell carcinoma(543;0.193)			GCAGCTTGGGTGGGTGCTTGG	0.577													4	2	---	---	---	---	
ETV3L	440695	broad.mit.edu	37	1	157071368	157071368	+	5'Flank	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157071368delA	uc001fqq.1	-							NM_001004341	NP_001004341	Q6ZN32	ETV3L_HUMAN	ets variant 3-like							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Hepatocellular(266;0.158)	Prostate(1639;0.184)				ctTAAGACTTAAAAAAAAAAA	0.025													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157531879	157531879	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157531879delT								FCRL5 (9569 upstream) : FCRL4 (11661 downstream)																							GGAATGTGGGTTTTCAAAAGT	0.299													4	2	---	---	---	---	
PYHIN1	149628	broad.mit.edu	37	1	158937961	158937962	+	Intron	INS	-	AA	AA			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158937961_158937962insAA	uc001ftb.2	+						PYHIN1_uc001ftc.2_Intron|PYHIN1_uc001ftd.2_Intron|PYHIN1_uc001fte.2_Intron	NM_152501	NP_689714	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1 alpha 1						cell cycle	nuclear speck				ovary(3)|pancreas(1)	4	all_hematologic(112;0.0378)					tacagaatgagaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163636070	163636071	+	IGR	DEL	GG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163636070_163636071delGG								NUF2 (310517 upstream) : PBX1 (892731 downstream)																							gttttatcttgGGCATAATACT	0.351													4	2	---	---	---	---	
ASTN1	460	broad.mit.edu	37	1	176850588	176850588	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176850588delT	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15						AGTAACAGTGTGATTTAGTCA	0.438											OREG0014002	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
TDRD5	163589	broad.mit.edu	37	1	179588010	179588010	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179588010delA	uc001gnf.1	+						TDRD5_uc010pnp.1_Intron|TDRD5_uc001gnh.1_Intron	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5						DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						AAAACTATTTAGTAAATAAGT	0.294													7	6	---	---	---	---	
CEP350	9857	broad.mit.edu	37	1	180005768	180005768	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180005768delT	uc001gnt.2	+						CEP350_uc009wxl.2_Intron|CEP350_uc001gnu.2_Intron	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4						aagtatgtactttttttagac	0.000													4	2	---	---	---	---	
RGL1	23179	broad.mit.edu	37	1	183849500	183849501	+	Intron	INS	-	AAAC	AAAC	rs113953745		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183849500_183849501insAAAC	uc001gqo.2	+						RGL1_uc010pof.1_Intron|RGL1_uc001gqm.2_Intron|RGL1_uc010pog.1_Intron|RGL1_uc010poh.1_Intron|RGL1_uc010poi.1_Intron	NM_015149	NP_055964	Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation						cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	protein binding|Ral guanyl-nucleotide exchange factor activity			breast(5)|ovary(4)|lung(2)	11						TAGCCTCCTTAAAACAAACAAA	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	187479335	187479336	+	IGR	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187479335_187479336delCA								PLA2G4A (521230 upstream) : None (None downstream)																							cctacacattcacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	198824815	198824816	+	IGR	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198824815_198824816insA								PTPRC (98270 upstream) : MIR181B1 (3186 downstream)																							TTTCCATGTTCAAAAAATAAAG	0.351													4	2	---	---	---	---	
WNT3A	89780	broad.mit.edu	37	1	228217442	228217442	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228217442delC	uc001hrq.1	+						WNT3A_uc001hrp.1_Intron	NM_033131	NP_149122	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family,						axis specification|cell proliferation in forebrain|cell-cell signaling|cellular response to retinoic acid|convergent extension|dermatome development|dorsal/ventral neural tube patterning|embryonic pattern specification|extracellular matrix organization|hemopoietic stem cell proliferation|hippocampus development|inner ear morphogenesis|mammary gland development|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of neuron projection development|notochord development|palate development|paraxial mesodermal cell fate commitment|positive regulation of catenin import into nucleus|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of receptor internalization|positive regulation of transcription from RNA polymerase II promoter|signalosome assembly|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuroblast division|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled-2 binding|receptor agonist activity|signal transducer activity|transcription coactivator activity			ovary(1)	1		Prostate(94;0.0405)				cttgtgcccacccccccccca	0.055													4	2	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	232008415	232008415	+	Intron	DEL	A	-	-	rs11305504		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232008415delA	uc001huz.2	+						TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|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)				ATCTGTTCTTAAAAAAAAAAA	0.348													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232917684	232917684	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232917684delA								SIPA1L2 (266441 upstream) : KIAA1383 (22954 downstream)																							CAAATTGCTTAAGAGACacat	0.199													4	2	---	---	---	---	
PCNXL2	80003	broad.mit.edu	37	1	233388827	233388827	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233388827delT	uc001hvl.2	-						PCNXL2_uc009xfu.2_Intron|PCNXL2_uc009xfv.1_Intron|PCNXL2_uc001hvq.1_5'Flank	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				ACCATACATGTGCCCAGCTGG	0.194													4	2	---	---	---	---	
B3GALNT2	148789	broad.mit.edu	37	1	235633937	235633938	+	Intron	INS	-	AT	AT			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235633937_235633938insAT	uc001hxc.2	-						B3GALNT2_uc001hxd.1_Intron	NM_152490	NP_689703	Q8NCR0	B3GL2_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 2						protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)			TTAAAAATGCATCAATCTTAAA	0.178													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	243002883	243002883	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243002883delA								PLD5 (314885 upstream) : CEP170 (284848 downstream)																							TTATCATAGGAAAATGGAAAT	0.214													4	2	---	---	---	---	
AKT3	10000	broad.mit.edu	37	1	243931666	243931666	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243931666delT	uc001iab.1	-						AKT3_uc001hzz.1_Intron	NM_005465	NP_005456	Q9Y243	AKT3_HUMAN	AKT3 kinase isoform 1						signal transduction	Golgi apparatus|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|lung(1)|breast(1)|central_nervous_system(1)	4	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			TTGCTAACAGttttttcacat	0.169													4	2	---	---	---	---	
ZNF695	57116	broad.mit.edu	37	1	247110970	247110971	+	Intron	INS	-	CA	CA	rs145847336	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247110970_247110971insCA	uc001ibx.2	-						ZNF695_uc001ica.2_Intron|ZNF695_uc009xgt.1_Intron|ZNF695_uc001iby.2_Intron			Q8IW36	ZN695_HUMAN	RecName: Full=Zinc finger protein 695; AltName: Full=Zinc finger protein SBZF3;						regulation of transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ACACGTTTATTCACAGTCTCTT	0.411													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	13990661	13990661	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13990661delA								None (None upstream) : FAM84A (782195 downstream)																							catatcaaggaaaggcactga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20050173	20050173	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20050173delG								OSR1 (491801 upstream) : TTC32 (46345 downstream)																							GCCAAAAAAAGGGGGGAAAAA	0.433													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	24736456	24736457	+	IGR	DEL	TG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24736456_24736457delTG								ITSN2 (153059 upstream) : NCOA1 (50722 downstream)																							GTAAGGAAAATGTGTGTGTGTG	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	30253313	30253313	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30253313delA								ALK (108881 upstream) : YPEL5 (116437 downstream)																							TCAGGGGGGGAAAAAAAAAGA	0.473													3	3	---	---	---	---	
TTC27	55622	broad.mit.edu	37	2	32892001	32892001	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32892001delT	uc002rom.2	+						TTC27_uc010ymx.1_Intron	NM_017735	NP_060205	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1						TTAACTGGTGTTTTTTTTTCC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	41259247	41259247	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41259247delA								SLC8A1 (519672 upstream) : None (None downstream)																							TGGAAATAACAAAAAAAATTG	0.303													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46132439	46132439	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46132439delA	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)			GGGAAGCTCCAAAAAAAAAGT	0.438													6	3	---	---	---	---	
RHOQ	23433	broad.mit.edu	37	2	46778463	46778463	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46778463delC	uc002rva.2	+							NM_012249	NP_036381	P17081	RHOQ_HUMAN	ras-like protein TC10 precursor						cortical actin cytoskeleton organization|insulin receptor signaling pathway|negative regulation of establishment of protein localization in plasma membrane|positive regulation of filopodium assembly|positive regulation of glucose import|positive regulation of transcription from RNA polymerase II promoter|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	actin filament|cytosol|plasma membrane	GBD domain binding|GTP binding|GTPase activity|profilin binding			skin(2)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			ctctactccacccgatgtgtg	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65793271	65793271	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65793271delC	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																		TCTTTCCTCACTGGTCCAGGT	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67174177	67174178	+	IGR	INS	-	T	T	rs138599547	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67174177_67174178insT								MEIS1 (374287 upstream) : ETAA1 (450264 downstream)																							ccagaagaggataaaacataag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	76901213	76901213	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76901213delT								C2orf3 (963102 upstream) : LRRTM4 (73645 downstream)																							CTGCACACAATTGCCCCTAAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90438548	90438549	+	Intron	INS	-	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90438548_90438549insT	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		tctgtcacttcttttagaatat	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96569190	96569190	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96569190delC	uc002sva.1	-						uc002suz.1_Intron|uc002svb.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		GCTACATGATCCCACTTACCT	0.388													4	2	---	---	---	---	
IL18R1	8809	broad.mit.edu	37	2	103004540	103004541	+	Intron	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103004540_103004541delCA	uc002tbw.3	+						IL18R1_uc010ywc.1_Intron|IL18R1_uc010ywd.1_Intron|IL18R1_uc010fiy.2_Intron	NM_003855	NP_003846	Q13478	IL18R_HUMAN	interleukin 18 receptor 1 precursor						innate immune response	integral to membrane|plasma membrane	interleukin-1 receptor activity			ovary(2)|pancreas(1)	3						cagagacagccacacacacaga	0.297													4	2	---	---	---	---	
UXS1	80146	broad.mit.edu	37	2	106758859	106758859	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106758859delT	uc002tdm.2	-						UXS1_uc002tdn.2_Intron|UXS1_uc002tdo.2_Intron|UXS1_uc010ywh.1_Intron	NM_025076	NP_079352	Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1						cellular metabolic process	Golgi cisterna membrane|integral to membrane	coenzyme binding|UDP-glucuronate decarboxylase activity			ovary(2)	2						tctcttgagatttttcctttg	0.075													4	2	---	---	---	---	
ST6GAL2	84620	broad.mit.edu	37	2	107449321	107449321	+	Intron	DEL	A	-	-	rs56781498	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107449321delA	uc002tdq.2	-						ST6GAL2_uc002tdr.2_Intron|ST6GAL2_uc002tds.3_Intron	NM_001142351	NP_001135823	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide						growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(4)|skin(1)	11						ACTTTTTTTTAAAAAAAAGCA	0.418													9	4	---	---	---	---	
RALB	5899	broad.mit.edu	37	2	121047044	121047045	+	Intron	INS	-	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121047044_121047045insT	uc002tmk.2	+						RALB_uc010yys.1_Intron|RALB_uc002tml.2_Intron|RALB_uc002tmm.2_Intron|RALB_uc010yyt.1_Intron	NM_002881	NP_002872	P11234	RALB_HUMAN	v-ral simian leukemia viral oncogene homolog B						apoptosis|cell cycle|cytokinesis|nerve growth factor receptor signaling pathway|Ras protein signal transduction|regulation of exocyst assembly|regulation of exocyst localization	cytosol|midbody|plasma membrane	GTP binding|GTPase activity|protein binding			lung(3)	3		Prostate(154;0.122)				AAATCTAGTGATTTTTTTTTTT	0.312													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	123301921	123301922	+	IGR	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123301921_123301922insA								TSN (776495 upstream) : None (None downstream)																							aacactatttgaaaagtgctta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	123876166	123876166	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123876166delA								None (None upstream) : CNTNAP5 (906698 downstream)																							tcaaatcatgatgacaccagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	124024931	124024932	+	IGR	DEL	AC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124024931_124024932delAC								None (None upstream) : CNTNAP5 (757932 downstream)																							aaggatggaaacaagaaataaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	124488510	124488510	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124488510delA								None (None upstream) : CNTNAP5 (294354 downstream)																							TTTCCTTTGGAAAAAAAAAAC	0.358													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	136822819	136822819	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136822819delT								DARS (79597 upstream) : CXCR4 (49101 downstream)																							CCATTAGGCATTTTAGTTCCC	0.403													4	2	---	---	---	---	
GALNT13	114805	broad.mit.edu	37	2	155083749	155083749	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155083749delA	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron|GALNT13_uc010foc.1_Intron	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						tctcactgagaaaagggtgac	0.124													4	2	---	---	---	---	
