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
SPEN	23013	broad.mit.edu	37	1	16256538	16256538	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16256538C>T	uc001axk.1	+	11	4007	c.3803C>T	c.(3802-3804)TCC>TTC	p.S1268F	SPEN_uc010obp.1_Missense_Mutation_p.S1227F	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1268					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CGACATGGTTCCTTCCATGAA	0.458													24	78	---	---	---	---	PASS
MAP3K6	9064	broad.mit.edu	37	1	27684801	27684801	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27684801G>A	uc001bny.1	-	21	3035	c.2786C>T	c.(2785-2787)TCT>TTT	p.S929F	MAP3K6_uc009vsw.1_Missense_Mutation_p.S921F|MAP3K6_uc001bnz.1_Missense_Mutation_p.S452F	NM_004672	NP_004663	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase	929					activation of JUN kinase activity		ATP binding|magnesium ion binding|MAP kinase kinase kinase activity			breast(4)|lung(3)|ovary(1)|central_nervous_system(1)	9		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GGGACTGGCAGAAGGGGCATC	0.652											OREG0013282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	50	188	---	---	---	---	PASS
PEF1	553115	broad.mit.edu	37	1	32096480	32096480	+	Intron	SNP	A	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32096480A>C	uc001bth.1	-						HCRTR1_uc010ogl.1_Intron|PEF1_uc001bte.1_3'UTR|PEF1_uc001btf.1_Intron|PEF1_uc001btg.1_Intron	NM_012392	NP_036524	Q9UBV8	PEF1_HUMAN	penta-EF-hand domain containing 1						response to calcium ion	cytoplasm|membrane	calcium ion binding|protein heterodimerization activity				0		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)|all_neural(195;0.186)		STAD - Stomach adenocarcinoma(196;0.0546)		ACACACAAAAACCTGCCATGA	0.527													9	17	---	---	---	---	PASS
DNAJC6	9829	broad.mit.edu	37	1	65831861	65831861	+	Silent	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65831861T>C	uc001dcd.1	+	4	518	c.354T>C	c.(352-354)ACT>ACC	p.T118T	DNAJC6_uc001dcc.1_Silent_p.T149T|DNAJC6_uc010opc.1_Silent_p.T105T|DNAJC6_uc001dce.1_Silent_p.T175T	NM_014787	NP_055602	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	118	Phosphatase tensin-type.				cellular membrane organization|post-Golgi vesicle-mediated transport	cytosol	heat shock protein binding|protein tyrosine phosphatase activity|SH3 domain binding			large_intestine(1)|lung(1)|ovary(1)	3						CTTATCGAACTGCCAAGTTTC	0.438													74	199	---	---	---	---	PASS
ST6GALNAC5	81849	broad.mit.edu	37	1	77510087	77510087	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77510087C>T	uc001dhi.2	+	3	635	c.460C>T	c.(460-462)CGC>TGC	p.R154C	ST6GALNAC5_uc010ori.1_Intron|ST6GALNAC5_uc009wbw.2_RNA	NM_030965	NP_112227	Q9BVH7	SIA7E_HUMAN	sialyltransferase 7E	154	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	sialyltransferase activity			pancreas(1)|skin(1)	2						GAGGATCCTCCGCAACCGCCA	0.637													7	13	---	---	---	---	PASS
RPF1	80135	broad.mit.edu	37	1	84945169	84945169	+	Silent	SNP	C	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84945169C>A	uc001djv.3	+	1	250	c.205C>A	c.(205-207)CGG>AGG	p.R69R		NM_025065	NP_079341	Q9H9Y2	RPF1_HUMAN	RNA processing factor 1	69					rRNA processing|translation	nucleolus	aminoacyl-tRNA ligase activity|ATP binding|rRNA binding				0						AATGTTCACGCGGTGGAAACA	0.612													5	30	---	---	---	---	PASS
IGSF3	3321	broad.mit.edu	37	1	117131468	117131468	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117131468C>T	uc001egr.1	-	8	2993	c.2288G>A	c.(2287-2289)GGC>GAC	p.G763D	IGSF3_uc001egq.1_Missense_Mutation_p.G783D|IGSF3_uc001egs.1_Missense_Mutation_p.G436D	NM_001007237	NP_001007238	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 2	763	Ig-like C2-type 6.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		GCTGAACAGGCCCCCCGACAC	0.617													3	34	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	146420167	146420167	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146420167G>A	uc001emp.3	+	24	4013	c.2815G>A	c.(2815-2817)GTT>ATT	p.V939I	uc010ozk.1_Missense_Mutation_p.V247I|uc010ozl.1_Missense_Mutation_p.V207I	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GCAACAGCGTGTTGGCTTGGC	0.463													6	64	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152186944	152186944	+	Silent	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152186944T>C	uc001ezt.1	-	3	7237	c.7161A>G	c.(7159-7161)TCA>TCG	p.S2387S		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	2387	26.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AAGATGAACCTGAGCTAGATC	0.572													6	332	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152282336	152282336	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152282336T>A	uc001ezu.1	-	3	5062	c.5026A>T	c.(5026-5028)AGT>TGT	p.S1676C		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1676	Ser-rich.|Filaggrin 10.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTCCTGGACTTGACCTTGCC	0.562									Ichthyosis				31	112	---	---	---	---	PASS
GBAP1	2630	broad.mit.edu	37	1	155188758	155188758	+	5'UTR	SNP	A	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155188758A>C	uc001fjd.2	-	1					RAG1AP1_uc010pey.1_Intron|GBAP1_uc001fjf.3_Intron|GBAP1_uc001fje.3_Intron					SubName: Full=cDNA FLJ56170, highly similar to Glucosylceramidase (EC 3.2.1.45);												0						GGATGCAGGTACCTGCCATAG	0.478													13	15	---	---	---	---	PASS
BCAN	63827	broad.mit.edu	37	1	156628842	156628842	+	Silent	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156628842G>A	uc001fpp.2	+	14	2988	c.2652G>A	c.(2650-2652)GAG>GAA	p.E884E		NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	884					cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ACCCAGAGGAGGACCCAGAAG	0.632													5	39	---	---	---	---	PASS
BCAN	63827	broad.mit.edu	37	1	156628843	156628843	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156628843G>C	uc001fpp.2	+	14	2989	c.2653G>C	c.(2653-2655)GAC>CAC	p.D885H		NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	885					cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCCAGAGGAGGACCCAGAAGG	0.632													5	39	---	---	---	---	PASS
ABL2	27	broad.mit.edu	37	1	179086363	179086363	+	Intron	SNP	T	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179086363T>G	uc001gmj.3	-						ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Intron|ABL2_uc009wxe.2_Intron|ABL2_uc001gmg.3_Intron|ABL2_uc001gmi.3_Intron|ABL2_uc001gmh.3_Intron|ABL2_uc010pne.1_Intron|ABL2_uc009wxf.1_3'UTR|ABL2_uc001gmk.2_3'UTR	NM_007314	NP_009298	P42684	ABL2_HUMAN	arg tyrosine kinase isoform b						axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	GAATGGCAGGTAAAGGTAGAG	0.189			T	ETV6	AML								6	9	---	---	---	---	PASS
CFH	3075	broad.mit.edu	37	1	196621079	196621079	+	5'UTR	SNP	G	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196621079G>T	uc001gtj.3	+	1					CFH_uc001gti.3_5'UTR|CFH_uc009wyw.2_5'UTR|CFH_uc009wyx.2_5'UTR	NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor						complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6						CTTGTGGCTTGTGGTTGATTT	0.398													7	25	---	---	---	---	PASS
LGTN	1939	broad.mit.edu	37	1	206772405	206772405	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206772405A>G	uc001heh.2	-	11	1453	c.1244T>C	c.(1243-1245)GTC>GCC	p.V415A	LGTN_uc009xbw.2_Missense_Mutation_p.V291A	NM_006893	NP_008824	P41214	EIF2D_HUMAN	ligatin	415					intracellular protein transport	cytoplasm	protein binding|receptor activity|translation initiation factor activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			GTAGTTAATGACGATCGTTCG	0.468													6	326	---	---	---	---	PASS
CR2	1380	broad.mit.edu	37	1	207641916	207641916	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207641916C>T	uc001hfw.2	+	3	584	c.490C>T	c.(490-492)CAT>TAT	p.H164Y	CR2_uc001hfv.2_Missense_Mutation_p.H164Y|CR2_uc009xch.2_Missense_Mutation_p.H164Y|CR2_uc009xci.1_5'Flank	NM_001877	NP_001868	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)	164	Sushi 3.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8						CCACAATGGACATCACACAAG	0.433													5	397	---	---	---	---	PASS
ARID4B	51742	broad.mit.edu	37	1	235377293	235377293	+	Silent	SNP	C	T	T	rs10588817		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235377293C>T	uc001hwq.2	-	17	2130	c.1632G>A	c.(1630-1632)GAG>GAA	p.E544E	ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwt.3_Silent_p.E225E	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	544	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			cctcctcctcctcttctgctt	0.224													5	338	---	---	---	---	PASS
ZAK	51776	broad.mit.edu	37	2	174123542	174123542	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174123542A>G	uc002uhz.2	+	17	1675	c.1475A>G	c.(1474-1476)AAG>AGG	p.K492R	uc002uib.2_Intron	NM_016653	NP_057737	Q9NYL2	MLTK_HUMAN	MLK-related kinase isoform 1	492					activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			lung(3)|stomach(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.176)			AAGATGACAAAGGTAGGGTTC	0.373													6	326	---	---	---	---	PASS
SP3	6670	broad.mit.edu	37	2	174777990	174777990	+	Missense_Mutation	SNP	T	C	C	rs144265071		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174777990T>C	uc002uig.2	-	6	2001	c.1837A>G	c.(1837-1839)ACC>GCC	p.T613A	SP3_uc002uie.2_Missense_Mutation_p.T545A|SP3_uc002uif.2_Missense_Mutation_p.T560A|SP3_uc010zel.1_Missense_Mutation_p.T610A	NM_003111	NP_003102	Q02447	SP3_HUMAN	Sp3 transcription factor isoform 1	613	Repressor domain.				negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	protein binding|zinc ion binding		EWSR1/SP3(3)	soft_tissue(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.185)			CCAAGATTGGTACCTCTAAAA	0.338													5	131	---	---	---	---	PASS
ALS2	57679	broad.mit.edu	37	2	202614458	202614458	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202614458T>C	uc002uyo.2	-	8	2148	c.1792A>G	c.(1792-1794)ACA>GCA	p.T598A	ALS2_uc002uyp.3_Missense_Mutation_p.T598A|ALS2_uc002uyq.2_Missense_Mutation_p.T598A	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1	598	RCC1 5.				cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						GGAACTGTTGTTGGAAAATCG	0.368													5	210	---	---	---	---	PASS
PECR	55825	broad.mit.edu	37	2	216908692	216908692	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216908692A>G	uc002vft.2	-	7	829	c.761T>C	c.(760-762)ATC>ACC	p.I254T	PECR_uc010zjq.1_RNA|PECR_uc002vfr.2_Missense_Mutation_p.I116T|PECR_uc002vfs.2_Missense_Mutation_p.I108T	NM_018441	NP_060911	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	254					fatty acid biosynthetic process|regulation of apoptosis	peroxisome	binding|trans-2-enoyl-CoA reductase (NADPH) activity				0		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	CTGTCCAGTGATGAAGGAAGC	0.502													4	99	---	---	---	---	PASS
MIR26B	407017	broad.mit.edu	37	2	219267407	219267407	+	RNA	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219267407C>T	hsa-mir-26b|MI0000084	+			c.39C>T			CTDSP1_uc002vhy.2_Intron|CTDSP1_uc002vhx.2_Intron|CTDSP1_uc002vhz.2_Intron|uc010zkd.1_RNA																	0						AGGTTGTGTGCTGTCCAGCCT	0.637													4	68	---	---	---	---	PASS
GIGYF2	26058	broad.mit.edu	37	2	233641145	233641145	+	Intron	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233641145A>G	uc002vti.3	+						GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Missense_Mutation_p.M186V|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron|KCNJ13_uc002vtp.2_Intron	NM_015575	NP_056390	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2 isoform b						cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		ATATTATTGCATGTACTCACC	0.363													6	367	---	---	---	---	PASS
XYLB	9942	broad.mit.edu	37	3	38390050	38390050	+	Missense_Mutation	SNP	G	T	T	rs146884889		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38390050G>T	uc003cic.2	+	2	176	c.67G>T	c.(67-69)GTT>TTT	p.V23F	XYLB_uc011ayp.1_5'UTR	NM_005108	NP_005099	O75191	XYLB_HUMAN	xylulokinase	23					D-xylose metabolic process|generation of precursor metabolites and energy|xylulose catabolic process		ATP binding|xylulokinase activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		GGTAAAGGTTGTTGCTGTTGA	0.428													126	355	---	---	---	---	PASS
STAB1	23166	broad.mit.edu	37	3	52553461	52553461	+	Intron	SNP	T	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52553461T>G	uc003dej.2	+						STAB1_uc003dek.1_5'UTR|STAB1_uc003del.2_5'Flank	NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor						cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GACAGGCAGGTGGGGGCCTGG	0.637													6	26	---	---	---	---	PASS
FLNB	2317	broad.mit.edu	37	3	58132610	58132610	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58132610A>G	uc003djj.2	+	34	5783	c.5618A>G	c.(5617-5619)GAT>GGT	p.D1873G	FLNB_uc010hne.2_Missense_Mutation_p.D1904G|FLNB_uc003djk.2_Missense_Mutation_p.D1862G|FLNB_uc010hnf.2_Missense_Mutation_p.D1849G|FLNB_uc003djl.2_Missense_Mutation_p.D1693G|FLNB_uc003djm.2_Missense_Mutation_p.D1680G|FLNB_uc010hng.1_5'Flank	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2	1873	Filamin 17.|Interaction with the cytoplasmic tail of GP1BA.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GACAATAAAGATGGGACATGC	0.537													4	85	---	---	---	---	PASS
ROBO1	6091	broad.mit.edu	37	3	78655981	78655981	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78655981T>C	uc003dqe.2	-	29	4854	c.4646A>G	c.(4645-4647)GAT>GGT	p.D1549G	ROBO1_uc003dqb.2_Missense_Mutation_p.D1510G|ROBO1_uc003dqc.2_Missense_Mutation_p.D1449G|ROBO1_uc003dqd.2_Missense_Mutation_p.D1504G|ROBO1_uc010hoh.2_Missense_Mutation_p.D741G|ROBO1_uc011bgl.1_Missense_Mutation_p.D1121G	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	1549	Cytoplasmic (Potential).				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TTCTCTGGGATCACCTGGATT	0.478													6	427	---	---	---	---	PASS
PROS1	5627	broad.mit.edu	37	3	93624946	93624946	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93624946C>A	uc003drb.3	-	5	729	c.388G>T	c.(388-390)GGA>TGA	p.G130*	PROS1_uc010hoo.2_5'UTR|PROS1_uc003dqz.3_5'UTR	NM_000313	NP_000304	P07225	PROS_HUMAN	protein S, alpha preproprotein	130	EGF-like 1.				leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)	CTCATATATCCATCTTCATTG	0.373													32	102	---	---	---	---	PASS
WDR52	55779	broad.mit.edu	37	3	113049451	113049451	+	Missense_Mutation	SNP	A	C	C	rs79365690		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113049451A>C	uc003ead.1	-	8	1236	c.1223T>G	c.(1222-1224)GTT>GGT	p.V408G	WDR52_uc010hqk.1_5'Flank			Q96MT7	WDR52_HUMAN	RecName: Full=WD repeat protein 52.; Flags: Fragment;	Error:Variant_position_missing_in_Q96MT7_after_alignment										central_nervous_system(1)	1						TTCCTCAACAACAGCCACTTT	0.408													30	201	---	---	---	---	PASS
SGEF	26084	broad.mit.edu	37	3	153943712	153943712	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153943712A>G	uc011bog.1	+	11	2214	c.2003A>G	c.(2002-2004)GAC>GGC	p.D668G	SGEF_uc011boh.1_Missense_Mutation_p.D668G|SGEF_uc011boi.1_5'UTR	NM_015595	NP_056410	Q96DR7	ARHGQ_HUMAN	Src homology 3 domain-containing guanine	668	PH.				regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TATGTTGAAGACACTGTGCTT	0.413													6	467	---	---	---	---	PASS
MCF2L2	23101	broad.mit.edu	37	3	183027516	183027516	+	Silent	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183027516C>T	uc003fli.1	-	10	1191	c.1101G>A	c.(1099-1101)GAG>GAA	p.E367E	MCF2L2_uc003flj.1_Silent_p.E367E|MCF2L2_uc003flp.1_3'UTR|MCF2L2_uc011bqs.1_RNA	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor	367	Spectrin.				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)			GGCTTTTTTCCTCCAGTTTTT	0.458													5	244	---	---	---	---	PASS
HTR3E	285242	broad.mit.edu	37	3	183823757	183823757	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183823757G>A	uc010hxq.2	+	7	1391	c.925G>A	c.(925-927)GGT>AGT	p.G309S	HTR3E_uc003fml.3_Missense_Mutation_p.G294S|HTR3E_uc003fmm.2_Missense_Mutation_p.G324S|HTR3E_uc010hxr.2_Missense_Mutation_p.G335S|HTR3E_uc003fmn.2_Missense_Mutation_p.G309S	NM_182589	NP_872395	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine receptor 3 subunit E	309	Helical; Name=3; (Potential).					integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			CCCCCTCATCGGTATGGCTCC	0.547													5	140	---	---	---	---	PASS
LPP	4026	broad.mit.edu	37	3	187897064	187897064	+	Intron	SNP	G	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187897064G>T	uc011bsg.1	+						FLJ42393_uc011bsh.1_RNA	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TCTTCGCAGCGGAGCTTCTTT	0.567			T	HMGA2|MLL|C12orf9	lipoma|leukemia								52	60	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506627	195506627	+	Missense_Mutation	SNP	T	G	G	rs145875920	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506627T>G	uc011bto.1	-	3	11900	c.11440A>C	c.(11440-11442)ACT>CCT	p.T3814P	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGTGCTGGTGACA	0.582													10	64	---	---	---	---	PASS
EPHA5	2044	broad.mit.edu	37	4	66467834	66467834	+	Silent	SNP	C	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66467834C>G	uc003hcy.2	-	3	628	c.435G>C	c.(433-435)GGG>GGC	p.G145G	EPHA5_uc003hcx.2_Silent_p.G76G|EPHA5_uc003hcz.2_Silent_p.G145G|EPHA5_uc011cah.1_Silent_p.G145G|EPHA5_uc011cai.1_Silent_p.G145G|EPHA5_uc003hda.2_Silent_p.G145G	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	145	Extracellular (Potential).				cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						CCTTACAGGTCCCCAGTCCTC	0.423										TSP Lung(17;0.13)			25	111	---	---	---	---	PASS
TMPRSS11B	132724	broad.mit.edu	37	4	69111349	69111349	+	5'UTR	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69111349A>G	uc003hdw.3	-	1						NM_182502	NP_872308	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B						proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1						gataacgatgacaatgctggt	0.299													6	231	---	---	---	---	PASS
UGT2B7	7364	broad.mit.edu	37	4	69972925	69972925	+	Silent	SNP	T	C	C	rs147582860	byFrequency	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69972925T>C	uc003heg.3	+	4	1081	c.1035T>C	c.(1033-1035)GAT>GAC	p.D345D	UGT2B7_uc010ihq.2_Silent_p.D345D	NM_001074	NP_001065	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2B7 precursor	345					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|skin(1)	2						ATAAACCAGATACCTTAGGTC	0.358													138	532	---	---	---	---	PASS
RCHY1	25898	broad.mit.edu	37	4	76419490	76419490	+	Intron	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76419490T>C	uc003hik.2	-						RCHY1_uc010iio.2_5'UTR|RCHY1_uc003hij.2_Intron|RCHY1_uc003hil.2_Intron|RCHY1_uc010iip.2_Intron|RCHY1_uc010iiq.2_Intron|RCHY1_uc010iir.2_Intron	NM_015436	NP_056251	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein autoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nuclear speck|ubiquitin ligase complex	electron carrier activity|p53 binding|protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			AAAAAAAATTTCCAGCCACAA	0.358													12	41	---	---	---	---	PASS
CCDC158	339965	broad.mit.edu	37	4	77244509	77244509	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77244509T>C	uc003hkb.3	-	23	3364	c.3211A>G	c.(3211-3213)AAC>GAC	p.N1071D		NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	1071	Potential.									skin(3)|ovary(2)|pancreas(1)	6						TCTAGTCTGTTCTGAAGCTTC	0.383													8	719	---	---	---	---	PASS
C4orf29	80167	broad.mit.edu	37	4	128905554	128905554	+	Silent	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128905554C>T	uc003ifr.2	+	3	471	c.153C>T	c.(151-153)AGC>AGT	p.S51S	C4orf29_uc003ifq.1_RNA|C4orf29_uc003ifs.2_5'UTR	NM_001039717	NP_001034806	Q0P651	CD029_HUMAN	hypothetical protein LOC80167 precursor	51						extracellular region				ovary(1)	1						TGGTTTCAAGCGATTATCCAG	0.318													75	272	---	---	---	---	PASS
PET112L	5188	broad.mit.edu	37	4	152680071	152680071	+	Silent	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152680071T>C	uc003iml.2	-	2	192	c.180A>G	c.(178-180)GAA>GAG	p.E60E	PET112L_uc003imm.3_Silent_p.E60E	NM_004564	NP_004555	O75879	GATB_HUMAN	PET112-like precursor	60						mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding				0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)			L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	CCCATTTGTGTTCACTAAGAA	0.363													6	247	---	---	---	---	PASS
DCHS2	54798	broad.mit.edu	37	4	155219151	155219151	+	Silent	SNP	A	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155219151A>T	uc003inw.2	-	18	4950	c.4950T>A	c.(4948-4950)CCT>CCA	p.P1650P		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	1650	Cadherin 14.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GCAGCCAGATAGGGAAGTATT	0.408													35	117	---	---	---	---	PASS
RAI14	26064	broad.mit.edu	37	5	34823798	34823798	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34823798T>G	uc003jir.2	+	15	2047	c.1851T>G	c.(1849-1851)AGT>AGG	p.S617R	RAI14_uc010iur.2_Missense_Mutation_p.S588R|RAI14_uc011coj.1_Missense_Mutation_p.S617R|RAI14_uc003jis.2_Missense_Mutation_p.S620R|RAI14_uc003jit.2_Missense_Mutation_p.S617R|RAI14_uc011cok.1_Missense_Mutation_p.S609R	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a	617	Potential.					cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)					CACTAAAAAGTCAGATGACAC	0.383													24	106	---	---	---	---	PASS
LIFR	3977	broad.mit.edu	37	5	38485983	38485983	+	Missense_Mutation	SNP	C	T	T	rs143995164		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38485983C>T	uc010ive.1	-	17	2767	c.2435G>A	c.(2434-2436)CGA>CAA	p.R812Q	LIFR_uc003jli.2_Missense_Mutation_p.R812Q	NM_001127671	NP_001121143	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor precursor	812	Fibronectin type-III 6.|Extracellular (Potential).				positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)					TGTATAGGCTCGCAAGACCAG	0.433			T	PLAG1	salivary adenoma								5	256	---	---	---	---	PASS
IPO11	51194	broad.mit.edu	37	5	61789862	61789862	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61789862G>A	uc003jtc.2	+	16	1691	c.1501G>A	c.(1501-1503)GGT>AGT	p.G501S	IPO11_uc011cqr.1_Missense_Mutation_p.G541S|IPO11_uc003jtb.1_Missense_Mutation_p.G501S	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2	501	HEAT 5.					cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		TTGGCTCATCGGTCAGTGGAT	0.343													4	326	---	---	---	---	PASS
MAST4	375449	broad.mit.edu	37	5	66459285	66459285	+	Silent	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66459285C>T	uc003jut.1	+	28	3779	c.3711C>T	c.(3709-3711)CAC>CAT	p.H1237H	MAST4_uc003juw.2_Silent_p.H1165H|MAST4_uc003jux.2_5'Flank	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	1429						cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TCGTCAGACACATCGTGAGGC	0.622													6	8	---	---	---	---	PASS
MEGF10	84466	broad.mit.edu	37	5	126776499	126776499	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126776499G>A	uc003kuh.3	+	19	2664	c.2302G>A	c.(2302-2304)GAC>AAC	p.D768N	MEGF10_uc003kui.3_Missense_Mutation_p.D768N	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor	768	Extracellular (Potential).|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.|EGF-like 14.				cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		AGCTGACTGCGACCACATTTC	0.493													40	151	---	---	---	---	PASS
SLC36A1	206358	broad.mit.edu	37	5	150843145	150843145	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150843145G>T	uc003luc.2	+	3	392	c.175G>T	c.(175-177)GGC>TGC	p.G59C	GM2A_uc011dcs.1_Intron|SLC36A1_uc003lub.1_Missense_Mutation_p.G59C|SLC36A1_uc010jhw.1_Missense_Mutation_p.G59C	NM_078483	NP_510968	Q7Z2H8	S36A1_HUMAN	solute carrier family 36 member 1	59	Helical; Name=1; (Potential).				cellular nitrogen compound metabolic process|ion transport	endoplasmic reticulum|integral to membrane|lysosomal membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			skin(1)	1		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glycine(DB00145)|L-Alanine(DB00160)	CCTGTTAAAAGGCAACATTGG	0.438													43	135	---	---	---	---	PASS
ZNF454	285676	broad.mit.edu	37	5	178369697	178369697	+	5'UTR	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178369697A>G	uc003mjo.1	+	2					ZNF454_uc010jkz.1_5'UTR|ZNF454_uc003mjp.2_Missense_Mutation_p.D4G	NM_182594	NP_872400	Q8N9F8	ZN454_HUMAN	zinc finger protein 454						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		AGGTGTGTGGACCCTTCTAGC	0.552													8	21	---	---	---	---	PASS
SYCP2L	221711	broad.mit.edu	37	6	10911079	10911079	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10911079G>T	uc003mzo.2	+	12	1191	c.895G>T	c.(895-897)GCT>TCT	p.A299S	SYCP2L_uc011din.1_Missense_Mutation_p.A140S|SYCP2L_uc010jow.2_Intron	NM_001040274	NP_001035364	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	299						nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			TCCGTGTATTGCTGCTTTTGC	0.418													131	464	---	---	---	---	PASS
BTN3A1	11119	broad.mit.edu	37	6	26413447	26413447	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26413447G>A	uc003nhv.2	+	10	1437	c.1069G>A	c.(1069-1071)GAG>AAG	p.E357K	BTN3A1_uc011dkj.1_3'UTR|BTN3A1_uc011dkk.1_Missense_Mutation_p.E305K|BTN3A1_uc010jqj.2_3'UTR	NM_007048	NP_008979	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1 isoform a	357	Cytoplasmic (Potential).|B30.2/SPRY.				lipid metabolic process	integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2						CCTTGTTTCTGAGGACCAGAG	0.498													38	176	---	---	---	---	PASS
POLH	5429	broad.mit.edu	37	6	43554938	43554938	+	Intron	SNP	T	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43554938T>G	uc003ovq.3	+						POLH_uc010jyu.2_Intron|POLH_uc011dvl.1_Intron|POLH_uc003ovr.3_5'UTR	NM_006502	NP_006493	Q9Y253	POLH_HUMAN	DNA-directed DNA polymerase eta						DNA replication|DNA synthesis involved in DNA repair|regulation of DNA repair|response to UV-C	cytoplasm|nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			breast(2)	2	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			TATGGCAGGGTGGGAGTGGAG	0.368								DNA_polymerases_(catalytic_subunits)	Xeroderma_Pigmentosum				27	47	---	---	---	---	PASS
CENPQ	55166	broad.mit.edu	37	6	49456071	49456071	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49456071A>G	uc003ozh.1	+	7	573	c.484A>G	c.(484-486)ATA>GTA	p.I162V		NM_018132	NP_060602	Q7L2Z9	CENPQ_HUMAN	centromere protein Q	162					CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)					TCAGGAAGAAATAGATAAAAT	0.299													5	205	---	---	---	---	PASS
KHDRBS2	202559	broad.mit.edu	37	6	62757853	62757853	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62757853T>C	uc003peg.2	-	3	513	c.266A>G	c.(265-267)AAG>AGG	p.K89R		NM_152688	NP_689901	Q5VWX1	KHDR2_HUMAN	KH domain-containing, RNA-binding, signal	89	KH.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)		CTGTAGCCTCTTCAAGGAGTT	0.358													6	507	---	---	---	---	PASS
KCNQ5	56479	broad.mit.edu	37	6	73713668	73713668	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73713668T>C	uc003pgk.2	+	2	783	c.436T>C	c.(436-438)TTT>CTT	p.F146L	KCNQ5_uc003pgj.3_Missense_Mutation_p.F146L|KCNQ5_uc011dyh.1_Missense_Mutation_p.F146L|KCNQ5_uc011dyi.1_Missense_Mutation_p.F146L|KCNQ5_uc010kat.2_Missense_Mutation_p.F146L|KCNQ5_uc011dyj.1_Missense_Mutation_p.F146L|KCNQ5_uc011dyk.1_5'UTR	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	146	Helical; Name=Segment S1; (Potential).				protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		TTTGTCAGTGTTTTCTACCAT	0.358													7	618	---	---	---	---	PASS
TMEM200A	114801	broad.mit.edu	37	6	130761752	130761752	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130761752G>C	uc003qca.2	+	3	1056	c.185G>C	c.(184-186)GGT>GCT	p.G62A	TMEM200A_uc010kfh.2_Missense_Mutation_p.G62A|TMEM200A_uc010kfi.2_Missense_Mutation_p.G62A|TMEM200A_uc003qcb.2_Missense_Mutation_p.G62A	NM_052913	NP_443145	Q86VY9	T200A_HUMAN	transmembrane protein 200A	62	Helical; (Potential).					integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TCCCCATCTGGTTTTTTTCTT	0.473													48	293	---	---	---	---	PASS
GPR126	57211	broad.mit.edu	37	6	142741085	142741085	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142741085A>T	uc010khc.2	+	22	3574	c.3163A>T	c.(3163-3165)AGC>TGC	p.S1055C	GPR126_uc010khd.2_Missense_Mutation_p.S1027C|GPR126_uc010khe.2_Missense_Mutation_p.S1055C|GPR126_uc010khf.2_Missense_Mutation_p.S1027C|GPR126_uc011edv.1_Missense_Mutation_p.S115C	NM_020455	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 alpha 1	1055	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		TGGCAAGAGAAGCAACCGGAC	0.468													121	429	---	---	---	---	PASS
MTHFD1L	25902	broad.mit.edu	37	6	151206821	151206821	+	Silent	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151206821T>C	uc003qob.2	+	6	862	c.594T>C	c.(592-594)TGT>TGC	p.C198C	MTHFD1L_uc011een.1_RNA|MTHFD1L_uc011eeo.1_Silent_p.C198C|MTHFD1L_uc003qoc.2_Silent_p.C145C|MTHFD1L_uc003qoa.1_Silent_p.C198C|MTHFD1L_uc010kil.1_RNA	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+	198	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.				folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		CCCATGAATGTTTTGTTTCAC	0.398													6	493	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94049879	94049879	+	Silent	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94049879A>G	uc003ung.1	+	37	2685	c.2214A>G	c.(2212-2214)AAA>AAG	p.K738K	COL1A2_uc011kib.1_Intron|COL1A2_uc010lfi.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	738			Missing (in OI2A).		axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CTGGTGCTAAAGGAGAAAGAG	0.507										HNSCC(75;0.22)			5	128	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	96113212	96113212	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96113212C>A	uc003uoh.1	-	5	433	c.346G>T	c.(346-348)GGT>TGT	p.G116C	uc011kil.1_Missense_Mutation_p.G106C					RecName: Full=Putative uncharacterized protein FLJ42280;																		TAGAGGTCACCCGAATGGCAG	0.507													12	69	---	---	---	---	PASS
ABCB8	11194	broad.mit.edu	37	7	150731895	150731895	+	Silent	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150731895C>T	uc003wil.3	+	6	888	c.795C>T	c.(793-795)TCC>TCT	p.S265S	ABCB8_uc003wii.2_Silent_p.S285S|ABCB8_uc003wij.3_Silent_p.S248S|ABCB8_uc010lpw.1_Silent_p.S67S|ABCB8_uc010lpx.2_Silent_p.S248S|ABCB8_uc011kvd.1_Silent_p.S160S|ABCB8_uc003wim.3_Silent_p.S43S|ABCB8_uc003wik.3_Silent_p.S248S	NM_007188	NP_009119	Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B, member 8	265	ABC transmembrane type-1.					ATP-binding cassette (ABC) transporter complex|integral to membrane|membrane fraction|mitochondrial inner membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(2)|upper_aerodigestive_tract(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTAAGTCATCCTTCAAGCTTG	0.572													22	87	---	---	---	---	PASS
CTSB	1508	broad.mit.edu	37	8	11710911	11710911	+	Missense_Mutation	SNP	C	T	T	rs151331859	byFrequency	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11710911C>T	uc003wum.2	-	4	377	c.53G>A	c.(52-54)CGG>CAG	p.R18Q	CTSB_uc011kxl.1_Missense_Mutation_p.R18Q|CTSB_uc003wun.2_Missense_Mutation_p.R18Q|CTSB_uc003wuo.2_Missense_Mutation_p.R18Q|CTSB_uc003wup.2_Missense_Mutation_p.R18Q|CTSB_uc003wuq.2_Missense_Mutation_p.R18Q|CTSB_uc010lsc.2_5'UTR|CTSB_uc003wur.2_Missense_Mutation_p.R18Q|CTSB_uc003wus.1_Missense_Mutation_p.R18Q|CTSB_uc003wut.1_Missense_Mutation_p.R18Q	NM_147780	NP_680090	P07858	CATB_HUMAN	cathepsin B preproprotein	18					proteolysis|regulation of apoptosis|regulation of catalytic activity	lysosome|melanosome	cysteine-type endopeptidase activity				0	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		GGGCCTGCTCCGGGCATTGGC	0.592													3	48	---	---	---	---	PASS
