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
PLA2G2F	64600	broad.mit.edu	37	1	20466689	20466689	+	Silent	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20466689C>T	uc009vpp.1	+	2	245	c.147C>T	c.(145-147)ACC>ACT	p.T49T		NM_022819	NP_073730	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	6					lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		AGTTCTTCACCGTGGCCATCC	0.592													11	80	---	---	---	---	PASS
SCMH1	22955	broad.mit.edu	37	1	41608634	41608634	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41608634C>T	uc001cgo.2	-	6	609	c.298G>A	c.(298-300)GAC>AAC	p.D100N	SCMH1_uc010ojr.1_Missense_Mutation_p.D53N|SCMH1_uc001cgp.2_Missense_Mutation_p.D39N|SCMH1_uc001cgr.2_Missense_Mutation_p.D39N|SCMH1_uc001cgs.2_Missense_Mutation_p.D110N|SCMH1_uc001cgt.2_Missense_Mutation_p.D39N|SCMH1_uc001cgq.2_Missense_Mutation_p.D53N|SCMH1_uc010ojs.1_RNA	NM_001031694	NP_001026864	Q96GD3	SCMH1_HUMAN	sex comb on midleg 1 isoform 1	100	MBT 1.				anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				CGCCAGAAGTCATTTTTGTTG	0.532													19	206	---	---	---	---	PASS
ZYG11B	79699	broad.mit.edu	37	1	53245528	53245528	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53245528T>C	uc001cuj.2	+	4	1150	c.955T>C	c.(955-957)TCT>CCT	p.S319P	ZYG11B_uc009vzg.2_RNA|ZYG11B_uc010onj.1_Missense_Mutation_p.S310P	NM_024646	NP_078922	Q9C0D3	ZY11B_HUMAN	zyg-11 homolog B	319							protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						TTCACAGGTGTCTGGGGAAGC	0.333													7	256	---	---	---	---	PASS
COL24A1	255631	broad.mit.edu	37	1	86362087	86362087	+	Silent	SNP	T	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86362087T>G	uc001dlj.2	-	29	2826	c.2784A>C	c.(2782-2784)TCA>TCC	p.S928S	COL24A1_uc001dli.2_Silent_p.S64S|COL24A1_uc010osd.1_Silent_p.S228S|COL24A1_uc001dlk.2_RNA|COL24A1_uc010ose.1_RNA|COL24A1_uc010osf.1_RNA	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	928	Collagen-like 7.				cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		CTGGTCCTCTTGATCCCTAGA	0.328													24	158	---	---	---	---	PASS
GBP3	2635	broad.mit.edu	37	1	89481094	89481094	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89481094A>G	uc001dmt.2	-	3	399	c.194T>C	c.(193-195)TTC>TCC	p.F65S	GBP3_uc010oss.1_5'UTR|GBP3_uc001dmu.2_5'UTR|GBP3_uc001dmv.2_RNA	NM_018284	NP_060754	Q9H0R5	GBP3_HUMAN	guanylate binding protein 3	65						integral to membrane	GTP binding|GTPase activity			ovary(1)|pancreas(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		GCCCAGAGAGAAGCCTGTAAA	0.458													5	194	---	---	---	---	PASS
BARHL2	343472	broad.mit.edu	37	1	91182297	91182297	+	Silent	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91182297T>C	uc001dns.2	-	1	498	c.456A>G	c.(454-456)AAA>AAG	p.K152K		NM_020063	NP_064447	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2	152						nucleus	sequence-specific DNA binding			ovary(1)	1		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)		CCGCCAGAGGTTTGCTGTCGC	0.562													4	82	---	---	---	---	PASS
BRDT	676	broad.mit.edu	37	1	92470105	92470105	+	Silent	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92470105G>A	uc001dok.3	+	17	2872	c.2523G>A	c.(2521-2523)CGG>CGA	p.R841R	BRDT_uc001dol.3_Silent_p.R841R|BRDT_uc010osz.1_Silent_p.R845R|BRDT_uc009wdf.2_Silent_p.R768R|BRDT_uc010ota.1_Silent_p.R795R|BRDT_uc010otb.1_Silent_p.R795R|BRDT_uc001dom.3_Silent_p.R841R	NM_207189	NP_997072	Q58F21	BRDT_HUMAN	testis-specific bromodomain protein	841					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		TAAAAGCTCGGACACAGGAAC	0.388													14	146	---	---	---	---	PASS
VAV3	10451	broad.mit.edu	37	1	108315355	108315355	+	Splice_Site	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108315355A>G	uc001dvk.1	-	5	609	c.555_splice	c.e5+1	p.P185_splice	VAV3_uc010ouw.1_Splice_Site_p.P185_splice|VAV3_uc001dvl.1_Splice_Site_p.P9_splice|VAV3_uc010oux.1_Splice_Site_p.P185_splice	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TAAAAGTCCTACGGGCTGATG	0.353													5	333	---	---	---	---	PASS
FLG2	388698	broad.mit.edu	37	1	152324078	152324078	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152324078C>A	uc001ezw.3	-	3	6257	c.6184G>T	c.(6184-6186)GGA>TGA	p.G2062*	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	2062							calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACTGAGGATCCTGACTCTCCA	0.532													52	357	---	---	---	---	PASS
FLG2	388698	broad.mit.edu	37	1	152326741	152326741	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152326741C>T	uc001ezw.3	-	3	3594	c.3521G>A	c.(3520-3522)GGT>GAT	p.G1174D	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1174	Ser-rich.						calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTGGTTGGACCTGAGCCAGA	0.483													9	56	---	---	---	---	PASS
GATAD2B	57459	broad.mit.edu	37	1	153785772	153785772	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153785772G>A	uc001fdb.3	-	8	1617	c.1373C>T	c.(1372-1374)ACC>ATC	p.T458I		NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	458	Potential.|GATA-type.|CR2.					nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CAGCCGGTTGGTGTGTTCAGC	0.448													15	379	---	---	---	---	PASS
PRCC	5546	broad.mit.edu	37	1	156764508	156764508	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156764508G>T	uc001fqa.2	+	5	1521	c.1231G>T	c.(1231-1233)GTG>TTG	p.V411L	PRCC_uc001fqb.2_Missense_Mutation_p.V379L	NM_005973	NP_005964	Q92733	PRCC_HUMAN	papillary renal cell carcinoma	411					cell cycle|mitotic cell cycle checkpoint	nucleus	protein binding		PRCC/TFE3(25)	kidney(25)|central_nervous_system(2)	27	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					AATCAACTTTGTGGAGATCAA	0.473			T	TFE3	papillary renal 								20	159	---	---	---	---	PASS
LAMC2	3918	broad.mit.edu	37	1	183196680	183196680	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183196680A>T	uc001gqa.2	+	10	1630	c.1316A>T	c.(1315-1317)GAC>GTC	p.D439V	LAMC2_uc001gpz.3_Missense_Mutation_p.D439V|LAMC2_uc010poa.1_Missense_Mutation_p.D139V	NM_005562	NP_005553	Q13753	LAMC2_HUMAN	laminin, gamma 2 isoform a precursor	439	Laminin EGF-like 5.				cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3						GAGAATCCTGACATTGAGTGT	0.527													8	66	---	---	---	---	PASS
APOBEC4	403314	broad.mit.edu	37	1	183617821	183617821	+	Silent	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183617821A>G	uc001gqn.2	-	2	368	c.96T>C	c.(94-96)CCT>CCC	p.P32P	RGL1_uc010pof.1_Intron|RGL1_uc001gqm.2_Intron|RGL1_uc010pog.1_Intron|RGL1_uc010poh.1_Intron	NM_203454	NP_982279	Q8WW27	ABEC4_HUMAN	apolipoprotein B	32					mRNA processing		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding				0						GAATATGGTAAGGACAATTAG	0.393													6	270	---	---	---	---	PASS
TPR	7175	broad.mit.edu	37	1	186292952	186292952	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186292952T>C	uc001grv.2	-	43	6460	c.6163A>G	c.(6163-6165)AGA>GGA	p.R2055G		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	2055					carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TGTTGTTCTCTAGAAACCTCC	0.453			T	NTRK1	papillary thyroid								4	162	---	---	---	---	PASS
DEGS1	8560	broad.mit.edu	37	1	224380110	224380110	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224380110T>C	uc001hoj.2	+	3	1013	c.902T>C	c.(901-903)GTG>GCG	p.V301A	DEGS1_uc001hoi.2_Missense_Mutation_p.V280A	NM_144780	NP_659004	O15121	DEGS1_HUMAN	degenerative spermatocyte homolog 1, lipid	301					sphingolipid metabolic process|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	electron carrier activity|protein binding|sphingolipid delta-4 desaturase activity				0	Breast(184;0.193)			GBM - Glioblastoma multiforme(131;0.00643)		TATGATTTTGTGATGGATGAT	0.398													6	161	---	---	---	---	PASS
PARP1	142	broad.mit.edu	37	1	226561930	226561930	+	Silent	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226561930A>G	uc001hqd.3	-	14	2238	c.2067T>C	c.(2065-2067)TAT>TAC	p.Y689Y		NM_001618	NP_001609	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase family, member 1	689	PARP alpha-helical.				cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nuclear envelope|nucleolus|transcription factor complex	DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding			lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1)	10	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CAATAACCTCATACTCCACCA	0.433								Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					32	263	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237886484	237886484	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237886484G>T	uc001hyl.1	+	74	10731	c.10611G>T	c.(10609-10611)AGG>AGT	p.R3537S	RYR2_uc010pxz.1_Missense_Mutation_p.R492S	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3537					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TACCAAACAGGACTGATGATA	0.398													31	285	---	---	---	---	PASS