OSBPL6	114880	broad.mit.edu	37	2	179260742	179260743	+	3'UTR	INS	-	GTGT	GTGT			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179260742_179260743insGTGT	uc002ulx.2	+	25					OSBPL6_uc002uly.2_3'UTR|OSBPL6_uc010zfe.1_3'UTR|OSBPL6_uc002ulz.2_3'UTR|OSBPL6_uc002uma.2_3'UTR	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			GCAGACTTCAAGTGTGTCTGTT	0.480													4	2	---	---	---	---	
PIKFYVE	200576	broad.mit.edu	37	2	209138183	209138183	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209138183delA	uc002vcz.2	+						PIKFYVE_uc010fun.1_Intron|PIKFYVE_uc002vcy.1_Intron|PIKFYVE_uc002vcv.2_Intron|PIKFYVE_uc002vcw.2_Intron|PIKFYVE_uc002vcx.2_Intron	NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type						cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10						atgaaaaaggaaaaaaaaAAT	0.139													4	2	---	---	---	---	
VWC2L	402117	broad.mit.edu	37	2	215425013	215425013	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215425013delT	uc002vet.2	+						VWC2L_uc010zjl.1_Intron	NM_001080500	NP_001073969	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain-containing							extracellular region					0						CCTACTCATCTTTTTTTAGTT	0.383													4	2	---	---	---	---	
FARSB	10056	broad.mit.edu	37	2	223493835	223493836	+	Intron	INS	-	ATG	ATG			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223493835_223493836insATG	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	ACTTGAAAGGTTTATTTTCCAG	0.426													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	227450476	227450476	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227450476delA								KIAA1486 (855005 upstream) : IRS1 (145558 downstream)																							AATCTGTTAGAAAAAAAAAAA	0.353													4	2	---	---	---	---	
WDR69	164781	broad.mit.edu	37	2	228778705	228778706	+	Intron	DEL	TC	-	-	rs71723734		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228778705_228778706delTC	uc002vpn.1	+						WDR69_uc010zlw.1_Intron|WDR69_uc002vpo.1_Intron	NM_178821	NP_849143	Q8N136	WDR69_HUMAN	WD repeat domain 69											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)		TATATCTGTAtctctctctctc	0.168													4	3	---	---	---	---	
CHL1	10752	broad.mit.edu	37	3	424573	424573	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:424573delG	uc003bou.2	+						CHL1_uc003bot.2_Intron|CHL1_uc003bow.1_Intron|CHL1_uc011asi.1_Intron|uc003box.1_Intron	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM						axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1)	12		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		AGTGACATATGAAAAAAAAAC	0.299													4	2	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191543	10191546	+	Frame_Shift_Del	DEL	ACAT	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191543_10191546delACAT	uc003bvc.2	+	3	749_752	c.536_539delACAT	c.(535-540)GACATCfs	p.D179fs	VHL_uc003bvd.2_Frame_Shift_Del_p.D138fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	179_180			I -> V (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.I180N(4)|p.D179fs*23(3)|p.L178_V181del(1)|p.D179A(1)|p.D179N(1)|p.D179fs*>36(1)|p.D179fs*36(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		AGGAGACTGGACATCGTCAGGTCG	0.520		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				39	19	---	---	---	---	
ATP2B2	491	broad.mit.edu	37	3	10432825	10432825	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10432825delC	uc003bvt.2	-						ATP2B2_uc003bvv.2_Intron|ATP2B2_uc003bvw.2_Intron|ATP2B2_uc010hdp.2_Intron|ATP2B2_uc010hdo.2_Intron	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6						ctactgtgtgcagggcacatg	0.174													4	2	---	---	---	---	
BAP1	8314	broad.mit.edu	37	3	52442523	52442523	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52442523delA	uc003ddx.2	-	4	337	c.222delT	c.(220-222)GATfs	p.D74fs	PHF7_uc003ddy.2_5'Flank|PHF7_uc003ddz.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	74					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TCACAATATCATCATCAATCA	0.483			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								21	14	---	---	---	---	
SFMBT1	51460	broad.mit.edu	37	3	53005812	53005812	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53005812delA	uc003dgf.2	-						SFMBT1_uc003dgg.2_Intron|SFMBT1_uc003dgh.2_Intron	NM_001005159	NP_001005159	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1						regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		gcagctaggcaaaagggggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	73197601	73197601	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73197601delT								PPP4R2 (82590 upstream) : PDZRN3 (234051 downstream)																							ATTGTGTTGCTTTGCTTCCTA	0.413													4	2	---	---	---	---	
GABRR3	200959	broad.mit.edu	37	3	97742150	97742151	+	Intron	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97742150_97742151insA	uc011bgr.1	-							NM_001105580	NP_001099050	A8MPY1	GBRR3_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 3						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity				0						GAGTTTAACTGAGAAATCTAAC	0.411											OREG0015688	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
RABL3	285282	broad.mit.edu	37	3	120428430	120428431	+	Intron	INS	-	AGACAAAGCAC	AGACAAAGCAC	rs141684205	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120428430_120428431insAGACAAAGCAC	uc003edx.2	-							NM_173825	NP_776186	Q5HYI8	RABL3_HUMAN	RAB, member of RAS oncogene family-like 3						small GTPase mediated signal transduction		GTP binding				0				GBM - Glioblastoma multiforme(114;0.151)		AGAAACACTTAATGTTTAATGT	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	120535760	120535760	+	IGR	DEL	A	-	-	rs113870704		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120535760delA								GTF2E1 (33845 upstream) : STXBP5L (91290 downstream)																							AGATGTGAAGAAAAAAAAATC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	126974898	126974898	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126974898delG								PLXNA1 (218670 upstream) : TPRA1 (317010 downstream)																							GGCACACCCTGGCAAGACAAG	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127070727	127070728	+	Intron	INS	-	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127070727_127070728insT	uc003ejj.2	-											Homo sapiens, clone IMAGE:4618125, mRNA.																		tttgtgggtcaggaatgcagaa	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	134149377	134149377	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134149377delT								AMOTL2 (55118 upstream) : ANAPC13 (47170 downstream)																							TCAAAGCCTGTTTTTTAaggg	0.229													4	2	---	---	---	---	
C3orf16	389161	broad.mit.edu	37	3	149495607	149495607	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149495607delG	uc003exl.2	-						C3orf16_uc011bnt.1_Intron	NM_001144960	NP_001138432	E9PHT4	E9PHT4_HUMAN	hypothetical protein LOC389161												0						gtgtatacatgtctcatttct	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151681992	151681993	+	IGR	DEL	CT	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151681992_151681993delCT								SUCNR1 (82342 upstream) : LOC401093 (298420 downstream)																							taattaatgactctcaactttt	0.000													4	2	---	---	---	---	
VEPH1	79674	broad.mit.edu	37	3	157222160	157222161	+	5'Flank	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157222160_157222161insA	uc003fbk.1	-						VEPH1_uc010hvu.1_5'Flank|VEPH1_uc003fbm.2_5'Flank|VEPH1_uc003fbn.2_5'Flank	NM_024621	NP_078897	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain homolog 1							plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			ATGCTGCATGTAAAAAAATTAC	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161013741	161013741	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161013741delG								NMD3 (42422 upstream) : C3orf57 (48840 downstream)																							CATTAAGAATGTGTCACAGTT	0.234													5	3	---	---	---	---	
MCF2L2	23101	broad.mit.edu	37	3	183007985	183007986	+	Intron	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183007985_183007986delCA	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc011bqr.1_Intron|uc003fln.1_Intron	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			CACACACAATCATACTATGATT	0.411													3	3	---	---	---	---	
YEATS2	55689	broad.mit.edu	37	3	183490566	183490567	+	Intron	INS	-	A	A	rs11425644	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183490566_183490567insA	uc003fly.2	+							NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2						histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			cacacacacacccacatacaca	0.119													4	2	---	---	---	---	
YEATS2	55689	broad.mit.edu	37	3	183490567	183490568	+	Intron	INS	-	ACA	ACA	rs73175334	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183490567_183490568insACA	uc003fly.2	+							NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2						histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			acacacacacccacatacacac	0.114													4	2	---	---	---	---	
OPA1	4976	broad.mit.edu	37	3	193331352	193331352	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193331352delT	uc003ftm.2	+						OPA1_uc003ftg.2_Intron|OPA1_uc003fth.2_Intron|OPA1_uc003fti.2_Intron|OPA1_uc003ftj.2_Intron|OPA1_uc003ftk.2_Intron|OPA1_uc003ftl.2_Intron|OPA1_uc003ftn.2_Intron	NM_015560	NP_056375	O60313	OPA1_HUMAN	optic atrophy 1 isoform 1						apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		TCCTTCtttgttttttttttg	0.224													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194276340	194276340	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194276340delT								ATP13A3 (87372 upstream) : TMEM44 (32063 downstream)																							tgcttcaagcttttttccccc	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6005635	6005637	+	IGR	DEL	TGT	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6005635_6005637delTGT								C4orf50 (15469 upstream) : JAKMIP1 (22289 downstream)																							gtgatggtgatgttgatgatggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10122105	10122106	+	IGR	DEL	TT	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10122105_10122106delTT								WDR1 (3532 upstream) : ZNF518B (319399 downstream)																							CCAGAGAAACTTTAAAAGCTTG	0.495													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13859113	13859113	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13859113delA	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																		actaactGACAAAAAGGCACA	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	35828234	35828234	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35828234delA								None (None upstream) : ARAP2 (121610 downstream)																							ATACTTACTCAAAAAAGGAGT	0.338													4	2	---	---	---	---	
KIAA1239	57495	broad.mit.edu	37	4	37448889	37448889	+	3'UTR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37448889delA	uc011bxz.1	+	7						NM_001144990	NP_001138462	Q9ULI1	K1239_HUMAN	hypothetical protein LOC57495												0						TACAGAAGGGAAAAAAATGTG	0.408													6	11	---	---	---	---	
RBM47	54502	broad.mit.edu	37	4	40460772	40460772	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40460772delT	uc003gvc.2	-						RBM47_uc003gvd.2_Intron|RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron|RBM47_uc003gvg.1_Intron	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3						GTGATAATTGTTTTTTTTTCC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49504997	49504998	+	IGR	INS	-	C	C	rs113932747		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49504997_49504998insC								CWH43 (440904 upstream) : None (None downstream)																							AATTTTAACGTCTTAAGATATT	0.297													4	2	---	---	---	---	
KDR	3791	broad.mit.edu	37	4	55970676	55970676	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55970676delT	uc003has.2	-						KDR_uc003hat.1_Intron	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor						angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)	CCTCAAGGACTTTCGGTGAAG	0.368			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			7	4	---	---	---	---	
DCK	1633	broad.mit.edu	37	4	71895356	71895357	+	3'UTR	INS	-	CT	CT			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71895356_71895357insCT	uc003hfx.2	+	7					DCK_uc011cbb.1_3'UTR	NM_000788	NP_000779	P27707	DCK_HUMAN	deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	tggttccagtatcagcatagtg	0.109													4	3	---	---	---	---	
AFF1	4299	broad.mit.edu	37	4	88016400	88016400	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88016400delA	uc003hqj.3	+						AFF1_uc011ccy.1_Intron|AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926	P51825	AFF1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		cctcctgagtagttgggacta	0.000													4	2	---	---	---	---	
SPARCL1	8404	broad.mit.edu	37	4	88412411	88412411	+	Intron	DEL	A	-	-	rs55638164		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88412411delA	uc010ikm.2	-						SPARCL1_uc011cdc.1_Intron|SPARCL1_uc003hqs.3_Intron|SPARCL1_uc011cdd.1_Intron	NM_001128310	NP_001121782	Q14515	SPRL1_HUMAN	SPARC-like 1 precursor						signal transduction	extracellular space|proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		TGTTTGTGATAGGGGGAGGAA	0.368													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	97738730	97738730	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97738730delT								PDHA2 (976106 upstream) : C4orf37 (741304 downstream)																							AAAGGATGGATTTTTTTTTTG	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	98221706	98221706	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98221706delT								None (None upstream) : C4orf37 (258328 downstream)																							TTGTCTCTTCTTGCTACAGTT	0.413													4	2	---	---	---	---	
AP1AR	55435	broad.mit.edu	37	4	113178967	113178967	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113178967delA	uc003iaj.3	+						AP1AR_uc010imm.1_Intron|AP1AR_uc003iak.3_Intron	NM_018569	NP_061039	Q63HQ0	AP1AR_HUMAN	adaptor-related protein complex 1 associated						protein transport	early endosome|Golgi apparatus|late endosome|transport vesicle					0						AGGCTTTGTTAAAAAAAAAAA	0.209													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	117266982	117266982	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117266982delA								MIR1973 (46058 upstream) : TRAM1L1 (737734 downstream)																							CTGCATCTTCACCTGCAACTT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	118118313	118118314	+	IGR	INS	-	T	T	rs148988789	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118118313_118118314insT								TRAM1L1 (111577 upstream) : NDST3 (836459 downstream)																							ctcaaaacttgtttttactatt	0.000													2	5	---	---	---	---	
TRPC3	7222	broad.mit.edu	37	4	122823082	122823082	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122823082delA	uc003ieg.2	-						TRPC3_uc010inr.2_Intron|TRPC3_uc003ief.2_Intron|TRPC3_uc011cgl.1_Intron	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,						axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2						CAGGTCAAACAAAAAAAGATT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	130586714	130586714	+	IGR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130586714delC								C4orf33 (552872 upstream) : None (None downstream)																							ACCATGTCATCCCTCTAAACC	0.368													4	2	---	---	---	---	