CRISPLD1	83690	broad.mit.edu	37	8	75937789	75937789	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75937789G>C	uc003yan.2	+	13	1628	c.1253G>C	c.(1252-1254)TGT>TCT	p.C418S	CRISPLD1_uc011lfk.1_Missense_Mutation_p.C230S|CRISPLD1_uc011lfl.1_Missense_Mutation_p.C230S	NM_031461	NP_113649	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain	418	LCCL 2.					extracellular region				ovary(1)|central_nervous_system(1)	2	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			AGAGTATACTGTCCTCGTAAC	0.299													23	79	---	---	---	---	PASS
ZNF623	9831	broad.mit.edu	37	8	144733782	144733782	+	3'UTR	SNP	A	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144733782A>C	uc003yzd.2	+	1					ZNF623_uc011lkp.1_3'UTR|ZNF623_uc003yzc.2_3'UTR	NM_014789	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			AGTGGGTGCCACCTGCCACTG	0.517													4	3	---	---	---	---	PASS
PTPRD	5789	broad.mit.edu	37	9	8518037	8518037	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8518037T>C	uc003zkk.2	-	20	2065	c.1354A>G	c.(1354-1356)AGA>GGA	p.R452G	PTPRD_uc003zkp.2_Missense_Mutation_p.R452G|PTPRD_uc003zkq.2_Missense_Mutation_p.R452G|PTPRD_uc003zkr.2_Missense_Mutation_p.R446G|PTPRD_uc003zks.2_Missense_Mutation_p.R442G|PTPRD_uc003zkl.2_Missense_Mutation_p.R452G|PTPRD_uc003zkm.2_Missense_Mutation_p.R439G|PTPRD_uc003zkn.2_Missense_Mutation_p.R452G|PTPRD_uc003zko.2_Missense_Mutation_p.R449G	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	452	Fibronectin type-III 2.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TAATAAACTCTATATCCTTGG	0.458										TSP Lung(15;0.13)			7	532	---	---	---	---	PASS
VCP	7415	broad.mit.edu	37	9	35062162	35062162	+	Intron	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35062162A>G	uc003zvy.2	-						VCP_uc003zvz.2_Intron|VCP_uc010mkh.1_5'UTR|VCP_uc010mki.1_Intron	NM_007126	NP_009057	P55072	TERA_HUMAN	valosin-containing protein						activation of caspase activity|double-strand break repair|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|retrograde protein transport, ER to cytosol	cytosol|endoplasmic reticulum|microsome|nucleus|proteasome complex	ATP binding|ATPase activity|lipid binding|polyubiquitin binding|protein domain specific binding|protein phosphatase binding			upper_aerodigestive_tract(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TCTGGTCAGAAGTGAAGTCAG	0.522													5	181	---	---	---	---	PASS
ZFAND5	7763	broad.mit.edu	37	9	74971943	74971943	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74971943G>A	uc004aiv.2	-	5	675	c.397C>T	c.(397-399)CAG>TAG	p.Q133*	ZFAND5_uc010mox.1_Nonsense_Mutation_p.Q30*|ZFAND5_uc010moy.1_Nonsense_Mutation_p.Q133*|ZFAND5_uc004aix.2_Nonsense_Mutation_p.Q133*|ZFAND5_uc004aiw.2_Nonsense_Mutation_p.Q133*|ZFAND5_uc004aiy.2_Nonsense_Mutation_p.Q133*	NM_006007	NP_005998	O76080	ZFAN5_HUMAN	zinc finger, AN1-type domain 5	133							DNA binding|zinc ion binding				0						GTACTGGGCTGAGAAACTGAT	0.383													114	486	---	---	---	---	PASS
GKAP1	80318	broad.mit.edu	37	9	86414181	86414181	+	Silent	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86414181T>C	uc004amy.2	-	4	775	c.279A>G	c.(277-279)CAA>CAG	p.Q93Q	GKAP1_uc004amz.2_Silent_p.Q93Q|GKAP1_uc011lsu.1_RNA	NM_025211	NP_079487	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1 isoform a	93					signal transduction	Golgi apparatus					0						GAAGATCATGTTGAGCGTTAC	0.353													6	498	---	---	---	---	PASS
NANS	54187	broad.mit.edu	37	9	100843297	100843297	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100843297T>C	uc004ayb.2	+	6	1445	c.803T>C	c.(802-804)CTT>CCT	p.L268P	NANS_uc004ayc.2_Missense_Mutation_p.L268P|TRIM14_uc004ayd.2_Intron|NANS_uc004aye.1_Missense_Mutation_p.L116P|TRIM14_uc004ayf.1_3'UTR	NM_018946	NP_061819	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid phosphate synthase	268					lipopolysaccharide biosynthetic process	cytoplasm	N-acetylneuraminate synthase activity|N-acylneuraminate cytidylyltransferase activity|N-acylneuraminate-9-phosphate synthase activity			skin(1)	1		Acute lymphoblastic leukemia(62;0.0559)				TCAGTGCGTCTTGTGGAGCGT	0.607													20	65	---	---	---	---	PASS
ZBTB6	10773	broad.mit.edu	37	9	125674096	125674096	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125674096G>T	uc004bnh.2	-	2	345	c.256C>A	c.(256-258)CTG>ATG	p.L86M		NM_006626	NP_006617	Q15916	ZBTB6_HUMAN	zinc finger and BTB domain containing 6	86	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TAGCAAGACAGTAACAATTTT	0.393													22	100	---	---	---	---	PASS
PMPCA	23203	broad.mit.edu	37	9	139305134	139305134	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139305134T>C	uc004chl.2	+	1	19	c.14T>C	c.(13-15)GTG>GCG	p.V5A	SDCCAG3_uc004chi.2_5'Flank|SDCCAG3_uc004chj.2_5'Flank|SDCCAG3_uc004chk.2_5'Flank|PMPCA_uc011mdy.1_Missense_Mutation_p.V5A|PMPCA_uc010nbk.2_RNA|PMPCA_uc010nbl.2_5'UTR|PMPCA_uc011mdz.1_5'UTR	NM_015160	NP_055975	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	5					proteolysis	mitochondrial inner membrane|mitochondrial matrix	metalloendopeptidase activity|zinc ion binding				0		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		GCGGCTGTGGTGCTGGCGGCG	0.721													8	21	---	---	---	---	PASS
PARD3	56288	broad.mit.edu	37	10	34626340	34626340	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34626340T>G	uc010qej.1	-	17	2432	c.2432A>C	c.(2431-2433)GAT>GCT	p.D811A	PARD3_uc010qek.1_Missense_Mutation_p.D808A|PARD3_uc010qel.1_Missense_Mutation_p.D811A|PARD3_uc010qem.1_Missense_Mutation_p.D795A|PARD3_uc010qen.1_Missense_Mutation_p.D795A|PARD3_uc010qeo.1_Missense_Mutation_p.D795A|PARD3_uc010qep.1_Missense_Mutation_p.D751A|PARD3_uc010qeq.1_Missense_Mutation_p.D751A|PARD3_uc001ixo.1_Missense_Mutation_p.D525A|PARD3_uc001ixp.1_Missense_Mutation_p.D673A|PARD3_uc001ixq.1_Missense_Mutation_p.D795A|PARD3_uc001ixr.1_Missense_Mutation_p.D808A|PARD3_uc001ixt.1_Missense_Mutation_p.D629A|PARD3_uc001ixu.1_Missense_Mutation_p.D754A|PARD3_uc001ixs.1_Missense_Mutation_p.D464A	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog	811	Interacts with PRKCZ (By similarity).				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				TGGATCAACATCTGGACTCAA	0.363													50	181	---	---	---	---	PASS
GRID1	2894	broad.mit.edu	37	10	87966375	87966375	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87966375G>A	uc001kdl.1	-	3	367	c.266C>T	c.(265-267)GCC>GTC	p.A89V	GRID1_uc009xsu.1_RNA	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	89	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	CGTGACCAAGGCCAAAATCCC	0.592										Multiple Myeloma(13;0.14)			6	20	---	---	---	---	PASS
C10orf4	118924	broad.mit.edu	37	10	95459948	95459948	+	Intron	SNP	A	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95459948A>C	uc001kiz.1	-						C10orf4_uc001kiv.1_Intron|C10orf4_uc001kja.1_Intron|C10orf4_uc001kjb.1_5'UTR|C10orf4_uc009xuh.1_Intron	NM_145246	NP_660289	Q70Z53	F10C1_HUMAN	FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)				gttatcttaaacagccacaat	0.149													14	33	---	---	---	---	PASS
TUBGCP2	10844	broad.mit.edu	37	10	135106637	135106637	+	Silent	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135106637C>T	uc001lmg.1	-	7	1287	c.930G>A	c.(928-930)CTG>CTA	p.L310L	TUBGCP2_uc001lmf.1_5'Flank|TUBGCP2_uc010qvc.1_Silent_p.L338L|TUBGCP2_uc009ybk.1_Silent_p.L310L|TUBGCP2_uc010qvd.1_Silent_p.L180L|TUBGCP2_uc001lmh.1_RNA	NM_006659	NP_006650	Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	310					G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		GCAGCTGCTCCAGCTGTGACA	0.617													3	24	---	---	---	---	PASS
ELP4	26610	broad.mit.edu	37	11	31616367	31616367	+	Silent	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31616367A>G	uc001mtb.2	+	4	467	c.432A>G	c.(430-432)GAA>GAG	p.E144E	ELP4_uc001mta.1_RNA|ELP4_uc001mtc.2_Silent_p.E144E|ELP4_uc010rdz.1_Silent_p.E144E	NM_019040	NP_061913	Q96EB1	ELP4_HUMAN	elongation protein 4 homolog	144					histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)					AATTTGATGAAGATGTATACA	0.308													5	228	---	---	---	---	PASS
EHF	26298	broad.mit.edu	37	11	34670585	34670585	+	Silent	SNP	G	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34670585G>C	uc001mvr.1	+	4	474	c.363G>C	c.(361-363)CTG>CTC	p.L121L	EHF_uc009yke.1_Silent_p.L121L|EHF_uc009ykf.1_Silent_p.L124L	NM_012153	NP_036285	Q9NZC4	EHF_HUMAN	ets homologous factor	121					cell proliferation|epithelial cell differentiation|multicellular organismal development|positive regulation of transcription, DNA-dependent		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			GTAGTGACCTGTTCCAGTCCA	0.512													27	129	---	---	---	---	PASS
PCNXL3	399909	broad.mit.edu	37	11	65391403	65391403	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65391403G>A	uc001oey.2	+	13	2515	c.2515G>A	c.(2515-2517)GTG>ATG	p.V839M	PCNXL3_uc009yqn.2_5'Flank|PCNXL3_uc001oez.2_5'Flank	NM_032223	NP_115599	Q9H6A9	PCX3_HUMAN	pecanex-like 3	839						integral to membrane					0						CTTCCAGAGCGTGCAGCCTGA	0.488													3	34	---	---	---	---	PASS
OPCML	4978	broad.mit.edu	37	11	132527098	132527098	+	Missense_Mutation	SNP	G	A	A	rs137852691		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132527098G>A	uc001qgs.2	-	2	334	c.284C>T	c.(283-285)CCA>CTA	p.P95L	OPCML_uc001qgu.2_Missense_Mutation_p.P88L|OPCML_uc010sck.1_Missense_Mutation_p.P95L|OPCML_uc001qgt.2_Missense_Mutation_p.P95L|OPCML_uc010scl.1_Missense_Mutation_p.P54L	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion	95	Ig-like C2-type 1.		P -> R (in ovarian cancer; somatic mutation).		cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GTACTGGGTTGGTGTATTGAC	0.532													45	188	---	---	---	---	PASS
GXYLT1	283464	broad.mit.edu	37	12	42503369	42503369	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42503369G>A	uc001rms.3	-	4	836	c.611C>T	c.(610-612)CCG>CTG	p.P204L	GXYLT1_uc001rmt.3_Missense_Mutation_p.P173L	NM_173601	NP_775872	Q4G148	GXLT1_HUMAN	glycosyltransferase 8 domain containing 3	204	Lumenal (Potential).				O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0						AAAACTTACCGGCAAGAACAA	0.328													16	63	---	---	---	---	PASS
LETMD1	25875	broad.mit.edu	37	12	51449626	51449626	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51449626T>G	uc001rxm.2	+	5	538	c.482T>G	c.(481-483)TTT>TGT	p.F161C	LETMD1_uc010smz.1_Missense_Mutation_p.F111C|LETMD1_uc010sna.1_Intron|LETMD1_uc001rxl.2_Missense_Mutation_p.F105C|LETMD1_uc009zlv.2_Intron|LETMD1_uc001rxs.2_Intron|LETMD1_uc009zlw.2_Missense_Mutation_p.F174C|LETMD1_uc001rxn.2_Missense_Mutation_p.F4C|LETMD1_uc001rxo.2_RNA|LETMD1_uc001rxp.2_Missense_Mutation_p.F44C|LETMD1_uc001rxq.2_Intron|LETMD1_uc001rxr.2_Intron|LETMD1_uc001rxt.2_Intron	NM_015416	NP_056231	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1 isoform 1	161	Mitochondrial intermembrane (Potential).|LETM1.					integral to membrane|mitochondrial outer membrane	protein binding			central_nervous_system(2)	2						AGGTACCTGTTTCCCAGGCAA	0.423													36	136	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78516003	78516003	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78516003G>A	uc001syp.2	+	16	4206	c.4033G>A	c.(4033-4035)GTG>ATG	p.V1345M	NAV3_uc001syo.2_Missense_Mutation_p.V1345M|NAV3_uc010sub.1_Missense_Mutation_p.V845M|NAV3_uc009zsf.2_Intron	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	1345	Ser-rich.					nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						AGGTGGTCTCGTGTGGGCTGC	0.507										HNSCC(70;0.22)			10	57	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88496844	88496844	+	Intron	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88496844C>T	uc001tar.2	-						CEP290_uc001taq.2_Translation_Start_Site|CEP290_uc001tat.2_Intron	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						TGGTCAAGCACTAGCCACTTT	0.299													8	23	---	---	---	---	PASS
FGD6	55785	broad.mit.edu	37	12	95604938	95604938	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95604938A>G	uc001tdp.3	-	2	346	c.122T>C	c.(121-123)GTT>GCT	p.V41A	FGD6_uc009zsx.2_Intron	NM_018351	NP_060821	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	41					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3						CGACTGTGGAACACTAGAAAT	0.483													7	378	---	---	---	---	PASS
SPIC	121599	broad.mit.edu	37	12	101876604	101876604	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101876604T>C	uc001tid.2	+	5	404	c.245T>C	c.(244-246)ATT>ACT	p.I82T	SPIC_uc009zua.2_5'UTR|SPIC_uc010svp.1_Missense_Mutation_p.I81T	NM_152323	NP_689536	Q8N5J4	SPIC_HUMAN	Spi-C transcription factor (Spi-1/PU.1 related)	82						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1						GAAGGAAATATTCATCAATCT	0.289													5	236	---	---	---	---	PASS
KIAA1033	23325	broad.mit.edu	37	12	105536914	105536914	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105536914A>G	uc001tld.2	+	20	1990	c.1903A>G	c.(1903-1905)AGT>GGT	p.S635G	KIAA1033_uc010swr.1_Missense_Mutation_p.S636G|KIAA1033_uc010sws.1_Missense_Mutation_p.S447G	NM_015275	NP_056090	Q2M389	WAHS7_HUMAN	hypothetical protein LOC23325	635					endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2						GTACATGTTCAGTGCTTTGCG	0.333													55	236	---	---	---	---	PASS
SSH1	54434	broad.mit.edu	37	12	109182653	109182653	+	Missense_Mutation	SNP	G	A	A	rs151176410	byFrequency	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109182653G>A	uc001tnm.2	-	15	2348	c.2261C>T	c.(2260-2262)TCC>TTC	p.S754F	SSH1_uc001tnl.2_Missense_Mutation_p.S442F	NM_018984	NP_061857	Q8WYL5	SSH1_HUMAN	slingshot 1 isoform 1	754					actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(4)	4						CAAAAGGAGGGACTTTGGCAG	0.527													39	167	---	---	---	---	PASS
DGKH	160851	broad.mit.edu	37	13	42703705	42703705	+	Silent	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42703705A>G	uc001uyl.1	+	3	342	c.321A>G	c.(319-321)GAA>GAG	p.E107E	DGKH_uc010tfh.1_Silent_p.E107E|DGKH_uc001uym.1_Silent_p.E107E	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	107	PH.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TATTTGATGAAGTTGACCTCT	0.343													6	474	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109859148	109859148	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109859148C>A	uc001vqt.1	+	35	5667	c.5541C>A	c.(5539-5541)AAC>AAA	p.N1847K	MYO16_uc010agk.1_Missense_Mutation_p.N1869K	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	1847					cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CCTCCTGCAACAGGCTGCCGT	0.577													5	30	---	---	---	---	PASS
PLEKHH1	57475	broad.mit.edu	37	14	68038462	68038462	+	Intron	SNP	C	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68038462C>G	uc001xjl.1	+						PLEKHH1_uc010tsw.1_Intron|PLEKHH1_uc001xjm.1_5'UTR|PLEKHH1_uc001xjn.1_5'UTR	NM_020715	NP_065766	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H							cytoskeleton	binding				0				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		AGGGGCCTGTCTTGCAGAGAG	0.587											OREG0022748	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	59	---	---	---	---	PASS
SERPINA3	12	broad.mit.edu	37	14	95081158	95081158	+	Missense_Mutation	SNP	A	G	G	rs145819878		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95081158A>G	uc001ydp.2	+	2	459	c.380A>G	c.(379-381)AAT>AGT	p.N127S	SERPINA3_uc001ydo.3_Missense_Mutation_p.N152S|SERPINA3_uc010avf.1_RNA|SERPINA3_uc001ydr.2_RNA|SERPINA3_uc001ydq.2_Missense_Mutation_p.N127S|SERPINA3_uc001yds.2_Missense_Mutation_p.N127S|SERPINA3_uc010avg.2_Missense_Mutation_p.N127S	NM_001085	NP_001076	P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A, member 3	127					acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis	extracellular region|nucleus	DNA binding|protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|skin(1)	6		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		CGCACCCTCAATCAGTCCAGC	0.532													22	59	---	---	---	---	PASS
TRPM1	4308	broad.mit.edu	37	15	31362150	31362150	+	Intron	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31362150A>G	uc001zfm.2	-						TRPM1_uc010azy.2_5'Flank|TRPM1_uc001zfl.2_5'Flank|TRPM1_uc001zfn.3_Silent_p.P99P|uc010ubn.1_RNA	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,						cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		GAAGAAGACCAGGTATCTGCA	0.458													5	37	---	---	---	---	PASS
C15orf55	256646	broad.mit.edu	37	15	34640772	34640772	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34640772T>A	uc001zif.2	+	2	774	c.619T>A	c.(619-621)TCC>ACC	p.S207T	C15orf55_uc010ucc.1_Missense_Mutation_p.S235T|C15orf55_uc010ucd.1_Missense_Mutation_p.S225T	NM_175741	NP_786883	Q86Y26	NUT_HUMAN	nuclear protein in testis	207						cytoplasm|nucleus			BRD4_ENST00000263377/C15orf55(24)|BRD3/C15orf55(3)	midline_organs(25)|ovary(2)|lung(2)|skin(1)	30		all_lung(180;2.78e-08)		all cancers(64;4.53e-18)|GBM - Glioblastoma multiforme(113;8.29e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0249)		CTCCAAAATTTCCAAGGACGT	0.557			T	BRD3|BRD4	lethal midline carcinoma								14	36	---	---	---	---	PASS
ADAL	161823	broad.mit.edu	37	15	43644189	43644189	+	3'UTR	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43644189T>C	uc010udo.1	+	12					ADAL_uc001zri.1_3'UTR	NM_001159280	NP_001152752	Q6DHV7	ADAL_HUMAN	adenosine deaminase-like isoform 1						adenosine catabolic process|inosine biosynthetic process|purine ribonucleoside monophosphate biosynthetic process		adenosine deaminase activity|metal ion binding				0		all_cancers(109;7.96e-11)|all_epithelial(112;2.96e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;9.31e-07)		TCAATCAAGTTCCTGCCATAT	0.353													5	27	---	---	---	---	PASS
SPG11	80208	broad.mit.edu	37	15	44920966	44920966	+	Silent	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44920966C>T	uc001ztx.2	-	10	1999	c.1968G>A	c.(1966-1968)AAG>AAA	p.K656K	SPG11_uc010ueh.1_Silent_p.K656K|SPG11_uc010uei.1_Silent_p.K656K|SPG11_uc001zua.1_Silent_p.K656K	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	656	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TCCAAGGAAACTTTATCATGA	0.358													27	564	---	---	---	---	PASS
POLG	5428	broad.mit.edu	37	15	89864148	89864148	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89864148C>G	uc002bns.3	-	18	3112	c.2830G>C	c.(2830-2832)GAG>CAG	p.E944Q	POLG_uc002bnr.3_Missense_Mutation_p.E944Q	NM_002693	NP_002684	P54098	DPOG1_HUMAN	DNA-directed DNA polymerase gamma	944					base-excision repair, gap-filling|cell death|DNA-dependent DNA replication	mitochondrial nucleoid	DNA binding|DNA-directed DNA polymerase activity|protease binding			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			TTGGCATGCTCACGGCTGATG	0.557								DNA_polymerases_(catalytic_subunits)					12	63	---	---	---	---	PASS
CREBBP	1387	broad.mit.edu	37	16	3860701	3860701	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3860701A>G	uc002cvv.2	-	3	1082	c.878T>C	c.(877-879)GTG>GCG	p.V293A	CREBBP_uc002cvw.2_Missense_Mutation_p.V293A	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	293	Interaction with SRCAP.				cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CTGGGGGTTCACTCCAGTGGC	0.478			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				54	158	---	---	---	---	PASS
BBS2	583	broad.mit.edu	37	16	56519576	56519576	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56519576C>A	uc002ejd.2	-	16	2219	c.1985G>T	c.(1984-1986)TGT>TTT	p.C662F		NM_031885	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2 protein	662					adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1						GTGATTGTTACAGCGAATTTT	0.388									Bardet-Biedl_syndrome				6	394	---	---	---	---	PASS
BBS2	583	broad.mit.edu	37	16	56532523	56532523	+	Intron	SNP	C	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56532523C>G	uc002ejd.2	-						BBS2_uc010ccg.2_3'UTR	NM_031885	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2 protein						adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1						TTTTAAGGTACAGACGTTCTT	0.373									Bardet-Biedl_syndrome				17	32	---	---	---	---	PASS
CCL22	6367	broad.mit.edu	37	16	57397559	57397559	+	3'UTR	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57397559T>C	uc002elh.2	+	3						NM_002990	NP_002981	O00626	CCL22_HUMAN	small inducible cytokine A22 precursor						cell-cell signaling|chemotaxis|immune response|inflammatory response|response to virus|signal transduction	extracellular space	chemokine activity				0						GAGCCCTACCTCCCTGCCATT	0.577													4	32	---	---	---	---	PASS
ABR	29	broad.mit.edu	37	17	915255	915255	+	Intron	SNP	G	C	C	rs113364180		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:915255G>C	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010vqf.1_Intron|ABR_uc010vqg.1_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron|ABR_uc002fsf.2_Missense_Mutation_p.C181W	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		TGGGTGGAGGGCAGCCCCCAC	0.662													10	60	---	---	---	---	PASS
CWC25	54883	broad.mit.edu	37	17	36977308	36977308	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36977308G>T	uc002hqu.2	-	2	190	c.37C>A	c.(37-39)CAC>AAC	p.H13N	CWC25_uc010wdv.1_5'UTR|CWC25_uc010wdx.1_RNA	NM_017748	NP_060218	Q9NXE8	CWC25_HUMAN	coiled-coil domain containing 49	13											0						GTCTGCGGGTGCCAGCTCTTC	0.532													8	116	---	---	---	---	PASS
CDK12	51755	broad.mit.edu	37	17	37681093	37681093	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37681093C>T	uc010cvv.2	+	12	3848	c.3262C>T	c.(3262-3264)CAG>TAG	p.Q1088*	CDK12_uc010wef.1_Nonsense_Mutation_p.Q1087*|CDK12_uc002hrw.3_Nonsense_Mutation_p.Q1088*	NM_016507	NP_057591	Q9NYV4	CDK12_HUMAN	Cdc2-related kinase, arginine/serine-rich	1088					mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1)	19						AGCACCACCTCAGCCTGCTCC	0.527										TCGA Ovarian(9;0.13)			18	69	---	---	---	---	PASS
KRT13	3860	broad.mit.edu	37	17	39659631	39659631	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39659631G>C	uc002hwu.1	-	3	706	c.643C>G	c.(643-645)CTG>GTG	p.L215V	KRT13_uc002hwv.1_Missense_Mutation_p.L215V|KRT13_uc002hww.2_Missense_Mutation_p.L108V|KRT13_uc010wfr.1_Missense_Mutation_p.L108V|KRT13_uc010cxo.2_Missense_Mutation_p.L215V|KRT13_uc002hwx.1_Missense_Mutation_p.L203V	NM_153490	NP_705694	P13646	K1C13_HUMAN	keratin 13 isoform a	215	Coil 1B.|Rod.				epidermis development	intermediate filament	structural molecule activity			ovary(2)|skin(2)|pancreas(1)	5		Breast(137;0.000286)				AGCTCATCCAGCACCCGGCGC	0.493													15	73	---	---	---	---	PASS
LSM12	124801	broad.mit.edu	37	17	42141197	42141197	+	Missense_Mutation	SNP	G	T	T	rs17854322		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42141197G>T	uc002iev.2	-	3	553	c.230C>A	c.(229-231)CCT>CAT	p.P77H	LSM12_uc010wit.1_Intron|LSM12_uc002iew.1_RNA	NM_152344	NP_689557	Q3MHD2	LSM12_HUMAN	LSM12 homolog	77							protein binding				0		Breast(137;0.0313)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.115)		AGCTAGGGGAGGAGGGGTTTC	0.438													72	264	---	---	---	---	PASS
ASPSCR1	79058	broad.mit.edu	37	17	79941541	79941541	+	Silent	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79941541C>T	uc002kcx.2	+	3	367	c.270C>T	c.(268-270)AAC>AAT	p.N90N	ASPSCR1_uc002kcw.1_Silent_p.N90N|ASPSCR1_uc002kcy.2_Silent_p.N90N|ASPSCR1_uc002kcz.2_Silent_p.N90N|ASPSCR1_uc002kda.2_Silent_p.N13N|ASPSCR1_uc002kdb.1_Silent_p.N13N	NM_024083	NP_076988	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region,	90							protein binding		ASPSCR1/TFE3(161)	soft_tissue(118)|kidney(43)|breast(1)	162	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GGCCTGAGAACATGGTGGGTC	0.647			T	TFE3	alveolar soft part sarcoma								28	76	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	18	14179258	14179258	+	5'UTR	SNP	T	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14179258T>G	uc010xag.1	+	1										RecName: Full=Putative ankyrin repeat domain-containing protein 20A5;																		atcgcggatttggggttggat	0.348													5	12	---	---	---	---	PASS
PIK3C3	5289	broad.mit.edu	37	18	39629582	39629582	+	Intron	SNP	G	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39629582G>C	uc002lap.2	+						PIK3C3_uc010xcl.1_Intron|PIK3C3_uc002laq.2_Intron|PIK3C3_uc002lar.1_3'UTR	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3						cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	midbody|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding			lung(8)|ovary(1)|breast(1)	10						AACAATTAATGACTACCAGTA	0.338										TSP Lung(28;0.18)			29	163	---	---	---	---	PASS
HAUS1	115106	broad.mit.edu	37	18	43700027	43700027	+	Splice_Site	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43700027G>A	uc002lbu.2	+	4	556	c.476_splice	c.e4+1	p.E159_splice	HAUS1_uc002lbv.2_Splice_Site_p.E83_splice	NM_138443	NP_612452	Q96CS2	HAUS1_HUMAN	coiled-coil domain containing 5						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole				ovary(1)	1						GTCTACAAGAGTAAGTAATTG	0.294													37	122	---	---	---	---	PASS
CNDP1	84735	broad.mit.edu	37	18	72234488	72234488	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72234488A>T	uc002llq.2	+	6	787	c.576A>T	c.(574-576)AAA>AAT	p.K192N	CNDP1_uc002lls.2_5'UTR	NM_032649	NP_116038	Q96KN2	CNDP1_HUMAN	carnosinase 1 precursor	192					proteolysis	extracellular region	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity|tripeptidase activity				0		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		TGAATATCAAATTCATCATTG	0.333													4	211	---	---	---	---	PASS
GADD45B	4616	broad.mit.edu	37	19	2477618	2477618	+	3'UTR	SNP	A	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2477618A>T	uc002lwb.1	+	4						NM_015675	NP_056490	O75293	GA45B_HUMAN	growth arrest and DNA-damage-inducible, beta						activation of MAPKKK activity|apoptosis|cell differentiation|multicellular organismal development|response to stress						0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGCAGCAGAATCTGTTGAG	0.542													12	37	---	---	---	---	PASS
MEGF8	1954	broad.mit.edu	37	19	42860310	42860310	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42860310G>T	uc002otl.3	+	24	4902	c.4267G>T	c.(4267-4269)GTC>TTC	p.V1423F	MEGF8_uc002otm.3_Missense_Mutation_p.V1031F	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1490	Extracellular (Potential).					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)				CGGGCAGCTGGTCTGGGAGAC	0.652													3	17	---	---	---	---	PASS
SHANK1	50944	broad.mit.edu	37	19	51219979	51219979	+	Silent	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51219979G>A	uc002psx.1	-	1	217	c.198C>T	c.(196-198)GAC>GAT	p.D66D		NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	66					cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		AGTGGGCGTCGTCTGGGACGG	0.672													7	43	---	---	---	---	PASS
MYADM	91663	broad.mit.edu	37	19	54377173	54377173	+	Silent	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54377173C>T	uc002qcl.2	+	3	538	c.390C>T	c.(388-390)CAC>CAT	p.H130H	MYADM_uc002qcm.2_Silent_p.H130H|MYADM_uc002qcn.2_Silent_p.H130H|MYADM_uc002qco.2_Silent_p.H130H|MYADM_uc002qcp.2_Silent_p.H130H	NM_001020820	NP_001018656	Q96S97	MYADM_HUMAN	myeloid-associated differentiation marker	130	MARVEL 1.					integral to membrane				ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.0488)		TCCTGTCCCACGGCCGTTCGC	0.667													14	52	---	---	---	---	PASS
NNAT	4826	broad.mit.edu	37	20	36150821	36150821	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36150821A>G	uc002xhd.2	+	2	261	c.134A>G	c.(133-135)CAG>CGG	p.Q45R	BLCAP_uc002xha.2_5'Flank|BLCAP_uc002xhb.2_Intron|BLCAP_uc002xhc.2_Intron|NNAT_uc002xhe.2_Intron	NM_005386	NP_005377	Q16517	NNAT_HUMAN	neuronatin isoform alpha	45					brain development|protein lipoylation|transport						0		Myeloproliferative disorder(115;0.00878)				CCAGGGACACAGCCCATTGCG	0.502													5	159	---	---	---	---	PASS
URB1	9875	broad.mit.edu	37	21	33688961	33688961	+	Silent	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33688961G>A	uc002ypn.2	-	38	6543	c.6450C>T	c.(6448-6450)TTC>TTT	p.F2150F		NM_014825	NP_055640	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog	2150						nucleolus	protein binding				0						TATACAGCCTGAATATGCTGC	0.602													6	36	---	---	---	---	PASS
SIM2	6493	broad.mit.edu	37	21	38084889	38084889	+	Silent	SNP	C	T	T	rs143395130	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38084889C>T	uc002yvr.2	+	3	371	c.315C>T	c.(313-315)TCC>TCT	p.S105S	SIM2_uc002yvq.2_Silent_p.S105S	NM_005069	NP_005060	Q14190	SIM2_HUMAN	single-minded homolog 2 long isoform	105	PAS 1.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1						TGTATATATCCGAGACCGCTT	0.373													6	591	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47981523	47981523	+	Intron	SNP	T	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47981523T>G	uc002zjo.2	+						DIP2A_uc011afz.1_Intron|DIP2A_uc002zjs.2_5'UTR|DIP2A_uc002zjt.2_5'Flank	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a						multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TCATGGCAGGTGTGCTGTGGA	0.557													13	17	---	---	---	---	PASS
PPIL2	23759	broad.mit.edu	37	22	22042006	22042006	+	Silent	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22042006C>T	uc010gtj.1	+	13	1088	c.972C>T	c.(970-972)TCC>TCT	p.S324S	PPIL2_uc002zvh.3_Silent_p.S324S|PPIL2_uc002zvi.3_Silent_p.S324S|PPIL2_uc002zvg.3_Silent_p.S324S|PPIL2_uc011aij.1_Silent_p.S303S|PPIL2_uc002zvk.3_Silent_p.S70S	NM_148175	NP_680480	Q13356	PPIL2_HUMAN	peptidylprolyl isomerase-like 2 isoform a	324	PPIase cyclophilin-type.				blood coagulation|leukocyte migration|protein folding|protein polyubiquitination	Golgi lumen|nucleus|ubiquitin ligase complex	peptidyl-prolyl cis-trans isomerase activity|ubiquitin-ubiquitin ligase activity			ovary(2)	2	Colorectal(54;0.105)					TCCACAGATCCATCCGGAACT	0.527													5	150	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22764457	22764457	+	RNA	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22764457C>T	uc011aim.1	+	58		c.6244C>T								Parts of antibodies, mostly variable regions.												0						AGCCCCCAAACTCCTCATCTA	0.592													6	142	---	---	---	---	PASS
TCN2	6948	broad.mit.edu	37	22	31022643	31022643	+	3'UTR	SNP	A	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31022643A>C	uc003aip.1	+	9					TCN2_uc003aiq.1_3'UTR|TCN2_uc003air.1_3'UTR	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor						cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CCCTGGGATCACCCCAGCCAC	0.607													5	8	---	---	---	---	PASS
SUN2	25777	broad.mit.edu	37	22	39132222	39132222	+	3'UTR	SNP	T	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39132222T>G	uc003awh.1	-	19					SUN2_uc011anz.1_3'UTR|SUN2_uc011aoa.1_3'UTR|SUN2_uc003awi.1_3'UTR|SUN2_uc010gxq.1_3'UTR|SUN2_uc010gxr.1_3'UTR|SUN2_uc010gxs.1_Intron	NM_015374	NP_056189	Q9UH99	SUN2_HUMAN	unc-84 homolog B						centrosome localization|cytoskeletal anchoring at nuclear membrane|mitotic spindle organization|nuclear envelope organization|nuclear matrix anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	endosome membrane|integral to membrane|nuclear inner membrane|SUN-KASH complex	lamin binding|microtubule binding			large_intestine(1)|skin(1)	2						AGCGGCGGGGTGCTGTTCACC	0.627													6	15	---	---	---	---	PASS