FBXO11	80204	broad.mit.edu	37	2	48050392	48050392	+	Silent	SNP	A	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48050392A>T	uc010fbl.2	-	12	1368	c.1254T>A	c.(1252-1254)ACT>ACA	p.T418T	FBXO11_uc002rwe.2_Silent_p.T418T|FBXO11_uc002rwf.2_Silent_p.T418T|FBXO11_uc002rwg.1_Silent_p.T418T|FBXO11_uc010fbk.2_5'UTR	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1	502	PbH1 5.				ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ATATTCCTCCAGTCTGCCCAT	0.383													45	401	---	---	---	---	PASS
PNPT1	87178	broad.mit.edu	37	2	55898455	55898455	+	Silent	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55898455T>C	uc002rzf.2	-	11	1028	c.975A>G	c.(973-975)AAA>AAG	p.K325K	PNPT1_uc002rzg.2_RNA	NM_033109	NP_149100	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	325					mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			aaaatTTACCTTTTAGTTGTT	0.323													5	163	---	---	---	---	PASS
GALNT5	11227	broad.mit.edu	37	2	158165091	158165091	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158165091A>C	uc002tzg.2	+	9	2788	c.2533A>C	c.(2533-2535)AAT>CAT	p.N845H	GALNT5_uc010zci.1_RNA	NM_014568	NP_055383	Q7Z7M9	GALT5_HUMAN	N-acetylgalactosaminyltransferase 5	845	Lumenal (Potential).|Ricin B-type lectin.				glycosaminoglycan biosynthetic process	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(3)|skin(1)	4						TCAACAATTTAATTACACCTG	0.393													37	159	---	---	---	---	PASS
SLC4A10	57282	broad.mit.edu	37	2	162761321	162761321	+	Silent	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162761321C>T	uc002ubx.3	+	14	1837	c.1653C>T	c.(1651-1653)ACC>ACT	p.T551T	SLC4A10_uc010zcr.1_RNA|SLC4A10_uc002uby.3_Silent_p.T521T|SLC4A10_uc010zcs.1_Silent_p.T532T	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate	551	Helical; (Potential).				bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5						CATCCATGACCGGGATAGCCT	0.403													5	370	---	---	---	---	PASS
UBR3	130507	broad.mit.edu	37	2	170806129	170806129	+	Silent	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170806129T>C	uc010zdi.1	+	23	3099	c.3099T>C	c.(3097-3099)GCT>GCC	p.A1033A	UBR3_uc002ufr.3_RNA|UBR3_uc010fqa.2_5'UTR|UBR3_uc002uft.3_5'UTR	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3	1033					sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0						CTGGTACAGCTCAAGTTTTCA	0.318													12	77	---	---	---	---	PASS
UBR3	130507	broad.mit.edu	37	2	170806130	170806130	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170806130C>T	uc010zdi.1	+	23	3100	c.3100C>T	c.(3100-3102)CAA>TAA	p.Q1034*	UBR3_uc002ufr.3_RNA|UBR3_uc010fqa.2_5'UTR|UBR3_uc002uft.3_5'UTR	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3	1034					sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0						TGGTACAGCTCAAGTTTTCAG	0.323													11	77	---	---	---	---	PASS
C2orf67	151050	broad.mit.edu	37	2	210896049	210896049	+	Intron	SNP	T	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210896049T>G	uc002vds.2	-						C2orf67_uc002vdt.2_Intron|uc002vdu.1_RNA	NM_152519	NP_689732	A0AUZ9	CB067_HUMAN	hypothetical protein LOC151050											ovary(3)	3		Renal(323;0.202)		Epithelial(149;0.00435)|Lung(261;0.0529)|LUSC - Lung squamous cell carcinoma(261;0.0551)|all cancers(144;0.0696)		TTAGTGGCTGTTCTGGATTAT	0.284													11	23	---	---	---	---	PASS
DOCK10	55619	broad.mit.edu	37	2	225635352	225635352	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225635352C>T	uc010fwz.1	-	54	6454	c.6215G>A	c.(6214-6216)GGG>GAG	p.G2072E	DOCK10_uc002vob.2_Missense_Mutation_p.G2066E|DOCK10_uc002voa.2_Missense_Mutation_p.G728E	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	2072	DHR-2.						GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GGCCATTGGCCCAGCATTAAC	0.453													4	143	---	---	---	---	PASS
PPARG	5468	broad.mit.edu	37	3	12434123	12434123	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12434123G>A	uc003bwx.2	+	4	582	c.491G>A	c.(490-492)CGG>CAG	p.R164Q	PPARG_uc003bwr.2_Missense_Mutation_p.R136Q|PPARG_uc003bws.2_Missense_Mutation_p.R136Q|PPARG_uc003bwu.2_Missense_Mutation_p.R136Q|PPARG_uc003bwv.2_Missense_Mutation_p.R136Q|PPARG_uc010hea.1_RNA|PPARG_uc003bwq.1_Missense_Mutation_p.R136Q|PPARG_uc003bwt.1_Missense_Mutation_p.R136Q|PPARG_uc003bww.1_Missense_Mutation_p.R164Q	NM_015869	NP_056953	P37231	PPARG_HUMAN	peroxisome proliferative activated receptor	164	Nuclear receptor.				activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation	cytosol|nucleoplasm	activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|kidney(1)	2					Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197)	GGTTTCTTCCGGAGAACAATC	0.279			T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy|familial partial L;diabetes mellitus|insulin-resistantI|with acanthosis nigricans and hypertension						21	132	---	---	---	---	PASS
TSEN2	80746	broad.mit.edu	37	3	12574197	12574197	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12574197A>G	uc003bxc.2	+	12	1762	c.1375A>G	c.(1375-1377)AGG>GGG	p.R459G	TSEN2_uc003bwz.2_Missense_Mutation_p.R400G|TSEN2_uc003bxa.2_Missense_Mutation_p.R433G|TSEN2_uc003bxb.2_Missense_Mutation_p.R459G|TSEN2_uc011aur.1_Missense_Mutation_p.R368G	NM_025265	NP_079541	Q8NCE0	SEN2_HUMAN	tRNA-intron nuclease 2 isoform 1	459					mRNA processing|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|nucleolus|tRNA-intron endonuclease complex	nucleic acid binding|tRNA-intron endonuclease activity			central_nervous_system(1)	1						TTCACGAGAGAGGAGTGACCA	0.323													7	480	---	---	---	---	PASS
EFHB	151651	broad.mit.edu	37	3	19947155	19947155	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19947155G>C	uc003cbl.3	-	6	1571	c.1375C>G	c.(1375-1377)CGA>GGA	p.R459G	EFHB_uc003cbm.2_Missense_Mutation_p.R329G	NM_144715	NP_653316	Q8N7U6	EFHB_HUMAN	EF hand domain family, member B	459					signal transduction	proteinaceous extracellular matrix	calcium ion binding				0						GCCATGGCTCGTCCATCATTA	0.383													6	79	---	---	---	---	PASS
CSRNP1	64651	broad.mit.edu	37	3	39185098	39185098	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39185098C>A	uc003cjg.2	-	5	1432	c.1218G>T	c.(1216-1218)GAG>GAT	p.E406D	CSRNP1_uc003cjh.2_Missense_Mutation_p.E406D	NM_033027	NP_149016	Q96S65	CSRN1_HUMAN	AXIN1 up-regulated 1	406					apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(4)|skin(1)	5						CCTCTTCCTCCTCCTCCCCAC	0.607													5	35	---	---	---	---	PASS
PHLDB2	90102	broad.mit.edu	37	3	111693466	111693466	+	3'UTR	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111693466G>A	uc010hqa.2	+	18					PHLDB2_uc003dyc.2_3'UTR|PHLDB2_uc003dyd.2_3'UTR|PHLDB2_uc003dyg.2_3'UTR|PHLDB2_uc003dyh.2_3'UTR|PHLDB2_uc003dyi.2_3'UTR|PHLDB2_uc003dyj.2_3'UTR	NM_001134438	NP_001127910	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,							cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6						TTACAAGAATGAAGCCATATT	0.418													4	27	---	---	---	---	PASS
WDR52	55779	broad.mit.edu	37	3	113049451	113049451	+	Missense_Mutation	SNP	A	C	C	rs79365690		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-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													21	145	---	---	---	---	PASS
CEP63	80254	broad.mit.edu	37	3	134268984	134268984	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134268984C>T	uc003eqo.1	+	12	1711	c.1262C>T	c.(1261-1263)ACT>ATT	p.T421I	CEP63_uc003eql.1_Missense_Mutation_p.T375I|CEP63_uc003eqm.2_Missense_Mutation_p.T375I|CEP63_uc003eqn.1_Missense_Mutation_p.T421I|CEP63_uc003eqp.1_Missense_Mutation_p.T50I	NM_025180	NP_079456	Q96MT8	CEP63_HUMAN	centrosomal protein 63 isoform a	421	Potential.				cell division|DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitosis|signal transduction in response to DNA damage|spindle assembly	centrosome|cytosol|spindle pole	protein binding			ovary(1)	1						TCCCATCTAACTCAGGAGTTA	0.408													10	175	---	---	---	---	PASS
LRRC33	375387	broad.mit.edu	37	3	196387147	196387147	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196387147C>A	uc003fwv.2	+	3	737	c.633C>A	c.(631-633)AAC>AAA	p.N211K		NM_198565	NP_940967	Q86YC3	LRC33_HUMAN	leucine rich repeat containing 33 precursor	211	Extracellular (Potential).|LRR 7.					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.9e-23)|all cancers(36;1.76e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		GGCACCTCAACCTGGCCTTCA	0.637													5	9	---	---	---	---	PASS
NPFFR2	10886	broad.mit.edu	37	4	73012865	73012865	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73012865C>G	uc003hgg.2	+	4	1003	c.905C>G	c.(904-906)ACC>AGC	p.T302S	NPFFR2_uc010iig.1_Missense_Mutation_p.T84S|NPFFR2_uc003hgi.2_Missense_Mutation_p.T203S|NPFFR2_uc003hgh.2_Missense_Mutation_p.T200S|NPFFR2_uc003hgj.2_RNA	NM_004885	NP_004876	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2 isoform 1	302	Extracellular (Potential).				detection of abiotic stimulus	actin cytoskeleton|integral to plasma membrane	neuropeptide receptor activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			CAGAATAAAACCAGTCCAGTC	0.473													10	134	---	---	---	---	PASS
RCHY1	25898	broad.mit.edu	37	4	76419490	76419490	+	Intron	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-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													8	18	---	---	---	---	PASS