USP38	84640	broad.mit.edu	37	4	144130979	144130980	+	Intron	INS	-	T	T	rs148666231	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144130979_144130980insT	uc003ijb.2	+						USP38_uc003ija.3_Intron|USP38_uc003ijc.2_Intron	NM_032557	NP_115946	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_hematologic(180;0.158)					AAATATCTAGATTTTTTTTATT	0.292													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	144220783	144220784	+	IGR	DEL	TC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144220783_144220784delTC								USP38 (77643 upstream) : GAB1 (37199 downstream)																							GTGATTCCTTTCAGCTAGTTTG	0.465													4	2	---	---	---	---	
ACCN5	51802	broad.mit.edu	37	4	156771262	156771262	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156771262delT	uc003ipe.1	-							NM_017419	NP_059115	Q9NY37	ACCN5_HUMAN	amiloride-sensitive cation channel 5,							integral to membrane|plasma membrane				ovary(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0464)|Kidney(143;0.058)|COAD - Colon adenocarcinoma(41;0.141)		ctcctaaagattttTTTTTTA	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	164092922	164092922	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164092922delG								NAF1 (4849 upstream) : NPY1R (152195 downstream)																							ggcacagagtggggagtttcc	0.000													4	2	---	---	---	---	
KLHL2	11275	broad.mit.edu	37	4	166210905	166210905	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166210905delT	uc003irb.2	+						KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron|KLHL2_uc010ira.2_Intron	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1						intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		CCAAGTTGGCTTTTTAGCAAG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	179413663	179413664	+	IGR	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179413663_179413664insA								LOC285501 (501760 upstream) : None (None downstream)																							ggataatcctgaaagcagcaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	181078593	181078593	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181078593delT								None (None upstream) : None (None downstream)																							tttgagtcgattttttataat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	182434412	182434412	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182434412delA								None (None upstream) : MGC45800 (625747 downstream)																							TCATAATTACAAAAAAAAAAT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190548442	190548442	+	IGR	DEL	T	-	-	rs66532963		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190548442delT								None (None upstream) : FRG1 (313532 downstream)																							ACAATGAGACTTTGGTTTTCA	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190565126	190565126	+	IGR	DEL	A	-	-	rs71876512		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190565126delA								None (None upstream) : FRG1 (296848 downstream)																							ATATCAGTAGAAAAAAAAAAC	0.368													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190604520	190604520	+	IGR	DEL	G	-	-	rs73876265		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190604520delG								None (None upstream) : FRG1 (257454 downstream)																							ctctcacagagtcacagccac	0.050													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27527398	27527398	+	IGR	DEL	T	-	-	rs35161615		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27527398delT								CDH9 (488709 upstream) : None (None downstream)																							TCTTCATCCATTTTTTTTTTT	0.323													3	4	---	---	---	---	
SEPP1	6414	broad.mit.edu	37	5	42810691	42810691	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42810691delA	uc011cps.1	-						SEPP1_uc011cpt.1_Intron|SEPP1_uc011cpu.1_Intron|SEPP1_uc011cpv.1_Intron|SEPP1_uc003jna.2_Intron			P49908	SEPP1_HUMAN	Homo sapiens cDNA FLJ37321 fis, clone BRAMY2018122.						response to oxidative stress	extracellular region	selenium binding				0						cctcccaagtagctgggatta	0.000													6	3	---	---	---	---	
DDX4	54514	broad.mit.edu	37	5	55059376	55059377	+	Intron	INS	-	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55059376_55059377insG	uc003jqg.3	+						DDX4_uc010ivz.2_Intron|DDX4_uc003jqh.3_Intron	NM_001136034	NP_001129506	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform						multicellular organismal development|sperm motility	perinuclear region of cytoplasm|pi-body|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|skin(1)	2		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				GCAAAACTTGACGACTTTTTAA	0.282													5	3	---	---	---	---	
RNF180	285671	broad.mit.edu	37	5	63508172	63508173	+	Intron	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63508172_63508173delCA	uc003jti.2	+						RNF180_uc003jth.3_Intron|RNF180_uc010iws.2_Intron	NM_001113561	NP_001107033	Q86T96	RN180_HUMAN	ring finger protein 180 isoform 1							integral to membrane|nuclear envelope	zinc ion binding				0		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)		GTGTTTTacgcacacacacaca	0.213													4	2	---	---	---	---	
ADAMTS6	11174	broad.mit.edu	37	5	64473886	64473886	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64473886delG	uc003jtp.2	-						ADAMTS6_uc003jto.2_Intron|ADAMTS6_uc003jtq.2_Intron	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		gagacctgaagggatgcagtg	0.000													4	2	---	---	---	---	
PPWD1	23398	broad.mit.edu	37	5	64882170	64882170	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64882170delA	uc003jtv.3	+						PPWD1_uc011cqv.1_Intron|PPWD1_uc011cqw.1_Intron	NM_015342	NP_056157	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		TTATGTGACTAATCAGTTTAG	0.199													4	2	---	---	---	---	
SGTB	54557	broad.mit.edu	37	5	64981458	64981458	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64981458delA	uc003jud.2	-							NM_019072	NP_061945	Q96EQ0	SGTB_HUMAN	small glutamine-rich tetratricopeptide repeat								binding				0		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)		TAATAAAATGAAAAAAAAAAG	0.313													8	4	---	---	---	---	
ANKRD31	256006	broad.mit.edu	37	5	74486433	74486434	+	Intron	DEL	TG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74486433_74486434delTG	uc003kdo.1	-									Q8N7Z5	ANR31_HUMAN	Homo sapiens cDNA FLJ40191 fis, clone TESTI2019280, weakly similar to Homo sapiens nasopharyngeal carcinoma susceptibility protein LZ16 mRNA.												0						tgCTTATATATGTGTGTGTGTG	0.163													4	2	---	---	---	---	
IQGAP2	10788	broad.mit.edu	37	5	75871050	75871051	+	Intron	DEL	TG	-	-	rs71961375		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75871050_75871051delTG	uc003kek.2	+							NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		ATTTTTTAAAtgtgtgtgtgtg	0.124													5	3	---	---	---	---	
JMY	133746	broad.mit.edu	37	5	78608021	78608021	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78608021delT	uc003kfx.3	+						JMY_uc003kfw.1_Intron	NM_152405	NP_689618	Q8N9B5	JMY_HUMAN	junction-mediating and regulatory protein						'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		ACTAAAACTGTGTATTAAAAA	0.164													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	88250874	88250875	+	Intron	INS	-	TAT	TAT	rs72543584	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88250874_88250875insTAT	uc003kjn.1	+											Homo sapiens mRNA; cDNA DKFZp586I041 (from clone DKFZp586I041).																		ATAATTTTTAGATTCCTGTCTA	0.317													1	5	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111701913	111701913	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111701913delC	uc003kpv.1	-						EPB41L4A_uc003kpw.1_Intron	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		CACAGCTCCACTCTCCTCTCC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116174650	116174651	+	IGR	DEL	AC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116174650_116174651delAC								SEMA6A (264099 upstream) : None (None downstream)																							ttagaaatagacacacacacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	125339765	125339765	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125339765delA								None (None upstream) : GRAMD3 (356023 downstream)																							TTTTATGTTCAAAAACATATA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	125568963	125568963	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125568963delT								None (None upstream) : GRAMD3 (126825 downstream)																							tatttttgactttttaaaaaa	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	127132256	127132256	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127132256delT								CTXN3 (137935 upstream) : FLJ33630 (143879 downstream)																							TTGCTAGGAATTTTTTTGGTT	0.393													4	2	---	---	---	---	
CHSY3	337876	broad.mit.edu	37	5	129495633	129495633	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129495633delT	uc003kvd.2	+							NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3							Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		AATAGTAGCATTTTTTTTTGA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	137996065	137996065	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137996065delT								HSPA9 (84950 upstream) : CTNNA1 (93042 downstream)																							gtgccatgcctacagcagtga	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139138105	139138105	+	5'Flank	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139138105delA	uc011czf.1	+											DQ592953																		GGGCAGCTTCAGGGCAGGAAG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139961056	139961056	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139961056delA								SLC35A4 (12373 upstream) : CD14 (50261 downstream)																							tgattccttgaaaaaaAAATT	0.184													4	2	---	---	---	---	
G3BP1	10146	broad.mit.edu	37	5	151179246	151179246	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151179246delA	uc003lun.2	+						G3BP1_uc003lum.2_Intron|G3BP1_uc011dcu.1_Intron|G3BP1_uc010jhz.2_Intron|G3BP1_uc003luq.2_Intron	NM_005754	NP_005745	Q13283	G3BP1_HUMAN	Ras-GTPase-activating protein SH3-domain-binding						Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			skin(3)|ovary(1)	4		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			actctggctcaaaaaaaaaaa	0.164													5	3	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156807528	156807528	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156807528delT	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron|CYFIP2_uc003lwv.2_5'Flank	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ggaaaggtggttttgtctcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157501681	157501681	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157501681delA								CLINT1 (215513 upstream) : EBF1 (621243 downstream)																							ATATCATCTGATGGGTGTTTT	0.373													4	2	---	---	---	---	
RNF145	153830	broad.mit.edu	37	5	158624044	158624044	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158624044delG	uc003lxp.2	-						RNF145_uc011ddy.1_Intron|RNF145_uc003lxo.1_Intron|RNF145_uc011ddz.1_Intron|RNF145_uc010jiq.1_Intron|RNF145_uc011dea.1_Intron	NM_144726	NP_653327	Q96MT1	RN145_HUMAN	ring finger protein 145							integral to membrane	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCTAGACATGGAAGATCCAA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	160494087	160494087	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160494087delT								LOC285629 (128454 upstream) : GABRB2 (221349 downstream)																							gccattgccatttttcaccta	0.000													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167350533	167350533	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167350533delG	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		AAGACGGCTTGGGTGACTTCA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173000922	173000922	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173000922delG								STC2 (244416 upstream) : LOC285593 (5724 downstream)																							gaaataatgtggggtttttgg	0.000													4	2	---	---	---	---	
C6orf105	84830	broad.mit.edu	37	6	11722609	11722610	+	Intron	DEL	TT	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11722609_11722610delTT	uc003nab.2	-						C6orf105_uc003naa.2_Intron|C6orf105_uc011dip.1_Intron	NM_032744	NP_116133	Q96IZ2	CF105_HUMAN	hypothetical protein LOC84830 isoform 2							integral to membrane					0	Ovarian(93;0.0848)|Breast(50;0.0871)	all_hematologic(90;0.135)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.193)			AACTGTCAGGTTTTTTTTGCAT	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14324345	14324346	+	IGR	DEL	TG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14324345_14324346delTG								CD83 (187199 upstream) : JARID2 (921388 downstream)																							TGTGTATAACTGTGTGTGTGTG	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19368178	19368180	+	IGR	DEL	ACA	-	-	rs78041733		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19368178_19368180delACA								MIR548A1 (796067 upstream) : ID4 (469437 downstream)																							tgaaatatggacaacgagatgga	0.177													2	4	---	---	---	---	
FLJ22536	401237	broad.mit.edu	37	6	22030064	22030065	+	Intron	DEL	AG	-	-	rs34276003		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22030064_22030065delAG	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0						agaggcagacagaaatggagac	0.208													3	4	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32520509	32520510	+	Intron	DEL	CA	-	-	rs148684238		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32520509_32520510delCA	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obm.1_RNA|HLA-DRB6_uc003obn.1_RNA	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						TTTTTAACTCCATGTTTGAGAA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	39222255	39222255	+	IGR	DEL	A	-	-	rs35667128		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39222255delA								KCNK5 (25004 upstream) : KCNK17 (44523 downstream)																							ctactataagaaaaaaccttc	0.000													3	3	---	---	---	---	
LRFN2	57497	broad.mit.edu	37	6	40404759	40404759	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40404759delG	uc003oph.1	-							NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III							cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)					gtatgtgtatgGGGTAGTGTT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50398227	50398227	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50398227delT								DEFB112 (381863 upstream) : TFAP2D (283030 downstream)																							ctcttgcttcttttttgtgtg	0.055													4	2	---	---	---	---	
TRAM2	9697	broad.mit.edu	37	6	52367753	52367754	+	3'UTR	INS	-	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52367753_52367754insG	uc003paq.2	-	11					EFHC1_uc011dwv.1_Intron	NM_012288	NP_036420	Q15035	TRAM2_HUMAN	translocation-associated membrane protein 2						collagen biosynthetic process|protein transport|transmembrane transport	integral to membrane	protein binding				0	Lung NSC(77;0.109)					GAGTGAGGACAGGAGGTGGCCT	0.515													5	3	---	---	---	---	