RBX1	9978	broad.mit.edu	37	22	41368598	41368598	+	3'UTR	SNP	G	T	T	rs15468		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41368598G>T	uc003azk.2	+	5						NM_014248	NP_055063	P62877	RBX1_HUMAN	ring-box 1						DNA repair|interspecies interaction between organisms|protein neddylation|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	Cul3-RING ubiquitin ligase complex|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytosol|nucleus|SCF ubiquitin ligase complex	NEDD8 ligase activity|protein binding|zinc ion binding			skin(1)	1						TTTCTGCTTTGTTTTTTCAGT	0.348													12	260	---	---	---	---	PASS
RBX1	9978	broad.mit.edu	37	22	41368620	41368620	+	3'UTR	SNP	G	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41368620G>T	uc003azk.2	+	5						NM_014248	NP_055063	P62877	RBX1_HUMAN	ring-box 1						DNA repair|interspecies interaction between organisms|protein neddylation|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	Cul3-RING ubiquitin ligase complex|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytosol|nucleus|SCF ubiquitin ligase complex	NEDD8 ligase activity|protein binding|zinc ion binding			skin(1)	1						TGCTGTTTCTGTAGCCATATT	0.348													16	159	---	---	---	---	PASS
FAM104B	90736	broad.mit.edu	37	X	55172537	55172537	+	Intron	SNP	G	A	A	rs1047054	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55172537G>A	uc004duh.1	-						FAM104B_uc004dug.1_Intron|FAM104B_uc004dui.3_Nonsense_Mutation_p.R111*	NM_138362	NP_612371	Q5XKR9	F104B_HUMAN	hypothetical protein LOC90736												0						GCTTGCCCTCGCTGCTGCAGG	0.438													4	49	---	---	---	---	PASS
CXorf26	51260	broad.mit.edu	37	X	75394758	75394758	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75394758A>G	uc004ecl.1	+	3	333	c.130A>G	c.(130-132)ATG>GTG	p.M44V		NM_016500	NP_057584	Q9BVG4	CX026_HUMAN	hypothetical protein LOC51260	44											0						CATGAGAGCAATGCAGCATGC	0.398													6	198	---	---	---	---	PASS
XIAP	331	broad.mit.edu	37	X	123020384	123020384	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123020384C>T	uc010nqu.2	+	2	998	c.872C>T	c.(871-873)GCT>GTT	p.A291V	XIAP_uc004etx.2_Missense_Mutation_p.A291V|XIAP_uc010nqv.2_Intron	NM_001167	NP_001158	P98170	XIAP_HUMAN	baculoviral IAP repeat-containing protein 4	291	BIR 3.				anti-apoptosis|apoptosis|induction of apoptosis by intracellular signals|response to DNA damage stimulus	cytosol	caspase inhibitor activity|ligase activity|protein binding|zinc ion binding			ovary(1)|lung(1)	2						GGATTTTATGCTTTAGGTAAA	0.383									X-linked_Lymphoproliferative_syndrome				3	52	---	---	---	---	PASS
HCFC1	3054	broad.mit.edu	37	X	153215018	153215018	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153215018C>T	uc004fjp.2	-	25	6582	c.6054G>A	c.(6052-6054)ATG>ATA	p.M2018I		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	2018					cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTGGAGAGGACATGGGCCGCT	0.552													72	114	---	---	---	---	PASS
FUNDC2	65991	broad.mit.edu	37	X	154282983	154282983	+	3'UTR	SNP	T	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154282983T>C	uc004fmw.2	+	5						NM_023934	NP_076423	Q9BWH2	FUND2_HUMAN	FUN14 domain containing 2							mitochondrion					0	all_cancers(53;3.51e-17)|all_epithelial(53;5.13e-11)|all_lung(58;3.84e-07)|Lung NSC(58;1.2e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CCTGGTTTTTTCCAGCCAGCA	0.488													8	100	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13499	13499	+	RNA	SNP	G	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13499G>A	uc004cox.3	+	1		c.1163G>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		TTTCCTCACAGGTTTCTACTC	0.458													25	23	---	---	---	---	PASS
SAMD11	148398	broad.mit.edu	37	1	876443	876443	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:876443delT	uc001abw.1	+						SAMD11_uc001abx.1_Intron	NM_152486	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11							nucleus					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		GTTCCCCACCTCAGTGTTCTA	0.697													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5880294	5880294	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5880294delT								None (None upstream) : NPHP4 (42576 downstream)																							ttggagattgttagaccctgg	0.000													4	2	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7785971	7785972	+	Intron	DEL	CA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7785971_7785972delCA	uc001aoi.2	+						CAMTA1_uc010nzv.1_Intron|CAMTA1_uc001aok.3_Intron	NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		GCGGGTGGGTCACACACACAGA	0.574													4	2	---	---	---	---	
PADI6	353238	broad.mit.edu	37	1	17718392	17718393	+	Intron	INS	-	CTT	CTT			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17718392_17718393insCTT	uc001bak.1	+							NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	TCCCAACCTGGCTCTGCCATGG	0.564													6	4	---	---	---	---	
ARHGEF10L	55160	broad.mit.edu	37	1	17950322	17950322	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17950322delT	uc001ban.2	+						ARHGEF10L_uc009vpe.1_Intron|ARHGEF10L_uc001bao.2_Intron|ARHGEF10L_uc001bap.2_Intron|ARHGEF10L_uc010ocr.1_Intron|ARHGEF10L_uc001baq.2_Intron|ARHGEF10L_uc010ocs.1_Intron|ARHGEF10L_uc001bar.2_Intron|ARHGEF10L_uc009vpf.2_5'Flank	NM_018125	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF)						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		AGAAAAAAACTTTTTTTTGAA	0.448													4	2	---	---	---	---	
UBXN11	91544	broad.mit.edu	37	1	26628435	26628435	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26628435delA	uc001blw.2	-						UBXN11_uc001blz.1_Intron|UBXN11_uc001blv.2_Intron|UBXN11_uc001bly.2_Intron|UBXN11_uc001blx.2_Intron|UBXN11_uc001bma.2_Intron|UBXN11_uc001bmb.1_Intron|UBXN11_uc010ofb.1_Intron|UBXN11_uc010ofc.1_Intron	NM_183008	NP_892120	Q5T124	UBX11_HUMAN	socius isoform 2							cytoplasm|cytoskeleton				ovary(1)	1						AAGGATGGGGAAGGGGTgaag	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	29659754	29659754	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29659754delT								PTPRU (6439 upstream) : None (None downstream)																							ctgaccatgattacaccagta	0.000													4	2	---	---	---	---	
CSMD2	114784	broad.mit.edu	37	1	34415985	34415986	+	Intron	DEL	AG	-	-	rs72033474		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34415985_34415986delAG	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				ctcctcCAGCagagagagagag	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	34726953	34726953	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34726953delA								C1orf94 (42224 upstream) : MIR552 (408247 downstream)																							aggttattccaggccttgaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35292390	35292390	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35292390delG								GJA4 (31044 upstream) : C1orf212 (26734 downstream)																							agctgtccccggcatctaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	40764106	40764106	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40764106delA								ZMPSTE24 (4251 upstream) : COL9A2 (2057 downstream)																							GAACCTTTGCAAAGGGGCTGG	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	41798741	41798742	+	IGR	INS	-	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41798741_41798742insG								SCMH1 (90953 upstream) : EDN2 (145707 downstream)																							aaaaaaattttggggggggtcg	0.015													4	2	---	---	---	---	
YBX1	4904	broad.mit.edu	37	1	43152307	43152307	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43152307delG	uc001chs.2	+							NM_004559	NP_004550	P67809	YBOX1_HUMAN	nuclease sensitive element binding protein 1						CRD-mediated mRNA stabilization|negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|positive regulation of cell division|transcription from RNA polymerase II promoter	CRD-mediated mRNA stability complex|extracellular region|histone pre-mRNA 3'end processing complex|nucleoplasm|stress granule|U12-type spliceosomal complex	double-stranded DNA binding|protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(4)|upper_aerodigestive_tract(1)	5	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCTTTGGGGTGGGGGCTCCCT	0.388													4	2	---	---	---	---	
GPX7	2882	broad.mit.edu	37	1	53067258	53067258	+	5'Flank	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53067258delT	uc001cue.2	+							NM_015696	NP_056511	Q96SL4	GPX7_HUMAN	glutathione peroxidase 7 precursor						response to oxidative stress	extracellular region	glutathione peroxidase activity				0					Glutathione(DB00143)	atcttggcccttgttgcccca	0.000													4	2	---	---	---	---	
PPAP2B	8613	broad.mit.edu	37	1	57002981	57002981	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57002981delC	uc001cyj.1	-							NM_177414	NP_803133	O14495	LPP3_HUMAN	phosphatidic acid phosphatase type 2B						canonical Wnt receptor signaling pathway involved in positive regulation of cell-cell adhesion|canonical Wnt receptor signaling pathway involved in positive regulation of endothelial cell migration|canonical Wnt receptor signaling pathway involved in positive regulation of wound healing|germ cell migration|homotypic cell-cell adhesion|negative regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|sphingolipid metabolic process	adherens junction|Golgi apparatus|integral to membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|protein binding|sphingosine-1-phosphate phosphatase activity				0						cctttccacacccccatgagg	0.219													4	2	---	---	---	---	
DOCK7	85440	broad.mit.edu	37	1	63089210	63089210	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63089210delT	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc009wah.1_Intron	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2						TGATTTATGCTTATAATACCA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	64147547	64147548	+	IGR	DEL	CT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64147547_64147548delCT								PGM1 (21633 upstream) : ROR1 (92142 downstream)																							caattccttactctctctctct	0.005													3	3	---	---	---	---	
ST6GALNAC3	256435	broad.mit.edu	37	1	76799497	76799497	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76799497delA	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_Intron|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541	Q8NDV1	SIA7C_HUMAN	sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5						tacagtagctagtgtttatca	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	83203794	83203794	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83203794delT								LPHN2 (745688 upstream) : None (None downstream)																							ACATGTTTTCTTTTTTTTTTC	0.249													4	2	---	---	---	---	
CLCA1	1179	broad.mit.edu	37	1	86950533	86950533	+	Intron	DEL	A	-	-	rs5744364		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86950533delA	uc001dlt.2	+						CLCA1_uc001dls.1_Intron	NM_001285	NP_001276	A8K7I4	CLCA1_HUMAN	chloride channel accessory 1 precursor						calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		CAGATGGGAGAAAAGTGATAA	0.443													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91940240	91940241	+	IGR	INS	-	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91940240_91940241insT								HFM1 (69814 upstream) : CDC7 (26163 downstream)																							catacctttcataaaatccttc	0.000													4	2	---	---	---	---	
BCAR3	8412	broad.mit.edu	37	1	94163618	94163618	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94163618delA	uc001dqb.2	-							NM_003567	NP_003558	O75815	BCAR3_HUMAN	breast cancer antiestrogen resistance 3						response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		TGTCCTACTGAAAGCCAGCTC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	100497391	100497393	+	IGR	DEL	CAC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100497391_100497393delCAC								SLC35A3 (8385 upstream) : HIAT1 (6396 downstream)																							CCCCTTCCTGCACCACCACCTGC	0.261													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142542406	142542406	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142542406delT								None (None upstream) : None (None downstream)																							tggagtggagtggagttgagt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143423574	143423574	+	IGR	DEL	C	-	-	rs112583144		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143423574delC								None (None upstream) : LOC100286793 (224065 downstream)																							gccacagttgccacactttgg	0.000													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145009261	145009262	+	Intron	DEL	TT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145009261_145009262delTT	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)		TTTGAATGTCTTAAGATACCAG	0.337			T	PDGFRB	MPD								4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145013762	145013762	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145013762delA	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|uc001emj.2_RNA	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)		AATGGATATGAAAATGAACAA	0.368			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145275507	145275508	+	Intron	INS	-	T	T	rs143422176	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145275507_145275508insT	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_Intron|NOTCH2NL_uc001emm.3_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		gagagccagtctgagttccaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149024527	149024527	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149024527delG								LOC645166 (71473 upstream) : LOC388692 (254949 downstream)																							gcccccacacgccacagtaac	0.000													4	2	---	---	---	---	
LOC388692	388692	broad.mit.edu	37	1	149287048	149287049	+	RNA	INS	-	A	A	rs143412331	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149287048_149287049insA	uc010pbf.1	+	1		c.7573_7574insA			LOC388692_uc001esg.3_5'Flank	NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0						TAGTTATTCACAGCTCAGCCCG	0.619													4	2	---	---	---	---	
GOLPH3L	55204	broad.mit.edu	37	1	150668380	150668380	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150668380delA	uc001evj.2	-						GOLPH3L_uc010pci.1_Intron	NM_018178	NP_060648	Q9H4A5	GLP3L_HUMAN	Golgi phosphoprotein 3-like							Golgi cisterna membrane				ovary(1)	1	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;1.2e-23)|all cancers(9;4.81e-23)|OV - Ovarian serous cystadenocarcinoma(6;1.93e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			TTCTCAATTTAAAAAAAAAAG	0.308													4	2	---	---	---	---	
ATP1A2	477	broad.mit.edu	37	1	160086327	160086327	+	Intron	DEL	G	-	-	rs72077824		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160086327delG	uc001fvc.2	+						ATP1A2_uc001fvb.2_Intron	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein						ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			GCTGGTGACAGGTGACCCCCC	0.617													4	2	---	---	---	---	
CD244	51744	broad.mit.edu	37	1	160801593	160801593	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160801593delA	uc009wtq.2	-						CD244_uc001fxa.2_Intron|CD244_uc009wtp.2_Intron|CD244_uc009wtr.2_Intron	NM_016382	NP_057466	Q9BZW8	CD244_HUMAN	CD244 natural killer cell receptor 2B4						blood coagulation|leukocyte migration	integral to membrane|plasma membrane	protein binding|receptor activity			ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			TCTTTATTGGACCACAGGTGG	0.448													4	2	---	---	---	---	
DDR2	4921	broad.mit.edu	37	1	162666244	162666244	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162666244delT	uc001gcf.2	+						DDR2_uc001gcg.2_Intron	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2						cell adhesion	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			GGTGTGTTTGTTTGGCTGTGA	0.577													4	2	---	---	---	---	
RCSD1	92241	broad.mit.edu	37	1	167603057	167603057	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167603057delT	uc001gem.2	+						RCSD1_uc010pli.1_Intron	NM_052862	NP_443094	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1											ovary(2)|central_nervous_system(2)|skin(1)	5	all_hematologic(923;0.215)					AGAAAGCATCTTTTCCAGTAC	0.458													4	2	---	---	---	---	
ASTN1	460	broad.mit.edu	37	1	176833823	176833824	+	Intron	DEL	TG	-	-	rs151315782	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176833823_176833824delTG	uc001glc.2	-						ASTN1_uc001glb.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						CAAAAATATCTGTCAAGCaaat	0.149													3	3	---	---	---	---	
ASTN1	460	broad.mit.edu	37	1	176833827	176833829	+	Intron	DEL	AAG	-	-	rs78225550		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176833827_176833829delAAG	uc001glc.2	-						ASTN1_uc001glb.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						AATATCTGTCAAGCaaatgaatg	0.153													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	182054282	182054282	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182054282delG								ZNF648 (23435 upstream) : GLUL (297387 downstream)																							CAGAGGCAAAGGACACCGCCT	0.602											OREG0014033	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
RGSL1	353299	broad.mit.edu	37	1	182528509	182528509	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182528509delT	uc009wxw.2	+						RGSL1_uc009wxx.1_Intron	NM_001137669	NP_001131141	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1							integral to membrane	signal transducer activity			central_nervous_system(1)	1						TTCCTCTGCCTCCCCTCCCAT	0.473													4	2	---	---	---	---	
C1orf26	54823	broad.mit.edu	37	1	185174195	185174195	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185174195delT	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988	Q5T5J6	SWT1_HUMAN	hypothetical protein LOC54823												0						TATGTTATTCTTTTTTTTGAG	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	191691088	191691088	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191691088delA								None (None upstream) : RGS18 (436504 downstream)																							ggctgtttataggagacagtt	0.000													4	2	---	---	---	---	
F13B	2165	broad.mit.edu	37	1	197025912	197025912	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197025912delA	uc001gtt.1	-							NM_001994	NP_001985	P05160	F13B_HUMAN	coagulation factor XIII B subunit precursor						blood coagulation	extracellular region				upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						ACTAGCGTTCAAAAAAAACTT	0.358													4	2	---	---	---	---	
KIF21B	23046	broad.mit.edu	37	1	200961703	200961705	+	Intron	DEL	CCT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200961703_200961705delCCT	uc001gvs.1	-						KIF21B_uc001gvr.1_Intron|KIF21B_uc009wzl.1_Intron|KIF21B_uc010ppn.1_Intron	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6						GCTTAAGCCGCCTGGGCAAGCTG	0.626													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	201536212	201536212	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201536212delA								RPS10P7 (36610 upstream) : NAV1 (81238 downstream)																							ACCGGAAGACAAAAAAAATGA	0.522													3	3	---	---	---	---	
FMOD	2331	broad.mit.edu	37	1	203265778	203265778	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203265778delA	uc010pqi.1	-							NM_002023		Q06828	FMOD_HUMAN	fibromodulin precursor						transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)			AGCAACCCTCAGGGGAATACA	0.517													4	2	---	---	---	---	
ZC3H11A	9877	broad.mit.edu	37	1	203816133	203816134	+	Intron	DEL	AA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203816133_203816134delAA	uc001hac.2	+						ZC3H11A_uc001had.2_Intron|ZC3H11A_uc001hae.2_Intron|ZC3H11A_uc001haf.2_Intron|ZC3H11A_uc010pqm.1_Intron|ZC3H11A_uc001hag.1_Intron	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A								nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			actctgtcttaaaaaaaaaaag	0.069													4	2	---	---	---	---	
CNTN2	6900	broad.mit.edu	37	1	205019151	205019151	+	Intron	DEL	T	-	-	rs79229240		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205019151delT	uc001hbr.2	+						CNTN2_uc001hbq.1_Intron	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor						axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			tccaaagaactctgtaaagtg	0.045													2	4	---	---	---	---	
DYRK3	8444	broad.mit.edu	37	1	206847193	206847193	+	Intron	DEL	A	-	-	rs71570024		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206847193delA	uc001hek.2	+									O43781	DYRK3_HUMAN	Homo sapiens regulatory erythroid kinase long form (RED) mRNA, alternatively spliced product, complete cds.						erythrocyte differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|central_nervous_system(1)	3	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			CAATATTCTGAAAAAAAAAAT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213483785	213483785	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213483785delT								RPS6KC1 (36978 upstream) : PROX1 (677501 downstream)																							gcctttgcactttttttttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	219736052	219736052	+	IGR	DEL	T	-	-	rs60400951		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219736052delT								LYPLAL1 (349846 upstream) : SLC30A10 (122717 downstream)																							TCCTTATAACTGTTTCATGCA	0.343													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	221493341	221493342	+	IGR	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221493341_221493342insA								HLX (434943 upstream) : LOC400804 (9928 downstream)																							GGGCATGACTGACCAAATTCCA	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229282993	229282994	+	IGR	INS	-	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229282993_229282994insC								RHOU (400584 upstream) : RAB4A (123885 downstream)																							GGGGAGAGAAGCCCCAGGAGGT	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229896665	229896665	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229896665delT								URB2 (100719 upstream) : GALNT2 (296871 downstream)																							GTTTATGTAATTTTTTTTTTT	0.363													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232222876	232222877	+	IGR	INS	-	A	A	rs143441388	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232222876_232222877insA								DISC1 (45860 upstream) : SIPA1L2 (310837 downstream)																							tatgactggagaaaaaaagtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	235675054	235675056	+	IGR	DEL	GTT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235675054_235675056delGTT								B3GALNT2 (7273 upstream) : GNG4 (35931 downstream)																							TCTATATGGAGTTGATCTATCTG	0.360													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	236807686	236807686	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236807686delG								HEATR1 (39872 upstream) : ACTN2 (42084 downstream)																							CATCATTCAAGTCAGCCTCTC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	240871371	240871371	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240871371delG								GREM2 (95909 upstream) : RGS7 (60184 downstream)																							ATACCTGGGTGCTGAGAAAAG	0.373													4	2	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245335384	245335387	+	Intron	DEL	TGTT	-	-	rs150517346		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245335384_245335387delTGTT	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TCCATCCACCTGTTTGTTTATCCA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	247401187	247401188	+	IGR	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247401187_247401188insA								ZNF124 (65869 upstream) : VN1R5 (18186 downstream)																							TATCTGTAGAGAAAAATAAGAC	0.282													4	2	---	---	---	---	
MYT1L	23040	broad.mit.edu	37	2	2298728	2298729	+	Intron	INS	-	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2298728_2298729insT	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		AAGTGATGTTCTTTTTTTTTTa	0.050													4	2	---	---	---	---	
TAF1B	9014	broad.mit.edu	37	2	10052500	10052504	+	Intron	DEL	TGTTC	-	-	rs141961934		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10052500_10052504delTGTTC	uc002qzz.2	+						TAF1B_uc010exc.2_Intron|TAF1B_uc002qzy.3_Intron|TAF1B_uc010yja.1_Intron|TAF1B_uc010exd.2_Intron	NM_005680	NP_005671	Q53T94	TAF1B_HUMAN	TBP-associated factor 1B						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					AGTTTCTTAATGTTCTGTTCTCATT	0.185													3	3	---	---	---	---	
TRIB2	28951	broad.mit.edu	37	2	12873168	12873168	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12873168delC	uc002rbv.3	+						TRIB2_uc010yjp.1_Intron	NM_021643	NP_067675	Q92519	TRIB2_HUMAN	tribbles homolog 2						negative regulation of fat cell differentiation|negative regulation of interleukin-10 biosynthetic process|negative regulation of protein kinase activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity	cytoplasm|cytoskeleton|nucleus	ATP binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity			stomach(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CTGCCAAGGGCCCACAGTGCT	0.443													4	2	---	---	---	---	
NBAS	51594	broad.mit.edu	37	2	15442641	15442641	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15442641delA	uc002rcc.1	-						NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4						TTGCACCCAGAAAGGGAATGG	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20315293	20315294	+	IGR	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20315293_20315294insA								LAPTM4A (63504 upstream) : SDC1 (85264 downstream)																							TGGAAGAACCCAACAGCCTAAG	0.525													4	2	---	---	---	---	
ADCY3	109	broad.mit.edu	37	2	25090158	25090158	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25090158delG	uc002rfs.3	-						ADCY3_uc010ykm.1_Intron	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3						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|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					agtaaaaaatggcagcctaga	0.000													4	2	---	---	---	---	
EHD3	30845	broad.mit.edu	37	2	31469331	31469331	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31469331delG	uc002rnu.2	+						EHD3_uc010ymt.1_Intron	NM_014600	NP_055415	Q9NZN3	EHD3_HUMAN	EH-domain containing 3						blood coagulation|endocytic recycling|protein homooligomerization	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding			skin(2)	2	Acute lymphoblastic leukemia(172;0.155)					GGAAAAGCCAGGGGGAGACAA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37986208	37986210	+	IGR	DEL	TGG	-	-	rs141557425	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37986208_37986210delTGG								CDC42EP3 (86882 upstream) : FAM82A1 (166252 downstream)																							ATGATGACAATGGTGGTGGTGGT	0.133													3	3	---	---	---	---	
KCNG3	170850	broad.mit.edu	37	2	42705697	42705698	+	Intron	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42705697_42705698insA	uc002rsn.2	-						KCNG3_uc002rsm.2_Intron	NM_133329	NP_579875	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G,							endoplasmic reticulum|voltage-gated potassium channel complex	protein binding			central_nervous_system(1)	1						AGGTAAAGCTTAAAAAAAAAAA	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58651958	58651959	+	IGR	DEL	TG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58651958_58651959delTG								FANCL (183443 upstream) : None (None downstream)																							AGATAATTGAtgtgtgtgtgtg	0.332													4	2	---	---	---	---	
BCL11A	53335	broad.mit.edu	37	2	60718075	60718076	+	Intron	INS	-	A	A	rs71400256		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60718075_60718076insA	uc002sae.1	-						BCL11A_uc002sab.2_Intron|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Intron|BCL11A_uc002sad.1_Intron|BCL11A_uc002saf.1_Intron	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1						negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleus|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(2)|skin(2)	13			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			AACTTTCAGATAAAAAAAAAAA	0.351			T	IGH@	B-CLL								3	3	---	---	---	---	
COMMD1	150684	broad.mit.edu	37	2	62184726	62184726	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62184726delA	uc002sbp.2	+							NM_152516	NP_689729	Q8N668	COMD1_HUMAN	MURR1						copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			TTTTCATTACAAAAAAAATTA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65712953	65712953	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65712953delT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																		TATCAACTACtttttttttaa	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67870574	67870574	+	IGR	DEL	G	-	-	rs76740132		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67870574delG								ETAA1 (233041 upstream) : C1D (398759 downstream)																							GGCTGGATTTGGGAGAGGGAT	0.403													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67990530	67990531	+	IGR	DEL	GA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67990530_67990531delGA								ETAA1 (352997 upstream) : C1D (278802 downstream)																							ATGCACACTTGAGAACTGCTCT	0.371													4	2	---	---	---	---	
ASPRV1	151516	broad.mit.edu	37	2	70203418	70203419	+	Intron	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70203418_70203419insA	uc002sga.2	-						ASPRV1_uc010fdn.1_Intron			Q53RT3	APRV1_HUMAN	Homo sapiens cDNA FLJ32260 fis, clone PROST1000334.						protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1						CCTTGGAAGCCAGGCCCAGCCC	0.604													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	80170411	80170412	+	Intron	INS	-	GT	GT	rs142438302	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80170411_80170412insGT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						TTAAAAAGAAAGTGGATTTTCT	0.257													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89879994	89879995	+	IGR	INS	-	GA	GA			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89879994_89879995insGA								FLJ40330 (773869 upstream) : None (None downstream)																							ggaatggaatgAGGGAATGTCA	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91771100	91771102	+	IGR	DEL	AGA	-	-	rs148733415		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91771100_91771102delAGA								None (None upstream) : LOC654342 (34090 downstream)																							catgacttatagaagaagtgtct	0.015													4	2	---	---	---	---	
SLC9A4	389015	broad.mit.edu	37	2	103104620	103104620	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103104620delT	uc002tbz.3	+							NM_001011552	NP_001011552	Q6AI14	SL9A4_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	apical plasma membrane|basolateral plasma membrane|integral to membrane	sodium:hydrogen antiporter activity			skin(2)|central_nervous_system(1)	3						AGTCCTGTGGTTTTCAACAGC	0.478													4	2	---	---	---	---	
MFSD9	84804	broad.mit.edu	37	2	103341032	103341032	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103341032delC	uc002tcb.2	-						MFSD9_uc010fja.2_Intron	NM_032718	NP_116107	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing						transmembrane transport	integral to membrane|plasma membrane	transporter activity			ovary(2)|breast(2)	4						TGTCCCTAGACCCCCCACGTG	0.388													4	2	---	---	---	---	