CENPE	1062	broad.mit.edu	37	4	104062252	104062252	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104062252G>T	uc003hxb.1	-	36	5563	c.5473C>A	c.(5473-5475)CTT>ATT	p.L1825I	CENPE_uc003hxc.1_Missense_Mutation_p.L1800I|CENPE_uc003hxd.1_5'Flank	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	1825	Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TTTGCCTTAAGTTCTTGAATC	0.284													11	179	---	---	---	---	PASS
NDST3	9348	broad.mit.edu	37	4	119036028	119036028	+	Silent	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119036028T>C	uc003ibx.2	+	4	1540	c.1137T>C	c.(1135-1137)CCT>CCC	p.P379P	NDST3_uc011cgf.1_Intron	NM_004784	NP_004775	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan	379	Lumenal (Potential).|Heparan sulfate N-deacetylase 3.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1						GGTGGTTTCCTCACATGTGGA	0.443													6	378	---	---	---	---	PASS
FGA	2243	broad.mit.edu	37	4	155507658	155507658	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155507658C>T	uc003iod.1	-	5	981	c.923G>A	c.(922-924)CGA>CAA	p.R308Q	FGA_uc003ioe.1_Missense_Mutation_p.R308Q|FGA_uc003iof.1_Intron	NM_000508	NP_000499	P02671	FIBA_HUMAN	fibrinogen, alpha polypeptide isoform alpha-E	308	By similarity.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|breast(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	CCCAGGGTTTCGGTTTCCAGT	0.572													4	147	---	---	---	---	PASS
CBR4	84869	broad.mit.edu	37	4	169923170	169923170	+	Intron	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169923170C>T	uc003iry.2	-						CBR4_uc011cjy.1_Intron|CBR4_uc003irz.1_3'UTR	NM_032783	NP_116172	Q8N4T8	CBR4_HUMAN	carbonic reductase 4						fatty acid biosynthetic process|protein homotetramerization	mitochondrial matrix	NADPH binding|NADPH dehydrogenase (quinone) activity|protein binding|quinone binding				0		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)		ATAATGGCTTCCCTATAAAAC	0.299													10	82	---	---	---	---	PASS
PRDM9	56979	broad.mit.edu	37	5	23527472	23527472	+	Missense_Mutation	SNP	G	A	A	rs112666693		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23527472G>A	uc003jgo.2	+	11	2457	c.2275G>A	c.(2275-2277)GAT>AAT	p.D759N		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	759	C2H2-type 10.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6						GGGCTTTCGCGATAAGTCACA	0.572										HNSCC(3;0.000094)			5	34	---	---	---	---	PASS
DAB2	1601	broad.mit.edu	37	5	39382743	39382743	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39382743C>T	uc003jlx.2	-	10	1849	c.1318G>A	c.(1318-1320)GGA>AGA	p.G440R	DAB2_uc003jlw.2_Missense_Mutation_p.G419R	NM_001343	NP_001334	P98082	DAB2_HUMAN	disabled homolog 2	440					cell proliferation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway, planar cell polarity pathway	clathrin coated vesicle membrane|coated pit	protein C-terminus binding			kidney(2)|skin(1)	3	all_lung(31;0.000197)		Epithelial(62;0.137)			CTGCCTCTTCCTGGTTTGGTA	0.483													7	310	---	---	---	---	PASS
NDUFS4	4724	broad.mit.edu	37	5	52899338	52899338	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52899338T>C	uc003jpe.2	+	2	183	c.155T>C	c.(154-156)CTC>CCC	p.L52P		NM_002495	NP_002486	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4	52					brain development|cAMP-mediated signaling|mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|positive regulation of fibroblast proliferation|reactive oxygen species metabolic process|regulation of protein phosphorylation|response to cAMP|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			central_nervous_system(1)	1		Lung NSC(810;8.27e-05)|Breast(144;0.0848)			NADH(DB00157)	GACACACAACTCATAACAGTT	0.403													6	254	---	---	---	---	PASS
NDUFAF2	91942	broad.mit.edu	37	5	60448551	60448551	+	Silent	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60448551A>G	uc003jsp.3	+	4	406	c.279A>G	c.(277-279)AAA>AAG	p.K93K	NDUFAF2_uc003jso.3_RNA	NM_174889	NP_777549	Q8N183	MIMIT_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	93						membrane|mitochondrion	electron carrier activity|NADH dehydrogenase (ubiquinone) activity				0		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)				AGAATGAAAAACACAGAGAAG	0.249													4	67	---	---	---	---	PASS
DIMT1L	27292	broad.mit.edu	37	5	61688718	61688718	+	Intron	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61688718G>A	uc003jta.2	-						DIMT1L_uc011cqq.1_3'UTR	NM_014473	NP_055288	Q9UNQ2	DIMT1_HUMAN	dimethyladenosine transferase							nucleolus	RNA binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity			central_nervous_system(1)	1		Lung NSC(810;8.94e-06)|Prostate(74;0.0235)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.122)		TGGAGCACTGGCCCTTTATAC	0.378													47	216	---	---	---	---	PASS
DIMT1L	27292	broad.mit.edu	37	5	61688719	61688719	+	Intron	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61688719C>T	uc003jta.2	-						DIMT1L_uc011cqq.1_3'UTR	NM_014473	NP_055288	Q9UNQ2	DIMT1_HUMAN	dimethyladenosine transferase							nucleolus	RNA binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity			central_nervous_system(1)	1		Lung NSC(810;8.94e-06)|Prostate(74;0.0235)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.122)		GGAGCACTGGCCCTTTATACA	0.378													49	222	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75490860	75490860	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75490860T>C	uc003kei.1	+	3	831	c.697T>C	c.(697-699)TTC>CTC	p.F233L		NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	233	Helical; (Potential).				neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		ATTCTTTGCCTTCCTTTCTTC	0.448													8	578	---	---	---	---	PASS
MEGF10	84466	broad.mit.edu	37	5	126793028	126793028	+	3'UTR	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126793028G>T	uc003kuh.3	+	26					MEGF10_uc003kui.3_3'UTR	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor						cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		GGACCGCTTGGTAGCCACTGG	0.418													8	15	---	---	---	---	PASS
HBEGF	1839	broad.mit.edu	37	5	139722271	139722271	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139722271C>T	uc003lfi.2	-	3	622	c.347G>A	c.(346-348)TGC>TAC	p.C116Y	HBEGF_uc010jfj.2_RNA	NM_001945	NP_001936	Q99075	HBEGF_HUMAN	heparin-binding EGF-like growth factor	116	Extracellular (Potential).|EGF-like.				epidermal growth factor receptor signaling pathway|muscle organ development|positive regulation of protein kinase B signaling cascade|positive regulation of wound healing	cell surface|extracellular space|integral to plasma membrane	epidermal growth factor receptor binding|eukaryotic cell surface binding|growth factor activity|heparin binding|receptor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCATGGATGCAGAAGTCCTT	0.527													4	142	---	---	---	---	PASS
PCDHA13	56136	broad.mit.edu	37	5	140389805	140389805	+	3'UTR	SNP	C	T	T	rs114341618	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140389805C>T	uc003lif.2	+	4					PCDHA1_uc003lha.2_3'UTR|PCDHA1_uc003lhb.2_3'UTR|PCDHA2_uc003lhd.2_3'UTR|PCDHA3_uc003lhf.2_3'UTR|PCDHA4_uc003lhi.2_3'UTR|PCDHA4_uc003lhh.1_Missense_Mutation_p.S897F|PCDHA5_uc003lhk.1_Missense_Mutation_p.S886F|PCDHA5_uc003lhl.2_3'UTR|PCDHA6_uc003lhn.2_3'UTR|PCDHA6_uc003lho.2_3'UTR|PCDHA7_uc003lhq.2_3'UTR|PCDHA8_uc003lhs.2_3'UTR|PCDHA9_uc003lhu.2_3'UTR|PCDHA10_uc003lhw.2_3'UTR|PCDHA10_uc003lhx.2_3'UTR|PCDHA11_uc003lia.2_3'UTR|PCDHA12_uc003lic.2_3'UTR|PCDHA13_uc003lie.1_Missense_Mutation_p.S900F|PCDHAC1_uc003lih.2_3'UTR|PCDHAC2_uc003lii.2_3'UTR	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGAGGCTTCCCAGCCCCGC	0.522													5	23	---	---	---	---	PASS
PECI	10455	broad.mit.edu	37	6	4130462	4130462	+	Intron	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4130462G>T	uc003mwf.2	-						C6orf201_uc003mwa.3_3'UTR|C6orf201_uc003mvz.3_RNA|C6orf201_uc003mwb.3_RNA|PECI_uc003mwc.2_5'UTR|PECI_uc003mwd.2_Intron|PECI_uc003mwe.2_Intron|PECI_uc010jnr.1_Intron	NM_206836	NP_996667	O75521	ECI2_HUMAN	peroxisomal D3,D2-enoyl-CoA isomerase isoform 2						fatty acid metabolic process	mitochondrion|peroxisomal matrix	dodecenoyl-CoA delta-isomerase activity|fatty-acyl-CoA binding				0	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GTTGTATGAAGTAGCCACAAT	0.368													6	108	---	---	---	---	PASS
SLC35B3	51000	broad.mit.edu	37	6	8413723	8413723	+	3'UTR	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8413723A>G	uc010joe.2	-	11					SLC35B3_uc003mya.2_Intron|SLC35B3_uc003myc.2_RNA|SLC35B3_uc003myb.2_3'UTR|SLC35B3_uc011did.1_3'UTR|SLC35B3_uc003myd.2_RNA	NM_001142541	NP_001136013	Q9H1N7	S35B3_HUMAN	solute carrier family 35, member B3						transmembrane transport	Golgi membrane|integral to membrane					0	Ovarian(93;0.0569)					TCCCTTTGGAAAGTTAATTAA	0.383													10	74	---	---	---	---	PASS