HCRTR2	3062	broad.mit.edu	37	6	55123132	55123132	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55123132delA	uc003pcl.2	+						HCRTR2_uc010jzv.2_Intron|HCRTR2_uc010jzw.1_Intron	NM_001526	NP_001517	O43614	OX2R_HUMAN	orexin receptor 2						feeding behavior	integral to plasma membrane	neuropeptide receptor activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|breast(1)	6	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			GTGGCAGTGGAAAAAAATTTG	0.279													4	2	---	---	---	---	
GFRAL	389400	broad.mit.edu	37	6	55266896	55266896	+	3'UTR	DEL	T	-	-	rs34070544		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55266896delT	uc003pcm.1	+	9						NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor							integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			tgcctcagccttcccgagtag	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57390726	57390728	+	Intron	DEL	TTG	-	-	rs34695317		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57390726_57390728delTTG	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		GTTTTGAGCATTGTTGTGGCACT	0.448													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57517065	57517065	+	IGR	DEL	A	-	-	rs67005360		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57517065delA								PRIM2 (3690 upstream) : GUSBL2 (729094 downstream)																							ACATTTTTTTAAGAGATCTTA	0.348													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	78267348	78267348	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78267348delT								HTR1B (94228 upstream) : None (None downstream)																							ACACTAGATCTTTTTTTTTTC	0.249													3	3	---	---	---	---	
TTK	7272	broad.mit.edu	37	6	80715274	80715274	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80715274delT	uc003pjc.2	+						TTK_uc003pjb.3_Intron	NM_003318	NP_003309	P33981	TTK_HUMAN	TTK protein kinase						mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1)	11		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		CTCTATCATATTTTTTTTAAG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	86699420	86699420	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86699420delA								SNHG5 (310969 upstream) : HTR1E (947604 downstream)																							GCCAAATTCTAAAAAAGAAAT	0.199													4	2	---	---	---	---	
FAM26E	254228	broad.mit.edu	37	6	116834762	116834762	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116834762delA	uc003pwy.2	+						BET3L_uc003pwx.2_5'Flank|BET3L_uc011ebh.1_Intron	NM_153711	NP_714922	Q8N5C1	FA26E_HUMAN	hypothetical protein LOC254228							integral to membrane					0		all_cancers(87;0.0608)|all_epithelial(87;0.05)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0242)|all cancers(137;0.0419)|OV - Ovarian serous cystadenocarcinoma(136;0.0671)|Epithelial(106;0.212)		TCAGAATGAGAAGGACCTGGG	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	121916381	121916381	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121916381delT								GJA1 (145509 upstream) : HSF2 (804315 downstream)																							TCACTTCTAgtttttttttgt	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	341417	341417	+	IGR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:341417delC								FAM20C (40706 upstream) : PDGFA (195482 downstream)																							CTCTGCTCAGCCCCCAGGTAG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4401598	4401598	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4401598delA								SDK1 (92969 upstream) : FOXK1 (281790 downstream)																							cactagctggaaaaggcaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	20631020	20631020	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20631020delT								ITGB8 (175642 upstream) : ABCB5 (24225 downstream)																							CAACGGAGTATTTTTTTTCCT	0.388													4	3	---	---	---	---	
CDCA7L	55536	broad.mit.edu	37	7	21951581	21951582	+	Intron	INS	-	A	A	rs143540822		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21951581_21951582insA	uc010kuk.2	-						CDCA7L_uc003sve.3_Intron|CDCA7L_uc010kul.2_Intron|CDCA7L_uc003svf.3_Intron|CDCA7L_uc011jyk.1_Intron	NM_018719	NP_061189	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like isoform 1						positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0						tattttaccacaaaaaaaaaAA	0.010													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	28293271	28293271	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28293271delG								JAZF1 (72834 upstream) : LOC402644 (25571 downstream)																							caacatcccagggcatcaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	49673525	49673526	+	IGR	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49673525_49673526delCA								CDC14C (706476 upstream) : VWC2 (139731 downstream)																							cagacctcctcacacacacaTC	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57719063	57719064	+	IGR	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57719063_57719064insA								ZNF716 (185798 upstream) : None (None downstream)																							aaacaatggggaaatttctacg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61775878	61775878	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61775878delT								None (None upstream) : LOC643955 (975794 downstream)																							CTGATTATTCTTTTTTTTTCT	0.318													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61859823	61859824	+	IGR	INS	-	A	A	rs138058730	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61859823_61859824insA								None (None upstream) : LOC643955 (891848 downstream)																							acagaatggacaaaaaaacagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64721668	64721668	+	IGR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64721668delC								INTS4L1 (27069 upstream) : ZNF92 (117100 downstream)																							CCACCACCTGCCCCTGGAATG	0.483													4	2	---	---	---	---	
LOC729156	729156	broad.mit.edu	37	7	66298679	66298679	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66298679delT	uc003tvj.1	-							NR_003934				Homo sapiens cDNA FLJ36054 fis, clone TESTI2018290.												0						CATCCATGTAttttttttttt	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84146566	84146566	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84146566delT								SEMA3A (322349 upstream) : SEMA3D (478308 downstream)																							ATGGCTTTCATTTTTTTTTTC	0.378													3	3	---	---	---	---	
GIGYF1	64599	broad.mit.edu	37	7	100285299	100285300	+	Intron	INS	-	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100285299_100285300insG	uc003uwg.1	-							NM_022574	NP_072096	O75420	PERQ1_HUMAN	PERQ amino acid rich, with GYF domain 1											large_intestine(1)|central_nervous_system(1)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					TCCACCCCCACCCCACAGCACC	0.678													4	2	---	---	---	---	
CREB3L2	64764	broad.mit.edu	37	7	137601571	137601572	+	Intron	DEL	AG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137601571_137601572delAG	uc003vtw.2	-						CREB3L2_uc003vtx.1_Intron|CREB3L2_uc003vty.3_Intron|CREB3L2_uc003vtv.2_Intron	NM_194071	NP_919047	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like						chondrocyte differentiation|positive regulation of transcription, DNA-dependent|response to endoplasmic reticulum stress|response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	cAMP response element binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		FUS/CREB3L2(158)	soft_tissue(158)|upper_aerodigestive_tract(1)|ovary(1)	160						cgagagcgacagagagagagag	0.208			T	FUS	fibromyxoid sarcoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142465862	142465862	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142465862delT	uc011krr.1	+						uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|TRY6_uc011ksn.1_Intron|uc003wan.1_Intron|TRY6_uc011kso.1_5'Flank					SubName: Full=V_segment translation product; Flags: Fragment;																		AAAATCCTCATATTCTTGGGT	0.423													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146270843	146270844	+	Intron	INS	-	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146270843_146270844insT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			ttagtgtcaaattttttgtgtg	0.050										HNSCC(39;0.1)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153286844	153286844	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153286844delT								ACTR3B (734381 upstream) : DPP6 (297575 downstream)																							TGGGCAACGATTTAGCAATGC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155765612	155765612	+	IGR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155765612delC								SHH (160645 upstream) : C7orf4 (567573 downstream)																							CTGGAGCAAGCCCCCACTGGG	0.438													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158291268	158291268	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158291268delT	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)		TCGGCTCTGGTTTTTTGTCCT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	866764	866764	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:866764delA	uc003wpj.1	+						uc003wpk.2_Intron					Homo sapiens cDNA clone IMAGE:4824304.																		ATTTCAAGGCAAATGGCTGAT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	6831247	6831248	+	IGR	DEL	TG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6831247_6831248delTG								DEFA4 (35461 upstream) : DEFA1B (3923 downstream)																							ACTTGTACTTTGTGTGTGTGTG	0.277													4	2	---	---	---	---	
DLC1	10395	broad.mit.edu	37	8	13355760	13355761	+	Intron	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13355760_13355761insA	uc003wwm.2	-						DLC1_uc003wwn.2_Intron|DLC1_uc011kxy.1_Intron	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						ACAGTTTTTGGAAAAATGTGGG	0.406													5	3	---	---	---	---	
CDCA2	157313	broad.mit.edu	37	8	25362380	25362380	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25362380delC	uc003xep.1	+						PPP2R2A_uc003xek.2_Intron|CDCA2_uc011lae.1_Intron|CDCA2_uc003xeq.1_Intron|CDCA2_uc003xer.1_Intron	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2						cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		tttctatgttcccctgctccc	0.134													4	2	---	---	---	---	
CYP7B1	9420	broad.mit.edu	37	8	65686307	65686307	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65686307delA	uc003xvj.2	-							NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,						bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				ggtatctggtaagggccttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	76811632	76811633	+	IGR	INS	-	GAT	GAT	rs149644747	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76811632_76811633insGAT								HNF4G (332573 upstream) : LOC100192378 (711482 downstream)																							AAgatgataaagatgatgatga	0.203													5	3	---	---	---	---	
HEY1	23462	broad.mit.edu	37	8	80678300	80678301	+	Intron	INS	-	A	A	rs141548462	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80678300_80678301insA	uc003ybm.2	-						HEY1_uc010lzq.2_Intron|HEY1_uc003ybl.2_Intron	NM_012258	NP_036390	Q9Y5J3	HEY1_HUMAN	hairy/enhancer-of-split related with YRPW motif						angiogenesis|negative regulation of Notch signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|Notch signaling pathway|transcription, DNA-dependent	nucleus	DNA binding|protein binding			lung(3)	3	all_lung(9;5.1e-05)		Epithelial(68;0.076)|all cancers(69;0.179)			TCAACAACAACAAAAAATACAT	0.401											OREG0018837	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	90630175	90630176	+	IGR	DEL	TC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90630175_90630176delTC								None (None upstream) : RIPK2 (139799 downstream)																							AAGTGTGAAGTCAAGACTATTC	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101516203	101516203	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101516203delA								RNF19A (193876 upstream) : ANKRD46 (5784 downstream)																							ttccatctttaaaaaaATGCC	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120419058	120419059	+	IGR	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120419058_120419059delCA								MAL2 (161147 upstream) : NOV (9493 downstream)																							ttacaatagccacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129242862	129242862	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129242862delT								MIR1208 (80428 upstream) : None (None downstream)																							atttcccccctttttttctca	0.000													4	2	---	---	---	---	
ADCY8	114	broad.mit.edu	37	8	132018295	132018296	+	Intron	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132018295_132018296delCA	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8						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	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			ctctctctGTcacacacacaca	0.050										HNSCC(32;0.087)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137054901	137054901	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137054901delT								KHDRBS3 (395055 upstream) : None (None downstream)																							TTTTTGAATCTTTTTGCATTT	0.403													4	2	---	---	---	---	
BAI1	575	broad.mit.edu	37	8	143566298	143566299	+	Intron	DEL	AT	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143566298_143566299delAT	uc003ywm.2	+							NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1						axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1)	8	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					AGGGTTGATGATGTGGCCTAGG	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143638573	143638573	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143638573delT								BAI1 (12206 upstream) : ARC (53837 downstream)																							TTAATATGTCTTTTTTTtttt	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	146196594	146196594	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146196594delA								ZNF16 (20320 upstream) : ZNF252 (2382 downstream)																							ccttatccttaaaaaagtggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	5146118	5146118	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5146118delT								JAK2 (17936 upstream) : INSL6 (17747 downstream)																							aacctttgggttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66510466	66510467	+	IGR	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66510466_66510467insA								LOC442421 (7439 upstream) : AQP7P1 (743800 downstream)																							GTTCCCCACTTTTTTGTGGCTG	0.228													2	7	---	---	---	---	