ST6GAL2	84620	broad.mit.edu	37	2	107455727	107455727	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107455727delC	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						TTTCTCACTTCCATATGATGC	0.522													4	2	---	---	---	---	
ZC3H6	376940	broad.mit.edu	37	2	113040625	113040625	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113040625delC	uc002thq.1	+							NM_198581	NP_940983	P61129	ZC3H6_HUMAN	zinc finger CCCH-type domain containing 6								nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4						taaatttagtcctatcttttg	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114826187	114826187	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114826187delG								ACTR3 (110020 upstream) : DPP10 (373712 downstream)																							GTACCGTGATGGGGAAGTAGT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118113817	118113819	+	IGR	DEL	ACA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118113817_118113819delACA								None (None upstream) : DDX18 (458436 downstream)																							AAAGTAAACCACAACAACAACAA	0.409													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	121097325	121097325	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121097325delG								RALB (45042 upstream) : INHBB (6394 downstream)																							AATGCTATCTGGGGTCAGCTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122666621	122666621	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122666621delA								TSN (141195 upstream) : None (None downstream)																							TCACAAGAGTAAGGCAGAAAA	0.383													4	2	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	124953196	124953197	+	Intron	DEL	AC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124953196_124953197delAC	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		CATATTAAATACACACACACAC	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132779686	132779686	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132779686delT								C2orf27B (220452 upstream) : NCRNA00164 (125478 downstream)																							AGCATTTTAGTAcagtcacac	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133169915	133169915	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133169915delA								NCRNA00164 (154373 upstream) : GPR39 (4232 downstream)																							GGTCCTACTTAAAAaaaaagt	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134549545	134549546	+	IGR	DEL	AG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134549545_134549546delAG								NCKAP5 (223514 upstream) : MGAT5 (462284 downstream)																							GAGCAGAGGCAGAGAGAGAGAC	0.500													4	2	---	---	---	---	
MGAT5	4249	broad.mit.edu	37	2	135204008	135204008	+	Intron	DEL	A	-	-	rs7604436	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135204008delA	uc002ttv.1	+						LOC151162_uc002ttw.3_5'Flank	NM_002410	NP_002401	Q09328	MGT5A_HUMAN	N-acetylglucosaminyltransferase V						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0964)		TAATTCACCCAAAAAAAAAGG	0.418													3	3	---	---	---	---	
ACVR2A	92	broad.mit.edu	37	2	148684420	148684420	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148684420delT	uc002twg.2	+						ACVR2A_uc010zbn.1_Intron|ACVR2A_uc002twh.2_Intron	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor						activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)		GGGATAGAGATTTTTTTTTTG	0.328													3	4	---	---	---	---	
CACNB4	785	broad.mit.edu	37	2	152754441	152754441	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152754441delT	uc002tya.2	-						CACNB4_uc002txy.2_Intron|CACNB4_uc002txz.2_Intron|CACNB4_uc010fnz.2_Intron|CACNB4_uc002tyb.2_Intron	NM_000726	NP_000717	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)	TGGCCCTTTGTTTTTTGGGTG	0.299													4	2	---	---	---	---	
GPD2	2820	broad.mit.edu	37	2	157368052	157368052	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157368052delT	uc002tzf.3	+						GPD2_uc010zch.1_Intron|GPD2_uc002tzd.3_Intron|GPD2_uc002tze.1_Intron	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,						cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1						AATCTGTCTCTTTTTTTTTCT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	159787916	159787916	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159787916delT								DAPL1 (115422 upstream) : TANC1 (37230 downstream)																							atacatttccttttttttttt	0.085													3	4	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	159948475	159948475	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159948475delG	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						TGTAAATATAGGGGGGGGTGT	0.398													4	2	---	---	---	---	
BAZ2B	29994	broad.mit.edu	37	2	160245639	160245640	+	Intron	INS	-	CC	CC	rs58342810	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160245639_160245640insCC	uc002uao.2	-						BAZ2B_uc002uap.2_Intron	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						caaccaaccaaacaaacaaaca	0.188													4	3	---	---	---	---	
BAZ2B	29994	broad.mit.edu	37	2	160245640	160245641	+	Intron	INS	-	AC	AC	rs77557920	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160245640_160245641insAC	uc002uao.2	-						BAZ2B_uc002uap.2_Intron	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						aaccaaccaaacaaacaaacaa	0.188													4	3	---	---	---	---	
XIRP2	129446	broad.mit.edu	37	2	167896947	167896947	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167896947delC	uc002udx.2	+						XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						caggaagtggcccactctcac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173207679	173207679	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173207679delT								DLX2 (240201 upstream) : ITGA6 (84403 downstream)																							TGACTTTCTCTTCCAGAAGAC	0.428													4	2	---	---	---	---	
ATF2	1386	broad.mit.edu	37	2	176024207	176024207	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176024207delT	uc002ujl.2	-						ATF2_uc010fqv.2_Intron|ATF2_uc002ujv.2_Intron|ATF2_uc002ujm.2_Intron|ATF2_uc002ujn.2_Intron|ATF2_uc002ujo.2_Intron|ATF2_uc002ujp.2_Intron|ATF2_uc002ujq.2_Intron|ATF2_uc002ujr.2_Intron|ATF2_uc010fqu.2_Intron|ATF2_uc002ujs.2_Intron|ATF2_uc002ujt.2_Intron|ATF2_uc002uju.2_Intron|ATF2_uc002ujw.1_Intron|ATF2_uc002ujx.1_Intron|ATF2_uc002ujy.1_Intron	NM_001880	NP_001871	P15336	ATF2_HUMAN	activating transcription factor 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nucleoplasm	protein dimerization activity|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(1)|breast(1)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.125)			AGCAGCAGTATTTTTTCCCCC	0.338													4	2	---	---	---	---	
PDE11A	50940	broad.mit.edu	37	2	178969319	178969319	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178969319delA	uc002ulr.2	-						PDE11A_uc002ult.1_Intron	NM_001077197	NP_001070665	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A isoform 3						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)			GATGTTAAACAAAAACATATC	0.284									Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				4	2	---	---	---	---	
CDK15	65061	broad.mit.edu	37	2	202746625	202746626	+	Intron	DEL	CA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202746625_202746626delCA	uc002uyt.2	+						CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc002uyu.1_Intron	NM_139158	NP_631897	Q96Q40	CDK15_HUMAN	PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)	catacacacgcacacacacaca	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	204468019	204468020	+	IGR	DEL	AG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204468019_204468020delAG								RAPH1 (67961 upstream) : CD28 (103178 downstream)																							CTGATGTGGCAGAGAGAGATAG	0.540													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	207264260	207264260	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207264260delC								ZDBF2 (85112 upstream) : ADAM23 (44108 downstream)																							CACATGGAAGCCCCAGGATGG	0.423													4	2	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	214675436	214675436	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214675436delT	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		AAGACTGGTCTTTAGTTTCGT	0.433													4	2	---	---	---	---	
DIRC3	729582	broad.mit.edu	37	2	218295077	218295077	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218295077delG	uc002vgn.1	-						DIRC3_uc002vgo.2_Intron					Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0						TCACTCAGGTGGTGACAAGGC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	222237427	222237428	+	IGR	DEL	AC	-	-	rs10578961		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222237427_222237428delAC								None (None upstream) : EPHA4 (45321 downstream)																							ACGGAAAAATACAATCAAGCAG	0.505											OREG0015236	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	223893334	223893334	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223893334delA								ACSL3 (83980 upstream) : KCNE4 (23528 downstream)																							CTGTACTAGCAAAGGGTAGCT	0.259													4	2	---	---	---	---	
AP1S3	130340	broad.mit.edu	37	2	224675457	224675457	+	Intron	DEL	A	-	-	rs67190454		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224675457delA	uc010fwx.1	-						AP1S3_uc002vnn.2_Intron|AP1S3_uc010fww.2_Intron|AP1S3_uc002vno.2_Intron	NM_001039569	NP_001034658	Q96PC3	AP1S3_HUMAN	adaptor-related protein complex 1, sigma 3						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane coat	protein transporter activity				0		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)		GTCCCACTTCAAAAAAAAAAT	0.318													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232821370	232821370	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232821370delA								NPPC (30411 upstream) : DIS3L2 (4923 downstream)																							TCAAAACCAGAAAAAAATATG	0.294													4	2	---	---	---	---	
GIGYF2	26058	broad.mit.edu	37	2	233712402	233712402	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233712402delA	uc002vti.3	+						GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc002vtq.3_Intron	NM_015575	NP_056390	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2 isoform b						cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		ACCATGCTTTAAAAAATGTGT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235639058	235639058	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235639058delG								ARL4C (233365 upstream) : SH3BP4 (221570 downstream)																							agagagcccaggcaggaccag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	240632760	240632760	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240632760delG								HDAC4 (309414 upstream) : NDUFA10 (267398 downstream)																							TGGAGCTCCTGGGGCTCACAC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	241412124	241412125	+	IGR	INS	-	T	T	rs138468687	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241412124_241412125insT								GPC1 (4630 upstream) : ANKMY1 (6714 downstream)																							cctggaggcaacccttcagaga	0.000													6	4	---	---	---	---	
PDCD1	5133	broad.mit.edu	37	2	242803666	242803667	+	5'Flank	DEL	AA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242803666_242803667delAA	uc002wcq.3	-						PDCD1_uc010fzt.2_5'Flank	NM_005018	NP_005009	Q15116	PDCD1_HUMAN	programmed cell death 1 precursor						apoptosis|humoral immune response|multicellular organismal development|T cell costimulation	integral to membrane	protein tyrosine phosphatase activity|signal transducer activity			ovary(1)	1		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219)		cacaatcctcaacacacacaca	0.030													4	2	---	---	---	---	
ATP2B2	491	broad.mit.edu	37	3	10509429	10509429	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10509429delT	uc003bvt.2	-						ATP2B2_uc003bvv.2_Intron|ATP2B2_uc003bvw.2_Intron|ATP2B2_uc010hdp.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						CGAGGTAACATTTTTGGCGGG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	12011707	12011707	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12011707delC								C3orf31 (123355 upstream) : SYN2 (34155 downstream)																							TATTGGGATGCCATCTGTaat	0.308													4	2	---	---	---	---	
NEK10	152110	broad.mit.edu	37	3	27161744	27161744	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27161744delT	uc010hfk.2	-						NEK10_uc010hfj.2_Intron			Q6ZWH5	NEK10_HUMAN	RecName: Full=Serine/threonine-protein kinase Nek10;          EC=2.7.11.1; AltName: Full=NimA-related protein kinase 10;								ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13						CAAATCACTATTTTTTTTTCA	0.264													4	2	---	---	---	---	
CTDSPL	10217	broad.mit.edu	37	3	38009946	38009946	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38009946delT	uc003chg.2	+						CTDSPL_uc003chh.2_Intron|CTDSPL_uc003chi.2_Intron	NM_001008392	NP_001008393	O15194	CTDSL_HUMAN	small CTD phosphatase 3 isoform 1							nucleus	metal ion binding|phosphoprotein phosphatase activity				0		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)		TTGCTTCTGATTTTTTTTCCT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	39081435	39081435	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39081435delA								SCN11A (89383 upstream) : WDR48 (12072 downstream)																							CATGTCCGCCAAGGGCTGAGG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	42391272	42391272	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42391272delG								CCK (83610 upstream) : LYZL4 (47305 downstream)																							GCAGACTGCAGGGACTTTGCC	0.473													4	2	---	---	---	---	
EXOSC7	23016	broad.mit.edu	37	3	45019509	45019509	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45019509delG	uc003coi.2	+						ZDHHC3_uc003cod.2_5'Flank|ZDHHC3_uc003cog.2_5'Flank|ZDHHC3_uc011bad.1_5'Flank|EXOSC7_uc003coh.1_Intron|EXOSC7_uc011bae.1_Intron|EXOSC7_uc010his.1_Intron|EXOSC7_uc003coj.2_Intron	NM_015004	NP_055819	Q15024	EXOS7_HUMAN	exosome component 7						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|protein binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)		catgttatgtgggaaacagca	0.229													4	2	---	---	---	---	
LARS2	23395	broad.mit.edu	37	3	45529499	45529499	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45529499delA	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155	Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	TGGAGGAGTCAGCCCCGCTTC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	48235661	48235662	+	IGR	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48235661_48235662insA								CDC25A (5860 upstream) : CAMP (29200 downstream)																							cctAAAAAAGTAAAAAAAAATG	0.282											OREG0015554	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ARHGEF3	50650	broad.mit.edu	37	3	57096016	57096016	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57096016delA	uc003dih.2	-						SPATA12_uc003dij.1_Intron	NM_001128615	NP_001122087	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		TGCCCTGAATAATGCCTTTGG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90052979	90052980	+	IGR	DEL	AC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90052979_90052980delAC								EPHA3 (521697 upstream) : None (None downstream)																							gcacacacatacacacacacac	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	97836266	97836266	+	IGR	DEL	T	-	-	rs63225260		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97836266delT								OR5AC2 (29322 upstream) : OR5H1 (15276 downstream)																							cgctggctccttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	104782011	104782012	+	IGR	DEL	AC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104782011_104782012delAC								None (None upstream) : ALCAM (303701 downstream)																							cacacgccaaacacacacacac	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112373726	112373726	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112373726delT								CCDC80 (13749 upstream) : CD200R1L (160830 downstream)																							accaaatgcattacatactgt	0.000													4	2	---	---	---	---	
HGD	3081	broad.mit.edu	37	3	120391743	120391744	+	Intron	INS	-	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120391743_120391744insC	uc003edw.2	-							NM_000187	NP_000178	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase						L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	homogentisate 1,2-dioxygenase activity|metal ion binding				0				GBM - Glioblastoma multiforme(114;0.158)		CCAGACTTTTGCCTTTTCAAGA	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127257232	127257232	+	5'Flank	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127257232delA	uc003ejk.2	-											Homo sapiens cDNA FLJ25806 fis, clone TST07194.																		TGAATTTAAGAaaaaaaaaat	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	128776501	128776501	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128776501delA								CCDC48 (16918 upstream) : GP9 (3144 downstream)																							ttaagttctgaatagatcctg	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	136521660	136521661	+	IGR	DEL	GA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136521660_136521661delGA								STAG1 (50415 upstream) : TMEM22 (16200 downstream)																							gtgtgtgtgtgagagagagaga	0.272													4	2	---	---	---	---	
PIK3CB	5291	broad.mit.edu	37	3	138413450	138413450	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138413450delT	uc011bmq.1	-						PIK3CB_uc011bmn.1_Intron|PIK3CB_uc011bmo.1_Intron|PIK3CB_uc011bmp.1_Intron	NM_006219	NP_006210	P42338	PK3CB_HUMAN	catalytic phosphatidylinositol 3-kinase beta						activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5						ATGCTTTTGGTTTTTTTTTTC	0.224													4	2	---	---	---	---	
PCOLCE2	26577	broad.mit.edu	37	3	142581342	142581342	+	Intron	DEL	T	-	-	rs58090088	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142581342delT	uc003evd.2	-							NM_013363	NP_037495	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2							extracellular region	collagen binding|heparin binding|peptidase activator activity			ovary(2)|skin(1)	3						ttcaattcccttactgtaatt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152306472	152306472	+	IGR	DEL	A	-	-	rs79812042		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152306472delA								MBNL1 (122904 upstream) : P2RY1 (246264 downstream)																							gtgtcttgggaaaaaaaaaaG	0.154													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161488113	161488113	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161488113delA								OTOL1 (266385 upstream) : None (None downstream)																							ggactgggggaaaaaagcctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176209764	176209764	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176209764delA								NAALADL2 (686338 upstream) : TBL1XR1 (528779 downstream)																							CCTTTATGAGAAAAAAAAAAT	0.363													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	178153999	178153999	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178153999delA								None (None upstream) : KCNMB2 (100225 downstream)																							ACAAATGCAGAAAATAAACCC	0.264													4	2	---	---	---	---	
KCNMB2	10242	broad.mit.edu	37	3	178545700	178545700	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178545700delA	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron|KCNMB2_uc003fje.2_Intron|KCNMB2_uc003fjf.2_Intron|KCNMB2_uc011bqa.1_Intron|KCNMB2_uc011bqb.1_Intron	NM_181361	NP_852006	Q9Y691	KCMB2_HUMAN	calcium-activated potassium channel beta 2						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of vasoconstriction	voltage-gated potassium channel complex	calcium-activated potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(1)	1	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)			TCCATAAGGGAAAAAAGAACT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	178601888	178601889	+	IGR	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178601888_178601889insA								KCNMB2 (39672 upstream) : ZMAT3 (139638 downstream)																							taacttcaaataaaaaaaaata	0.000													4	2	---	---	---	---	
USP13	8975	broad.mit.edu	37	3	179458439	179458440	+	Intron	INS	-	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179458439_179458440insT	uc003fkh.2	+						USP13_uc003fkf.2_Intron	NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TTCACAATTTATTTTTTTCTGG	0.421													4	2	---	---	---	---	
DGKG	1608	broad.mit.edu	37	3	185918813	185918813	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185918813delG	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	AGCCGGCACTGGGTGCCAGTT	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191656749	191656749	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191656749delC								PYDC2 (477506 upstream) : FGF12 (202935 downstream)																							tgccatggttcccccttcctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193278994	193278995	+	IGR	INS	-	GT	GT			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193278994_193278995insGT								ATP13A4 (6298 upstream) : OPA1 (31938 downstream)																							ACTAACCAAGAGTGTGGCTGGG	0.594													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197134429	197134429	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197134429delC								DLG1 (108286 upstream) : BDH1 (102226 downstream)																							AAGAGCTTTTCCCAGCACAGA	0.498													4	2	---	---	---	---	
ZFYVE28	57732	broad.mit.edu	37	4	2399768	2399769	+	Intron	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2399768_2399769insA	uc003gex.1	-						ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						atgggagggggggtcctggcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3607288	3607289	+	IGR	INS	-	C	C	rs141113002	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3607288_3607289insC								LRPAP1 (73064 upstream) : ADRA2C (160786 downstream)																							CCTTTCAGCCACCCCCTCCCCC	0.644													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14028985	14028985	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14028985delG								BOD1L (399657 upstream) : CPEB2 (976537 downstream)																							CCTCAGGCATGGGTTCGAAAG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14323762	14323762	+	IGR	DEL	C	-	-	rs34037819		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14323762delC								BOD1L (694434 upstream) : CPEB2 (681760 downstream)																							ccttctctttcccctttccag	0.000													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18145115	18145115	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18145115delT								LCORL (121730 upstream) : None (None downstream)																							agctaccttGTTTTAGCAGTG	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	22662631	22662632	+	IGR	DEL	TG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22662631_22662632delTG								GPR125 (144959 upstream) : GBA3 (31916 downstream)																							tctctggtgctgaaaaaaatta	0.139													4	2	---	---	---	---	
CCDC149	91050	broad.mit.edu	37	4	24893143	24893145	+	Intron	DEL	CAT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24893143_24893145delCAT	uc011bxr.1	-						CCDC149_uc003grc.2_Intron|CCDC149_uc003grb.2_Intron|CCDC149_uc003grd.2_Intron|CCDC149_uc003gre.2_Intron	NM_173463	NP_775734	B4DZG3	B4DZG3_HUMAN	coiled-coil domain containing 149 isoform 1												0		Breast(46;0.173)				TGACCACCACCATCATCACCTCT	0.409													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49210300	49210301	+	IGR	INS	-	G	G	rs116114182		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49210300_49210301insG								CWH43 (146207 upstream) : None (None downstream)																							ggaccacctTTTTatgtctttc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49246087	49246087	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49246087delC								CWH43 (181994 upstream) : None (None downstream)																							CAAAAACAAACAAAAAAAAAT	0.249													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	61920602	61920602	+	IGR	DEL	G	-	-	rs5858667		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61920602delG								None (None upstream) : LPHN3 (146372 downstream)																							TATGGAAAGAGTGGGTGTTGA	0.388													4	2	---	---	---	---	
PARM1	25849	broad.mit.edu	37	4	75930803	75930803	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75930803delC	uc003hih.1	+							NM_015393	NP_056208	Q6UWI2	PARM1_HUMAN	prostatic androgen-repressed message-1						positive regulation of telomerase activity	early endosome|endosome membrane|Golgi membrane|integral to membrane|late endosome|plasma membrane				ovary(1)	1						CAACAATCAGCCCCCCACATC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	83140204	83140204	+	IGR	DEL	A	-	-	rs113631274		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83140204delA								RASGEF1B (747143 upstream) : HNRNPD (134263 downstream)																							GTCTCAGGGGAAAAAAAAAAA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	83322313	83322313	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83322313delT								HNRNPD (27164 upstream) : HNRPDL (22036 downstream)																							ATCTACCTAATTTTTTTGGTA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	85107461	85107461	+	Intron	DEL	A	-	-	rs72060175		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85107461delA	uc010ikd.1	-						uc003hoz.1_Intron					Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																		AGTTGTAGAGAAAAAAAAAAA	0.299													3	3	---	---	---	---	
GRID2	2895	broad.mit.edu	37	4	94578790	94578790	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94578790delA	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	ATGTAGGAGGAAAAAAAAAAC	0.373													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	139335453	139335453	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139335453delT								SLC7A11 (171950 upstream) : CCRN4L (601490 downstream)																							TGTATTCCCATGACAGCTGTT	0.463													4	2	---	---	---	---	
ARHGAP10	79658	broad.mit.edu	37	4	148668306	148668306	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148668306delT	uc003ilf.2	+						ARHGAP10_uc003ile.1_Intron	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		GTCCTTCATCTTTTTTTTTTT	0.398													6	4	---	---	---	---	
FNIP2	57600	broad.mit.edu	37	4	159756286	159756286	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159756286delT	uc003iqe.3	+							NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2						DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		TTATTCAGAGTTTTTTTTTTA	0.294													4	2	---	---	---	---	
CPE	1363	broad.mit.edu	37	4	166389979	166389979	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166389979delA	uc003irg.3	+							NM_001873	NP_001864	P16870	CBPE_HUMAN	carboxypeptidase E preproprotein						cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TCTTTTGCTTAAAAAACCTTA	0.289													4	2	---	---	---	---	
WDR17	116966	broad.mit.edu	37	4	177065247	177065247	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177065247delC	uc003iuj.2	+						WDR17_uc003iuk.2_Intron|WDR17_uc003ium.3_Intron|WDR17_uc003iul.1_Intron	NM_170710	NP_733828	Q8IZU2	WDR17_HUMAN	WD repeat domain 17 isoform 1											ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		ccccaaggttcacttatactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	177281502	177281502	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177281502delT								SPCS3 (28108 upstream) : VEGFC (323189 downstream)																							GACTTGGGTCTTTTTTTTTCA	0.303													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180389425	180389425	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180389425delT								None (None upstream) : None (None downstream)																							AAGGCATTGGTTTTTATCCTT	0.373													4	2	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183424416	183424416	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183424416delT	uc003ivd.1	+							NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		ATATTTAGACTTTCAACCTGT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190565934	190565934	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190565934delG								None (None upstream) : FRG1 (296040 downstream)																							ACAGGTGAAAGGCGGAGCTAG	0.453													7	4	---	---	---	---	
AHRR	57491	broad.mit.edu	37	5	370567	370567	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:370567delG	uc003jav.2	+						AHRR_uc003jaw.2_Intron|AHRR_uc010isy.2_Intron|AHRR_uc010isz.2_Intron	NM_020731	NP_065782	A9YTQ3	AHRR_HUMAN	arylhydrocarbon receptor repressor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			breast(2)	2			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			GGGTCCCTCAGGAGGGAGCTT	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	788771	788772	+	IGR	DEL	TT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:788771_788772delTT								TPPP (95261 upstream) : ZDHHC11 (6948 downstream)																							GAGCACATTCTTAATACGCCAG	0.569													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4174829	4174829	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4174829delC								IRX1 (573313 upstream) : LOC340094 (859643 downstream)																							ctgaggctcactgactttaag	0.000													4	2	---	---	---	---	
LOC285692	285692	broad.mit.edu	37	5	9741041	9741041	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9741041delG	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0						TAGTTCTTTTGATGTGTCCTA	0.373													4	2	---	---	---	---	
TRIO	7204	broad.mit.edu	37	5	14347770	14347771	+	Intron	INS	-	A	A	rs173948	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14347770_14347771insA	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					ATTGTTGCTGCATTAAAAGCTT	0.455													4	2	---	---	---	---	
ANKH	56172	broad.mit.edu	37	5	14752804	14752805	+	Intron	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14752804_14752805insA	uc003jfm.3	-							NM_054027	NP_473368	Q9HCJ1	ANKH_HUMAN	progressive ankylosis protein						locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1						AGGACTGCAGCGGGGAGAGGGC	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23049361	23049362	+	IGR	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23049361_23049362insA								CDH12 (195630 upstream) : PRDM9 (458362 downstream)																							TTCTTTGCTATAAAATTCTAAT	0.307													4	2	---	---	---	---	
PDZD2	23037	broad.mit.edu	37	5	31770927	31770928	+	Intron	INS	-	A	A	rs5867101		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31770927_31770928insA	uc003jhl.2	+							NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						CTCAAATTTAGAAAAAAAAAAA	0.421													4	3	---	---	---	---	
RAI14	26064	broad.mit.edu	37	5	34693284	34693284	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34693284delT	uc003jir.2	+						RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Intron|RAI14_uc010ius.1_Intron|RAI14_uc003jis.2_Intron|RAI14_uc003jit.2_Intron|RAI14_uc011cok.1_Intron	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)					taaggtcaccttctgaggtta	0.075													4	2	---	---	---	---	