TCP11	6954	broad.mit.edu	37	6	35088304	35088304	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35088304C>A	uc003okd.2	-	7	1055	c.874G>T	c.(874-876)GCA>TCA	p.A292S	TCP11_uc003ojz.1_Missense_Mutation_p.A217S|TCP11_uc003oka.2_Missense_Mutation_p.A217S|TCP11_uc003okb.2_Missense_Mutation_p.A216S|TCP11_uc003okc.2_Missense_Mutation_p.A216S|TCP11_uc011dsu.1_Missense_Mutation_p.A274S|TCP11_uc011dsv.1_Missense_Mutation_p.A241S|TCP11_uc011dsw.1_Missense_Mutation_p.A246S	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1	279					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5						TTGTTGGCTGCCTCATTGGGA	0.572													9	143	---	---	---	---	PASS
BRPF3	27154	broad.mit.edu	37	6	36177586	36177586	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36177586T>C	uc003olv.3	+	5	1984	c.1760T>C	c.(1759-1761)ATG>ACG	p.M587T	BRPF3_uc010jwb.2_Missense_Mutation_p.M587T|BRPF3_uc011dtj.1_RNA|BRPF3_uc010jwc.2_RNA|BRPF3_uc011dtk.1_Missense_Mutation_p.M587T	NM_015695	NP_056510	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	587					histone H3 acetylation|platelet activation|platelet degranulation	cytosol|extracellular region|MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding			ovary(1)|skin(1)	2						CAGGCTGCCATGGAGCTGGAG	0.498													9	70	---	---	---	---	PASS
FILIP1	27145	broad.mit.edu	37	6	76024808	76024808	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76024808G>T	uc003pia.2	-	5	1113	c.740C>A	c.(739-741)GCA>GAA	p.A247E	FILIP1_uc003phy.1_Missense_Mutation_p.A247E|FILIP1_uc003phz.2_Missense_Mutation_p.A148E|FILIP1_uc010kbe.2_Missense_Mutation_p.A250E|FILIP1_uc003pib.1_5'UTR	NM_015687	NP_056502	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	247	Potential.									skin(3)|ovary(1)	4						CAGCATGAGTGCAAAGGATTT	0.413													18	313	---	---	---	---	PASS
C6orf164	63914	broad.mit.edu	37	6	88074934	88074934	+	Intron	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88074934C>T	uc003plr.2	+						C6orf163_uc003pls.2_RNA					Homo sapiens DC18 mRNA, complete cds.												0						AACTGGGAATCATGACAAATT	0.418													11	108	---	---	---	---	PASS
VNN1	8876	broad.mit.edu	37	6	133032934	133032934	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133032934C>T	uc003qdo.2	-	2	275	c.255G>A	c.(253-255)TGG>TGA	p.W85*		NM_004666	NP_004657	O95497	VNN1_HUMAN	vanin 1 precursor	85	CN hydrolase.				acute inflammatory response|anti-apoptosis|cell-cell adhesion|cellular component movement|chronic inflammatory response|innate immune response|pantothenate metabolic process|positive regulation of T cell differentiation in thymus|response to oxidative stress	anchored to membrane|integral to membrane|plasma membrane	GPI anchor binding|pantetheine hydrolase activity			ovary(3)	3	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		TGTTGAAGTTCCAGCCATAAA	0.453													5	200	---	---	---	---	PASS
RAET1G	353091	broad.mit.edu	37	6	150239429	150239429	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150239429T>C	uc010kii.1	-	4	791	c.723A>G	c.(721-723)ATA>ATG	p.I241M	uc003qni.1_Intron|RAET1G_uc003qnm.2_Intron	NM_001001788	NP_001001788	Q6H3X3	RET1G_HUMAN	retinoic acid early transcript 1G precursor	241	Helical; (Potential).				antigen processing and presentation|immune response	integral to membrane|MHC class I protein complex	protein binding				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		GCCTGGAGCATATGAGGAGAC	0.607													5	380	---	---	---	---	PASS
OPRM1	4988	broad.mit.edu	37	6	154360384	154360384	+	5'Flank	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154360384T>C	uc003qpr.2	+						OPRM1_uc011efb.1_Intron|OPRM1_uc011efc.1_Intron|OPRM1_uc011efd.1_Intron|OPRM1_uc011efe.1_Missense_Mutation_p.L30P|OPRM1_uc003qpn.2_5'Flank|OPRM1_uc003qpo.1_5'Flank|OPRM1_uc011eff.1_5'Flank|OPRM1_uc011efg.1_5'Flank|OPRM1_uc011efh.1_5'Flank|OPRM1_uc003qpq.1_5'Flank|OPRM1_uc003qpt.1_5'Flank|OPRM1_uc011efi.1_5'Flank|OPRM1_uc003qpp.2_5'Flank|OPRM1_uc003qps.2_5'Flank	NM_000914	NP_000905	P35372	OPRM_HUMAN	opioid receptor, mu 1 isoform MOR-1						behavior|negative regulation of cell proliferation|sensory perception	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	mu-opioid receptor activity|protein binding			ovary(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tramadol(DB00193)	CCTCCCTCCCTTCCAGCCTCC	0.587													5	124	---	---	---	---	PASS
DAGLB	221955	broad.mit.edu	37	7	6461459	6461459	+	Intron	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6461459C>T	uc003sqa.2	-						DAGLB_uc003spz.2_Missense_Mutation_p.A70T|DAGLB_uc011jwt.1_Intron|DAGLB_uc011jwu.1_Intron|DAGLB_uc003sqb.2_Intron|DAGLB_uc003sqc.2_Intron|DAGLB_uc011jwv.1_Intron|DAGLB_uc003sqd.3_Intron|DAGLB_uc011jww.1_Intron	NM_139179	NP_631918	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta isoform 1						lipid catabolic process|platelet activation	integral to membrane|plasma membrane	acylglycerol lipase activity|metal ion binding|triglyceride lipase activity			ovary(2)|central_nervous_system(1)	3		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		GTTGCAGAAGCGGCCGTCAGC	0.602													7	33	---	---	---	---	PASS
COL28A1	340267	broad.mit.edu	37	7	7516789	7516789	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7516789A>G	uc003src.1	-	14	1304	c.1187T>C	c.(1186-1188)GTA>GCA	p.V396A	COL28A1_uc011jxe.1_Missense_Mutation_p.V79A|COL28A1_uc003srd.2_5'UTR	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	collagen, type XXVIII precursor	396	Collagen-like 3.				cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			skin(3)	3		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CTCTCCTGGTACTCCCTCAGG	0.333													5	89	---	---	---	---	PASS
ANGPT2	285	broad.mit.edu	37	8	6366472	6366472	+	Silent	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6366472A>G	uc003wqj.3	-	8	1640	c.1311T>C	c.(1309-1311)TGT>TGC	p.C437C	MCPH1_uc003wqi.2_Intron|ANGPT2_uc003wqk.3_Silent_p.C436C|ANGPT2_uc010lri.2_Silent_p.C385C|ANGPT2_uc003wql.3_Silent_p.C436C	NM_001147	NP_001138	O15123	ANGP2_HUMAN	angiopoietin 2 isoform a precursor	437	Fibrinogen C-terminal.				angiogenesis|blood coagulation|leukocyte migration|negative regulation of blood vessel endothelial cell migration|negative regulation of positive chemotaxis|Tie receptor signaling pathway	extracellular space	metal ion binding|receptor tyrosine kinase binding			upper_aerodigestive_tract(1)	1		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		GCATTTGTGAACATTTGCAAA	0.418													7	334	---	---	---	---	PASS
PSD3	23362	broad.mit.edu	37	8	18413784	18413784	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18413784C>A	uc003wza.2	-	15	2966	c.2863G>T	c.(2863-2865)GAC>TAC	p.D955Y	PSD3_uc003wyx.3_Missense_Mutation_p.D284Y|PSD3_uc003wyy.2_Missense_Mutation_p.D421Y|PSD3_uc003wyz.2_Missense_Mutation_p.D256Y	NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide	956					regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		ACCTTCTTGTCGGGGGGATAT	0.483													27	209	---	---	---	---	PASS
XPO7	23039	broad.mit.edu	37	8	21827777	21827777	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21827777T>A	uc003xaa.3	+	4	484	c.382T>A	c.(382-384)TAT>AAT	p.Y128N	XPO7_uc010lti.2_Missense_Mutation_p.Y128N|XPO7_uc010ltj.1_RNA|XPO7_uc010ltk.2_Missense_Mutation_p.Y129N	NM_015024	NP_055839	Q9UIA9	XPO7_HUMAN	exportin 7 isoform b	128					mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		GAAGGATGACTATGTCTTCAG	0.393													16	84	---	---	---	---	PASS
REEP4	80346	broad.mit.edu	37	8	21996193	21996193	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21996193G>T	uc003xau.1	-	7	1120	c.667C>A	c.(667-669)CAG>AAG	p.Q223K	REEP4_uc010ltt.1_3'UTR	NM_025232	NP_079508	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	223						integral to membrane				skin(1)	1				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)		CGCAGGCTCTGGCTGCGGATT	0.677													3	36	---	---	---	---	PASS
KCNU1	157855	broad.mit.edu	37	8	36790510	36790510	+	Silent	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36790510C>A	uc010lvw.2	+	26	3091	c.3004C>A	c.(3004-3006)CGA>AGA	p.R1002R	KCNU1_uc003xjw.2_RNA	NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	1002	Cytoplasmic (Potential).					voltage-gated potassium channel complex	binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TGGCTTATACCGAATAATTGA	0.428													38	314	---	---	---	---	PASS
CLVS1	157807	broad.mit.edu	37	8	62370953	62370953	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62370953C>T	uc003xuh.2	+	5	1153	c.829C>T	c.(829-831)CCT>TCT	p.P277S	CLVS1_uc003xui.2_RNA|CLVS1_uc010lyp.2_Intron	NM_173519	NP_775790	Q8IUQ0	CLVS1_HUMAN	retinaldehyde binding protein 1-like 1	277	CRAL-TRIO.				lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity	p.P277L(1)		skin(4)|ovary(1)	5						AACTCTTCCTCCTTATGACAT	0.438													8	184	---	---	---	---	PASS
CLVS1	157807	broad.mit.edu	37	8	62412012	62412012	+	Splice_Site	SNP	A	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62412012A>T	uc003xuh.2	+	6	1302	c.978_splice	c.e6-2	p.R326_splice	CLVS1_uc003xui.2_Splice_Site|CLVS1_uc010lyp.2_Splice_Site_p.I248_splice	NM_173519	NP_775790	Q8IUQ0	CLVS1_HUMAN	retinaldehyde binding protein 1-like 1						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5						CCCTCTTGTTAGATCTCAGTC	0.433													17	177	---	---	---	---	PASS