ZNF367	195828	broad.mit.edu	37	9	99169725	99169729	+	Intron	DEL	CGCCA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99169725_99169729delCGCCA	uc004awf.2	-						ZNF367_uc004awg.2_Intron	NM_153695	NP_710162	Q7RTV3	ZN367_HUMAN	zinc finger protein 367						regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0167)				ACATAAACAGCGCCATGCTGAGAAA	0.371													13	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	103487157	103487157	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103487157delG								MURC (136986 upstream) : LPPR1 (303874 downstream)																							CTGTGTTGCTGGAAGTCTGAG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110622302	110622302	+	IGR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110622302delC								KLF4 (370255 upstream) : ACTL7B (994569 downstream)																							TCTAAAGAGTCCCCAGTGATT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110971563	110971563	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110971563delT								KLF4 (719516 upstream) : ACTL7B (645308 downstream)																							cccacttccctcttctgtaaa	0.000													4	2	---	---	---	---	
CEP110	11064	broad.mit.edu	37	9	123888360	123888360	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123888360delT	uc004bkx.1	+						CEP110_uc004bky.1_Intron|CEP110_uc004bkz.1_Intron|CEP110_uc004bla.1_Intron	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						ACAGTTGGGCTTTTTTTTTTC	0.303													5	3	---	---	---	---	
VAV2	7410	broad.mit.edu	37	9	136636901	136636901	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136636901delT	uc004ces.2	-						VAV2_uc004cer.2_Intron|VAV2_uc004cet.1_Intron	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		GAAGTCCCAATTCAGGAGGCT	0.537													6	6	---	---	---	---	
SEC16A	9919	broad.mit.edu	37	9	139352107	139352108	+	Intron	DEL	TA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139352107_139352108delTA	uc004chx.2	-						SEC16A_uc004chu.2_5'Flank|SEC16A_uc004chv.3_Intron|SEC16A_uc004chw.2_Intron|SEC16A_uc010nbn.2_Intron	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		CAAAGCCTTGTACTGCCCTGAG	0.604													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11856071	11856071	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11856071delT								ECHDC3 (50007 upstream) : C10orf47 (9326 downstream)																							AAGAGTTTTGTTTTTTTTTAA	0.358													4	2	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12588371	12588372	+	Intron	DEL	AG	-	-	rs146132552		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12588371_12588372delAG	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		TGACAGAGACAGAGAGCAGTAA	0.446													3	3	---	---	---	---	
FAM188A	80013	broad.mit.edu	37	10	15890089	15890090	+	Intron	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15890089_15890090insA	uc001iod.1	-						FAM188A_uc001ioe.1_Intron|FAM188A_uc001iof.1_Intron	NM_024948	NP_079224	Q9H8M7	F188A_HUMAN	chromosome 10 open reading frame 97						apoptosis	nucleus	calcium ion binding			ovary(1)	1						GGAACCTTTTGAAAAAAAAATC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	19093152	19093153	+	IGR	INS	-	G	G	rs142874627	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19093152_19093153insG								ARL5B (126212 upstream) : None (None downstream)																							tgtatggctgagaggcctcagg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	25912613	25912614	+	IGR	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25912613_25912614insA								GPR158 (21458 upstream) : MYO3A (310388 downstream)																							ccagggcaatcaggcaaaagaa	0.000													4	2	---	---	---	---	
YME1L1	10730	broad.mit.edu	37	10	27415453	27415453	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27415453delA	uc001iti.2	-						YME1L1_uc001itj.2_Intron|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_Intron	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1						protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						TGCAGTTACCAAAAAAAAAAG	0.134													4	3	---	---	---	---	
ARMC4	55130	broad.mit.edu	37	10	28273726	28273727	+	Intron	INS	-	AT	AT			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28273726_28273727insAT	uc009xky.2	-						ARMC4_uc010qds.1_5'Flank|ARMC4_uc010qdt.1_5'Flank|ARMC4_uc001itz.2_Intron|ARMC4_uc010qdu.1_5'Flank	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4								binding			ovary(4)|skin(2)	6						GCAATAACTTCCATACTTTACT	0.238													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29110021	29110021	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29110021delT								BAMBI (138153 upstream) : LYZL1 (467969 downstream)																							tgttgccatctttatgccatg	0.199													4	2	---	---	---	---	
CCNY	219771	broad.mit.edu	37	10	35816011	35816012	+	Intron	INS	-	A	A	rs148894770	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35816011_35816012insA	uc001iyw.3	+						CCNY_uc001iyu.3_Intron|CCNY_uc001iyv.3_Intron|CCNY_uc001iyx.3_Intron|CCNY_uc009xmb.2_Intron|CCNY_uc010qet.1_Intron	NM_145012	NP_659449	Q8ND76	CCNY_HUMAN	cyclin Y isoform 1						cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein kinase binding				0						TATCCAGAAGCAGACACCTAGA	0.406													3	3	---	---	---	---	
HNRNPF	3185	broad.mit.edu	37	10	43888354	43888355	+	Intron	DEL	AA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43888354_43888355delAA	uc009xmh.1	-						HNRNPF_uc001jar.2_Intron|HNRNPF_uc001jas.2_Intron|HNRNPF_uc001jat.2_Intron|HNRNPF_uc001jav.2_Intron|HNRNPF_uc001jau.2_Intron	NM_001098208	NP_001091678	P52597	HNRPF_HUMAN	heterogeneous nuclear ribonucleoprotein F						regulation of RNA splicing	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding				0						TGCCACAACTAAACCTCACATT	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	66234315	66234315	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66234315delT								REEP3 (852344 upstream) : ANXA2P3 (350970 downstream)																							gggaaaaaaaTTTTTAAATCA	0.224													4	2	---	---	---	---	
CCAR1	55749	broad.mit.edu	37	10	70533029	70533029	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70533029delG	uc001joo.2	+						CCAR1_uc010qiz.1_Intron|CCAR1_uc010qjb.1_Intron	NM_018237	NP_060707	Q8IX12	CCAR1_HUMAN	cell-cycle and apoptosis regulatory protein 1						apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7						ATTGTTTGAAGACATATTTAT	0.294													8	4	---	---	---	---	
KIAA1274	27143	broad.mit.edu	37	10	72300042	72300043	+	Intron	DEL	TG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72300042_72300043delTG	uc001jrd.3	+						KIAA1274_uc001jre.3_Intron	NM_014431	NP_055246	Q9ULE6	PALD_HUMAN	KIAA1274											ovary(2)|central_nervous_system(1)	3						gtgtgtggaatgtgtgtgtgtg	0.248													4	2	---	---	---	---	
ADK	132	broad.mit.edu	37	10	76445647	76445647	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76445647delT	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_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)	GGTTAAGGAATTTTTTTTTTG	0.303													4	3	---	---	---	---	
MYST4	23522	broad.mit.edu	37	10	76787932	76787932	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76787932delT	uc001jwn.1	+						MYST4_uc001jwo.1_Intron|MYST4_uc001jwp.1_Intron	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic						histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)					TTCAAATTGATTTTTTTTTTT	0.318			T	CREBBP	AML								4	2	---	---	---	---	
PDLIM1	9124	broad.mit.edu	37	10	96998112	96998112	+	Intron	DEL	T	-	-	rs45543839		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96998112delT	uc001kkh.2	-						PDLIM1_uc001kki.2_Intron|PDLIM1_uc009xuv.2_Intron|PDLIM1_uc001kkj.1_3'UTR	NM_020992	NP_066272	O00151	PDLI1_HUMAN	PDZ and LIM domain 1						response to oxidative stress	cytoplasm|cytoskeleton	zinc ion binding				0		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		ATTTTTCTCATTTTACATGTT	0.483													5	5	---	---	---	---	
SLIT1	6585	broad.mit.edu	37	10	98917797	98917797	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98917797delG	uc001kmw.2	-						SLIT1_uc009xvh.1_Intron|ARHGAP19_uc001kmy.2_Intron|SLIT1_uc001kmz.2_Intron	NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		taccttctctgggcctcagtt	0.159													4	2	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100433461	100433461	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100433461delT	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600	Q8WWQ2	HPSE2_HUMAN	heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		ATTTCTTGTATTTTTTTTTTC	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	107176447	107176449	+	IGR	DEL	AGG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107176447_107176449delAGG								SORCS3 (151454 upstream) : None (None downstream)																							AGAAagaagaaggaggaggagga	0.163													4	2	---	---	---	---	
KIAA1598	57698	broad.mit.edu	37	10	118746965	118746966	+	Intron	DEL	TT	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118746965_118746966delTT	uc009xyw.2	-						KIAA1598_uc001lcz.3_Intron|KIAA1598_uc010qso.1_Intron|KIAA1598_uc010qsp.1_Intron|KIAA1598_uc010qsq.1_Intron	NM_001127211	NP_001120683	A0MZ66	SHOT1_HUMAN	shootin1 isoform a						axon guidance	axon					0				all cancers(201;0.00494)		gtatccggtgttaagaattagt	0.000													4	2	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127575513	127575516	+	Intron	DEL	TCTT	-	-	rs143617895		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127575513_127575516delTCTT	uc001ljg.1	-							NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TTTCCCCATGTCTTTCTGTCTCTT	0.412													4	2	---	---	---	---	
GALNTL4	374378	broad.mit.edu	37	11	11618483	11618484	+	Intron	INS	-	T	T	rs10765872	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11618483_11618484insT	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		tagttgtgggattttttgtaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15340777	15340778	+	IGR	INS	-	A	A	rs80274963	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15340777_15340778insA								INSC (72025 upstream) : SOX6 (647218 downstream)																							AAAGAGAGGGGAAAAAAAAGTT	0.376													3	3	---	---	---	---	
SAA4	6291	broad.mit.edu	37	11	18257617	18257617	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18257617delC	uc001mny.2	-							NM_006512	NP_006503	P35542	SAA4_HUMAN	serum amyloid A4, constitutive precursor						acute-phase response	high-density lipoprotein particle					0						tcctccctttctttctttctt	0.050													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	20780017	20780017	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20780017delA	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						AGTGTATGCTAAGCtaaggag	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	24100378	24100378	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24100378delT								None (None upstream) : LUZP2 (418178 downstream)																							attttgaaacttttttttcct	0.134													4	2	---	---	---	---	
LGR4	55366	broad.mit.edu	37	11	27478494	27478494	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27478494delT	uc001mrj.3	-						LGR4_uc001mrk.3_Intron	NM_018490	NP_060960	Q9BXB1	LGR4_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1						TCTGTTCTGATTTTTTTTTCC	0.323													4	2	---	---	---	---	
BDNFOS	497258	broad.mit.edu	37	11	27529434	27529434	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27529434delT	uc001mrm.2	+						LIN7C_uc001mrl.2_5'Flank|LIN7C_uc009yii.2_5'Flank|BDNFOS_uc009yij.2_Intron|BDNFOS_uc009yik.2_Intron|BDNFOS_uc009yil.2_Intron|BDNFOS_uc001mrp.2_Intron|BDNFOS_uc009yim.2_Intron|BDNFOS_uc009yin.2_Intron|BDNFOS_uc009yio.2_Intron|BDNFOS_uc009yip.2_Intron|BDNFOS_uc001mrn.2_Intron|BDNFOS_uc009yiq.2_Intron|BDNFOS_uc001mro.2_Intron|BDNFOS_uc009yir.2_Intron|BDNFOS_uc009yis.2_Intron|BDNFOS_uc009yit.2_Intron|BDNFOS_uc009yiu.2_Intron|BDNFOS_uc009yiv.2_Intron|BDNFOS_uc009yiw.2_Intron|BDNFOS_uc009yix.2_Intron|BDNFOS_uc009yiy.2_Intron|BDNFOS_uc009yiz.2_Intron|BDNFOS_uc001mrq.3_Intron|BDNFOS_uc001mrr.3_Intron|BDNFOS_uc009yja.2_Intron|BDNFOS_uc009yjb.2_Intron	NR_002832				Homo sapiens non-coding transcript BT2C (BDNF) mRNA, complete sequence; alternatively spliced.												0						TCAGTCCAGATAGTATAGTTT	0.269													4	2	---	---	---	---	
CSTF3	1479	broad.mit.edu	37	11	33129180	33129181	+	Intron	INS	-	ACA	ACA	rs141819230	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33129180_33129181insACA	uc001muh.2	-							NM_001326	NP_001317	Q12996	CSTF3_HUMAN	cleavage stimulation factor subunit 3 isoform 1						mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	protein binding|RNA binding				0						GAAAAAATTTGACAAGTCTGTC	0.391													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44526313	44526314	+	IGR	DEL	AC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44526313_44526314delAC								ALX4 (194597 upstream) : CD82 (60827 downstream)																							cattctacagacacacacacac	0.173													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	51570583	51570583	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51570583delA								OR4C46 (54374 upstream) : None (None downstream)																							acaaaaagagagagtttcaaa	0.000													4	2	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70799264	70799264	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70799264delT	uc001oqc.2	-							NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			AGtgctacactttgaacactg	0.184													4	2	---	---	---	---	
MRPL48	51642	broad.mit.edu	37	11	73516338	73516339	+	Intron	INS	-	T	T	rs11335180		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73516338_73516339insT	uc001ouh.3	+						MRPL48_uc009ytt.2_Intron|MRPL48_uc010rri.1_Intron|MRPL48_uc009ytu.2_Intron	NM_016055	NP_057139	Q96GC5	RM48_HUMAN	mitochondrial ribosomal protein L48 precursor						translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0						tgatgctgttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74241461	74241462	+	IGR	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74241461_74241462delCA								LIPT2 (36706 upstream) : POLD3 (62167 downstream)																							aaatttctgtcaccttgtgaaa	0.035													4	2	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	78687972	78687972	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78687972delC	uc001ozl.3	-							NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						CACGTGCTTTCCAACATAGCT	0.338													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83437792	83437795	+	Intron	DEL	AAAC	-	-	rs113643684		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83437792_83437795delAAAC	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				ATCTGCCTGAaaacaaacaaacaa	0.382													4	2	---	---	---	---	
GRM5	2915	broad.mit.edu	37	11	88387664	88387664	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88387664delG	uc001pcq.2	-						GRM5_uc009yvm.2_Intron	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	AAGGAAGTATGGGGAAAGGGA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93301170	93301171	+	IGR	DEL	TC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93301170_93301171delTC								C11orf75 (24624 upstream) : KIAA1731 (93645 downstream)																							ATGTTGCACTTCAGAAAACCAA	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	98291282	98291282	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98291282delG								None (None upstream) : CNTN5 (600589 downstream)																							gggtctatttgggattgtaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	110823669	110823669	+	IGR	DEL	G	-	-	rs35282135		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110823669delG								ARHGAP20 (239757 upstream) : C11orf53 (303038 downstream)																							GAGGCTGAGAGGGTCAGAGCA	0.512													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134868572	134868572	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134868572delT								B3GAT1 (586760 upstream) : None (None downstream)																							tccaatctggttttttttttc	0.000													4	2	---	---	---	---	