SLC1A3	6507	broad.mit.edu	37	5	36682621	36682621	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36682621delA	uc003jkj.3	+						SLC1A3_uc011cox.1_Intron|SLC1A3_uc010iuy.2_Intron	NM_004172	NP_004163	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity						D-aspartate import|L-glutamate import|neurotransmitter uptake	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		L-Glutamic Acid(DB00142)	ctgGGTTATTAAAAAAAAAAG	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	54180773	54180773	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54180773delT								SNX18 (338358 upstream) : ESM1 (92923 downstream)																							GCCAGGGACCTTCTAGAATCT	0.318													4	2	---	---	---	---	
ELOVL7	79993	broad.mit.edu	37	5	60098792	60098792	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60098792delA	uc003jsi.3	-						ELOVL7_uc010iwk.2_Intron|ELOVL7_uc003jsj.3_Intron	NM_024930	NP_079206	A1L3X0	ELOV7_HUMAN	elongation of very long chain fatty acids-like						fatty acid elongation, polyunsaturated fatty acid|fatty acid elongation, saturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)				ATTTTTAcggaaaaagacagt	0.025													4	2	---	---	---	---	
CCNB1	891	broad.mit.edu	37	5	68468903	68468903	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68468903delA	uc003jvm.2	+						CCNB1_uc011crd.1_Intron|CCNB1_uc010ixb.2_Intron	NM_031966	NP_114172	P14635	CCNB1_HUMAN	cyclin B1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitotic cell cycle spindle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|mitotic spindle stabilization|positive regulation of attachment of spindle microtubules to kinetochore|positive regulation of mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of cyclin-dependent protein kinase activity	condensed nuclear chromosome outer kinetochore|cytosol|microtubule organizing center|nucleoplasm|spindle pole					0		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		cccagccTGTAAATGTGCTGT	0.060													4	2	---	---	---	---	
MCCC2	64087	broad.mit.edu	37	5	70898709	70898709	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70898709delT	uc003kbs.3	+						MCCC2_uc010iyv.1_Intron|MCCC2_uc003kbt.3_Intron|MCCC2_uc003kbu.1_Intron	NM_022132	NP_071415	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)						leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)	1		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	TGTTGTGTGGTTTTTTTTTTT	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	72413175	72413176	+	IGR	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72413175_72413176insA								FCHO2 (26827 upstream) : TMEM171 (3212 downstream)																							cTACTTCCCACAAAAAATCACG	0.040													4	2	---	---	---	---	
SERINC5	256987	broad.mit.edu	37	5	79455260	79455260	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79455260delT	uc003kgj.2	-						SERINC5_uc003kgk.2_Intron|SERINC5_uc003kgl.2_Intron|SERINC5_uc003kgm.2_Intron|SERINC5_uc011ctj.1_Intron	NM_178276	NP_840060	Q86VE9	SERC5_HUMAN	developmentally regulated protein TPO1						phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(167;0.00328)|all_lung(232;0.00356)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.93e-46)|Epithelial(54;5.59e-40)|all cancers(79;1.89e-34)		CTGAGGTGTGTTTTTTTTTTA	0.229													4	2	---	---	---	---	
NBPF22P	285622	broad.mit.edu	37	5	85581309	85581310	+	Intron	DEL	TC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85581309_85581310delTC	uc003kiq.2	+							NR_003719				SubName: Full=Putative uncharacterized protein NBPF22P;												0						ACCTGATGCTtctctctctctc	0.356													3	3	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	90331107	90331107	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90331107delT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron|GPR98_uc003kjx.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CCATCTTCCCTTGGTGTCACC	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	101966053	101966054	+	IGR	DEL	CA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101966053_101966054delCA								SLCO6A1 (131333 upstream) : PAM (235473 downstream)																							GAGCACACAGCACACACACACA	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	110854009	110854009	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110854009delT								STARD4 (5776 upstream) : C5orf13 (144314 downstream)																							ttttgttttgtttttgctgct	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116123441	116123441	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116123441delA								SEMA6A (212890 upstream) : None (None downstream)																							GACACAAGAGAAAAAATGAAA	0.423													4	2	---	---	---	---	
PRR16	51334	broad.mit.edu	37	5	119922472	119922472	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119922472delT	uc003ksq.2	+						PRR16_uc003ksp.2_Intron	NM_016644	NP_057728	Q569H4	PRR16_HUMAN	proline rich 16											pancreas(2)|ovary(1)	3		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		atttgaccagttagtaaccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	122822822	122822823	+	IGR	INS	-	T	T	rs151325322	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122822822_122822823insT								CEP120 (63570 upstream) : CSNK1G3 (24970 downstream)																							GTATAGTACCGTTTTTTTTTTC	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123275723	123275723	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123275723delG								CSNK1G3 (323261 upstream) : ZNF608 (696887 downstream)																							gaaggttgcaggactaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	125876374	125876374	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125876374delA								GRAMD3 (46523 upstream) : ALDH7A1 (2544 downstream)																							GTAGACACAGAAAAAGGAATA	0.438													4	2	---	---	---	---	
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139869710	139869710	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139869710delC	uc003lfs.1	+						ANKHD1_uc003lfq.1_Intron|ANKHD1_uc003lfr.2_Intron|ANKHD1_uc003lft.1_Intron|ANKHD1_uc003lfu.1_Intron|ANKHD1_uc003lfv.1_Intron	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGTTTGACCTTTTTGTTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	155066912	155066912	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155066912delT								KIF4B (669227 upstream) : SGCD (68151 downstream)																							agagagcaagtttttaaaaag	0.000													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155295760	155295760	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155295760delA	uc003lwa.1	+							NM_172244	NP_758447	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 2						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AAGTTAGCTGAAATGGATAAG	0.323													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168444772	168444772	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168444772delA	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron|uc003mad.1_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGTCTATGAGAAAAAAAAGCT	0.393													4	2	---	---	---	---	
FBXW11	23291	broad.mit.edu	37	5	171380973	171380973	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171380973delC	uc003mbm.1	-						FBXW11_uc011dey.1_Intron|FBXW11_uc003mbl.1_Intron|FBXW11_uc003mbn.1_Intron	NM_012300	NP_036432	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11 isoform						cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of circadian rhythm|positive regulation of proteolysis|positive regulation of transcription, DNA-dependent|protein dephosphorylation|protein destabilization|protein polyubiquitination|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	centrosome|cytosol|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)|breast(1)	2	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTACTTACTGCCCAGCACTAT	0.448													4	2	---	---	---	---	
UBTD2	92181	broad.mit.edu	37	5	171679324	171679324	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171679324delT	uc003mbp.1	-							NM_152277	NP_689490	Q8WUN7	UBTD2_HUMAN	dendritic cell-derived ubiquitin-like protein							cytoplasm					0	Renal(175;0.000159)|Lung NSC(126;0.00976)|all_lung(126;0.0156)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GAAGTTGGCCTTTTTTTTTCC	0.463													4	2	---	---	---	---	
ERGIC1	57222	broad.mit.edu	37	5	172272450	172272450	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172272450delC	uc003mbw.3	+							NM_001031711	NP_001026881	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate						ER to Golgi vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TCTGGCCAGTCCCCAGGGCCC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173235164	173235164	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173235164delC								BOD1 (191498 upstream) : CPEB4 (80167 downstream)																							ATGATCTCTGCAGTTGTACAC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180021787	180021790	+	IGR	DEL	GTGT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180021787_180021790delGTGT								SCGB3A1 (3300 upstream) : FLT4 (6717 downstream)																							gtgtgtgtgggtgtgtgtgtgagg	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	2268462	2268463	+	Intron	DEL	GT	-	-	rs35373504		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2268462_2268463delGT	uc003mts.1	+											Homo sapiens cDNA FLJ13567 fis, clone PLACE1008331.																		atgtagaggggtgtgtgtgtgt	0.000													6	3	---	---	---	---	
SERPINB6	5269	broad.mit.edu	37	6	2957354	2957354	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2957354delG	uc003muk.2	-						SERPINB6_uc003mui.2_5'Flank|SERPINB6_uc003muj.2_RNA|SERPINB6_uc003mul.2_Intron|SERPINB6_uc003mum.2_Intron|SERPINB6_uc003mun.2_Intron|SERPINB6_uc003muo.2_Intron	NM_004568	NP_004559	P35237	SPB6_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	centrosome|cytosol|protein complex	protease binding|serine-type endopeptidase inhibitor activity				0	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	ggcagaggctggacggacagg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	5817538	5817538	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5817538delC								FARS2 (45722 upstream) : NRN1 (180697 downstream)																							TGTCCTTCCTCCAGGAGTCTG	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	7506281	7506282	+	IGR	DEL	GT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7506281_7506282delGT								RIOK1 (88013 upstream) : DSP (35588 downstream)																							TTTCCATTGAGTGTGTGTGTTG	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	13868796	13868796	+	IGR	DEL	G	-	-	rs67634664		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13868796delG								CCDC90A (54007 upstream) : RNF182 (56407 downstream)																							GGAATGGGACGGGGGGGGCAC	0.468													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	31340582	31340583	+	IGR	INS	-	A	A	rs150349624	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31340582_31340583insA								HLA-B (15593 upstream) : MICA (26978 downstream)																							agttcagaaagaaaaaaaaacc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	34537730	34537730	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34537730delG								SPDEF (13639 upstream) : C6orf106 (17336 downstream)																							cagaactcgaggccagccagg	0.234													4	2	---	---	---	---	
DAAM2	23500	broad.mit.edu	37	6	39789477	39789477	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39789477delA	uc003oow.2	+						DAAM2_uc010jxc.2_Intron|DAAM2_uc003oox.2_Intron|DAAM2_uc003oov.3_Intron	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					GGGGGTTGACATCTGAACATA	0.552													4	2	---	---	---	---	
SUPT3H	8464	broad.mit.edu	37	6	45256594	45256594	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45256594delC	uc003oxo.2	-						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron	NM_181356	NP_852001	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog isoform 2						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3						CATCCTCTGTCCATTGATCCA	0.343													4	2	---	---	---	---	
GPR116	221395	broad.mit.edu	37	6	46834436	46834437	+	Intron	INS	-	A	A	rs73736673	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46834436_46834437insA	uc003oyo.3	-						GPR116_uc011dwj.1_Intron|GPR116_uc011dwk.1_Intron|GPR116_uc003oyp.3_Intron|GPR116_uc003oyq.3_Intron|GPR116_uc010jzi.1_Intron	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)			TTCTCCCAATTAAAAAAAAAGG	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	52039936	52039936	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52039936delG								MIR133B (26097 upstream) : IL17A (11249 downstream)																							AAACCAGAAAGTCCATAGCAG	0.443													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57438708	57438709	+	Intron	INS	-	T	T	rs150105211		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57438708_57438709insT	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)		GTTTTAGTGCATTTTTTTTCCC	0.386													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57496558	57496559	+	Intron	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57496558_57496559insA	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)		gcacagcaggcaaaaatgaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	72389936	72389936	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72389936delC								C6orf155 (259488 upstream) : RIMS1 (206714 downstream)																							AGGAACAGAACCCCTGACAGG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	73206777	73206777	+	IGR	DEL	T	-	-	rs68033720		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73206777delT								RIMS1 (94270 upstream) : KCNQ5 (124794 downstream)																							AATTTTAGGGTTTTTTTTTTT	0.398													4	3	---	---	---	---	
SENP6	26054	broad.mit.edu	37	6	76331010	76331011	+	Intron	INS	-	GG	GG			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76331010_76331011insGG	uc003pid.3	+						SENP6_uc003pie.3_Intron|SENP6_uc003pic.2_Intron	NM_015571	NP_056386	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6 isoform 1						proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)				ATTATAGCTTTCTAATCTGAGC	0.302													6	3	---	---	---	---	
ZNF292	23036	broad.mit.edu	37	6	87946111	87946112	+	Intron	INS	-	G	G	rs2274582	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87946111_87946112insG	uc003plm.3	+							NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		TAGGTTGttttttttttttttt	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92039640	92039642	+	IGR	DEL	TGG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92039640_92039642delTGG								MAP3K7 (742733 upstream) : None (None downstream)																							CTTTTTTCTCTGGTGGTGGTGGT	0.419													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	109075145	109075145	+	Intron	DEL	C	-	-	rs67814311		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109075145delC	uc003pso.1	+						uc003psp.1_Intron					Homo sapiens mRNA sequence.																		AGttttctttctttttttttt	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	123416933	123416934	+	IGR	DEL	TG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123416933_123416934delTG								CLVS2 (31870 upstream) : TRDN (120549 downstream)																							tccagatgtttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
HDDC2	51020	broad.mit.edu	37	6	125622050	125622051	+	Intron	DEL	TT	-	-	rs142233585		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125622050_125622051delTT	uc003qaa.1	-						HDDC2_uc003qab.1_Intron	NM_016063	NP_057147	Q7Z4H3	HDDC2_HUMAN	HD domain containing 2								metal ion binding|phosphoric diester hydrolase activity				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0186)		CGTCAAATTATTCTGTTACTGA	0.347													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	131047601	131047602	+	IGR	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131047601_131047602insA								TMEM200A (283393 upstream) : LOC285733 (100722 downstream)																							GAAAACACAGGAAAAAAAATCA	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	132405503	132405503	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132405503delC								CTGF (132985 upstream) : MOXD1 (211692 downstream)																							TCCTTCTGAACAGACCTTCAC	0.418													4	2	---	---	---	---	
PLEKHG1	57480	broad.mit.edu	37	6	151134996	151134996	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151134996delG	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron|PLEKHG1_uc011eem.1_Intron|PLEKHG1_uc003qnz.2_Intron	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		ttattcacatggatggtgaaa	0.234													4	2	---	---	---	---	
NOX3	50508	broad.mit.edu	37	6	155733287	155733288	+	Intron	DEL	CT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155733287_155733288delCT	uc003qqm.2	-							NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3								electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		CTGCCCACACCTCTCTCTCTCG	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	161214708	161214708	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161214708delT								PLG (40363 upstream) : MAP3K4 (198114 downstream)																							atattgtaccttttttcctaa	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164530239	164530239	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164530239delA								QKI (535347 upstream) : None (None downstream)																							TGTATTTTTTAAGGGCCTCGT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1832702	1832702	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1832702delT								ELFN1 (45112 upstream) : MAD1L1 (22726 downstream)																							ATctgcccccttttctaggtt	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	20630970	20630970	+	IGR	DEL	T	-	-	rs112224373		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20630970delT								ITGB8 (175592 upstream) : ABCB5 (24275 downstream)																							CACTGTCCGATTTTTTTTTCC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25228552	25228552	+	IGR	DEL	G	-	-	rs73285424	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25228552delG								C7orf31 (8735 upstream) : NPVF (35641 downstream)																							CCTGGGTGCTGGGAGAAGGGA	0.502													4	2	---	---	---	---	
LOC441204	441204	broad.mit.edu	37	7	26485975	26485976	+	Intron	INS	-	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26485975_26485976insT	uc003sxy.1	+						LOC441204_uc003sxz.2_Intron					Homo sapiens cDNA FLJ31922 fis, clone NT2RP7005219.												0						atccctccccatttccctgact	0.000													4	2	---	---	---	---	
CREB5	9586	broad.mit.edu	37	7	28726090	28726091	+	Intron	INS	-	AA	AA			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28726090_28726091insAA	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron|CREB5_uc003szs.2_Intron|CREB5_uc011jzr.1_Intron	NM_182898	NP_878901	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						CGGGTTGGAGGAAAaaagaaaa	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	29588497	29588497	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29588497delT	uc003tab.2	-											Homo sapiens, clone IMAGE:4347271, mRNA.																		AGCAGCCATGTTTTAAGTCCT	0.458													4	2	---	---	---	---	
FAM183B	340286	broad.mit.edu	37	7	38728649	38728649	+	5'Flank	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38728649delA	uc011kbd.1	-							NR_028347				Homo sapiens cDNA FLJ42138 fis, clone TESTI2036684.												0						GAATCTGGGGAAGCCAAGAAA	0.448													4	2	---	---	---	---	
POU6F2	11281	broad.mit.edu	37	7	39291999	39292000	+	Intron	DEL	AC	-	-	rs140090404	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39291999_39292000delAC	uc003thb.1	+						POU6F2_uc010kxo.2_Intron	NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1						agacagacagacacacacacac	0.233													3	5	---	---	---	---	
EGFR	1956	broad.mit.edu	37	7	55123416	55123417	+	Intron	INS	-	CA	CA	rs139576133	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55123416_55123417insCA	uc003tqk.2	+						EGFR_uc003tqh.2_Intron|EGFR_uc003tqi.2_Intron|EGFR_uc003tqj.2_Intron|EGFR_uc010kzg.1_Intron	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	cacacacacaccacacacacac	0.396		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57698974	57698975	+	IGR	DEL	AC	-	-	rs145904451	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57698974_57698975delAC								ZNF716 (165709 upstream) : None (None downstream)																							TAAAAAATGTACAGTGAGGGAA	0.272													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61661760	61661761	+	IGR	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61661760_61661761insA								None (None upstream) : None (None downstream)																							AATTATATCACACATGATAGTT	0.317													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62499408	62499408	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62499408delG								None (None upstream) : LOC643955 (252264 downstream)																							GGCAGCAGGAGGGGGGATGAG	0.488													4	2	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	70747491	70747491	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70747491delC	uc003tvy.2	+							NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				gatgcccattccgtatttgtt	0.343													4	2	---	---	---	---	
GTF2I	2969	broad.mit.edu	37	7	74131524	74131524	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74131524delT	uc003uau.2	+						GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron|uc003uaz.2_Intron	NM_032999	NP_127492	P78347	GTF2I_HUMAN	general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0						AAAATGCTACTTTTTTTTTTG	0.294													4	2	---	---	---	---	
CD36	948	broad.mit.edu	37	7	79998981	79998981	+	5'UTR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79998981delG	uc003uhc.2	+	1						NM_001127444	NP_001120916	P16671	CD36_HUMAN	CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1						ggcagcctttggtacccctgt	0.179													4	2	---	---	---	---	
SEMA3A	10371	broad.mit.edu	37	7	83824112	83824112	+	5'UTR	DEL	G	-	-	rs78303093		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83824112delG	uc003uhz.2	-	1						NM_006080	NP_006071	Q14563	SEM3A_HUMAN	semaphorin 3A precursor						axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4						CCTCCaaaaagaaaaaaaaaa	0.373													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	89471683	89471683	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89471683delT								ZNF804B (505339 upstream) : DPY19L2P4 (277031 downstream)																							agctgTGGGCTTTTCCCATCC	0.244													4	2	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90732046	90732046	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90732046delA	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						ACCAAATCAGAAAAAAAAAAA	0.353													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	95206946	95206946	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95206946delT								ASB4 (39877 upstream) : PDK4 (5869 downstream)																							TTTCtttttctttttttcttt	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98146509	98146509	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98146509delA								BAIAP2L1 (116082 upstream) : NPTX2 (100088 downstream)																							TGTTCTGGTTAAAAAAAAATT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117110663	117110663	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117110663delT								ASZ1 (43086 upstream) : CFTR (9354 downstream)																							TCACATCAACTTTTTTTTCAT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	118335388	118335388	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118335388delA								ANKRD7 (452606 upstream) : None (None downstream)																							GCATTAAATCAAAAAAAATTC	0.353													4	2	---	---	---	---	
TSPAN12	23554	broad.mit.edu	37	7	120492551	120492551	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120492551delT	uc003vjk.2	-							NM_012338	NP_036470	O95859	TSN12_HUMAN	transmembrane 4 superfamily member 12						angiogenesis|cell surface receptor linked signaling pathway|regulation of angiogenesis|retina layer formation	integral to plasma membrane|membrane fraction					0	all_neural(327;0.117)					cctcagggtgtggcactcaga	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	122870256	122870256	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122870256delA								SLC13A1 (30231 upstream) : IQUB (221982 downstream)																							AAACAATAAGAAAAAAATAAG	0.343													4	2	---	---	---	---	
SND1	27044	broad.mit.edu	37	7	127471717	127471717	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127471717delG	uc003vmi.2	+						SND1_uc010lle.2_Intron	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						GCCTCAGTGTGGGAACTATTG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	140896726	140896726	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140896726delG								MRPS33 (181945 upstream) : AGK (354352 downstream)																							GAGTGGGGATGGGGTGAGATG	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	144856324	144856324	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144856324delA								TPK1 (323178 upstream) : CNTNAP2 (957129 downstream)																							ACTTCCAGCCAAATCATTCCT	0.383													4	2	---	---	---	---	
GALNTL5	168391	broad.mit.edu	37	7	151665679	151665680	+	Intron	DEL	GA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151665679_151665680delGA	uc003wkp.2	+						GALNTL5_uc003wkq.2_Intron|GALNTL5_uc003wkr.2_Intron|GALNTL5_uc003wks.2_Intron|GALNTL5_uc010lqf.2_Intron	NM_145292	NP_660335	Q7Z4T8	GLTL5_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		CTCGGATGGTGAGAGAAAGGAG	0.530													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152101925	152101925	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152101925delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		ATCTTttttgtttttttgttt	0.139			N		medulloblastoma								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152381432	152381432	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152381432delT								XRCC2 (8182 upstream) : ACTR3B (75419 downstream)																							CTCAGCCTCATCTCCTGGCAT	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	154947719	154947719	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154947719delT								HTR5A (70260 upstream) : INSIG1 (141767 downstream)																							GGTAATACCCTTTCCAGTGCT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157225913	157225914	+	IGR	DEL	CA	-	-	rs112053347		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157225913_157225914delCA								DNAJB6 (15781 upstream) : PTPRN2 (105837 downstream)																							cactcacatgcacacacacaca	0.183													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	12430743	12430744	+	Intron	INS	-	T	T	rs137908130		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12430743_12430744insT	uc003wvy.3	-						uc003wwa.2_5'Flank					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		TTTCAGTCATCtttttttttga	0.257													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	15172220	15172220	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15172220delT								SGCZ (76428 upstream) : TUSC3 (225510 downstream)																							ACTCCTTTCCTTTTTTTTCTT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	29694589	29694589	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29694589delG								C8orf75 (88964 upstream) : LOC286135 (84440 downstream)																							GCCAGGGTATGGGAGACCAAA	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	29739470	29739470	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29739470delT								C8orf75 (133845 upstream) : LOC286135 (39559 downstream)																							AATTGCATGATTTTTTTTTCA	0.463													4	2	---	---	---	---	
RNF122	79845	broad.mit.edu	37	8	33406740	33406740	+	Intron	DEL	A	-	-	rs71899502		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33406740delA	uc003xjo.1	-							NM_024787	NP_079063	Q9H9V4	RN122_HUMAN	ring finger protein 122							endoplasmic reticulum|Golgi apparatus|integral to membrane	zinc ion binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0966)|Kidney(114;0.116)		actccaactcaaaaaaaaaag	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	35680655	35680655	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35680655delG								UNC5D (28475 upstream) : KCNU1 (961187 downstream)																							tggacagcgtggggagcagag	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	38080760	38080761	+	IGR	INS	-	CACA	CACA	rs139121543	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38080760_38080761insCACA								BAG4 (12223 upstream) : DDHD2 (8248 downstream)																							CCACCTTGCTGCACAGCTTCAA	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54599968	54599968	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54599968delA								OPRK1 (435774 upstream) : ATP6V1H (28148 downstream)																							AAGGATTTTCAAAGGTGCTTG	0.413													4	2	---	---	---	---	
XKR4	114786	broad.mit.edu	37	8	56279365	56279366	+	Intron	DEL	CT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56279365_56279366delCT	uc003xsf.2	+							NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)			tggaattaccctctctctccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	57211248	57211248	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57211248delG								CHCHD7 (80074 upstream) : SDR16C5 (1322 downstream)																							TTTGTCTGGTGGCCCAGATTT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	74690329	74690329	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74690329delG								STAU2 (30386 upstream) : UBE2W (2003 downstream)																							gtaaagaagaggcaaatttgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81863360	81863360	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81863360delG								ZNF704 (76344 upstream) : PAG1 (16688 downstream)																							TATCGCTCCTGGGCTCCTCTG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	89603972	89603973	+	IGR	INS	-	T	T	rs141011653	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89603972_89603973insT								MMP16 (264255 upstream) : None (None downstream)																							GTCTGATAGAGGTTAGTTTTTA	0.426													1	5	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100741196	100741196	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100741196delT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTCAACAGACTTTTTTTTTCT	0.423													4	2	---	---	---	---	
RNF19A	25897	broad.mit.edu	37	8	101322672	101322672	+	5'Flank	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101322672delG	uc003yjk.1	-							NM_183419	NP_904355	Q9NV58	RN19A_HUMAN	ring finger protein 19						microtubule cytoskeleton organization|protein modification process	centrosome|integral to membrane	ligase activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)			AGGTCGGGGTGGCTGGAGCTG	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103705154	103705154	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103705154delG								KLF10 (37171 upstream) : AZIN1 (133383 downstream)																							CCGGGGCTTTGGAGCTGCACG	0.517													4	2	---	---	---	---	