RAD54B	25788	broad.mit.edu	37	8	95419896	95419896	+	Silent	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95419896C>T	uc003ygk.2	-	5	650	c.552G>A	c.(550-552)CTG>CTA	p.L184L	RAD54B_uc010may.1_5'UTR|RAD54B_uc003ygl.1_RNA	NM_012415	NP_036547	O95073	FSBP_HUMAN	RAD54 homolog B	Error:Variant_position_missing_in_O95073_after_alignment					double-strand break repair via homologous recombination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA translocase activity|protein binding	p.L184L(1)		kidney(2)|lung(1)|skin(1)	4	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			CACAAATCATCAGTGTTTGGC	0.378								Direct_reversal_of_damage|Homologous_recombination					8	261	---	---	---	---	PASS
LAPTM4B	55353	broad.mit.edu	37	8	98831370	98831370	+	Silent	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98831370T>C	uc003yia.2	+	5	840	c.684T>C	c.(682-684)CCT>CCC	p.P228P	LAPTM4B_uc010mbg.2_Intron	NM_018407	NP_060877	Q86VI4	LAP4B_HUMAN	lysosomal associated transmembrane protein 4	281					transport	endomembrane system|integral to membrane	protein binding			skin(1)	1	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)			TTTTGCAGCCTCCTAATTTTC	0.373													7	617	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113564842	113564842	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113564842C>A	uc003ynu.2	-	26	4501	c.4342G>T	c.(4342-4344)GAT>TAT	p.D1448Y	CSMD3_uc003yns.2_Missense_Mutation_p.D720Y|CSMD3_uc003ynt.2_Missense_Mutation_p.D1408Y|CSMD3_uc011lhx.1_Missense_Mutation_p.D1344Y	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1448	Extracellular (Potential).|CUB 8.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TTTCCAGGATCTACCTCAATC	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			13	178	---	---	---	---	PASS
TATDN1	83940	broad.mit.edu	37	8	125535229	125535229	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125535229A>C	uc003yrd.2	-	2	79	c.37T>G	c.(37-39)TTG>GTG	p.L13V	TATDN1_uc003yre.2_RNA|TATDN1_uc010mdm.2_Intron|TATDN1_uc003yrf.2_Missense_Mutation_p.L13V	NM_032026	NP_114415	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1 isoform a	13						nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GGGTCAGTCAAGTTGATACCA	0.313													24	229	---	---	---	---	PASS
CNTLN	54875	broad.mit.edu	37	9	17457562	17457562	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17457562A>T	uc003zmz.2	+	19	3178	c.3152A>T	c.(3151-3153)GAA>GTA	p.E1051V	CNTLN_uc003zmy.2_Missense_Mutation_p.E1052V|CNTLN_uc010mio.2_Missense_Mutation_p.E731V	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1	1052	Potential.					centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)		AAAGAAAAAGAAGATTTACTA	0.269													10	124	---	---	---	---	PASS
NFX1	4799	broad.mit.edu	37	9	33318728	33318728	+	Splice_Site	SNP	G	A	A	rs137968719		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33318728G>A	uc003zsq.2	+	8	1650	c.1589_splice	c.e8-1	p.V530_splice	SUGT1P1_uc010mjq.1_Intron|NFX1_uc011lnw.1_Splice_Site_p.V530_splice|NFX1_uc003zso.2_Splice_Site_p.V530_splice|NFX1_uc003zsp.1_Splice_Site_p.V530_splice|NFX1_uc010mjr.1_Splice_Site_p.V530_splice|NFX1_uc003zsr.2_Splice_Site_p.V530_splice	NM_002504	NP_002495	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1						inflammatory response|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|ligase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		TTCTCTTCAAGTATGCTATTG	0.383													13	239	---	---	---	---	PASS
PIGO	84720	broad.mit.edu	37	9	35090534	35090534	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35090534T>G	uc003zwd.2	-	8	3179	c.2783A>C	c.(2782-2784)CAT>CCT	p.H928P	PIGO_uc003zwc.1_3'UTR|PIGO_uc003zwe.2_Missense_Mutation_p.H511P|PIGO_uc003zwf.2_Missense_Mutation_p.H511P|PIGO_uc003zwg.1_Missense_Mutation_p.H491P	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	928				PFTVPWQAVSAWALMATQTFYSTGHQPVFPAIHWHAAFVGF PEGHGSCTWLPALLVGANTFASHLLFAVGCPLLLLWPFLCE SQGL -> KYLSSDSLKDNSDVSSAPLVFKEVLLLMFLSLT EGPMPHTTRKVFLVSSLLPAIAKQIDPSCWFPGFMERRDKE SSKTPCGNAASS (in Ref. 8).	C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			ACAGGAGCCATGACCCTCTGG	0.582													5	21	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	66459898	66459898	+	5'Flank	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66459898A>G	uc010mng.1	-						uc004aeb.2_5'Flank|uc004aec.2_RNA					Homo sapiens cDNA, FLJ98602.																		cagtgtctggacattaaaatc	0.000													3	5	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	66468984	66468984	+	RNA	SNP	A	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66468984A>C	uc004aec.2	+	5		c.2551A>C								Homo sapiens, clone IMAGE:5213378, mRNA.																		gggaggaaagaaattgagggc	0.129													3	3	---	---	---	---	PASS
C9orf89	84270	broad.mit.edu	37	9	95874559	95874559	+	Missense_Mutation	SNP	T	A	A	rs147126180		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95874559T>A	uc004atd.2	+	5	602	c.424T>A	c.(424-426)TGC>AGC	p.C142S	C9orf89_uc004ate.2_RNA|C9orf89_uc004atf.2_RNA	NM_032310	NP_115686	Q96LW7	BINCA_HUMAN	chromosome 9 open reading frame 89	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					negative regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|nucleus	CARD domain binding				0						GCTCCTGTACTGCTATCCGCC	0.667													4	31	---	---	---	---	PASS
FBP1	2203	broad.mit.edu	37	9	97382755	97382755	+	Silent	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97382755A>G	uc004auw.3	-	2	520	c.189T>C	c.(187-189)TCT>TCC	p.S63S	FBP1_uc010mrl.2_Silent_p.S63S	NM_000507	NP_000498	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1	63					gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)	TCACGTTGGTAGAACCAGCAA	0.453													4	79	---	---	---	---	PASS
C9orf84	158401	broad.mit.edu	37	9	114476772	114476772	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114476772A>T	uc004bfr.2	-	15	2311	c.2176T>A	c.(2176-2178)TTG>ATG	p.L726M	C9orf84_uc011lwt.1_RNA|C9orf84_uc004bfq.2_Missense_Mutation_p.L687M|C9orf84_uc010mug.2_Missense_Mutation_p.L637M	NM_173521	NP_775792	Q5VXU9	CI084_HUMAN	hypothetical protein LOC158401 isoform 1	726										ovary(2)	2						TGACATTGCAATTCTTGTATC	0.368													15	589	---	---	---	---	PASS
ST6GALNAC4	27090	broad.mit.edu	37	9	130678772	130678772	+	5'UTR	SNP	A	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130678772A>C	uc004bss.2	-	2					ST6GALNAC4_uc004bst.2_Intron	NM_175039	NP_778204	Q9H4F1	SIA7D_HUMAN	sialyltransferase 7D isoform a						glycolipid metabolic process|protein glycosylation	integral to Golgi membrane|nucleus|soluble fraction	(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity				0						GGAGCCGGGCACCTGCCAAGA	0.617													5	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	29079435	29079435	+	RNA	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29079435G>T	uc001iuk.1	-	2		c.2640C>A								Homo sapiens mRNA; cDNA DKFZp434F083 (from clone DKFZp434F083).																		CCACACTAAAGATCATTCTTG	0.463													6	68	---	---	---	---	PASS
ERCC6	2074	broad.mit.edu	37	10	50713893	50713893	+	Intron	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50713893G>T	uc001jhs.3	-						ERCC6_uc001jhr.3_5'UTR	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent						base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding			lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1)	16						ATAATGGCTTGATAGCAAATA	0.343								Direct_reversal_of_damage|NER					8	144	---	---	---	---	PASS
SUPV3L1	6832	broad.mit.edu	37	10	70949126	70949126	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70949126T>C	uc001jpe.1	+	5	731	c.676T>C	c.(676-678)TCT>CCT	p.S226P	SUPV3L1_uc010qjd.1_Missense_Mutation_p.S95P	NM_003171	NP_003162	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 precursor	226	Helicase ATP-binding.				DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2						CTCAGCAAAGTCTGGAGTGTA	0.408													5	164	---	---	---	---	PASS
FAM160B1	57700	broad.mit.edu	37	10	116621368	116621368	+	3'UTR	SNP	A	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116621368A>C	uc001lcb.2	+	17					FAM160B1_uc001lcc.2_Intron	NM_020940	NP_065991	Q5W0V3	F16B1_HUMAN	hypothetical protein LOC57700 isoform a											lung(1)	1						ACTCAGTTCCACCCAGCCACA	0.383													10	30	---	---	---	---	PASS
RRM1	6240	broad.mit.edu	37	11	4133183	4133183	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4133183G>A	uc001lyw.3	+	7	860	c.541G>A	c.(541-543)GAA>AAA	p.E181K	RRM1_uc009yeh.1_Missense_Mutation_p.E84K|RRM1_uc009yei.2_Missense_Mutation_p.E141K|RRM1_uc010qyc.1_Missense_Mutation_p.E84K	NM_001033	NP_001024	P23921	RIR1_HUMAN	ribonucleoside-diphosphate reductase M1 chain	181					deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	GATCCACAAAGAAGACATTGA	0.418													26	180	---	---	---	---	PASS