SLCO1B3	28234	broad.mit.edu	37	12	21031070	21031092	+	Intron	DEL	TAATTCCATAGGTGAAATTCACC	-	-	rs6144640		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21031070_21031092delTAATTCCATAGGTGAAATTCACC	uc001rek.2	+						SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron|SLCO1B3_uc001reo.2_Intron	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					TAGGTGAATTTAATTCCATAGGTGAAATTCACCTAATTCTATA	0.278													4	2	---	---	---	---	
CCDC91	55297	broad.mit.edu	37	12	28645157	28645158	+	Intron	INS	-	C	C			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28645157_28645158insC	uc001riq.2	+						CCDC91_uc001rio.2_Intron|CCDC91_uc009zjk.2_Intron|CCDC91_uc001rir.2_Intron|CCDC91_uc009zjl.2_Intron	NM_018318	NP_060788	Q7Z6B0	CCD91_HUMAN	GGA binding partner						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)					TGTTTTTTTTTCATTCTATAAA	0.317													4	2	---	---	---	---	
DENND5B	160518	broad.mit.edu	37	12	31595513	31595513	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31595513delT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2						TGTTTTTTTCTTTTTTTTTTT	0.279													4	3	---	---	---	---	
PDZRN4	29951	broad.mit.edu	37	12	41744648	41744651	+	Intron	DEL	TGTC	-	-	rs142616909		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41744648_41744651delTGTC	uc010skn.1	+							NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				GACTGGAGTTTGTCTGACCCAGAA	0.431													3	3	---	---	---	---	
LRP1	4035	broad.mit.edu	37	12	57555782	57555783	+	Intron	DEL	GT	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57555782_57555783delGT	uc001snd.2	+							NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1						aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	acgcatatgagtgtgtgtgtgt	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	59800630	59800631	+	IGR	DEL	AC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59800630_59800631delAC								LRIG3 (486368 upstream) : SLC16A7 (189217 downstream)																							ACACATACAGACACACACACAC	0.361													4	2	---	---	---	---	
FAM19A2	338811	broad.mit.edu	37	12	62204767	62204768	+	Intron	INS	-	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62204767_62204768insT	uc001sqw.2	-						FAM19A2_uc001sqv.2_Intron|FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		agaattgatgattttttttttc	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77766300	77766300	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77766300delT								E2F7 (306940 upstream) : NAV3 (458769 downstream)																							TACTATGCCCTTTTTTTTTCC	0.343													4	2	---	---	---	---	
NAV3	89795	broad.mit.edu	37	12	78392511	78392511	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78392511delT	uc001syp.2	+						NAV3_uc001syo.2_Intron	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						AAACAGGTCCTTCCAAATGCA	0.264										HNSCC(70;0.22)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80496638	80496638	+	IGR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80496638delC								PPP1R12A (167403 upstream) : PTPRQ (341488 downstream)																							ttttttttctccTTTGTTTCA	0.164													4	2	---	---	---	---	
MGAT4C	25834	broad.mit.edu	37	12	86801881	86801882	+	Intron	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86801881_86801882delCA	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						cacatacacgcacacacacaca	0.287													4	2	---	---	---	---	
UHRF1BP1L	23074	broad.mit.edu	37	12	100536987	100536987	+	5'Flank	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100536987delT	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_5'Flank	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2						tgcttgtttgttttttttttt	0.189													5	3	---	---	---	---	
UBE3B	89910	broad.mit.edu	37	12	109922064	109922065	+	Intron	INS	-	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109922064_109922065insG	uc001top.2	+						UBE3B_uc001toq.2_Intron|UBE3B_uc001tol.1_Intron|UBE3B_uc001tom.2_Intron|UBE3B_uc001ton.2_Intron|UBE3B_uc001too.1_Intron|UBE3B_uc009zvj.1_Intron|UBE3B_uc001tor.2_Intron	NM_130466	NP_569733	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			ovary(2)|lung(2)	4						TGAGATAAAACATAATACAAAA	0.391													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114491808	114491809	+	IGR	DEL	AC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114491808_114491809delAC								RBM19 (87632 upstream) : TBX5 (299927 downstream)																							gccaagtcctactcacatgacc	0.104													4	2	---	---	---	---	
MSI1	4440	broad.mit.edu	37	12	120809163	120809164	+	5'Flank	DEL	CC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120809163_120809164delCC	uc001tye.1	-							NM_002442	NP_002433	O43347	MSI1H_HUMAN	musashi 1						nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGGGTCCTTTCCGGCAGTGGCG	0.540													3	6	---	---	---	---	
CAMKK2	10645	broad.mit.edu	37	12	121709300	121709301	+	Intron	INS	-	T	T	rs151124517	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121709300_121709301insT	uc001tzu.2	-						CAMKK2_uc001tzt.2_Intron|CAMKK2_uc001tzv.2_Intron|CAMKK2_uc001tzw.2_Intron|CAMKK2_uc001tzx.2_Intron|CAMKK2_uc001tzy.2_Intron|CAMKK2_uc001uaa.1_Intron|CAMKK2_uc001uab.2_Intron|CAMKK2_uc001uac.2_Intron	NM_006549	NP_006540	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase						calcium-mediated signaling|MAPKKK cascade|positive regulation of transcription, DNA-dependent|protein autophosphorylation|regulation of protein kinase activity	cytoplasm	ATP binding|calcium ion binding|calmodulin binding|calmodulin-dependent protein kinase activity|protein tyrosine kinase activity			lung(1)|large_intestine(1)|stomach(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					tGTAAAACCCATTTTTTAAAGA	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	123405460	123405461	+	IGR	INS	-	A	A	rs147231924	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123405460_123405461insA								VPS37B (24748 upstream) : ABCB9 (8079 downstream)																							acccctgtcttaaaaaaaaaat	0.054													4	2	---	---	---	---	
MPHOSPH9	10198	broad.mit.edu	37	12	123665790	123665790	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123665790delA	uc001uel.2	-						MPHOSPH9_uc010tal.1_Intron|MPHOSPH9_uc010tam.1_Intron|MPHOSPH9_uc001uem.2_Intron	NM_022782	NP_073619	Q99550	MPP9_HUMAN	M-phase phosphoprotein 9						M phase of mitotic cell cycle	centriole|Golgi membrane					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		ATTATACCACAAAATTAAACG	0.224													55	37	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126627938	126627938	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126627938delA								TMEM132B (484349 upstream) : LOC100128554 (299089 downstream)																							ggtaatggccaaaaaaacaag	0.015													4	2	---	---	---	---	
TMEM132C	92293	broad.mit.edu	37	12	129029187	129029188	+	Intron	INS	-	G	G	rs148559032	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129029187_129029188insG	uc001uhs.3	+							NM_001136103	NP_001129575	Q8N3T6	T132C_HUMAN	transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1						gcacaattatagcggggggaat	0.054													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130604607	130604608	+	IGR	DEL	AC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130604607_130604608delAC								LOC100190940 (77720 upstream) : FZD10 (42424 downstream)																							acactgtgaaacacacacccac	0.307													4	2	---	---	---	---	
TPTE2	93492	broad.mit.edu	37	13	20000806	20000807	+	Intron	INS	-	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20000806_20000807insG	uc001umd.2	-						TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_Intron|TPTE2_uc010tcl.1_Intron	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid							endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TAATAATCTTTTCTAGTTGCAA	0.213													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30580026	30580026	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30580026delA								UBL3 (155206 upstream) : KATNAL1 (196742 downstream)																							ctataatcccaatcaatttat	0.000													4	2	---	---	---	---	
NHLRC3	387921	broad.mit.edu	37	13	39618052	39618052	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39618052delA	uc001uxc.2	+						NHLRC3_uc001uxb.1_Intron|NHLRC3_uc001uxd.2_Intron|NHLRC3_uc001uxe.2_Intron	NM_001012754	NP_001012772	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3 isoform a							extracellular region				skin(1)	1		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		AAGGAACTTTAAAAAAAAAAC	0.328													8	4	---	---	---	---	
DHRS12	79758	broad.mit.edu	37	13	52348370	52348372	+	Intron	DEL	CTC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52348370_52348372delCTC	uc001vfq.2	-						DHRS12_uc001vfr.1_Intron|DHRS12_uc001vfs.1_Intron			A0PJE2	DHR12_HUMAN	RecName: Full=Dehydrogenase/reductase SDR family member 12;          EC=1.1.-.-;								binding|oxidoreductase activity				0		Breast(56;0.00173)|Prostate(109;0.00899)|Lung NSC(96;0.0199)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.81e-08)		TACATGTATTCTCCTACAGTATT	0.291													4	2	---	---	---	---	
TBC1D4	9882	broad.mit.edu	37	13	76040511	76040511	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76040511delG	uc001vjl.1	-						TBC1D4_uc010aer.2_Intron|TBC1D4_uc010aes.2_Intron	NM_014832	NP_055647	O60343	TBCD4_HUMAN	TBC1 domain family, member 4							cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		TGAACATTTTGTTCATTGACA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	77272849	77272850	+	IGR	DEL	GT	-	-	rs111584566		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77272849_77272850delGT								LMO7 (838845 upstream) : KCTD12 (181454 downstream)																							TTCTTTCCTGgtgtgtgtgtgt	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	81678691	81678691	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81678691delT								SPRY2 (763605 upstream) : None (None downstream)																							TTGCTACAACTTTTTAAAAAC	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	83549234	83549234	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83549234delT								None (None upstream) : SLITRK1 (902110 downstream)																							GTAGGTGAAGTTTTTTTTTAA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	104830078	104830078	+	IGR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104830078delC								None (None upstream) : None (None downstream)																							ctcccacaatcccccctagct	0.000													4	2	---	---	---	---	
SLC7A7	9056	broad.mit.edu	37	14	23244455	23244465	+	Intron	DEL	GTGTACCATTC	-	-	rs151185590	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23244455_23244465delGTGTACCATTC	uc001wgr.3	-						SLC7A7_uc001wgs.3_Intron|SLC7A7_uc001wgt.3_Intron|SLC7A7_uc001wgu.3_Intron|SLC7A7_uc001wgv.3_Intron	NM_003982	NP_003973	Q9UM01	YLAT1_HUMAN	solute carrier family 7 member 7						blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity			ovary(1)|breast(1)	2	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		TAGAGCAGAGGTGTACCATTCCTTAGAGCAT	0.412													4	2	---	---	---	---	
TMEM63C	57156	broad.mit.edu	37	14	77711841	77711841	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77711841delT	uc001xtf.2	+						TMEM63C_uc010asq.1_Intron	NM_020431	NP_065164	Q9P1W3	TM63C_HUMAN	transmembrane protein 63C							integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		tattagtccatttgcactctg	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	86148760	86148760	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86148760delA								FLRT2 (54491 upstream) : None (None downstream)																							GCCAAGAGGGAAAAAAAGGTC	0.294													4	2	---	---	---	---	
C14orf159	80017	broad.mit.edu	37	14	91673696	91673696	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91673696delC	uc001xzb.2	+						C14orf159_uc001xyx.2_Intron|C14orf159_uc001xyw.2_Intron|C14orf159_uc001xzc.2_Intron|C14orf159_uc001xza.2_Intron|C14orf159_uc001xyv.2_Intron|C14orf159_uc001xyz.2_Intron|C14orf159_uc001xze.2_Intron	NM_001102366	NP_001095836	Q7Z3D6	CN159_HUMAN	hypothetical protein LOC80017 isoform a							mitochondrion				central_nervous_system(2)|ovary(1)	3		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		gaaaaaaaaacccacaacaga	0.000													4	2	---	---	---	---	
INF2	64423	broad.mit.edu	37	14	105206706	105206706	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105206706delA	uc010tyi.1	+						ADSSL1_uc001ypd.2_Intron|ADSSL1_uc001ype.2_Intron|ADSSL1_uc001ypf.2_Intron	NM_022489	NP_071934	Q27J81	INF2_HUMAN	inverted formin 2 isoform 1						actin cytoskeleton organization	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm	actin binding|Rho GTPase binding				0		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		aagtacacacagccacacatg	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20016069	20016069	+	IGR	DEL	C	-	-	rs28764803		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20016069delC								None (None upstream) : GOLGA6L6 (721025 downstream)																							tcaaaagaaacgttcaactct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20577988	20577990	+	IGR	DEL	TCT	-	-	rs112150497		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20577988_20577990delTCT								None (None upstream) : GOLGA6L6 (159104 downstream)																							GAGGTAATTGTCTTCATCTCATG	0.167													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20607082	20607083	+	Intron	DEL	AA	-	-	rs28755877		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20607082_20607083delAA	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																		GTCAGCATTTAAAAAAAAAAAA	0.332													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20852492	20852494	+	IGR	DEL	ATA	-	-	rs149564981		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20852492_20852494delATA								GOLGA8C (71466 upstream) : BCL8 (17562 downstream)																							cttgcttaatataatgagaggag	0.118													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	38721591	38721591	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38721591delT								SPRED1 (72142 upstream) : FAM98B (24737 downstream)																							TCtgatcatatttttttcctg	0.134													4	2	---	---	---	---	
C15orf33	196951	broad.mit.edu	37	15	49785613	49785614	+	Intron	INS	-	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49785613_49785614insT	uc001zxl.2	-						C15orf33_uc001zxm.2_Intron	NM_152647	NP_689860	Q96M60	CO033_HUMAN	hypothetical protein LOC196951											ovary(1)	1		all_lung(180;0.00187)		all cancers(107;3.45e-08)|GBM - Glioblastoma multiforme(94;0.000124)		ATGTCATTTTGTACACGCACCA	0.406													4	2	---	---	---	---	