BAALC	79870	broad.mit.edu	37	8	104157671	104157672	+	Intron	DEL	AA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104157671_104157672delAA	uc003yld.2	+						BAALC_uc003yle.2_Intron	NM_024812	NP_079088	Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic isoform 1							centrosome|membrane|nucleus					0			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)			cacattctctaaatacactact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	111875933	111875934	+	IGR	DEL	AA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111875933_111875934delAA								KCNV1 (887857 upstream) : None (None downstream)																							ctatatcaccaaaaggaaacat	0.000													4	2	---	---	---	---	
TSNARE1	203062	broad.mit.edu	37	8	143445373	143445373	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143445373delA	uc003ywk.2	-						TSNARE1_uc003ywl.3_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					TCTCTAACTGAAACCTCAATT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144223516	144223516	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144223516delG								C8orf31 (87796 upstream) : LY6H (15816 downstream)																							gaaggcatgtggaggcagagg	0.209													4	2	---	---	---	---	
KIAA1875	340390	broad.mit.edu	37	8	145169270	145169270	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145169270delC	uc011lkz.1	+	2	1804	c.123delC	c.(121-123)ATCfs	p.I41fs	KIAA1875_uc003zbd.3_RNA					SubName: Full=Putative uncharacterized protein DKFZp434F0427; Flags: Fragment;											large_intestine(1)	1						GTGTGCACATCCTGCAGGTGC	0.642													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	145931075	145931075	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145931075delG								ARHGAP39 (19881 upstream) : ZNF251 (15220 downstream)																							TACCAGCTCTGGATAAGCATC	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	2273543	2273543	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2273543delA								SMARCA2 (79922 upstream) : FLJ35024 (149159 downstream)																							GGCCATCAGGAAAAAGAAAAT	0.383													4	2	---	---	---	---	
KDM4C	23081	broad.mit.edu	37	9	6995678	6995678	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6995678delT	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						AGGTTTTAAAttttttttttt	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	25824585	25824585	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25824585delT								TUSC1 (145729 upstream) : None (None downstream)																							tgatctatccttgagaatgaa	0.000													4	2	---	---	---	---	
CNTFR	1271	broad.mit.edu	37	9	34592554	34592555	+	5'Flank	DEL	CA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34592554_34592555delCA	uc003zup.1	-						CNTFR_uc003zuq.1_5'Flank	NM_147164	NP_671693	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor						nervous system development	anchored to membrane|extrinsic to membrane|plasma membrane	ciliary neurotrophic factor receptor activity|receptor binding			ovary(3)|central_nervous_system(1)|skin(1)	5	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)		TGGACCCCCCCACACACACACC	0.525											OREG0019155	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	34601870	34601872	+	IGR	DEL	GAG	-	-	rs71891438		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34601870_34601872delGAG								CNTFR (12148 upstream) : C9orf23 (8621 downstream)																							agaagagagagaggaggacagcg	0.099													3	3	---	---	---	---	
SIGMAR1	10280	broad.mit.edu	37	9	34634946	34634946	+	3'UTR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34634946delC	uc003zvb.2	-	4					SIGMAR1_uc003zva.3_3'UTR|SIGMAR1_uc003zuz.2_3'UTR|SIGMAR1_uc003zvc.2_3'UTR|SIGMAR1_uc003zvd.2_RNA	NM_005866	NP_005857	Q99720	SGMR1_HUMAN	sigma non-opioid intracellular receptor 1						ergosterol biosynthetic process|lipid transport	cell junction|endoplasmic reticulum membrane|growth cone|integral to plasma membrane|lipid particle|nuclear inner membrane|nuclear outer membrane	C-8 sterol isomerase activity|drug binding				0					Dextromethorphan(DB00514)	CCACATCATACCCCCAAAGGA	0.542													4	2	---	---	---	---	
FRMPD1	22844	broad.mit.edu	37	9	37736856	37736857	+	Intron	DEL	GT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37736856_37736857delGT	uc004aag.1	+						FRMPD1_uc004aah.1_Intron|FRMPD1_uc011lqm.1_Intron|FRMPD1_uc011lqn.1_Intron	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1							cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		gtgcgtgagagtgtgtgtgtgt	0.366													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66461393	66461394	+	5'Flank	INS	-	AC	AC			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66461393_66461394insAC	uc004aeb.2	-						uc004aec.2_Intron					Homo sapiens cDNA clone IMAGE:3941306, partial cds.																		gctgtatttgtatgtactttat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68418927	68418928	+	IGR	INS	-	A	A	rs62545510		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68418927_68418928insA								FAM27B (624738 upstream) : MIR1299 (583311 downstream)																							catgcatacaccccatacagac	0.050													7	4	---	---	---	---	
MAMDC2	256691	broad.mit.edu	37	9	72658403	72658403	+	5'Flank	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72658403delA	uc004ahm.2	+						MAMDC2_uc004ahn.2_5'Flank	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						TCCACCGGCTAAAAAAAGTGG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	76280748	76280748	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76280748delT								ANXA1 (495441 upstream) : RORB (831504 downstream)																							agatactgtcttttttaagtg	0.050													4	2	---	---	---	---	
PCSK5	5125	broad.mit.edu	37	9	78573646	78573646	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78573646delT	uc004ajz.2	+						PCSK5_uc004ajy.2_Intron|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						gggcaaacgatttagctctat	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85546268	85546268	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85546268delG								FLJ46321 (936098 upstream) : RASEF (51049 downstream)																							ATATCACTCTGGTCATTATCA	0.353													4	2	---	---	---	---	
NAA35	60560	broad.mit.edu	37	9	88579602	88579602	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88579602delT	uc004aoi.3	+						NAA35_uc004aoj.3_Intron|NAA35_uc004aok.1_Intron	NM_024635	NP_078911	Q5VZE5	NAA35_HUMAN	corneal wound healing-related protein						smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3						ttcacttgggtttatctgttc	0.000													4	2	---	---	---	---	
C9orf79	286234	broad.mit.edu	37	9	90495573	90495573	+	5'Flank	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90495573delA	uc004app.3	+						C9orf79_uc004apo.1_5'Flank	NM_178828	NP_849150	Q6ZUB1	CI079_HUMAN	chromosome 9 open reading frame 79							integral to membrane				ovary(3)	3						GCAGGAAGGCAAAAGGCACCC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93119866	93119866	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93119866delA								LOC100129066 (785192 upstream) : DIRAS2 (252248 downstream)																							atgacattgcaaaaaaaaggc	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	101674553	101674553	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101674553delA								GALNT12 (62195 upstream) : COL15A1 (31585 downstream)																							agagagacagaaaaaaaaaaG	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111404105	111404105	+	IGR	DEL	T	-	-	rs77074915	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111404105delT								None (None upstream) : ACTL7B (212766 downstream)																							cagctttctcttttTTTCCTG	0.164													4	2	---	---	---	---	
PTPN3	5774	broad.mit.edu	37	9	112168483	112168483	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112168483delG	uc004bed.2	-						PTPN3_uc004beb.2_Intron|PTPN3_uc004bec.2_Intron|PTPN3_uc010mtu.2_Intron|PTPN3_uc011lwg.1_Intron|PTPN3_uc011lwh.1_Intron|PTPN3_uc011lwd.1_Intron|PTPN3_uc011lwe.1_Intron|PTPN3_uc011lwf.1_Intron	NM_002829	NP_002820	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type						negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3						actgggagctgggggctcatg	0.015													4	2	---	---	---	---	
RGS3	5998	broad.mit.edu	37	9	116299970	116299970	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116299970delG	uc004bhq.2	+						RGS3_uc004bhr.2_Intron|RGS3_uc004bhs.2_Intron|RGS3_uc004bht.2_Intron|RGS3_uc010muy.2_Intron|RGS3_uc004bhu.2_Intron|RGS3_uc004bhv.2_Intron	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3						TGCTGGATCTGGGCGAAGAGG	0.527													4	2	---	---	---	---	
DFNB31	25861	broad.mit.edu	37	9	117228266	117228267	+	Intron	INS	-	C	C	rs138194289	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117228266_117228267insC	uc004biz.3	-						DFNB31_uc004biy.3_Intron|DFNB31_uc004bja.3_Intron	NM_015404	NP_056219	Q9P202	WHRN_HUMAN	CASK-interacting protein CIP98 isoform 1						inner ear receptor stereocilium organization|retina homeostasis|sensory perception of light stimulus|sensory perception of sound	cytoplasm|growth cone|stereocilium				ovary(4)|central_nervous_system(1)|pancreas(1)	6						TCCTCTCCACGCATCGTAACAA	0.554													4	2	---	---	---	---	
DAB2IP	153090	broad.mit.edu	37	9	124490246	124490246	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124490246delT	uc004bln.2	+							NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform						activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2						CAGTGTTGTCTTTTTTTGTAA	0.328													4	2	---	---	---	---	
FNBP1	23048	broad.mit.edu	37	9	132678572	132678572	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132678572delT	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc011mbu.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848	Q96RU3	FNBP1_HUMAN	formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		TAAAGTAAGCTTATAGTCAGT	0.284			T	MLL	AML								4	2	---	---	---	---	
ABL1	25	broad.mit.edu	37	9	133690986	133690986	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133690986delG	uc004bzv.2	+							NM_007313	NP_009297	P00519	ABL1_HUMAN	c-abl oncogene 1, receptor tyrosine kinase						actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)	ctcttggccagggtccctgct	0.000			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	138154007	138154008	+	IGR	DEL	TG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138154007_138154008delTG								OLFM1 (140976 upstream) : KIAA0649 (217640 downstream)																							tctgcatgtctgtgtgtgtgca	0.000													4	2	---	---	---	---	
LARP4B	23185	broad.mit.edu	37	10	867059	867059	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:867059delG	uc001ifs.1	-							NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B								nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3						GTGCCTCCTTGGGATGTCTGT	0.433													4	2	---	---	---	---	
PFKFB3	5209	broad.mit.edu	37	10	6263049	6263050	+	Intron	DEL	TG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6263049_6263050delTG	uc001ije.2	+						PFKFB3_uc001ijd.2_Intron|PFKFB3_uc009xii.2_Intron|PFKFB3_uc010qaw.1_Intron|PFKFB3_uc001ijf.2_Intron	NM_004566	NP_004557	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(2)|central_nervous_system(1)	3						CATGTGGCTTtgtgtgtgtgtg	0.104													4	2	---	---	---	---	
PRKCQ	5588	broad.mit.edu	37	10	6528953	6528954	+	Intron	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6528953_6528954insA	uc001ijj.1	-						PRKCQ_uc009xim.1_Intron|PRKCQ_uc001iji.1_Intron|PRKCQ_uc009xin.1_Intron|PRKCQ_uc010qax.1_Intron	NM_006257	NP_006248	Q04759	KPCT_HUMAN	protein kinase C, theta						axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6						CCTCAGCTTTGAAAAAAAAATC	0.515													4	2	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11107663	11107664	+	Intron	INS	-	C	C	rs145741845	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11107663_11107664insC	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						gacaaaccccaccccccgccat	0.099													3	3	---	---	---	---	
PRPF18	8559	broad.mit.edu	37	10	13682291	13682292	+	Intron	INS	-	G	G	rs139922369	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13682291_13682292insG	uc001imq.2	+						uc001imr.1_RNA			Q99633	PRP18_HUMAN	Homo sapiens mRNA; cDNA DKFZp434L162 (from clone DKFZp434L162).						mRNA processing|RNA splicing	nuclear speck|spliceosomal complex				central_nervous_system(1)	1						cttcactatctgtTGACAGTTG	0.198													2	7	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	13738095	13738096	+	Intron	INS	-	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13738095_13738096insT	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						CTAACCTCAACTTTTTTCCTTG	0.505													4	2	---	---	---	---	
KIF5B	3799	broad.mit.edu	37	10	32300020	32300020	+	3'UTR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32300020delA	uc001iwe.3	-	26						NM_004521	NP_004512	P33176	KINH_HUMAN	kinesin family member 5B						stress granule disassembly|vesicle transport along microtubule	kinesin complex|microtubule|perinuclear region of cytoplasm|vesicle	ATP binding|microtubule binding|microtubule motor activity		KIF5B/ALK(4)	lung(4)|ovary(1)	5		Prostate(175;0.0137)				TTCTCTTAAGAAAAAAAAAGG	0.269													4	3	---	---	---	---	
ZNF365	22891	broad.mit.edu	37	10	64271617	64271617	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64271617delA	uc001jmc.2	+							NM_199451	NP_955523	Q70YC4	TALAN_HUMAN	zinc finger protein 365 isoform C											ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					GAAGGCCTAGAAGGCCTGGAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	78561029	78561029	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78561029delA								C10orf11 (243905 upstream) : KCNMA1 (68330 downstream)																							gccaaactccaagggacatat	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80062398	80062399	+	Intron	INS	-	G	G	rs72515558	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80062398_80062399insG	uc010qlp.1	+						uc001jzw.1_Intron					SubName: Full=cDNA FLJ57363;																		AGCTGTAAAAATCTGCCACACT	0.470													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	89828582	89828582	+	IGR	DEL	G	-	-	rs113311284		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89828582delG								PTEN (100051 upstream) : RNLS (63475 downstream)																							ATTAACAACAGGACTCAATGC	0.388													0	6	---	---	---	---	
SLC16A12	387700	broad.mit.edu	37	10	91238903	91238903	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91238903delG	uc001kgm.2	-							NM_213606	NP_998771	Q6ZSM3	MOT12_HUMAN	solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			skin(1)	1						acctacAGCTGGGGACAAAGA	0.114													4	2	---	---	---	---	
MARCH5	54708	broad.mit.edu	37	10	94090973	94090973	+	Intron	DEL	T	-	-	rs140276544	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94090973delT	uc001khx.1	+						MARCH5_uc010qno.1_Intron	NM_017824	NP_060294	Q9NX47	MARH5_HUMAN	membrane-associated ring finger (C3HC4) 5						cell aging|protein autoubiquitination|protein localization in mitochondrion|protein polyubiquitination|regulation of mitochondrial fission	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane	GTPase binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1						TGGTGGTGACTTTTTTCAGCA	0.378													4	2	---	---	---	---	
SUFU	51684	broad.mit.edu	37	10	104368229	104368230	+	Intron	DEL	GG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104368229_104368230delGG	uc001kvy.1	+						SUFU_uc001kvw.1_Intron|SUFU_uc001kvx.2_Intron|SUFU_uc009xxe.1_Intron|SUFU_uc009xxf.1_Intron	NM_016169	NP_057253	Q9UMX1	SUFU_HUMAN	suppressor of fused						negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			central_nervous_system(4)|skin(2)|breast(1)	7		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		ggcaagcccaggggaacttcag	0.000			D|F|S		medulloblastoma	medulloblastoma			Medulloblastoma_associated_with_Germline_SUFU_Mutation				4	2	---	---	---	---	
KIAA1598	57698	broad.mit.edu	37	10	118660503	118660503	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118660503delA	uc009xyw.2	-						KIAA1598_uc001lcz.3_Intron|KIAA1598_uc010qso.1_Intron|KIAA1598_uc010qsp.1_Intron|KIAA1598_uc010qsq.1_Intron|KIAA1598_uc001lcy.3_Intron	NM_001127211	NP_001120683	A0MZ66	SHOT1_HUMAN	shootin1 isoform a						axon guidance	axon					0				all cancers(201;0.00494)		CTAGAGTTACAAAAAAGGGGT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130262725	130262734	+	IGR	DEL	CCTCCTCCTC	-	-	rs66913631		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130262725_130262734delCCTCCTCCTC								MKI67 (338257 upstream) : None (None downstream)																							ctagacttctcctcctcctccctcctcctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133143031	133143032	+	IGR	INS	-	T	T	rs144672047	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133143031_133143032insT								TCERG1L (33047 upstream) : PPP2R2D (604928 downstream)																							ACTACAGCAGGTTGTCTGACAC	0.411													1	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133344799	133344800	+	IGR	DEL	CA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133344799_133344800delCA								TCERG1L (234815 upstream) : PPP2R2D (403160 downstream)																							CCCCTTTTGTCACCAGCAGCTT	0.574													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	1771572	1771572	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1771572delG	uc001lub.1	-											Homo sapiens cDNA FLJ76511 complete cds.																		TCCCTGAGCTGGGTCCTCTTC	0.612													4	2	---	---	---	---	
ZNF195	7748	broad.mit.edu	37	11	3396835	3396835	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3396835delA	uc001lxt.2	-						ZNF195_uc001lxv.2_Intron|ZNF195_uc001lxs.2_Intron|ZNF195_uc010qxr.1_Intron|ZNF195_uc009ydz.2_Intron|ZNF195_uc001lxu.2_Intron	NM_001130520	NP_001123992	O14628	ZN195_HUMAN	zinc finger protein 195 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		CAGTTACTGGAAATGGAAAAG	0.443													4	2	---	---	---	---	
INSC	387755	broad.mit.edu	37	11	15197822	15197823	+	Intron	INS	-	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15197822_15197823insT	uc001mly.2	+						INSC_uc001mlz.2_Intron|INSC_uc001mma.2_Intron|INSC_uc010rcs.1_Intron|INSC_uc001mmb.2_Intron|INSC_uc001mmc.2_Intron	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a						cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5						tgtgctaggtgtttttttttta	0.163													5	4	---	---	---	---	
SLC6A5	9152	broad.mit.edu	37	11	20665454	20665454	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20665454delT	uc001mqd.2	+						SLC6A5_uc009yic.2_Intron	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter						synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	TGGTAGGAAGTAAAAGCAAAT	0.502													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	20999981	20999981	+	Intron	DEL	A	-	-	rs66504544		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20999981delA	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						TGTCTTCATGAAAAAAAAAGC	0.249													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21246750	21246750	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21246750delG	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						acattctggtggcagctctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	27761156	27761156	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27761156delA								BDNF (17551 upstream) : KIF18A (281007 downstream)																							TGTCTGTCTCAACAGTCATCC	0.403													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	30046885	30046885	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30046885delA								KCNA4 (8397 upstream) : FSHB (205678 downstream)																							tctggggcagAAAAAAAAGAA	0.184													4	2	---	---	---	---	
EIF3M	10480	broad.mit.edu	37	11	32613748	32613748	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32613748delA	uc001mtu.2	+						EIF3M_uc010ref.1_Intron	NM_006360	NP_006351	Q7L2H7	EIF3M_HUMAN	eukaryotic translation initiation factor 3,							eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)|breast(1)|skin(1)	3	Breast(20;0.109)					CACAACCCATAAAGTTGCTAG	0.318													4	2	---	---	---	---	
PHF21A	51317	broad.mit.edu	37	11	45987668	45987668	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45987668delT	uc001ncc.3	-						PHF21A_uc001ncb.3_Intron|PHF21A_uc009ykx.2_Intron|PHF21A_uc001nce.2_Intron|PHF21A_uc001nca.1_Intron	NM_001101802	NP_001095272	Q96BD5	PF21A_HUMAN	BRAF35/HDAC2 complex isoform a						blood coagulation|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|transcription, DNA-dependent	histone deacetylase complex	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2						ctggcaccccttttcttccca	0.000													4	2	---	---	---	---	
CKAP5	9793	broad.mit.edu	37	11	46791247	46791247	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46791247delA	uc001ndi.1	-						CKAP5_uc009ylg.1_Intron|CKAP5_uc001ndj.1_Intron|CKAP5_uc001ndh.1_Intron	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2						tgccatctctaaaaaaaaaaa	0.119													4	2	---	---	---	---	
LRP4	4038	broad.mit.edu	37	11	46912171	46912172	+	Intron	INS	-	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46912171_46912172insT	uc001ndn.3	-							NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein						endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)		CACAGAATGAAtttttttttta	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49859909	49859910	+	IGR	INS	-	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49859909_49859910insT								LOC440040 (27942 upstream) : OR4C13 (114065 downstream)																							TAGAAATCCTACCAAAGAGTCA	0.356													4	2	---	---	---	---	
SLC22A20	440044	broad.mit.edu	37	11	64994393	64994394	+	Intron	DEL	AT	-	-	rs67392513		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64994393_64994394delAT	uc010roc.1	+							NM_001004326	NP_001004326	A6NK97	S22AK_HUMAN	solute carrier family 22, member 20						ion transport	integral to membrane	transmembrane transporter activity			central_nervous_system(1)	1						acacacacacatacacacGTTC	0.178													4	2	---	---	---	---	
C11orf80	79703	broad.mit.edu	37	11	66581711	66581711	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66581711delT	uc001ojf.2	+						C11orf80_uc001ojg.2_Intron|C11orf80_uc001ojh.2_Intron|C11orf80_uc001oji.2_Intron|C11orf80_uc010rpl.1_Intron|C11orf80_uc001ojj.2_Intron	NM_024650	NP_078926	Q8N6T0	CK080_HUMAN	hypothetical protein LOC79703												0						GCATTGCATGTTTTTTTTTGT	0.269													3	3	---	---	---	---	
C11orf51	25906	broad.mit.edu	37	11	71817517	71817517	+	3'UTR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71817517delC	uc009ytc.1	-	4					LRTOMT_uc010rqv.1_Intron|LRTOMT_uc010rqw.1_Intron|LRTOMT_uc001ors.3_Intron			P60006	CK051_HUMAN	Homo sapiens HSPC020 mRNA, complete cds.							intracellular					0						gccacaaatgctggcctcaaa	0.109													4	2	---	---	---	---	
CLPB	81570	broad.mit.edu	37	11	72119263	72119263	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72119263delA	uc001osj.2	-						CLPB_uc010rqx.1_Intron|CLPB_uc010rqy.1_Intron|CLPB_uc001osk.2_Intron|CLPB_uc009ytg.2_Intron|CLPB_uc010rqz.1_Intron	NM_030813	NP_110440	Q9H078	CLPB_HUMAN	caseinolytic peptidase B						cellular response to heat		ATP binding|nucleoside-triphosphatase activity|protein binding			pancreas(1)	1						ggtataatggaaaaaaagcaa	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	83079664	83079665	+	Intron	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83079664_83079665insA	uc001pag.2	+											Homo sapiens cDNA clone IMAGE:5296561.																		TAATTCACAGGAAAAATCCTTG	0.312													4	2	---	---	---	---	
PDGFD	80310	broad.mit.edu	37	11	103964855	103964856	+	Intron	INS	-	ATT	ATT	rs72520944		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103964855_103964856insATT	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484	Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		ttgcctcttaaaccagccctct	0.000													0	6	---	---	---	---	
NNMT	4837	broad.mit.edu	37	11	114126757	114126758	+	5'Flank	INS	-	T	T	rs73009004		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114126757_114126758insT	uc001por.1	+							NM_006169	NP_006160	P40261	NNMT_HUMAN	nicotinamide N-methyltransferase						xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)	ttttttttttgttttttttgcc	0.297													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124592684	124592684	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124592684delA								SPA17 (27999 upstream) : NRGN (17145 downstream)																							CCCCATGTTTAAAAAAAAACC	0.418													4	2	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126467792	126467792	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126467792delC	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		ACAGTTCTGTCTAAAACAGAG	0.443													4	2	---	---	---	---	
SNX19	399979	broad.mit.edu	37	11	130747921	130747922	+	3'UTR	DEL	CC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130747921_130747922delCC	uc001qgk.3	-	11					SNX19_uc009zcw.2_3'UTR|SNX19_uc010sce.1_3'UTR|SNX19_uc010scf.1_3'UTR|SNX19_uc010scg.1_3'UTR	NM_014758	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|lung(2)	4	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		CAGTTTTTTTCCTGTTCTATCT	0.455													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133233969	133233969	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133233969delC	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		TGCGGTAAGTCCCAGCTCCAA	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134934461	134934461	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134934461delT								B3GAT1 (652649 upstream) : None (None downstream)																							GGAAAGCAGAttttttttttt	0.179													3	3	---	---	---	---	
ERC1	23085	broad.mit.edu	37	12	1437789	1437790	+	Intron	DEL	TT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1437789_1437790delTT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			tttctctctctttcgcttcccc	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4310344	4310344	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4310344delT								PARP11 (327736 upstream) : CCND2 (72558 downstream)																							cagcatattctcccttgattt	0.144													4	2	---	---	---	---	
DYRK4	8798	broad.mit.edu	37	12	4689428	4689428	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4689428delG	uc009zeh.1	+							NM_003845	NP_003836	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation							Golgi apparatus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|skin(1)	3			Colorectal(7;0.103)			TAGGACCCCAGGGAGGCTACT	0.587													4	2	---	---	---	---	
RIMKLB	57494	broad.mit.edu	37	12	8835611	8835611	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8835611delG	uc001quu.2	+						RIMKLB_uc009zgf.1_Intron	NM_020734	NP_065785	Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0						tacagtatgtggacttttcag	0.000													4	2	---	---	---	---	
DERA	51071	broad.mit.edu	37	12	16135558	16135558	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16135558delT	uc001rde.2	+						DERA_uc010shx.1_Intron	NM_015954	NP_057038	Q9Y315	DEOC_HUMAN	deoxyribose-phosphate aldolase-like						deoxyribonucleoside catabolic process|deoxyribonucleotide catabolic process	cytoplasm	deoxyribose-phosphate aldolase activity|protein binding				0		Hepatocellular(102;0.121)				TTCTTCCACATTTTTTTTTGT	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	26439470	26439470	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26439470delT								SSPN (33617 upstream) : ITPR2 (48817 downstream)																							TGCATCTTGCTTTTGCCCTCT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	28051477	28051477	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28051477delC								KLHDC5 (95505 upstream) : PTHLH (59541 downstream)																							TGTTATTTTTCTTTTAGGAGT	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	44113297	44113297	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44113297delG								ADAMTS20 (167573 upstream) : PUS7L (9117 downstream)																							agaaacaggtggggggactct	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	58252695	58252695	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58252695delT								CTDSP2 (11948 upstream) : XRCC6BP1 (82750 downstream)																							gttaataggctttttctctgt	0.000													4	2	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	82025125	82025125	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82025125delA	uc001szo.1	-						PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6						TTGTCTGATGAAAAAAAATAC	0.308													4	2	---	---	---	---	
TMTC2	160335	broad.mit.edu	37	12	83244004	83244004	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83244004delC	uc001szt.2	+						TMTC2_uc001szr.1_Intron|TMTC2_uc001szs.1_Intron|TMTC2_uc010suk.1_Intron	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2						gttaacattgccttgtttgat	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	101050017	101050018	+	IGR	DEL	AC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101050017_101050018delAC								GAS2L3 (31334 upstream) : ANO4 (61286 downstream)																							atacacacagacacacacacgc	0.396													4	2	---	---	---	---	
HCFC2	29915	broad.mit.edu	37	12	104472519	104472519	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104472519delC	uc001tkj.3	+						HCFC2_uc009zul.2_Intron	NM_013320	NP_037452	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2						regulation of transcription from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleus	transcription coactivator activity			ovary(2)|central_nervous_system(1)	3						agaataataaccatttgatta	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108657379	108657379	+	IGR	DEL	G	-	-	rs5800816		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108657379delG								WSCD2 (13068 upstream) : CMKLR1 (24443 downstream)																							CCCCACAAAAGCATCCAGTCC	0.478													2	4	---	---	---	---	
ACACB	32	broad.mit.edu	37	12	109626138	109626138	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109626138delA	uc001tob.2	+						ACACB_uc001toc.2_Intron	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	cttcccttccattgccttcct	0.000													4	2	---	---	---	---	
BRAP	8315	broad.mit.edu	37	12	112097878	112097878	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112097878delA	uc001tsn.3	-						BRAP_uc010syh.1_Intron|BRAP_uc009zvv.2_Intron	NM_006768	NP_006759	Q7Z569	BRAP_HUMAN	BRCA1 associated protein						MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1						accctgtctcaaaaaaaaaag	0.134													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112976902	112976902	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112976902delG								PTPN11 (29186 upstream) : RPH3A (35999 downstream)																							AAAGTGCAGTGGGATTCTTTA	0.358													4	2	---	---	---	---	
KDM2B	84678	broad.mit.edu	37	12	121906123	121906123	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121906123delA	uc001uat.2	-						KDM2B_uc001uaq.2_5'Flank|KDM2B_uc010szy.1_5'Flank|KDM2B_uc001uar.2_Intron|KDM2B_uc001uas.2_Intron|KDM2B_uc001uau.2_Intron	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2						TCATTCATTCAAAAAAAAAGT	0.433													4	2	---	---	---	---	