OR52I1	390037	broad.mit.edu	37	11	4616186	4616186	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4616186G>C	uc010qyi.1	+	1	918	c.918G>C	c.(916-918)GAG>GAC	p.E306D		NM_001005169	NP_001005169	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I,	306	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		AATTGCTGGAGGGAATATGGA	0.468													8	48	---	---	---	---	PASS
CCKBR	887	broad.mit.edu	37	11	6290923	6290923	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6290923C>T	uc001mcp.2	+	2	369	c.176C>T	c.(175-177)ACT>ATT	p.T59I	CCKBR_uc001mcq.2_5'UTR|CCKBR_uc001mcr.2_Missense_Mutation_p.T59I|CCKBR_uc001mcs.2_Missense_Mutation_p.T59I	NM_176875	NP_795344	P32239	GASR_HUMAN	cholecystokinin B receptor	59	Helical; Name=1; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	ATTAGAATCACTCTTTACGCA	0.527													6	54	---	---	---	---	PASS
ELP4	26610	broad.mit.edu	37	11	31541630	31541630	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31541630T>C	uc001mtb.2	+	2	286	c.251T>C	c.(250-252)CTT>CCT	p.L84P	ELP4_uc001mta.1_RNA|ELP4_uc001mtc.2_Missense_Mutation_p.L84P|ELP4_uc010rdz.1_Missense_Mutation_p.L84P	NM_019040	NP_061913	Q96EB1	ELP4_HUMAN	elongation protein 4 homolog	84					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)					GGAACAGTTCTTCTAATTGGT	0.318													74	664	---	---	---	---	PASS
RNASEH2C	84153	broad.mit.edu	37	11	65488243	65488243	+	5'UTR	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65488243C>T	uc001ofn.2	-	1					RNASEH2C_uc001ofm.2_5'Flank	NM_032193	NP_115569	Q8TDP1	RNH2C_HUMAN	ribonuclease H2, subunit C						RNA catabolic process	nucleus|ribonuclease H2 complex					0						CCCTCCTACGCGACGCCAGGG	0.706													2	2	---	---	---	---	PASS
PCF11	51585	broad.mit.edu	37	11	82877319	82877319	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82877319A>G	uc001ozx.3	+	5	1725	c.1380A>G	c.(1378-1380)ATA>ATG	p.I460M	PCF11_uc010rsu.1_Missense_Mutation_p.I460M	NM_015885	NP_056969	O94913	PCF11_HUMAN	pre-mRNA cleavage complex II protein Pcf11	460					mRNA 3'-end processing|mRNA cleavage|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage factor complex				ovary(1)	1						AGGATACAATAACAGAAGAGT	0.383													5	105	---	---	---	---	PASS
GRM5	2915	broad.mit.edu	37	11	88781056	88781056	+	5'UTR	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88781056C>A	uc001pcq.2	-	1					GRM5_uc009yvm.2_5'UTR|GRM5_uc009yvn.1_5'UTR	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	GAAAGGAGTTCAAGCCAATAA	0.463													4	20	---	---	---	---	PASS
ALG9	79796	broad.mit.edu	37	11	111741006	111741006	+	Silent	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111741006A>G	uc001pmb.2	-	3	318	c.219T>C	c.(217-219)GCT>GCC	p.A73A	ALG9_uc001ply.2_5'UTR|ALG9_uc001plz.2_5'UTR|ALG9_uc010rwm.1_Silent_p.A73A|ALG9_uc010rwn.1_Intron|ALG9_uc010rwo.1_5'UTR|ALG9_uc009yyh.1_5'UTR	NM_001077690	NP_001071158	Q9H6U8	ALG9_HUMAN	asparagine-linked glycosylation 9 protein	73	Lumenal (Potential).				dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity			large_intestine(1)|ovary(1)	2		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)		TGCTCAGGAGAGCAGCACATA	0.428													4	70	---	---	---	---	PASS
TNFRSF1A	7132	broad.mit.edu	37	12	6443404	6443404	+	Silent	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6443404G>A	uc001qnu.2	-	2	327	c.46C>T	c.(46-48)CTG>TTG	p.L16L	TNFRSF1A_uc001qnt.2_5'UTR|TNFRSF1A_uc010sey.1_5'UTR|TNFRSF1A_uc010sez.1_Intron|TNFRSF1A_uc009zek.2_Silent_p.L16L|TNFRSF1A_uc010sfa.1_Silent_p.L16L	NM_001065	NP_001056	P19438	TNR1A_HUMAN	tumor necrosis factor receptor 1 precursor	16					apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|inflammatory response|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of inflammatory response|positive regulation of transcription from RNA polymerase II promoter|prostaglandin metabolic process	extracellular region|integral to plasma membrane|membrane raft	tumor necrosis factor receptor activity			lung(2)|skin(1)	3						AACAGCTCCAGGAGCACCTGG	0.522													5	88	---	---	---	---	PASS
PRB1	5542	broad.mit.edu	37	12	11506350	11506350	+	Silent	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11506350C>T	uc001qzw.1	-	4	724	c.687G>A	c.(685-687)CAG>CAA	p.Q229Q	PRB1_uc001qzu.1_Intron|PRB1_uc001qzv.1_Intron	NM_005039	NP_005030	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1 isoform 1	290	12.|15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].		Missing (in clone CP-4).|Missing (in clone CP-5).			extracellular region					0			OV - Ovarian serous cystadenocarcinoma(49;0.185)			GACCTTGGGGCTGGTTGCCTC	0.602													8	10	---	---	---	---	PASS
ATF7IP	55729	broad.mit.edu	37	12	14577910	14577910	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14577910C>T	uc001rbw.2	+	2	1219	c.1061C>T	c.(1060-1062)ACA>ATA	p.T354I	ATF7IP_uc010shs.1_Missense_Mutation_p.T354I|ATF7IP_uc001rbu.2_Missense_Mutation_p.T354I|ATF7IP_uc001rbv.1_Missense_Mutation_p.T354I|ATF7IP_uc001rbx.2_Missense_Mutation_p.T354I|ATF7IP_uc010sht.1_Missense_Mutation_p.T354I|ATF7IP_uc001rby.3_Missense_Mutation_p.T354I|ATF7IP_uc001rbz.1_Missense_Mutation_p.T354I|ATF7IP_uc001rca.2_Missense_Mutation_p.T354I|ATF7IP_uc001rcb.2_5'Flank	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	354	Glu-rich.				DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5						ACTCTAGAAACAGATGATACA	0.338													9	76	---	---	---	---	PASS
KRT7	3855	broad.mit.edu	37	12	52629134	52629134	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52629134G>T	uc001saa.1	+	2	647	c.520G>T	c.(520-522)GAG>TAG	p.E174*	KRT7_uc009zmf.1_Nonsense_Mutation_p.E174*	NM_005556	NP_005547	P08729	K2C7_HUMAN	keratin 7	174	Rod.|Coil 1B.				cytoskeleton organization|DNA replication|interphase|interspecies interaction between organisms|regulation of translation	Golgi apparatus|keratin filament|nucleus	protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.105)		GGATGTGGTGGAGGACTTCAA	0.627													10	70	---	---	---	---	PASS
KRT6C	286887	broad.mit.edu	37	12	52865858	52865858	+	Silent	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52865858G>T	uc001sal.3	-	2	795	c.747C>A	c.(745-747)CTC>CTA	p.L249L		NM_173086	NP_775109	P48668	K2C6C_HUMAN	keratin 6C	249	Coil 1B.|Rod.			L -> F (in Ref. 1; AAC41769).	cytoskeleton organization	keratin filament	structural molecule activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.0828)		ACTTGTTCTTGAGGTCCTCCA	0.552													5	70	---	---	---	---	PASS
PAN2	9924	broad.mit.edu	37	12	56713467	56713467	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56713467G>A	uc001skx.2	-	22	3413	c.3040C>T	c.(3040-3042)CGG>TGG	p.R1014W	PAN2_uc001skw.2_Missense_Mutation_p.R162W|PAN2_uc001skz.2_Missense_Mutation_p.R1013W|PAN2_uc001sky.2_Missense_Mutation_p.R1010W	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	1014	Exonuclease.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process	cytosol|nucleus	nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity			ovary(2)|skin(2)|large_intestine(1)|breast(1)	6						CCCTGGCCCCGAACACAGGTA	0.493													4	173	---	---	---	---	PASS
MDM1	56890	broad.mit.edu	37	12	68720392	68720392	+	Intron	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68720392G>A	uc001stz.2	-						MDM1_uc010stc.1_Intron|MDM1_uc009zqv.1_Intron|MDM1_uc001sua.3_Silent_p.F181F|MDM1_uc010std.1_3'UTR	NM_017440	NP_059136	Q8TC05	MDM1_HUMAN	mouse Mdm1 nuclear protein homolog isoform 1							nucleus				ovary(3)|skin(2)	5			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		TGAAACCAATGAAGAATTCTA	0.313													16	163	---	---	---	---	PASS
BBS10	79738	broad.mit.edu	37	12	76740157	76740157	+	Silent	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76740157A>G	uc001syd.1	-	2	1692	c.1608T>C	c.(1606-1608)TAT>TAC	p.Y536Y		NM_024685	NP_078961	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	536					cellular protein metabolic process|nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	cilium	ATP binding			ovary(1)|skin(1)	2						ATGGTTCATAATAATCAGTTA	0.348									Bardet-Biedl_syndrome				27	310	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88496844	88496844	+	Intron	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-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													11	17	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88512291	88512291	+	Silent	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88512291A>G	uc001tar.2	-	17	2024	c.1680T>C	c.(1678-1680)GCT>GCC	p.A560A	CEP290_uc001tat.2_Silent_p.A322A|CEP290_uc009zsl.1_RNA	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	560	Potential.				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						CTCTTTCTTGAGCCATTTGAC	0.303													6	287	---	---	---	---	PASS
EEA1	8411	broad.mit.edu	37	12	93202807	93202807	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93202807T>A	uc001tck.2	-	18	2590	c.2325A>T	c.(2323-2325)GAA>GAT	p.E775D		NM_003566	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1, 162kD	775	Potential.				early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3						CCTTCTCCATTTCAAGTTGTT	0.348													46	313	---	---	---	---	PASS