KIAA1370	56204	broad.mit.edu	37	15	52943717	52943717	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52943717delC	uc002acg.3	-						KIAA1370_uc002ach.3_Intron|KIAA1370_uc010bfg.1_Intron|KIAA1370_uc010ugf.1_Intron	NM_019600	NP_062546	Q32MH5	K1370_HUMAN	hypothetical protein LOC56204												0				all cancers(107;0.0803)		ATACCTCCTGCCCCCACATAC	0.318													4	2	---	---	---	---	
RAB27A	5873	broad.mit.edu	37	15	55518708	55518709	+	Intron	DEL	TG	-	-	rs71888593		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55518708_55518709delTG	uc002aco.2	-						RAB27A_uc002acr.2_Intron|RAB27A_uc002acp.2_Intron|RAB27A_uc002acq.2_Intron	NM_183234	NP_899057	P51159	RB27A_HUMAN	Ras-related protein Rab-27A						small GTPase mediated signal transduction	dendrite|exocytic vesicle|late endosome|lysosome|melanosome	GTP binding|GTPase activity			ovary(1)	1				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		TTTATGTATTtgtgtgtgtgtg	0.257													4	2	---	---	---	---	
ALDH1A2	8854	broad.mit.edu	37	15	58454704	58454704	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58454704delC	uc010ugw.1	-						AQP9_uc010ugx.1_Intron|AQP9_uc002aez.2_Intron	NM_170697	NP_733798	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 3						negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	agctccctatccttaaaggtg	0.070													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	61386194	61386194	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61386194delC	uc002agx.2	-							NM_134261	NP_599023	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						CACGTGATGGCCAGAGATATT	0.498													4	2	---	---	---	---	
SV2B	9899	broad.mit.edu	37	15	91805832	91805832	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91805832delT	uc002bqv.2	+						SV2B_uc002bqt.2_Intron|SV2B_uc010uqv.1_Intron|SV2B_uc002bqu.3_Intron	NM_014848	NP_055663	Q7L1I2	SV2B_HUMAN	synaptic vesicle protein 2B homolog						neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			ttctgcccccttcctcctccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96271061	96271061	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96271061delA								LOC145820 (219987 upstream) : NR2F2 (598096 downstream)																							TTCTAAGAGTAAAGGGAGAAA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98431444	98431444	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98431444delA								LOC91948 (13785 upstream) : ARRDC4 (31340 downstream)																							GTTGACCAGGAATCCCACTTT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5878414	5878414	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5878414delA								FAM86A (730625 upstream) : A2BP1 (190718 downstream)																							ATAAAGGATGAAAAAAATGCA	0.219													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7595318	7595319	+	Intron	INS	-	C	C	rs140308010	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7595318_7595319insC	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|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)		GGTGCGGGTCATGGGGGTGGAG	0.569													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8578249	8578250	+	IGR	DEL	CA	-	-	rs74007814		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8578249_8578250delCA								A2BP1 (814909 upstream) : TMEM114 (41253 downstream)																							CCAAAATGCGcacacacacaca	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29231205	29231206	+	Intron	DEL	CA	-	-	rs150954013		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29231205_29231206delCA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		atagtactcgcacacacacgca	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32123215	32123215	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32123215delG								ZNF267 (194589 upstream) : HERC2P4 (39395 downstream)																							tattctagaaGGATAAATTAT	0.035													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33393654	33393654	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33393654delG								SLC6A10P (497191 upstream) : MIR1826 (571854 downstream)																							aagcccaggaggttgaggctg	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	62534585	62534585	+	IGR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62534585delC								CDH8 (464549 upstream) : None (None downstream)																							CATTAGAGGACCCAGAATACA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66153144	66153145	+	IGR	INS	-	ACAG	ACAG			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66153144_66153145insACAG								LOC283867 (542941 upstream) : CDH5 (247380 downstream)																							atacctccttcacttctgccac	0.000													4	2	---	---	---	---	
VAT1L	57687	broad.mit.edu	37	16	77953122	77953122	+	Intron	DEL	A	-	-	rs11288720		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77953122delA	uc002ffg.1	+							NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.								oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1						CTAGGTGTCCAGGGGAAAACA	0.333													3	3	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	82735215	82735215	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82735215delT	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		cagtccttcctttttttttgg	0.000													5	3	---	---	---	---	
OSGIN1	29948	broad.mit.edu	37	16	83984144	83984149	+	Intron	DEL	ACACAC	-	-	rs12932950		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83984144_83984149delACACAC	uc002fha.2	+						OSGIN1_uc002fhb.2_Intron|OSGIN1_uc002fhc.2_5'Flank	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1						cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						gcacacacgtacacacacatgcacac	0.000													4	2	---	---	---	---	
LOC728392	728392	broad.mit.edu	37	17	5402935	5402935	+	3'UTR	DEL	T	-	-	rs3215215		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5402935delT	uc010vtc.1	-	2						NM_001162371	NP_001155843			hypothetical protein LOC728392												0						CTTTTGAGTCTTAAGATGACA	0.458													1	6	---	---	---	---	
GABARAP	11337	broad.mit.edu	37	17	7145230	7145233	+	Intron	DEL	AATC	-	-	rs75210172		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7145230_7145233delAATC	uc002gfb.2	-						PHF23_uc002gfa.2_5'Flank|PHF23_uc010vtt.1_5'Flank|PHF23_uc010cma.2_5'Flank	NM_007278	NP_009209	O95166	GBRAP_HUMAN	GABA(A) receptor-associated protein						protein targeting|synaptic transmission	autophagic vacuole membrane|Golgi membrane|microtubule|plasma membrane	beta-tubulin binding|GABA receptor binding				0						CAACTATCTTAATCAGACGGAGGT	0.480													6	4	---	---	---	---	
RICH2	9912	broad.mit.edu	37	17	12796862	12796862	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12796862delT	uc002gnr.3	+						RICH2_uc010vvk.1_Intron|RICH2_uc010vvl.1_Intron|RICH2_uc002gns.3_Intron|RICH2_uc010vvm.1_Intron|RICH2_uc010vvn.1_Intron	NM_014859	NP_055674	Q17R89	RHG44_HUMAN	Rho GTPase-activating protein RICH2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0						tgatagacgcttccactccct	0.000													4	2	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21313451	21313451	+	Intron	DEL	C	-	-	rs147481555		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21313451delC	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)	CTGGCAGTGTCCCCCAGGAGT	0.657										Prostate(3;0.18)			6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21347614	21347614	+	IGR	DEL	T	-	-	rs112809292		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21347614delT								KCNJ12 (24435 upstream) : C17orf51 (83958 downstream)																							tttcaaaaacttttttttttg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21365888	21365888	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21365888delT								KCNJ12 (42709 upstream) : C17orf51 (65684 downstream)																							tccagcccactttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21514558	21514558	+	IGR	DEL	T	-	-	rs11328023		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21514558delT								C17orf51 (36827 upstream) : FAM27L (310812 downstream)																							attaaaaaaatctaccccaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	29715078	29715079	+	IGR	DEL	TG	-	-	rs140340790		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29715078_29715079delTG								NF1 (6173 upstream) : RAB11FIP4 (3563 downstream)																							ACCCTAACTATGTGTGTATGGG	0.208													2	4	---	---	---	---	
MYO1D	4642	broad.mit.edu	37	17	31022483	31022483	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31022483delT	uc002hho.1	-						MYO1D_uc002hhp.1_Intron	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)			ttggccatccttccttgtctt	0.000													4	2	---	---	---	---	
C17orf57	124989	broad.mit.edu	37	17	45468628	45468629	+	Intron	DEL	TG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45468628_45468629delTG	uc002iln.2	+						C17orf57_uc002ilm.2_Intron|C17orf57_uc010daz.1_Intron	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989								calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3						TTTTTGACTTTGATTTTGATAC	0.124													4	2	---	---	---	---	
C17orf57	124989	broad.mit.edu	37	17	45468631	45468632	+	Intron	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45468631_45468632insA	uc002iln.2	+						C17orf57_uc002ilm.2_Intron|C17orf57_uc010daz.1_Intron	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989								calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3						TTGACTTTGATTTTGATACTTA	0.124													4	2	---	---	---	---	
TTLL6	284076	broad.mit.edu	37	17	46839995	46839995	+	3'UTR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46839995delC	uc010wlo.1	-	17					TTLL6_uc002iob.2_3'UTR|TTLL6_uc010dbi.2_RNA|TTLL6_uc002ioc.2_3'UTR|TTLL6_uc002iod.2_3'UTR	NM_001130918	NP_001124390	Q8N841	TTLL6_HUMAN	tubulin tyrosine ligase-like family, member 6							cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity				0						AAACACTACTCCCGAAGTTGC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	50571220	50571220	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50571220delT								CA10 (333843 upstream) : None (None downstream)																							AGCTCAGATATTACAGACACT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	58611483	58611483	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58611483delA								APPBP2 (7903 upstream) : PPM1D (66071 downstream)																							ttgtcaacctaaaatagttaa	0.000													4	2	---	---	---	---	
SMURF2	64750	broad.mit.edu	37	17	62547477	62547477	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62547477delA	uc002jep.1	-						SMURF2_uc002jeq.1_Intron|SMURF2_uc002jer.1_Intron	NM_022739	NP_073576	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2						BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			cctgtctcagaaaaaaaaaaa	0.169													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	63284806	63284806	+	IGR	DEL	C	-	-	rs111332446		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63284806delC								RGS9 (60987 upstream) : AXIN2 (239879 downstream)																							CTCCTGACCTCCCCAGACTAG	0.507													4	2	---	---	---	---	
ARSG	22901	broad.mit.edu	37	17	66274059	66274059	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66274059delG	uc002jhc.2	+						SLC16A6_uc002jgz.1_Intron|SLC16A6_uc002jha.1_Intron	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			AGTGCCTTTTGTTTCTTGCCA	0.428													4	2	---	---	---	---	
WIPI1	55062	broad.mit.edu	37	17	66447180	66447180	+	Intron	DEL	A	-	-	rs78191101	byFrequency	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66447180delA	uc010dey.2	-						WIPI1_uc002jhd.3_Intron|WIPI1_uc010wqo.1_Intron|WIPI1_uc002jhe.3_Intron	NM_017983	NP_060453	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting						macroautophagy|vesicle targeting, trans-Golgi to endosome	autophagic vacuole membrane|clathrin-coated vesicle|cytosol|endosome membrane|PAS complex|pre-autophagosomal structure membrane|trans-Golgi network	androgen receptor binding|estrogen receptor binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding				0						CTGAGCTTGCATTGACAGTGA	0.562													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66843868	66843869	+	IGR	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66843868_66843869delCA								FAM20A (246773 upstream) : ABCA8 (19564 downstream)																							cacacaaatgcacacacacaca	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	69621208	69621208	+	IGR	DEL	C	-	-	rs57052177	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69621208delC								None (None upstream) : SOX9 (495953 downstream)																							CATTTTTTTTCCCCAAAGAGC	0.373													4	2	---	---	---	---	
SRP68	6730	broad.mit.edu	37	17	74051723	74051723	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74051723delT	uc002jqk.1	-						SRP68_uc010wsu.1_Intron|SRP68_uc002jql.1_Intron|SRP68_uc002jqj.1_5'Flank	NM_014230	NP_055045	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa						response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			ovary(1)	1						tagtcccagctactctggagg	0.000													6	6	---	---	---	---	
SRP68	6730	broad.mit.edu	37	17	74051728	74051729	+	Intron	INS	-	G	G			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74051728_74051729insG	uc002jqk.1	-						SRP68_uc010wsu.1_Intron|SRP68_uc002jql.1_Intron|SRP68_uc002jqj.1_5'Flank	NM_014230	NP_055045	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa						response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			ovary(1)	1						ccagctactctggaggctgagg	0.000													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75797482	75797482	+	IGR	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75797482delG								SEPT9 (300806 upstream) : FLJ45079 (77627 downstream)																							TCTTACGTTTGGAGGTTTTGT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	24780398	24780399	+	IGR	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24780398_24780399insA								C18orf16 (9748 upstream) : CDH2 (750531 downstream)																							ATTATGGATTCAAATTCTGGGC	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38544638	38544638	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38544638delA								None (None upstream) : KC6 (515600 downstream)																							tacatgtggcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	56059769	56059769	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56059769delT	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc002lhg.2_Intron|NEDD4L_uc002lhh.2_Intron|NEDD4L_uc010dpn.2_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						CAGAAAGGTGTTTTTTTTTTC	0.438													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57851463	57851464	+	IGR	INS	-	CTC	CTC	rs149739906	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57851463_57851464insCTC								PMAIP1 (279925 upstream) : MC4R (187100 downstream)																							TCATTTGCCCGCTCTTTCGGCT	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	69956172	69956172	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69956172delA								None (None upstream) : CBLN2 (247743 downstream)																							TGACATCCTCAAAAAAAAACT	0.353													4	3	---	---	---	---	