PSMD9	5715	broad.mit.edu	37	12	122343961	122343961	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122343961delG	uc001ubl.2	+						PSMD9_uc009zxj.2_Intron|PSMD9_uc001ubm.2_Intron	NM_002813	NP_002804	O00233	PSMD9_HUMAN	proteasome 26S non-ATPase subunit 9						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of insulin secretion|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of insulin secretion|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|proteasome regulatory particle assembly|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	nucleus|proteasome regulatory particle	bHLH transcription factor binding|transcription coactivator activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000117)|Epithelial(86;0.000415)|BRCA - Breast invasive adenocarcinoma(302;0.231)		tctgttgtgtggatctgtGAG	0.159													4	2	---	---	---	---	
GPR133	283383	broad.mit.edu	37	12	131574932	131574932	+	Intron	DEL	C	-	-	rs5801949		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131574932delC	uc001uit.3	+						GPR133_uc010tbm.1_Intron|GPR133_uc009zyo.2_Intron|GPR133_uc001uiv.1_Intron	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		CACTGCTGGTCTTTGGGTTCC	0.517													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21301980	21301980	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21301980delA	uc001unn.1	-											Homo sapiens cDNA FLJ30846 fis, clone FEBRA2002783.																		tttgttggccaaagcaagtct	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21528132	21528133	+	IGR	DEL	TG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21528132_21528133delTG								XPO4 (51219 upstream) : LATS2 (19045 downstream)																							GTTTTTTGGTTGTGTGTGTGTG	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27618357	27618357	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27618357delC								GPR12 (283435 upstream) : USP12 (24081 downstream)																							GTCCATCAGACCCCCATGGAA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	39245481	39245481	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39245481delA								UFM1 (308339 upstream) : FREM2 (15692 downstream)																							AGCACTAAGCAAAAAAAATGG	0.408													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	42934726	42934726	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42934726delT								AKAP11 (37324 upstream) : TNFSF11 (202146 downstream)																							CCAAGAGGACTTTTTTTTTTT	0.393													2	4	---	---	---	---	
DHRS12	79758	broad.mit.edu	37	13	52348464	52348466	+	Intron	DEL	CTC	-	-	rs34933807		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52348464_52348466delCTC	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	0.286													4	3	---	---	---	---	
DIAPH3	81624	broad.mit.edu	37	13	60680881	60680881	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60680881delA	uc001vht.2	-						DIAPH3_uc001vhw.1_Intron|DIAPH3_uc010aed.1_Intron|DIAPH3_uc010aee.1_Intron	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		agagtaaagcaaagggccaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71978606	71978607	+	IGR	INS	-	A	A	rs78937073		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71978606_71978607insA								None (None upstream) : DACH1 (33491 downstream)																							TATGATCTTGCTCCATTTTTGC	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73114147	73114147	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73114147delA								DACH1 (672817 upstream) : C13orf37 (168348 downstream)																							CTACAGAGCTAAAAAAGATAA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73154518	73154518	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73154518delA								DACH1 (713188 upstream) : C13orf37 (127977 downstream)																							CCACATGGCCAAAAAAAAATC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78600046	78600047	+	Intron	DEL	GA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78600046_78600047delGA	uc001vks.2	+											Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																		ctggtctgttgacattaaaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111171552	111171553	+	IGR	DEL	TG	-	-	rs72048022		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111171552_111171553delTG								COL4A2 (6181 upstream) : RAB20 (3861 downstream)																							GGGTCTCGACTGTGTATGCAGG	0.619													4	4	---	---	---	---	
ARHGEF7	8874	broad.mit.edu	37	13	111946452	111946452	+	3'UTR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111946452delC	uc001vrs.2	+	20					ARHGEF7_uc001vrr.2_3'UTR|ARHGEF7_uc001vrt.2_3'UTR|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron|ARHGEF7_uc010tjo.1_Intron|ARHGEF7_uc010tjp.1_3'UTR|ARHGEF7_uc001vry.1_3'UTR	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			GCAGTCAGAGCCCAGTGTTAA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20757196	20757197	+	IGR	INS	-	A	A	rs138729134	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20757196_20757197insA								OR11H4 (45272 upstream) : TTC5 (106 downstream)																							tttgtataaAGAAAAAAATGGG	0.183													4	2	---	---	---	---	
RNASE4	6038	broad.mit.edu	37	14	21164524	21164524	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21164524delT	uc001vxy.3	+						RNASE4_uc001vxx.3_Intron|RNASE4_uc001vya.2_Intron	NM_002937	NP_002928	P34096	RNAS4_HUMAN	ribonuclease, RNase A family, 4 precursor						mRNA cleavage	extracellular region	nucleic acid binding|pancreatic ribonuclease activity			central_nervous_system(1)	1	all_cancers(95;0.00304)		Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	GBM - Glioblastoma multiforme(265;0.0133)		CCACAAGCTGTTTAAAATAAA	0.458													4	2	---	---	---	---	
FLJ10357	55701	broad.mit.edu	37	14	21540953	21540953	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21540953delA	uc001vzp.2	+						NDRG2_uc010tll.1_5'Flank|FLJ10357_uc001vzn.1_Intron|FLJ10357_uc001vzo.1_Intron|FLJ10357_uc010aij.2_Intron|FLJ10357_uc010tln.1_Intron	NM_018071	NP_060541	Q8TER5	ARH40_HUMAN	hypothetical protein LOC55701						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;5.79e-11)|Epithelial(56;8.35e-09)|all cancers(55;4.23e-08)	GBM - Glioblastoma multiforme(265;0.0197)		CATTCACAACAAATTCTCCCT	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22890773	22890774	+	Intron	DEL	CT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22890773_22890774delCT	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wds.1_Intron|uc001wdv.3_5'Flank|uc001wdt.1_Intron|uc001wdu.2_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																		GACCTTTAAACTCAAAAGTGGA	0.371													4	2	---	---	---	---	
THTPA	79178	broad.mit.edu	37	14	23989143	23989143	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23989143delT	uc001wkb.3	+						uc001wkc.1_Intron			Q9BU02	THTPA_HUMAN	Homo sapiens thiamine triphosphatase mRNA, complete cds.						dephosphorylation|generation of precursor metabolites and energy|thiamine metabolic process	cytosol|nucleolus|soluble fraction	thiamin-triphosphatase activity				0	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)	Thiamine(DB00152)	AGAAGTGGTCTTAGGGACAAG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	30595127	30595127	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30595127delA								PRKD1 (198228 upstream) : G2E3 (433202 downstream)																							GTCTGAAGCCAAAAAAATGGC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	31013213	31013213	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31013213delT								PRKD1 (616314 upstream) : G2E3 (15116 downstream)																							TGGTCTGCTGTTTTTTTTGTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49917660	49917660	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49917660delG								None (None upstream) : SDCCAG1 (115367 downstream)																							CATTTCCTCTGGGGACAAGGT	0.413													4	2	---	---	---	---	
SAV1	60485	broad.mit.edu	37	14	51108110	51108110	+	Intron	DEL	A	-	-	rs71441301		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51108110delA	uc001wyg.1	-						SAV1_uc001wyh.1_Intron	NM_021818	NP_068590	Q9H4B6	SAV1_HUMAN	WW45 protein						hippo signaling cascade	cytoplasm|nucleus	identical protein binding			breast(1)	1	all_epithelial(31;0.000611)|Breast(41;0.0333)					CACAGAGATTAAAAAAAAAAA	0.358													2	4	---	---	---	---	
ERO1L	30001	broad.mit.edu	37	14	53150340	53150343	+	Intron	DEL	ATGG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53150340_53150343delATGG	uc001wzv.2	-						ERO1L_uc001wzw.2_Intron|ERO1L_uc010aof.2_Intron	NM_014584	NP_055399	Q96HE7	ERO1A_HUMAN	ERO1-like precursor						chaperone mediated protein folding requiring cofactor|electron transport chain|protein thiol-disulfide exchange|response to temperature stimulus|transport	endoplasmic reticulum lumen|endoplasmic reticulum membrane|microsome	disulfide oxidoreductase activity|flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor				0	Breast(41;0.226)					AAATTATCCAATGGATGGTTTCAG	0.260													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	56798416	56798416	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56798416delG								PELI2 (30386 upstream) : C14orf101 (247922 downstream)																							GTGCCAGGTAGGGGGGAAGGG	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66285370	66285371	+	IGR	DEL	AC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66285370_66285371delAC								FUT8 (75409 upstream) : C14orf53 (667738 downstream)																							tacataccatacacacacacac	0.000													4	2	---	---	---	---	
DNAL1	83544	broad.mit.edu	37	14	74155331	74155331	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74155331delA	uc001xoq.3	+						DNAL1_uc010aru.2_Intron|DNAL1_uc010arv.2_Intron	NM_031427	NP_113615	Q4LDG9	DNAL1_HUMAN	axonemal dynein light chain 1												0				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)		ttctcaaaacaaaaaaaagca	0.129													4	2	---	---	---	---	
CLMN	79789	broad.mit.edu	37	14	95725078	95725079	+	Intron	DEL	GT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95725078_95725079delGT	uc001yef.2	-							NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)		tgtatctgtggtgtgtgtgtgg	0.000													4	2	---	---	---	---	
AK7	122481	broad.mit.edu	37	14	96881352	96881352	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96881352delA	uc001yfn.2	+							NM_152327	NP_689540	Q96M32	KAD7_HUMAN	adenylate kinase 7						cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		ttggcctcccaaagtactggg	0.139													4	2	---	---	---	---	
HHIPL1	84439	broad.mit.edu	37	14	100136833	100136834	+	Intron	DEL	GC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100136833_100136834delGC	uc010avs.2	+							NM_001127258	NP_001120730	Q96JK4	HIPL1_HUMAN	HHIP-like protein 1 isoform a						carbohydrate metabolic process	extracellular region|membrane	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding|scavenger receptor activity			skin(2)	2		Melanoma(154;0.128)				tttagtggttgcgtctgcttag	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	102069739	102069739	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102069739delC								DIO3 (39950 upstream) : C14orf72 (127035 downstream)																							ACTCAGTCCTCCCACAGCTAC	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	103983979	103983980	+	IGR	INS	-	AG	AG	rs72520899	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103983979_103983980insAG								MARK3 (13815 upstream) : CKB (2016 downstream)																							CACAGGCAGACGACTGTAGCTC	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20128011	20128014	+	IGR	DEL	TAAT	-	-	rs145049235		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20128011_20128014delTAAT								None (None upstream) : GOLGA6L6 (609080 downstream)																							AAGTTTAAAATAATTAACCAGAAG	0.289													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20611011	20611011	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20611011delG	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																		gttacattttgggggagtcaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22505434	22505434	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22505434delT								OR4N3P (91049 upstream) : MIR1268 (7795 downstream)																							ttgctttttgtttttttctga	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22512282	22512283	+	IGR	DEL	AC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22512282_22512283delAC								OR4N3P (97897 upstream) : MIR1268 (946 downstream)																							gcacacacagacacacacacac	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22539625	22539626	+	IGR	DEL	CA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22539625_22539626delCA								MIR1268 (26345 upstream) : GOLGA8DP (162659 downstream)																							acacacataccacacagataca	0.069													4	2	---	---	---	---	
GOLGA6L1	283767	broad.mit.edu	37	15	22741010	22741011	+	Intron	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22741010_22741011insA	uc010tzx.1	+							NM_001001413	NP_001001413			golgi autoantigen, golgin subfamily a, 6-like 1												0						gaaactctgccaaaaaaaaaaa	0.158													4	3	---	---	---	---	
ATP10A	57194	broad.mit.edu	37	15	26049237	26049237	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26049237delT	uc010ayu.2	-							NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		tgtgtgtgtgtgtgtgtgtgg	0.204													4	2	---	---	---	---	
ATP10A	57194	broad.mit.edu	37	15	26049239	26049239	+	Intron	DEL	T	-	-	rs60187154		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26049239delT	uc010ayu.2	-							NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		tgtgtgtgtgtgtgtgtggtg	0.204													4	2	---	---	---	---	
ATP10A	57194	broad.mit.edu	37	15	26097715	26097715	+	Intron	DEL	C	-	-	rs75091697		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26097715delC	uc010ayu.2	-						ATP10A_uc001zax.2_Intron	NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		ctccgaagttcccttctctcc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	32508736	32508736	+	Intron	DEL	A	-	-	rs141891898		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32508736delA	uc001zfv.1	-											Homo sapiens cDNA FLJ43588 fis, clone SKNSH2009991.																		TTGCCAGTTTAAAAAAAAATT	0.388													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	35091522	35091522	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35091522delC	uc001zit.1	+											Homo sapiens cDNA FLJ34768 fis, clone NT2NE2002791.																		CTCTCTGAAGCCCACAGAGCT	0.532													4	2	---	---	---	---	
MEIS2	4212	broad.mit.edu	37	15	37353028	37353028	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37353028delA	uc001zjr.2	-						MEIS2_uc001zjl.2_Intron|MEIS2_uc010ucj.1_Intron|MEIS2_uc001zjm.2_Intron|MEIS2_uc001zjn.2_Intron|MEIS2_uc001zjo.2_Intron|MEIS2_uc001zjp.2_Intron|MEIS2_uc001zjs.2_Intron|MEIS2_uc001zju.2_Intron|MEIS2_uc001zjt.2_Intron	NM_170675	NP_733775	O14770	MEIS2_HUMAN	Meis homeobox 2 isoform c						negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)	2		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)		GAATGGCCCTAAAAATAAGAA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	45294696	45294696	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45294696delT								C15orf43 (23277 upstream) : SORD (20645 downstream)																							AACTTAATGGTTTTTTTTTTG	0.338													4	2	---	---	---	---	
SQRDL	58472	broad.mit.edu	37	15	45929777	45929777	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45929777delT	uc001zvt.2	+						SQRDL_uc001zvu.2_Intron|SQRDL_uc001zvv.2_Intron	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor								oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		AATTTGGGGCTTTTTTTCTGG	0.433													4	2	---	---	---	---	
MYEF2	50804	broad.mit.edu	37	15	48433101	48433102	+	3'UTR	INS	-	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48433101_48433102insC	uc001zwi.3	-	17					SLC24A5_uc001zwe.2_Intron|SLC24A5_uc010bel.2_Intron|MYEF2_uc001zwg.3_3'UTR|MYEF2_uc001zwh.3_3'UTR|MYEF2_uc001zwj.3_3'UTR|SLC24A5_uc001zwk.2_5'Flank	NM_016132	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2						transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding|nucleotide binding|RNA binding			lung(2)|ovary(1)	3		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		TAGATATGTCATTAAAAATCTG	0.342													4	2	---	---	---	---	
DUT	1854	broad.mit.edu	37	15	48634453	48634455	+	3'UTR	DEL	CAC	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48634453_48634455delCAC	uc001zws.2	+	7					DUT_uc001zwt.2_3'UTR|DUT_uc001zwu.2_RNA|DUT_uc001zwv.2_3'UTR|DUT_uc001zww.2_3'UTR	NM_001025248	NP_001020419	P33316	DUT_HUMAN	deoxyuridine triphosphatase isoform 1 precursor						DNA replication|dUTP metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process	mitochondrion|nucleoplasm	dUTP diphosphatase activity|protein binding				0		all_lung(180;0.00265)		all cancers(107;2.66e-09)|GBM - Glioblastoma multiforme(94;6.76e-07)		TAAAAAAAAACACAAAGAAGTTT	0.300								Modulation_of_nucleotide_pools					4	2	---	---	---	---	
TNFAIP8L3	388121	broad.mit.edu	37	15	51361487	51361488	+	Intron	INS	-	T	T	rs141098038	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51361487_51361488insT	uc001zyy.2	-							NM_207381	NP_997264	Q5GJ75	TP8L3_HUMAN	tumor necrosis factor, alpha-induced protein												0				all cancers(107;0.000389)|GBM - Glioblastoma multiforme(94;0.00338)		AGGAATGGGGATTTGTGTGTTT	0.460													5	3	---	---	---	---	
MYO5C	55930	broad.mit.edu	37	15	52497502	52497502	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52497502delC	uc010bff.2	-						MYO5C_uc010uga.1_Intron|uc002abv.2_RNA	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)		GTTTGGGACACCAGGGTGTGT	0.488													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	61171490	61171490	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61171490delT	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						cttggagaagttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	65023496	65023496	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65023496delG								OAZ2 (28034 upstream) : RBPMS2 (8602 downstream)																							GGAAAAAGGTGGGGGCGTGTC	0.512											OREG0023184	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70587072	70587073	+	IGR	DEL	TT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70587072_70587073delTT								TLE3 (196816 upstream) : UACA (359822 downstream)																							GTTTGTGGGCTTAAGAATATTG	0.119													4	2	---	---	---	---	
PSTPIP1	9051	broad.mit.edu	37	15	77289209	77289209	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77289209delG	uc002bcf.2	+						PSTPIP1_uc010bkt.1_Intron|PSTPIP1_uc010umo.1_Intron|PSTPIP1_uc010bku.1_Intron|PSTPIP1_uc002bcg.2_Intron|PSTPIP1_uc010bkv.1_Intron|PSTPIP1_uc010bkw.1_Intron	NM_003978	NP_003969	O43586	PPIP1_HUMAN	proline-serine-threonine phosphatase interacting						cell adhesion|signal transduction	cleavage furrow|lamellipodium|perinuclear region of cytoplasm	catalytic activity			ovary(1)	1						CTGGAGCCCTGGGGGATGGGG	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	85859032	85859032	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85859032delG								PDE8A (176662 upstream) : AKAP13 (64839 downstream)																							gtaaggaccaggagttagaga	0.144													4	2	---	---	---	---	
SLCO3A1	28232	broad.mit.edu	37	15	92707545	92707545	+	3'UTR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92707545delA	uc002bqx.2	+	10					SLCO3A1_uc002bqy.2_Intron	NM_013272	NP_037404	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)			TTACAAGAAGAAAAAAAAATG	0.308													4	2	---	---	---	---	
LUC7L	55692	broad.mit.edu	37	16	239632	239633	+	Intron	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:239632_239633insA	uc002cgc.1	-						LUC7L_uc002cga.1_3'UTR|LUC7L_uc002cgd.1_Intron|LUC7L_uc002cge.1_Intron|LUC7L_uc002cgb.1_Intron	NM_201412	NP_958815	Q9NQ29	LUC7L_HUMAN	LUC7-like isoform b								metal ion binding			central_nervous_system(1)	1		all_cancers(16;1.1e-06)|all_epithelial(16;2.71e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.0138)|all_lung(18;0.0306)				AAACACAATGGAAAAAAAAATA	0.277													4	2	---	---	---	---	
UNKL	64718	broad.mit.edu	37	16	1431173	1431173	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1431173delC	uc010brn.1	-						UNKL_uc002cln.2_5'Flank|UNKL_uc002clo.2_5'Flank|UNKL_uc002clp.2_5'Flank			Q9H9P5	UNKL_HUMAN	SubName: Full=Putative ubiquitin-protein ligase;          EC=6.3.2.19; Flags: Fragment;							cytoplasm|nucleus	ligase activity|nucleic acid binding|zinc ion binding				0		Hepatocellular(780;0.0893)				GGTCGACTTTCCACCCGAGTG	0.448													4	2	---	---	---	---	
TSC2	7249	broad.mit.edu	37	16	2113549	2113549	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2113549delT	uc002con.2	+						TSC2_uc010bsd.2_Intron|TSC2_uc002coo.2_Intron|TSC2_uc010uvv.1_Intron|TSC2_uc010uvw.1_Intron|TSC2_uc002cop.2_Intron	NM_000548	NP_000539	P49815	TSC2_HUMAN	tuberous sclerosis 2 isoform 1						cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)				GTCATACCCCTTTCCCAGGAG	0.637			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5858736	5858737	+	IGR	DEL	TA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5858736_5858737delTA								FAM86A (710947 upstream) : A2BP1 (210395 downstream)																							gttattggtgtataagaaagat	0.000													6	3	---	---	---	---	
GRIN2A	2903	broad.mit.edu	37	16	10174893	10174893	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10174893delT	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	CAGAGTGGTCTTTTTGCCTTT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11516876	11516876	+	IGR	DEL	G	-	-	rs74966130		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11516876delG								C16orf75 (71259 upstream) : LITAF (124706 downstream)																							CCAGGGATGTGGGGGGCTTTT	0.592													4	3	---	---	---	---	
ABCC6	368	broad.mit.edu	37	16	16285790	16285790	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16285790delC	uc002den.3	-						ABCC6_uc010bvo.2_Intron|ABCC6_uc010uzz.1_Intron	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6						response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		tgcaaagcttccagttaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	19950265	19950266	+	IGR	INS	-	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19950265_19950266insC								GPRC5B (53433 upstream) : GPR139 (92777 downstream)																							gacacaGTTTGCCCCCAAGTTA	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20136558	20136558	+	IGR	DEL	T	-	-	rs141303250		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20136558delT								GPR139 (51458 upstream) : GP2 (185254 downstream)																							CGAAGCTTTCTTTTTTTGGTT	0.378													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22640984	22640985	+	IGR	DEL	GA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22640984_22640985delGA								LOC653786 (52798 upstream) : HS3ST2 (184875 downstream)																							ccaaagtgctgagattacaggc	0.000													4	2	---	---	---	---	
GSG1L	146395	broad.mit.edu	37	16	27931556	27931556	+	Intron	DEL	T	-	-	rs36018954		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27931556delT	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						TGGGCGAAGGTGGTGAGGAAT	0.473													4	3	---	---	---	---	
STX4	6810	broad.mit.edu	37	16	31046917	31046917	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31046917delG	uc002eal.2	+						STX4_uc002eak.2_Intron|STX4_uc002eam.2_Intron	NM_004604	NP_004595	Q12846	STX4_HUMAN	syntaxin 4						intracellular protein transport|platelet activation|post-Golgi vesicle-mediated transport	basolateral plasma membrane|cell surface|cytosol|integral to membrane|plasma membrane enriched fraction|specific granule|vacuole	SNAP receptor activity				0						TTACTCACGTGGGACCTGGTG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32431977	32431978	+	IGR	INS	-	T	T	rs141924012		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32431977_32431978insT								HERC2P4 (268103 upstream) : TP53TG3B (252863 downstream)																							gttttcttaaatttttaaaaac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33370073	33370074	+	IGR	DEL	TC	-	-	rs113975885		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33370073_33370074delTC								SLC6A10P (473610 upstream) : MIR1826 (595434 downstream)																							TTTTTGTTGTTCTCAACCTGAG	0.436													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33533217	33533217	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33533217delA								SLC6A10P (636754 upstream) : MIR1826 (432291 downstream)																							ATATTACTTTAAAAAACTTTT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55155844	55155845	+	IGR	INS	-	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55155844_55155845insG								IRX5 (187451 upstream) : IRX6 (202626 downstream)																							aacacggtctaggggaaatgac	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79800947	79800947	+	IGR	DEL	G	-	-	rs11349360		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79800947delG								MAF (166325 upstream) : DYNLRB2 (773907 downstream)																							agatctgaaagtcaaactggc	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86291279	86291279	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86291279delC								IRF8 (335070 upstream) : LOC732275 (74177 downstream)																							ACTCAGGAGGCCTCAGCAGCC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88207913	88207913	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88207913delA								BANP (96990 upstream) : ZNF469 (285966 downstream)																							acaaaatcctaaatatgtaca	0.000													4	2	---	---	---	---	
GALNS	2588	broad.mit.edu	37	16	88900469	88900469	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88900469delC	uc002fly.3	-						GALNS_uc010cid.2_Intron|GALNS_uc002flz.3_Intron	NM_000512	NP_000503	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfate sulfatase							lysosome	metal ion binding|N-acetylgalactosamine-4-sulfatase activity|N-acetylgalactosamine-6-sulfatase activity			large_intestine(2)	2				BRCA - Breast invasive adenocarcinoma(80;0.0496)	Hyaluronidase(DB00070)	CTGTAGCCCTCCACACATGGG	0.701													4	2	---	---	---	---	
SPG7	6687	broad.mit.edu	37	16	89582797	89582798	+	Intron	DEL	AA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89582797_89582798delAA	uc002fnj.2	+						SPG7_uc002fni.2_Intron	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 isoform 1						cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		taaaaataccaaaaaaaaaaaa	0.025													4	2	---	---	---	---	
MNT	4335	broad.mit.edu	37	17	2301823	2301823	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2301823delA	uc002fur.2	-							NM_020310	NP_064706	Q99583	MNT_HUMAN	MAX binding protein						multicellular organismal development|negative regulation of cell proliferation|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			skin(1)	1				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		GAGGGAGAAGAAAATGAATTC	0.527													4	2	---	---	---	---	
METT10D	79066	broad.mit.edu	37	17	2378866	2378866	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2378866delA	uc002fut.2	-						METT10D_uc002fuu.3_Intron|METT10D_uc010cka.2_Intron|METT10D_uc002fuv.2_Intron|METT10D_uc010vqx.1_Intron|METT10D_uc010vqy.1_Intron	NM_024086	NP_076991	Q86W50	MET16_HUMAN	methyltransferase 10 domain containing								methyltransferase activity				0						TGTCAGCGCCAAAAAAAGTTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6207802	6207803	+	IGR	INS	-	CA	CA	rs138793359	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6207802_6207803insCA								WSCD1 (180057 upstream) : AIPL1 (119257 downstream)																							ACATAGAGACTcacacacacac	0.342													4	2	---	---	---	---	
GAS7	8522	broad.mit.edu	37	17	10048616	10048617	+	Intron	INS	-	G	G	rs139273408	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10048616_10048617insG	uc002gmg.1	-							NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						CAGAGAAGCACGGGGGAAAGTA	0.480			T	MLL	AML*								4	2	---	---	---	---	
MYH13	8735	broad.mit.edu	37	17	10239270	10239270	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10239270delG	uc002gmk.1	-							NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle						muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						ATTTTACAGTGGGGAGGCCAG	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	10675069	10675070	+	IGR	INS	-	TG	TG			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10675069_10675070insTG								TMEM220 (41423 upstream) : PIRT (50723 downstream)																							AAGTTGTCGGCtgtgtgtgtct	0.292													4	2	---	---	---	---	
FLCN	201163	broad.mit.edu	37	17	17126844	17126844	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17126844delT	uc002gra.3	-						PLD6_uc010cpn.2_Intron|FLCN_uc002grb.3_Intron	NM_144997	NP_659434	Q8NFG4	FLCN_HUMAN	folliculin isoform 1						regulation of protein phosphorylation	cytoplasm|nucleus|plasma membrane	protein binding			thyroid(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)	3						tccgaggctgttaccagagca	0.189									Birt-Hogg-Dub__syndrome|Familial_Non-VHL_Clear_Cell_Renal_Cancer				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21518137	21518140	+	IGR	DEL	GAGG	-	-	rs112566972		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21518137_21518140delGAGG								C17orf51 (40406 upstream) : FAM27L (307230 downstream)																							ACAAAATTTAGAGGGTGACTATTT	0.431													1	5	---	---	---	---	
TMEM97	27346	broad.mit.edu	37	17	26654811	26654811	+	3'UTR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26654811delT	uc002hat.2	+	3						NM_014573	NP_055388	Q5BJF2	TMM97_HUMAN	transmembrane protein 97						cholesterol homeostasis|regulation of cell growth	integral to membrane|lysosome|nuclear membrane|plasma membrane|rough endoplasmic reticulum	protein binding				0	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		TAGGCGAAAGTTTTTTTTGTT	0.353													4	2	---	---	---	---	
SSH2	85464	broad.mit.edu	37	17	28032479	28032479	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28032479delA	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_Intron|SSH2_uc002heq.2_Intron|SSH2_uc002her.2_Intron|SSH2_uc010csc.1_Intron	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						GTGCTGTATCAAAAaaaaact	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	29712694	29712695	+	IGR	DEL	TC	-	-	rs144879970		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29712694_29712695delTC								NF1 (3789 upstream) : RAB11FIP4 (5947 downstream)																							CACTGTAGAGTCTGcaaagttc	0.297													2	4	---	---	---	---	
C17orf75	64149	broad.mit.edu	37	17	30669323	30669323	+	5'Flank	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30669323delC	uc002hhg.2	-							NM_022344	NP_071739	Q9HAS0	NJMU_HUMAN	hypothetical protein LOC64149						spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			AGTCTCTTCTCCCCACAGGGG	0.542													4	2	---	---	---	---	