FBXO21	23014	broad.mit.edu	37	12	117595706	117595706	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117595706A>G	uc001twk.2	-	10	1549	c.1510T>C	c.(1510-1512)TCC>CCC	p.S504P	FBXO21_uc001twj.2_Missense_Mutation_p.S497P|FBXO21_uc009zwq.2_Missense_Mutation_p.S437P|FBXO21_uc001twl.1_Missense_Mutation_p.S117P	NM_033624	NP_296373	O94952	FBX21_HUMAN	F-box only protein 21 isoform 1	504					ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			kidney(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)		AGCCCGATGGAGTAGCAGACA	0.562													5	101	---	---	---	---	PASS
KLHDC1	122773	broad.mit.edu	37	14	50206889	50206889	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50206889G>A	uc001www.2	+	11	998	c.970G>A	c.(970-972)GCC>ACC	p.A324T	SDCCAG1_uc010anj.1_Intron|KLHDC1_uc010tqg.1_Missense_Mutation_p.A279T|KLHDC1_uc010tqh.1_Missense_Mutation_p.A239T	NM_172193	NP_751943	Q8N7A1	KLDC1_HUMAN	kelch domain containing 1	324	Kelch 6.					cytoplasm				pancreas(1)	1	all_epithelial(31;0.00244)|Breast(41;0.00964)					TGACTTACTTGCCTTGGATAC	0.333													34	199	---	---	---	---	PASS
C14orf37	145407	broad.mit.edu	37	14	58471373	58471373	+	3'UTR	SNP	T	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58471373T>G	uc001xdc.2	-	8					C14orf37_uc010tro.1_3'UTR	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						ATGTGGCAGGTTGTTCTTTTT	0.383													9	35	---	---	---	---	PASS
KIAA0586	9786	broad.mit.edu	37	14	58954623	58954623	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58954623T>C	uc001xdv.3	+	22	3368	c.3095T>C	c.(3094-3096)ATC>ACC	p.I1032T	KIAA0586_uc010trr.1_Missense_Mutation_p.I1149T|KIAA0586_uc001xdt.3_Missense_Mutation_p.I1064T|KIAA0586_uc001xdu.3_Missense_Mutation_p.I1093T|KIAA0586_uc010trs.1_Missense_Mutation_p.I1023T|KIAA0586_uc010trt.1_Missense_Mutation_p.I968T|KIAA0586_uc010tru.1_Missense_Mutation_p.I968T	NM_014749	NP_055564	E9PGW8	E9PGW8_HUMAN	talpid3 protein	1032										ovary(1)	1						ATGCCTGCCATCATGCTTGTT	0.393													5	205	---	---	---	---	PASS
ATP6V1D	51382	broad.mit.edu	37	14	67805178	67805178	+	3'UTR	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67805178G>A	uc001xjf.2	-	9					ATP6V1D_uc001xje.2_Intron	NM_015994	NP_057078	Q9Y5K8	VATD_HUMAN	H(+)-transporting two-sector ATPase						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting two-sector ATPase complex, catalytic domain|vacuolar proton-transporting V-type ATPase complex	protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)|lung(1)	2				all cancers(60;0.000739)|OV - Ovarian serous cystadenocarcinoma(108;0.00597)|BRCA - Breast invasive adenocarcinoma(234;0.00957)		GCTAAATTATGATTCTGCAAA	0.333													3	12	---	---	---	---	PASS
UBR7	55148	broad.mit.edu	37	14	93693406	93693406	+	3'UTR	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93693406C>A	uc001ybm.3	+	11					UBR7_uc001ybn.3_3'UTR|UBR7_uc010auq.2_3'UTR	NM_175748	NP_786924	Q8N806	UBR7_HUMAN	ubiquitin protein ligase E3 component n-recognin								ubiquitin-protein ligase activity|zinc ion binding				0						CTTTCTCATTCAAGCCAATGA	0.463													9	81	---	---	---	---	PASS
MIR665	100126315	broad.mit.edu	37	14	101341381	101341381	+	RNA	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101341381G>T	hsa-mir-665|MI0005563	+			c.12G>T																				0						CTCCTCGAGGGGTCTCTGCCT	0.612													5	73	---	---	---	---	PASS
GJD2	57369	broad.mit.edu	37	15	35044996	35044996	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35044996G>T	uc001zis.1	-	2	649	c.649C>A	c.(649-651)CAA>AAA	p.Q217K	uc001zit.1_5'Flank	NM_020660	NP_065711	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	217	Helical; (Potential).				synaptic transmission	connexon complex|integral to membrane	gap junction channel activity				0		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		AGAAAATATTGGCCAACCAGG	0.488													8	102	---	---	---	---	PASS
DUOX2	50506	broad.mit.edu	37	15	45402703	45402703	+	Silent	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45402703G>A	uc010bea.2	-	9	1166	c.963C>T	c.(961-963)GAC>GAT	p.D321D	DUOX2_uc001zun.2_Silent_p.D321D	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	321	Extracellular (Potential).|Peroxidase-like; mediates peroxidase activity (By similarity).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		AGATGCTGGGGTCTAGGAAAG	0.582													4	54	---	---	---	---	PASS
IGDCC3	9543	broad.mit.edu	37	15	65628159	65628159	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65628159T>A	uc002aos.2	-	3	797	c.545A>T	c.(544-546)GAC>GTC	p.D182V		NM_004884	NP_004875	Q8IVU1	IGDC3_HUMAN	putative neuronal cell adhesion molecule	182	Extracellular (Potential).|Ig-like C2-type 2.									ovary(3)	3						CCTCTCATTGTCCGTGTCAAT	0.592													14	131	---	---	---	---	PASS
CYP1A2	1544	broad.mit.edu	37	15	75047169	75047169	+	Missense_Mutation	SNP	C	T	T	rs28399424	byFrequency	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75047169C>T	uc002ayr.1	+	7	1355	c.1291C>T	c.(1291-1293)CGG>TGG	p.R431W		NM_000761	NP_000752	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A,	431					alkaloid metabolic process|exogenous drug catabolic process|methylation|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative deethylation|oxidative demethylation|steroid catabolic process|toxin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|caffeine oxidase activity|demethylase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding			ovary(3)|breast(1)	4					Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Aciclovir(DB00787)|Alosetron(DB00969)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Anagrelide(DB00261)|Azelastine(DB00972)|Bortezomib(DB00188)|Caffeine(DB00201)|Carmustine(DB00262)|Chlordiazepoxide(DB00475)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Clomipramine(DB01242)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Desloratadine(DB00967)|Diazepam(DB00829)|Dibucaine(DB00527)|Diclofenac(DB00586)|Duloxetine(DB00476)|Enoxacin(DB00467)|Esomeprazole(DB00736)|Estradiol(DB00783)|Estrone(DB00655)|Fluorouracil(DB00544)|Flutamide(DB00499)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Grepafloxacin(DB00365)|Haloperidol(DB00502)|Hesperetin(DB01094)|Imipramine(DB00458)|Ketoconazole(DB01026)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Melatonin(DB01065)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mirtazapine(DB00370)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pefloxacin(DB00487)|Pimozide(DB01100)|Propafenone(DB01182)|Propranolol(DB00571)|Quinidine(DB00908)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifampin(DB01045)|Riluzole(DB00740)|Rofecoxib(DB00533)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Tacrine(DB00382)|Telithromycin(DB00976)|Terfenadine(DB00342)|Theophylline(DB00277)|Thiabendazole(DB00730)|Tizanidine(DB00697)|Tolbutamide(DB01124)|Verapamil(DB00661)|Warfarin(DB00682)|Zileuton(DB00744)|Zolmitriptan(DB00315)	CCGGCCTGAGCGGTTCCTCAC	0.617													4	44	---	---	---	---	PASS
SEC11A	23478	broad.mit.edu	37	15	85213235	85213235	+	3'UTR	SNP	A	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85213235A>T	uc002blb.1	-	6					SEC11A_uc002blc.1_3'UTR	NM_014300	NP_055115	P67812	SC11A_HUMAN	SEC11-like 1						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	endoplasmic reticulum membrane|integral to membrane|microsome	protein binding|serine-type peptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(143;0.199)			TCCCAGGAACAGCAAGGCAGG	0.448													15	209	---	---	---	---	PASS
ITPRIPL2	162073	broad.mit.edu	37	16	19127313	19127313	+	Silent	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19127313C>T	uc002dfu.3	+	1	2060	c.1530C>T	c.(1528-1530)TAC>TAT	p.Y510Y	ITPRIPL2_uc002dft.2_Silent_p.Y206Y	NM_001034841	NP_001030013	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-triphosphate receptor interacting	510	Cytoplasmic (Potential).					integral to membrane				skin(2)	2						TCCGGGCCTACGGGGGTCCCC	0.677													4	40	---	---	---	---	PASS
KIAA0556	23247	broad.mit.edu	37	16	27629751	27629751	+	Silent	SNP	C	T	T	rs144603611		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27629751C>T	uc002dow.2	+	3	93	c.69C>T	c.(67-69)TAC>TAT	p.Y23Y		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	23										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						TTCAGGGTTACGCTAAGGACA	0.502													4	152	---	---	---	---	PASS
PHKB	5257	broad.mit.edu	37	16	47698832	47698832	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47698832A>C	uc002eev.3	+	25	2425	c.2373A>C	c.(2371-2373)AAA>AAC	p.K791N	PHKB_uc002eeu.3_Intron|PHKB_uc002eew.3_5'Flank	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a	791	Calmodulin-binding (Potential).				glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				TTACCCAGAAATTTTCTTCCT	0.438													27	215	---	---	---	---	PASS