FSD1	79187	broad.mit.edu	37	19	4316064	4316064	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4316064delT	uc002lzy.2	+						FSD1_uc002lzz.2_Intron|FSD1_uc002maa.2_Intron	NM_024333	NP_077309	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing						cell division|mitosis	cleavage furrow|microtubule|microtubule organizing center|nucleus				skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		gcacttggccttttttttttg	0.000													4	2	---	---	---	---	
ZNF266	10781	broad.mit.edu	37	19	9538504	9538504	+	Intron	DEL	G	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9538504delG	uc002mlm.2	-						ZNF266_uc002mln.2_Intron|ZNF266_uc002mlo.2_Intron|ZNF266_uc010dwp.2_Intron|ZNF266_uc010dwq.2_Intron	NM_006631	NP_006622	Q14584	ZN266_HUMAN	zinc finger protein 266						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						ccttccccaaggaaactcttg	0.000													4	2	---	---	---	---	
OLFM2	93145	broad.mit.edu	37	19	10021395	10021396	+	Intron	DEL	GG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10021395_10021396delGG	uc002mmp.2	-							NM_058164	NP_477512	O95897	NOE2_HUMAN	olfactomedin 2 precursor							extracellular region				large_intestine(1)|skin(1)	2						ggatagagatggatggatagaa	0.089													4	4	---	---	---	---	
OLFM2	93145	broad.mit.edu	37	19	10021404	10021405	+	Intron	INS	-	C	C			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10021404_10021405insC	uc002mmp.2	-							NM_058164	NP_477512	O95897	NOE2_HUMAN	olfactomedin 2 precursor							extracellular region				large_intestine(1)|skin(1)	2						tggatggatagaagaatggatC	0.089													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	15917666	15917666	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15917666delA								OR10H5 (11861 upstream) : OR10H1 (151 downstream)																							cctcccaagtagctagggtta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24564777	24564777	+	IGR	DEL	G	-	-	rs2198819	by1000genomes	TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24564777delG								LOC100101266 (218528 upstream) : None (None downstream)																							tatcttctgagaagagctaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24575195	24575196	+	IGR	INS	-	TTGA	TTGA	rs111495385		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24575195_24575196insTTGA								LOC100101266 (228946 upstream) : None (None downstream)																							tgaaactttctttgagcagttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27847262	27847262	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27847262delA								None (None upstream) : LOC148189 (434140 downstream)																							ctgctccatcaaaaaaaaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	33765107	33765108	+	IGR	DEL	TG	-	-	rs67711448		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33765107_33765108delTG								SLC7A10 (48351 upstream) : CEBPA (25734 downstream)																							TGGCTGAGTCtgtgtgtgtgtg	0.436													5	3	---	---	---	---	
SIPA1L3	23094	broad.mit.edu	37	19	38569079	38569080	+	Intron	DEL	CA	-	-	rs66830496		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38569079_38569080delCA	uc002ohk.2	+							NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CGCATACATGcacacacacaca	0.248													2	4	---	---	---	---	
XRCC1	7515	broad.mit.edu	37	19	44049433	44049433	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44049433delC	uc002owt.2	-						XRCC1_uc010xwp.1_Intron	NM_006297	NP_006288	P18887	XRCC1_HUMAN	X-ray repair cross complementing protein 1						base-excision repair|single strand break repair	nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(2)|large_intestine(1)|prostate(1)|breast(1)	7		Prostate(69;0.0153)				TGCCCCTCATCCCACAACTCC	0.383								Other_BER_factors					4	2	---	---	---	---	
SNAR-A4	100169956	broad.mit.edu	37	19	50627126	50627127	+	5'Flank	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50627126_50627127insA	uc010ybw.1	-							NR_024242				Homo sapiens small ILF3/NF90-associated RNA A3 (SNAR-A3), non-coding RNA.												0						atctcaaaaacaaacaaacaaa	0.005													5	4	---	---	---	---	
ZNF175	7728	broad.mit.edu	37	19	52084427	52084427	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52084427delA	uc002pxb.2	+							NM_007147	NP_009078	Q9Y473	ZN175_HUMAN	zinc finger protein 175						response to virus	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		CTCATTTTTGAAAAAAAAAAA	0.348													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	4175763	4175764	+	Intron	INS	-	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4175763_4175764insT	uc002wkq.2	+											Homo sapiens cDNA clone IMAGE:6422495, partial cds.																		ttcacttctgcacgtccaatga	0.074													4	2	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8660742	8660742	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8660742delT	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						TGTTACTAAGTTTTTTAGAAA	0.244													4	2	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8698724	8698724	+	Intron	DEL	G	-	-	rs73613688		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8698724delG	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron|PLCB1_uc002wnd.1_Intron	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						aaaattatctgggcatagtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	10615830	10615830	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10615830delA								C20orf94 (11805 upstream) : JAG1 (2502 downstream)																							TGTGGGGTGGAAAAAAAATGT	0.413													4	2	---	---	---	---	
PLUNC	51297	broad.mit.edu	37	20	31828385	31828388	+	Intron	DEL	GACA	-	-	rs33949511		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31828385_31828388delGACA	uc002wyv.2	+						PLUNC_uc002wyt.3_Intron|PLUNC_uc002wyu.3_Intron	NM_130852	NP_570913	Q9NP55	PLUNC_HUMAN	palate, lung and nasal epithelium associated						innate immune response	extracellular region	lipid binding				0						tggatggatggacagatggttaga	0.137													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36825955	36825956	+	IGR	INS	-	GT	GT			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36825955_36825956insGT								TGM2 (32255 upstream) : KIAA1755 (12951 downstream)																							TGCATATGTGCGTGTGTGTGTg	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55228511	55228511	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55228511delT								TFAP2C (14175 upstream) : BMP7 (515298 downstream)																							ATCTCCTGCCTTTTTTTCCAC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10087063	10087063	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10087063delT								None (None upstream) : TPTE (819680 downstream)																							tggaatggaattggaatggaa	0.000													5	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11072388	11072389	+	Intron	INS	-	T	T	rs140345115		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11072388_11072389insT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tggttcacgccgtgattccagc	0.000													2	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11093534	11093534	+	Intron	DEL	A	-	-	rs111962813		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11093534delA	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GAACTTGCCTAAAGCCACATC	0.313													6	3	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36711328	36711329	+	Intron	DEL	TC	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36711328_36711329delTC	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						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						GAGCTTGCCTTCTACCTAAAAA	0.262			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36980726	36980726	+	Intron	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36980726delT	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						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						cttatacatgttttttttagt	0.015			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				3	3	---	---	---	---	
DOPEY2	9980	broad.mit.edu	37	21	37650078	37650079	+	Intron	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37650078_37650079insA	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						tcagcctcctgagtagctggga	0.000													12	8	---	---	---	---	
DOPEY2	9980	broad.mit.edu	37	21	37650082	37650082	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37650082delA	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						cctcctgagtagctgggatta	0.000													16	7	---	---	---	---	
MX2	4600	broad.mit.edu	37	21	42745186	42745186	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42745186delA	uc002yzf.1	+						MX2_uc011aer.1_Intron	NM_002463	NP_002454	P20592	MX2_HUMAN	myxovirus resistance protein 2						response to virus|type I interferon-mediated signaling pathway	cytoplasm|nucleus	GTP binding|GTPase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				CAGAGAGAGCAAGGAACCCAA	0.408													4	2	---	---	---	---	
ADARB1	104	broad.mit.edu	37	21	46617820	46617821	+	Intron	DEL	AG	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46617820_46617821delAG	uc002zgy.2	+						ADARB1_uc002zgr.2_Intron|ADARB1_uc002zgs.2_Intron|ADARB1_uc002zgw.2_Intron|ADARB1_uc002zgv.2_Intron|ADARB1_uc002zgt.2_Intron|ADARB1_uc010gpx.2_Intron|ADARB1_uc002zgq.2_Intron|ADARB1_uc002zgu.2_Intron	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2						adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)		gttattgcctagtggggacaga	0.000													4	2	---	---	---	---	
DEPDC5	9681	broad.mit.edu	37	22	32300361	32300361	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32300361delA	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alu.2_Intron|DEPDC5_uc003alv.2_Intron|DEPDC5_uc003alw.2_Intron|DEPDC5_uc011alx.1_Intron|DEPDC5_uc010gwk.2_Intron|DEPDC5_uc011aly.1_Intron	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8						GAAATGAGGTAAAAAAAAATT	0.373													4	2	---	---	---	---	
EFCAB6	64800	broad.mit.edu	37	22	43943457	43943457	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43943457delA	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc010gzj.1_Intron	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				cagtctctacaaaaaaccaac	0.000													4	2	---	---	---	---	
EFCAB6	64800	broad.mit.edu	37	22	44133315	44133316	+	Intron	DEL	CA	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44133315_44133316delCA	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron|EFCAB6_uc003beb.3_Intron	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				caccatcactcacacacacata	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	46413112	46413112	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46413112delT								LOC730668 (6455 upstream) : LOC100271722 (22677 downstream)																							GATTTATGGATTTtttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	4799759	4799760	+	IGR	INS	-	T	T			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4799759_4799760insT								None (None upstream) : None (None downstream)																							TTCTCAGTGTGTTTTAGTTGTC	0.475													4	2	---	---	---	---	
PRRG1	5638	broad.mit.edu	37	X	37265250	37265251	+	Intron	INS	-	A	A			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37265250_37265251insA	uc004ddn.2	+						PRRG1_uc004ddo.2_Intron|PRRG1_uc010ngx.1_Intron	NM_000950	NP_000941	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1							extracellular region|integral to plasma membrane	calcium ion binding			ovary(1)|breast(1)	2						AGTAAGTTGATATAGAGCCCCT	0.391													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	41970884	41970884	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41970884delA								CASK (188597 upstream) : PPP1R2P9 (665735 downstream)																							TGGAACTAGGAAACCCATTTA	0.234													4	2	---	---	---	---	
SHROOM4	57477	broad.mit.edu	37	X	50506031	50506031	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50506031delA	uc004dpe.2	-						SHROOM4_uc004dpd.3_Intron	NM_020717	NP_065768	Q9ULL8	SHRM4_HUMAN	shroom family member 4						actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding			upper_aerodigestive_tract(1)	1	Ovarian(276;0.236)					tatcatgtgtatgttgaagca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	65663621	65663621	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65663621delT								HEPH (176393 upstream) : EDA2R (151862 downstream)																							TGGCCACTCATTTTTTTTTTC	0.358													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	69484898	69484898	+	IGR	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69484898delC								P2RY4 (5244 upstream) : ARR3 (3287 downstream)																							GTTCCGTCCTCCCCCACTGAG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	75654672	75654672	+	IGR	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75654672delA								MAGEE1 (2928 upstream) : MIR384 (485026 downstream)																							AGCTACAGTCAATGTGACTGA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	93283076	93283076	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:93283076delT								FAM133A (315815 upstream) : None (None downstream)																							GCAATACTCATTTTTTTTTCT	0.408													4	2	---	---	---	---	
LOC442459	442459	broad.mit.edu	37	X	98785374	98785374	+	Intron	DEL	A	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:98785374delA	uc011mrd.1	-							NR_024608				Homo sapiens DNA repair protein mRNA, complete cds.												0						aagttaatggaaaaaaaagag	0.000													4	2	---	---	---	---	
ENOX2	10495	broad.mit.edu	37	X	129844395	129844395	+	Intron	DEL	C	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129844395delC	uc004evw.2	-						ENOX2_uc004evx.2_Intron|ENOX2_uc004evy.2_Intron	NM_182314	NP_872114	Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2 isoform b						cell growth|electron transport chain|regulation of growth|transport|ultradian rhythm	cytosol|external side of plasma membrane|extracellular space	nucleic acid binding|nucleotide binding|protein disulfide oxidoreductase activity			ovary(1)	1						GCCAAGtttgccccacagggg	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	133392450	133392452	+	IGR	DEL	GGT	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133392450_133392452delGGT								CCDC160 (12644 upstream) : PHF6 (114890 downstream)																							cttggccaggggtggtggtggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13444848	13444848	+	IGR	DEL	T	-	-			TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13444848delT								None (None upstream) : None (None downstream)																							CTAGGCAGTATTTTTAGTGCA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59004691	59004692	+	IGR	DEL	AG	-	-	rs71687730		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59004691_59004692delAG								None (None upstream) : None (None downstream)																							aaagaaagttagttaataatgg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59004694	59004695	+	IGR	DEL	TA	-	-	rs67126218		TCGA-CJ-5680-01A-11D-1534-10	TCGA-CJ-5680-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59004694_59004695delTA								None (None upstream) : None (None downstream)																							gaaagttagttaataatggcat	0.000													6	3	---	---	---	---	