PPP1R1B	84152	broad.mit.edu	37	17	37782057	37782058	+	5'Flank	INS	-	AC	AC	rs149893244	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37782057_37782058insAC	uc002hrz.2	+						PPP1R1B_uc002hsa.2_5'Flank|PPP1R1B_uc010cvx.2_5'Flank|PPP1R1B_uc002hsb.2_5'Flank|PPP1R1B_uc002hsc.2_5'Flank	NM_032192	NP_115568	Q9UD71	PPR1B_HUMAN	protein phosphatase 1, regulatory (inhibitor)						signal transduction	cytosol	protein kinase inhibitor activity|protein phosphatase inhibitor activity				0	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TGTACACGTCTACACACACCCT	0.554													5	3	---	---	---	---	
ORMDL3	94103	broad.mit.edu	37	17	38084961	38084961	+	5'Flank	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38084961delA	uc002htj.1	-						ORMDL3_uc002hti.1_5'Flank|ORMDL3_uc002htk.1_5'Flank	NM_139280	NP_644809	Q8N138	ORML3_HUMAN	ORM1-like 3						ceramide metabolic process	integral to membrane|SPOTS complex	protein binding				0	Colorectal(19;0.000442)		Lung(15;0.0234)			CCTGACTCTGAATGGCAGTTC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39485069	39485069	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39485069delG								KRTAP17-1 (13122 upstream) : KRT33A (17302 downstream)																							CCCATTCAATGGGGAAGCTGG	0.597													4	2	---	---	---	---	
SOST	50964	broad.mit.edu	37	17	41831443	41831444	+	3'UTR	INS	-	C	C	rs72580126		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41831443_41831444insC	uc002iec.1	-	2						NM_025237	NP_079513	Q9BQB4	SOST_HUMAN	sclerostin precursor						negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of ossification|negative regulation of protein complex assembly|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway		heparin binding|protein binding				0		Breast(137;0.00725)		UCEC - Uterine corpus endometrioid carcinoma (308;0.177)|BRCA - Breast invasive adenocarcinoma(366;0.0741)		TTGGGTGGCAGTATTATGCTCT	0.322													1	5	---	---	---	---	
SOST	50964	broad.mit.edu	37	17	41831675	41831675	+	3'UTR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41831675delT	uc002iec.1	-	2						NM_025237	NP_079513	Q9BQB4	SOST_HUMAN	sclerostin precursor						negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of ossification|negative regulation of protein complex assembly|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway		heparin binding|protein binding				0		Breast(137;0.00725)		UCEC - Uterine corpus endometrioid carcinoma (308;0.177)|BRCA - Breast invasive adenocarcinoma(366;0.0741)		TCCTTGAACCTTTCACTTCTC	0.552													4	2	---	---	---	---	
FAM117A	81558	broad.mit.edu	37	17	47798090	47798090	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47798090delT	uc002ipk.2	-						FAM117A_uc010wlz.1_Intron	NM_030802	NP_110429	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A											ovary(1)	1						ACTACCCCTCttttttttttg	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48338701	48338701	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48338701delT								COL1A1 (59701 upstream) : TMEM92 (13136 downstream)																							AGGGTGCAtcttaggaagatt	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53459022	53459022	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53459022delG								HLF (56596 upstream) : MMD (10953 downstream)																							atccagtgctgggtctattgt	0.000													4	2	---	---	---	---	
MSI2	124540	broad.mit.edu	37	17	55666859	55666860	+	Intron	INS	-	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55666859_55666860insC	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412	Q96DH6	MSI2H_HUMAN	musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		GACTTGCCAAACCTGCCATAGC	0.589			T	HOXA9	CML								6	3	---	---	---	---	
MARCH10	162333	broad.mit.edu	37	17	60821555	60821555	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60821555delA	uc010ddr.2	-						MARCH10_uc002jag.3_Intron|MARCH10_uc010dds.2_Intron|MARCH10_uc002jah.2_Intron	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190								ligase activity|zinc ion binding				0						CTCTTGGAGGAAAAAAAACGC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	71092330	71092331	+	IGR	INS	-	G	G	rs141707910	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71092330_71092331insG								SLC39A11 (3477 upstream) : SSTR2 (68829 downstream)																							attgaggctcaggaaagctctg	0.054													4	7	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71472294	71472294	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71472294delA	uc010dfm.2	-							NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						GCAAACAAACAAAAAAAAGGT	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	72099725	72099726	+	IGR	INS	-	A	A	rs150938551	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72099725_72099726insA								C17orf54 (275049 upstream) : RPL38 (100069 downstream)																							CTCTCTGGGCCAAAAACCGGGT	0.550													2	4	---	---	---	---	
TTYH2	94015	broad.mit.edu	37	17	72223281	72223281	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72223281delT	uc002jkc.2	+						TTYH2_uc010wqw.1_Intron	NM_032646	NP_116035	Q9BSA4	TTYH2_HUMAN	tweety 2 isoform 1							chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4						gccccgctaatttttttattt	0.000													4	2	---	---	---	---	
TSPAN10	83882	broad.mit.edu	37	17	79608643	79608644	+	5'Flank	INS	-	GA	GA	rs144965665	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79608643_79608644insGA	uc010die.2	+						TSPAN10_uc002kaw.1_5'Flank|TSPAN10_uc010did.1_5'Flank	NM_031945	NP_114151	Q9H1Z9	TSN10_HUMAN	tetraspanin 10							integral to membrane				ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.175)|Lung NSC(278;0.192)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			TTTGGACTGCTGAGTGTTGGTG	0.208													3	3	---	---	---	---	
THOC1	9984	broad.mit.edu	37	18	241383	241383	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:241383delT	uc002kkj.3	-						THOC1_uc002kkk.3_Intron|THOC1_uc002kkl.2_Intron	NM_005131	NP_005122	Q96FV9	THOC1_HUMAN	THO complex 1						apoptosis|intronless viral mRNA export from host nucleus|mRNA processing|regulation of transcription elongation, DNA-dependent|RNA splicing|signal transduction|transcription, DNA-dependent	cytoplasm|nuclear matrix|nuclear speck|THO complex part of transcription export complex	DNA binding|protein binding|RNA binding			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				TGCCAGGAACTTTTTTTTAAA	0.338													4	2	---	---	---	---	
SMCHD1	23347	broad.mit.edu	37	18	2747815	2747815	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2747815delA	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0						ttGAGGAAATAAAGTTTATAT	0.259													4	2	---	---	---	---	
SMCHD1	23347	broad.mit.edu	37	18	2772085	2772086	+	Intron	DEL	TG	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2772085_2772086delTG	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0						GTGTTTTCTTTGTGTGTGTGTG	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10068946	10068947	+	IGR	INS	-	A	A	rs149106837	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10068946_10068947insA								VAPA (108929 upstream) : APCDD1 (385678 downstream)																							TTGCCTCAGGTAAAAAAAATAA	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11035106	11035106	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11035106delA								FAM38B (333127 upstream) : GNAL (654030 downstream)																							GAGTGTGTAGAAGGGGATGGA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	12214935	12214935	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12214935delG								IMPA2 (184059 upstream) : CIDEA (39383 downstream)																							AGGGAGGCCAGGGAAGATCAG	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	26161888	26161888	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26161888delA								CDH2 (404443 upstream) : None (None downstream)																							ACACTGAAGGAAAAAAAAAGC	0.458													4	3	---	---	---	---	
ASXL3	80816	broad.mit.edu	37	18	31164227	31164227	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31164227delG	uc010dmg.1	+						ASXL3_uc002kxq.2_Intron	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						CAGAAGACTTGGGGGGGCATA	0.343													4	2	---	---	---	---	
PSTPIP2	9050	broad.mit.edu	37	18	43571641	43571641	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43571641delC	uc002lbp.3	-						PSTPIP2_uc002lbq.3_Intron	NM_024430	NP_077748	Q9H939	PPIP2_HUMAN	proline-serine-threonine phosphatase interacting							membrane				ovary(1)	1						TAGGATTCATCCATGAATAAC	0.234													4	2	---	---	---	---	
C18orf25	147339	broad.mit.edu	37	18	43834305	43834305	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43834305delA	uc002lbw.2	+						C18orf25_uc002lbx.2_Intron	NM_145055	NP_659492	Q96B23	CR025_HUMAN	ARKadia-like 1 isoform a											central_nervous_system(2)	2						TCATATAACTAAGGGAGTCTT	0.343													4	2	---	---	---	---	
KIAA0427	9811	broad.mit.edu	37	18	46253836	46253836	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46253836delG	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron	NM_014772	NP_055587	O43310	CTIF_HUMAN	hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0						ggtagaatttgggaggtccaa	0.000													4	2	---	---	---	---	
ALPK2	115701	broad.mit.edu	37	18	56238260	56238260	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56238260delT	uc002lhj.3	-							NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase								ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						GACATCtttctttttttttct	0.234													4	2	---	---	---	---	
CCBE1	147372	broad.mit.edu	37	18	57282909	57282909	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57282909delC	uc002lib.2	-							NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)				GTTTATTTAACCAGCTGCCTC	0.343													4	2	---	---	---	---	
PHLPP1	23239	broad.mit.edu	37	18	60478221	60478221	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60478221delT	uc002lis.2	+							NM_194449	NP_919431	O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein						apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0						ctaaatctaattactggtcct	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	61272923	61272924	+	IGR	DEL	CA	-	-	rs113585124		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61272923_61272924delCA								SERPINB13 (6491 upstream) : SERPINB4 (31571 downstream)																							tacatgcgcccacacacacaca	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76700395	76700395	+	IGR	DEL	A	-	-	rs34335530		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76700395delA								None (None upstream) : SALL3 (39880 downstream)																							CATGGTCACCAGACTCCTGCA	0.587													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	980530	980531	+	IGR	INS	-	C	C	rs142263320	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:980530_980531insC								ARID3A (7739 upstream) : WDR18 (3797 downstream)																							CTTCCTGGTTACCCCCCCTTCA	0.604													4	4	---	---	---	---	
AP3D1	8943	broad.mit.edu	37	19	2145759	2145760	+	Intron	DEL	CA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2145759_2145760delCA	uc002luz.2	-						AP3D1_uc002luy.2_Intron|AP3D1_uc002lva.2_Intron	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1						eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGCCACCTCCACACACACACA	0.545													5	3	---	---	---	---	
NDUFA7	4701	broad.mit.edu	37	19	8383044	8383044	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8383044delT	uc002mjm.1	-							NM_005001	NP_004992	O95182	NDUA7_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0					NADH(DB00157)	tttttgtttgtttttttttga	0.100													4	2	---	---	---	---	
SLC1A6	6511	broad.mit.edu	37	19	15070505	15070505	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15070505delC	uc002naa.1	-						SLC1A6_uc010dzu.1_Intron|SLC1A6_uc010xod.1_Intron	NM_005071	NP_005062	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity						synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)|skin(1)	6					L-Glutamic Acid(DB00142)	ttcctgaatgccccaccattc	0.080													4	2	---	---	---	---	
CYP4F22	126410	broad.mit.edu	37	19	15648967	15648967	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15648967delT	uc002nbh.3	+							NM_173483	NP_775754	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F,							endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen			ovary(1)|pancreas(1)	2						tgagcttcactttttttttta	0.000													5	3	---	---	---	---	
ZNF714	148206	broad.mit.edu	37	19	21299358	21299358	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21299358delC	uc002npo.3	+						ZNF714_uc002npl.2_Intron|ZNF714_uc010ecp.1_Intron|ZNF714_uc002npn.2_Intron	NM_182515	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTTTCTTTTTCTTCTGTGTCT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30255216	30255217	+	IGR	DEL	CT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30255216_30255217delCT								C19orf12 (48764 upstream) : CCNE1 (47684 downstream)																							CCCCAGGAAACTCTCAACTGCC	0.223													4	2	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50752697	50752697	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50752697delT	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		ggtctctgcctctctgtctct	0.000													6	3	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50752730	50752731	+	Intron	INS	-	GT	GT	rs146824061		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50752730_50752731insGT	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		cctgtctctggctctgtcccct	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	55023723	55023724	+	IGR	DEL	TG	-	-	rs75136440	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55023723_55023724delTG								LAIR2 (1828 upstream) : KIR3DX1 (20185 downstream)																							CTGCTCTCTCTGTGTGTGTGTG	0.436													4	2	---	---	---	---	
SHISA7	729956	broad.mit.edu	37	19	55948787	55948787	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55948787delA	uc002qkz.3	-							NM_001145176	NP_001138648	A6NL88	SHSA7_HUMAN	shisa homolog 7 precursor							integral to membrane					0						AGGTTGCATTAAAAAAAAATC	0.388													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	5705759	5705759	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5705759delA								GPCPD1 (114087 upstream) : C20orf196 (25284 downstream)																							TGTCTTCACCAAAAGGGTTTC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12355446	12355446	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12355446delA								BTBD3 (448204 upstream) : SPTLC3 (634181 downstream)																							cctggagaagaaaggtgcttg	0.000													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	14913886	14913886	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14913886delA	uc002wou.2	+						MACROD2_uc002wot.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				ACAATCATAGAAACAGATAAC	0.313													4	2	---	---	---	---	
RALGAPA2	57186	broad.mit.edu	37	20	20579050	20579051	+	Intron	INS	-	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20579050_20579051insC	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						GCATCACATTTCCCCCTATTAA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25909449	25909449	+	IGR	DEL	G	-	-	rs2103812	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25909449delG								FAM182B (60663 upstream) : LOC100134868 (80986 downstream)																							tgccacttttgaaaccatcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26145379	26145379	+	IGR	DEL	T	-	-	rs112012044		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26145379delT								C20orf191 (50702 upstream) : MIR663 (43443 downstream)																							AAAGACAAAATTATGCCACTA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26213040	26213041	+	IGR	INS	-	A	A	rs77211147		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26213040_26213041insA								MIR663 (24126 upstream) : None (None downstream)																							GAGAAGAGGGGAAAAAAGATGT	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29422533	29422534	+	IGR	DEL	AA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29422533_29422534delAA								None (None upstream) : FRG1B (189345 downstream)																							CTGGAGACATAAATAGAGGAAG	0.282													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29600270	29600270	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29600270delA								None (None upstream) : FRG1B (11609 downstream)																							caaaaaatacaaacgactaat	0.000													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29633600	29633600	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29633600delA	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						CAGCATTCTCACCCTATTAAA	0.313													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29650318	29650321	+	Intron	DEL	TATC	-	-	rs140814196		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29650318_29650321delTATC	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						gcttgccatttatctcagcaccat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31186099	31186100	+	Intron	INS	-	T	T	rs146682465	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31186099_31186100insT	uc002wxy.2	+											RecName: Full=Putative uncharacterized protein MGC163334;																		ccaactcatccttaacagcact	0.000													4	3	---	---	---	---	
ZNF341	84905	broad.mit.edu	37	20	32378919	32378920	+	Frame_Shift_Ins	INS	-	C	C	rs143800289	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32378919_32378920insC	uc002wzy.2	+	15	2181_2182	c.2161_2162insC	c.(2161-2163)TCCfs	p.S721fs	ZNF341_uc002wzx.2_Frame_Shift_Ins_p.S714fs|ZNF341_uc010geq.2_Frame_Shift_Ins_p.S631fs|ZNF341_uc010ger.2_RNA|ZNF341_uc002wzz.2_Frame_Shift_Ins_p.S148fs	NM_032819	NP_116208	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	721					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						CAAGGGCTTTTCCCGCCACAAA	0.663													5	4	---	---	---	---	
DLGAP4	22839	broad.mit.edu	37	20	35128390	35128391	+	Intron	DEL	GT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35128390_35128391delGT	uc002xff.2	+						DLGAP4_uc010zvp.1_Intron|DLGAP4_uc002xfg.2_Intron|DLGAP4_uc002xfh.2_Intron|DLGAP4_uc002xfi.2_Intron|DLGAP4_uc002xfj.2_Intron	NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a						cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				CCTTGTCCTCGTGTGTGTGTGC	0.624													3	3	---	---	---	---	
BPI	671	broad.mit.edu	37	20	36943571	36943571	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36943571delT	uc002xib.2	+							NM_001725	NP_001716	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein						defense response to bacterium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of macrophage activation|negative regulation of tumor necrosis factor production	extracellular region|integral to plasma membrane	lipid binding|lipopolysaccharide binding			ovary(4)	4		Myeloproliferative disorder(115;0.00878)				attatccctattttacaggtg	0.139													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41776032	41776034	+	Intron	DEL	CAT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41776032_41776034delCAT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				AAACGCCAACCATCATCATCATC	0.315													4	2	---	---	---	---	
RIMS4	140730	broad.mit.edu	37	20	43404377	43404377	+	Intron	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43404377delG	uc002xms.2	-						RIMS4_uc010ggu.2_Intron	NM_182970	NP_892015	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4						exocytosis|neurotransmitter transport	cell junction|synapse				ovary(4)|central_nervous_system(1)	5		Myeloproliferative disorder(115;0.0122)				ggtctggtttggggacacctg	0.184													4	2	---	---	---	---	
SULF2	55959	broad.mit.edu	37	20	46326525	46326525	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46326525delT	uc002xto.2	-						SULF2_uc002xtr.2_Intron|SULF2_uc002xtq.2_Intron|SULF2_uc010ghv.1_Intron	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor						bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6						GTCCCCATGCTTAGCCCCAAA	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	47233567	47233567	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47233567delT								LOC284749 (234186 upstream) : PREX1 (7226 downstream)																							GTGGGttttgtttttttttta	0.269													4	2	---	---	---	---	
PREX1	57580	broad.mit.edu	37	20	47400627	47400627	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47400627delC	uc002xtw.1	-							NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CAAATAAAGACCCAGGAGTCG	0.458													4	2	---	---	---	---	
ADNP	23394	broad.mit.edu	37	20	49546474	49546475	+	Intron	DEL	GT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49546474_49546475delGT	uc002xvt.1	-						ADNP_uc002xvu.1_Intron	NM_015339	NP_056154	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						TGTGTGGGGGGTGTGTGTGTGT	0.470											OREG0026034	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52531843	52531844	+	IGR	INS	-	GG	GG	rs35398128		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52531843_52531844insGG								SUMO1P1 (39595 upstream) : BCAS1 (28235 downstream)																							agagagagagagggaggggggt	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56582273	56582273	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56582273delG								PMEPA1 (295732 upstream) : C20orf85 (143710 downstream)																							tgtggctcctggggcctccct	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59371108	59371108	+	IGR	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59371108delC								MIR646 (487483 upstream) : CDH4 (456451 downstream)																							TTTATTTATTCCAAGACGTGA	0.468													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	59951062	59951063	+	Intron	INS	-	TGC	TGC			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59951062_59951063insTGC	uc002ybn.1	+							NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			gatggtcttggtggtggtgata	0.010													8	4	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60465131	60465134	+	Intron	DEL	TGGA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60465131_60465134delTGGA	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			gatgcatgggtggatggatggatg	0.000													4	2	---	---	---	---	
TAF4	6874	broad.mit.edu	37	20	60637458	60637458	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60637458delT	uc002ybs.2	-						hsa-mir-3195|MI0014240_5'Flank	NM_003185	NP_003176	O00268	TAF4_HUMAN	TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			TTATTGATACTTTTTTTTTTT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9655804	9655804	+	IGR	DEL	A	-	-	rs78775969		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9655804delA								None (None upstream) : None (None downstream)																							tccttctcagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11064923	11064923	+	Intron	DEL	G	-	-	rs145287985		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11064923delG	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)		ccggccacttgggaggctgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11178616	11178617	+	IGR	INS	-	A	A			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11178616_11178617insA								BAGE (79679 upstream) : None (None downstream)																							aaggtcttcagggtcttcaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14830995	14830995	+	IGR	DEL	G	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14830995delG								C21orf99 (340426 upstream) : POTED (151503 downstream)																							CGCAGCAGCTGGGGAAATTAC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	16065991	16065992	+	IGR	INS	-	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16065991_16065992insG								SAMSN1 (110268 upstream) : NRIP1 (267564 downstream)																							TAGAAAAAAAAGGAAAGTCTCC	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26283252	26283253	+	IGR	DEL	CA	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26283252_26283253delCA								None (None upstream) : NCRNA00158 (474881 downstream)																							CCCTCCCCACCACACACACACA	0.223													4	2	---	---	---	---	
JAM2	58494	broad.mit.edu	37	21	27010533	27010533	+	5'Flank	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27010533delT	uc002ylp.1	+						JAM2_uc011ace.1_5'Flank|JAM2_uc002ylq.1_5'Flank|JAM2_uc011acf.1_5'Flank|JAM2_uc010glh.1_5'Flank|JAM2_uc002ylr.1_5'Flank|JAM2_uc010gli.1_5'Flank	NM_021219	NP_067042	P57087	JAM2_HUMAN	junctional adhesion molecule 2 precursor						blood coagulation|cell-cell adhesion|leukocyte migration	integral to plasma membrane|tight junction					0						TTTGTGTATATTTTTAGGGAG	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	30376502	30376502	+	IGR	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30376502delA								RNF160 (11225 upstream) : RWDD2B (1580 downstream)																							ctgtctccagaaaaaaaaaaa	0.114													4	2	---	---	---	---	
DSCR3	10311	broad.mit.edu	37	21	38635951	38635951	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38635951delA	uc002ywf.1	-						DSCR3_uc010gnm.1_Intron|DSCR3_uc010gnn.1_Intron|DSCR3_uc010gnl.2_Intron|DSCR3_uc011aeg.1_Intron|DSCR3_uc011aeh.1_Intron	NM_006052	NP_006043	O14972	DSCR3_HUMAN	Down syndrome critical region protein 3						vacuolar transport	nucleus|retromer complex					0						TTACGCTGACAAACACGTTTC	0.323													4	2	---	---	---	---	
PCP4	5121	broad.mit.edu	37	21	41291895	41291896	+	Intron	DEL	GT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41291895_41291896delGT	uc002yyp.2	+							NM_006198	NP_006189	P48539	PCP4_HUMAN	Purkinje cell protein 4						central nervous system development	cytosol|nucleus				large_intestine(1)	1		Prostate(19;2.65e-06)|all_epithelial(19;0.138)				gtgtgtgttggtgtgtgtgtgg	0.000													4	2	---	---	---	---	
PRDM15	63977	broad.mit.edu	37	21	43285243	43285243	+	Intron	DEL	C	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43285243delC	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						actcctcagtccccactcccc	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44198084	44198085	+	IGR	INS	-	C	C			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44198084_44198085insC								PDE9A (2468 upstream) : WDR4 (65121 downstream)																							AGGCAACGCAGCCCCCTGTGAT	0.535													4	2	---	---	---	---	
AGPAT3	56894	broad.mit.edu	37	21	45298197	45298198	+	Intron	INS	-	AC	AC	rs140992633	by1000genomes	TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45298197_45298198insAC	uc002zdv.2	+							NM_020132	NP_064517	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		GTGAGTTAGATACACACACACA	0.540													4	2	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45824752	45824753	+	Intron	INS	-	TGA	TGA			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45824752_45824753insTGA	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						gacagtgactgtgatgatagtg	0.114													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	21630505	21630506	+	IGR	INS	-	T	T			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21630505_21630506insT								LOC400891 (212050 upstream) : POM121L8P (6208 downstream)																							tatCATCCCACttttttttttt	0.025													5	3	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26204604	26204604	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26204604delT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						AGGTTGTCCCTctaagcagaa	0.274													4	2	---	---	---	---	
MIAT	440823	broad.mit.edu	37	22	27110615	27110615	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27110615delT	uc003adf.1	+											Homo sapiens cDNA: FLJ22849 fis, clone KAIA987.												0						CCCCTCTTCCTCTTCCTCCCC	0.522													4	2	---	---	---	---	
OSBP2	23762	broad.mit.edu	37	22	31278756	31278756	+	Intron	DEL	A	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31278756delA	uc003aiy.1	+						OSBP2_uc011ala.1_Intron|OSBP2_uc010gwc.1_Intron|OSBP2_uc011alb.1_Intron|OSBP2_uc003aiz.1_Intron|OSBP2_uc003aja.1_Intron|OSBP2_uc011alc.1_Intron|OSBP2_uc003ajb.2_Intron|OSBP2_uc011ald.1_Intron	NM_030758	NP_110385	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2						GGATCTGTGGAAAAAACAAAT	0.478													4	2	---	---	---	---	
TRIOBP	11078	broad.mit.edu	37	22	38169184	38169185	+	Intron	INS	-	TGGT	TGGT	rs139675202		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38169184_38169185insTGGT	uc003atr.2	+						TRIOBP_uc003atu.2_Intron|TRIOBP_uc003atw.2_Intron|TRIOBP_uc010gxh.2_Intron	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6						actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					AGGGCTCAAAGtggttggttgg	0.277													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45048978	45048979	+	IGR	INS	-	G	G	rs71800987		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45048978_45048979insG								NCRNA00207 (80649 upstream) : PRR5 (15614 downstream)																							GTgaagaaggtaagatgaaagt	0.015													4	2	---	---	---	---	
GYG2	8908	broad.mit.edu	37	X	2774822	2774822	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2774822delT	uc004cqs.1	+						GYG2_uc004cqt.1_Intron|GYG2_uc004cqu.1_Intron|GYG2_uc004cqv.1_Intron|GYG2_uc004cqw.1_Intron|GYG2_uc004cqx.1_Intron|GYG2_uc010ndc.1_Intron	NM_003918	NP_003909	O15488	GLYG2_HUMAN	glycogenin 2 isoform b						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|soluble fraction	glycogenin glucosyltransferase activity			ovary(1)|kidney(1)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				tctatctatctatctatcatc	0.189													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	40914554	40914555	+	IGR	DEL	TT	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40914554_40914555delTT								LOC100132831 (222105 upstream) : USP9X (30333 downstream)																							tctttctttctttttttttttt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	139435586	139435586	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139435586delT								CXorf66 (387909 upstream) : SOX3 (149566 downstream)																							CCCACCCCGCtttttttttga	0.249													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	154946368	154946368	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154946368delT								TMLHE (103751 upstream) : SPRY3 (51083 downstream)																							TAATCATAACTTTTTTTTAAT	0.090													4	2	---	---	---	---	
PRKY	5616	broad.mit.edu	37	Y	7173587	7173587	+	Intron	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:7173587delT	uc004fre.2	+							NM_002760	NP_002751			RecName: Full=Serine/threonine-protein kinase PRKX;          EC=2.7.11.1; AltName: Full=Protein kinase PKX1;												0						ACAGGATGCCTCCCATCATGT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13290743	13290743	+	IGR	DEL	T	-	-			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13290743delT								None (None upstream) : None (None downstream)																							ttttattttattttttttgag	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13429086	13429087	+	IGR	INS	-	G	G			TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13429086_13429087insG								None (None upstream) : None (None downstream)																							tctgcccctactgggggctgcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59021805	59021806	+	IGR	DEL	TA	-	-	rs150313998		TCGA-B0-5706-01A-11D-1534-10	TCGA-B0-5706-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59021805_59021806delTA								None (None upstream) : None (None downstream)																							gactgaaaactatgagcaaaat	0.104													4	2	---	---	---	---	