FTSJD1	55783	broad.mit.edu	37	16	71319019	71319019	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71319019C>T	uc010cga.2	-	3	1211	c.805G>A	c.(805-807)GGT>AGT	p.G269S	FTSJD1_uc002ezy.3_Missense_Mutation_p.G269S|FTSJD1_uc002ezz.3_Missense_Mutation_p.G269S	NM_001099642	NP_001093112	Q8IYT2	FTSJ1_HUMAN	FtsJ methyltransferase domain containing 1	269						integral to membrane	methyltransferase activity|nucleic acid binding			skin(1)	1						AAAGAGCCACCGTTTCCAAGA	0.388													18	110	---	---	---	---	PASS
PKD1L3	342372	broad.mit.edu	37	16	71978060	71978060	+	Silent	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71978060C>T	uc010vmm.1	-	24	3732	c.3732G>A	c.(3730-3732)TCG>TCA	p.S1244S		NM_181536	NP_853514			polycystin 1-like 3 precursor												0						CTGGTACTGACGAAGAACATT	0.383													9	454	---	---	---	---	PASS
ELAC2	60528	broad.mit.edu	37	17	12897814	12897814	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12897814T>C	uc002gnz.3	-	22	2131	c.2036A>G	c.(2035-2037)GAT>GGT	p.D679G	ELAC2_uc002gnu.3_Missense_Mutation_p.D76G|ELAC2_uc002gnv.3_Missense_Mutation_p.D307G|ELAC2_uc002gnw.3_Missense_Mutation_p.D335G|ELAC2_uc002gnx.3_Missense_Mutation_p.D439G|ELAC2_uc010vvo.1_Missense_Mutation_p.D477G|ELAC2_uc010vvp.1_Missense_Mutation_p.D660G|ELAC2_uc010vvq.1_Missense_Mutation_p.D678G|ELAC2_uc010vvr.1_Missense_Mutation_p.D639G	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1	679					tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0						GAGGGTGGCATCTTTCCCTGG	0.552									Hereditary_Prostate_Cancer				5	206	---	---	---	---	PASS
DHRS13	147015	broad.mit.edu	37	17	27225663	27225663	+	Silent	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27225663C>T	uc002hde.3	-	5	1057	c.930G>A	c.(928-930)CTG>CTA	p.L310L	FLOT2_uc002hdc.2_5'Flank|DHRS13_uc002hdd.3_Silent_p.L260L|DHRS13_uc010wba.1_Silent_p.L229L|uc002hdf.2_RNA	NM_144683	NP_653284	Q6UX07	DHR13_HUMAN	dehydrogenase/reductase (SDR family) member 13	310						extracellular region	binding|oxidoreductase activity				0	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.59e-06)|all cancers(11;9.27e-06)|BRCA - Breast invasive adenocarcinoma(11;5.78e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)			CAAGCCCTGCCAGCCTCTTGC	0.627													3	18	---	---	---	---	PASS
TMIGD1	388364	broad.mit.edu	37	17	28656364	28656364	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28656364A>G	uc002hfa.1	-	3	339	c.266T>C	c.(265-267)GTC>GCC	p.V89A	TMIGD1_uc010csh.1_Missense_Mutation_p.V89A	NM_206832	NP_996663	Q6UXZ0	TMIG1_HUMAN	transmembrane and immunoglobulin domain	89	Extracellular (Potential).|Ig-like C2-type 1.					integral to membrane					0						GATGGAAGAGACACAGACAGA	0.488													5	171	---	---	---	---	PASS
ACLY	47	broad.mit.edu	37	17	40054059	40054059	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40054059C>A	uc002hyg.2	-	13	1535	c.1372G>T	c.(1372-1374)GAG>TAG	p.E458*	ACLY_uc002hyh.2_Nonsense_Mutation_p.E458*|ACLY_uc002hyi.2_Nonsense_Mutation_p.E512*|ACLY_uc010wfx.1_Nonsense_Mutation_p.E512*|ACLY_uc010wfy.1_Nonsense_Mutation_p.E197*	NM_001096	NP_001087	P53396	ACLY_HUMAN	ATP citrate lyase isoform 1	458				SES -> YESMVDEV (in Ref. 1; CAA45614).	ATP catabolic process|cellular carbohydrate metabolic process|citrate metabolic process|coenzyme A metabolic process|energy reserve metabolic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	citrate lyase complex|cytosol|nucleus	ATP binding|ATP citrate synthase activity|citrate (pro-3S)-lyase activity|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			ovary(2)|central_nervous_system(1)	3		Breast(137;0.000143)				GCCCTGGACTCAGAAAAAGAT	0.567													10	75	---	---	---	---	PASS
PSME3	10197	broad.mit.edu	37	17	40986168	40986168	+	Intron	SNP	T	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40986168T>G	uc002ibr.2	+						PSME3_uc002ibp.2_Intron|PSME3_uc002ibq.2_Intron|PSME3_uc002ibs.2_5'UTR|PSME3_uc010whd.1_Intron	NM_005789	NP_005780	P61289	PSME3_HUMAN	proteasome activator subunit 3 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome activator complex	endopeptidase activator activity|identical protein binding|MDM2 binding|p53 binding				0		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		GACAGGCAGGTGCTGTCCTCA	0.468													6	7	---	---	---	---	PASS
NBR1	4077	broad.mit.edu	37	17	41345527	41345527	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41345527C>A	uc010czd.2	+	12	1536	c.1396C>A	c.(1396-1398)CAG>AAG	p.Q466K	NBR1_uc010diz.2_Missense_Mutation_p.Q466K|NBR1_uc010whu.1_Missense_Mutation_p.Q466K|NBR1_uc010whv.1_Missense_Mutation_p.Q466K|NBR1_uc010whw.1_Missense_Mutation_p.Q445K|NBR1_uc010whx.1_Missense_Mutation_p.Q275K	NM_031862	NP_114068	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	466					macroautophagy|protein oligomerization	autophagic vacuole|cytoplasmic vesicle|cytosol|late endosome|lysosome|sarcomere	ubiquitin binding|zinc ion binding			skin(1)	1		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		TCACAAAGGCCAGCAATTTGG	0.522													16	113	---	---	---	---	PASS
TEX14	56155	broad.mit.edu	37	17	56676681	56676681	+	Silent	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56676681G>T	uc010dcz.1	-	14	2161	c.2043C>A	c.(2041-2043)GGC>GGA	p.G681G	TEX14_uc002iwr.1_Silent_p.G675G|TEX14_uc002iws.1_Silent_p.G675G|TEX14_uc010dda.1_Silent_p.G455G	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a	681						cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CATCCTCACTGCCAAAACAAC	0.478													8	188	---	---	---	---	PASS
LAMA3	3909	broad.mit.edu	37	18	21508604	21508604	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21508604T>C	uc002kuq.2	+	64	8397	c.8311T>C	c.(8311-8313)TCA>CCA	p.S2771P	LAMA3_uc002kur.2_Missense_Mutation_p.S2715P|LAMA3_uc002kus.3_Missense_Mutation_p.S1162P|LAMA3_uc002kut.3_Missense_Mutation_p.S1106P	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	2771	Laminin G-like 3.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GCGATCTGCCTCATTCTCCAG	0.438													21	133	---	---	---	---	PASS
CIRBP	1153	broad.mit.edu	37	19	1271824	1271824	+	Intron	SNP	T	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1271824T>G	uc002lrr.3	+						C19orf23_uc010xgk.1_5'Flank|CIRBP_uc010dsg.1_3'UTR|CIRBP_uc002lrt.2_Intron|CIRBP_uc010xgl.1_Intron|CIRBP_uc002lrv.3_Intron|CIRBP_uc002lru.2_Intron	NM_001280	NP_001271	Q14011	CIRBP_HUMAN	cold inducible RNA binding protein						mRNA stabilization|positive regulation of translation|response to cold|response to UV|stress granule assembly	nucleoplasm|stress granule	mRNA 3'-UTR binding|nucleotide binding|protein binding|SSU rRNA binding|translation repressor activity				0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GACAGGCTGGTGGAGATTTTG	0.627													5	8	---	---	---	---	PASS
SAFB	6294	broad.mit.edu	37	19	5648215	5648215	+	Intron	SNP	A	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5648215A>C	uc002mcf.2	+						SAFB_uc010xiq.1_3'UTR|SAFB_uc002mcg.2_Intron|SAFB_uc002mce.3_Intron|SAFB_uc010xir.1_Intron|SAFB_uc010xis.1_Intron|SAFB_uc010xit.1_Intron|SAFB_uc010xiu.1_Intron	NM_002967	NP_002958	Q15424	SAFB1_HUMAN	scaffold attachment factor B						chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GAGATTGGAAACCCAGCCATA	0.333													6	6	---	---	---	---	PASS
OR7G1	125962	broad.mit.edu	37	19	9225926	9225926	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9225926C>T	uc002mks.1	-	1	514	c.514G>A	c.(514-516)GTT>ATT	p.V172I		NM_001005192	NP_001005192	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G,	172	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2						GGGATTTCAACGTTTTTGCAG	0.453													7	95	---	---	---	---	PASS
SMARCA4	6597	broad.mit.edu	37	19	11132522	11132522	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11132522C>A	uc002mqf.3	+	19	3022	c.2738C>A	c.(2737-2739)CCG>CAG	p.P913Q	SMARCA4_uc010dxp.2_Missense_Mutation_p.P913Q|SMARCA4_uc010dxo.2_Missense_Mutation_p.P913Q|SMARCA4_uc002mqg.1_Missense_Mutation_p.P913Q|SMARCA4_uc010dxq.2_Missense_Mutation_p.P913Q|SMARCA4_uc010dxr.2_Missense_Mutation_p.P913Q|SMARCA4_uc002mqj.3_Missense_Mutation_p.P913Q|SMARCA4_uc010dxs.2_Missense_Mutation_p.P913Q|SMARCA4_uc010dxt.1_Missense_Mutation_p.P133Q|SMARCA4_uc002mqh.3_Missense_Mutation_p.P36Q|SMARCA4_uc002mqi.1_Missense_Mutation_p.P116Q	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	913	Helicase ATP-binding.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				ACGGGCACACCGCTGCAGAAC	0.612			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				3	30	---	---	---	---	PASS
PRKCSH	5589	broad.mit.edu	37	19	11558317	11558317	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11558317C>T	uc002mrt.2	+	11	1249	c.913C>T	c.(913-915)CCG>TCG	p.P305S	PRKCSH_uc002mru.2_Missense_Mutation_p.P305S|PRKCSH_uc010xlz.1_Missense_Mutation_p.P305S|PRKCSH_uc010dya.2_Intron|PRKCSH_uc002mrv.1_Missense_Mutation_p.P305S|PRKCSH_uc010dyb.2_Missense_Mutation_p.P305S	NM_002743	NP_002734	P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H isoform 1	305					innate immune response|intracellular protein kinase cascade|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen	calcium ion binding|protein kinase C binding				0						GGAGGAGCAGCCGCCAGTGCC	0.448													3	20	---	---	---	---	PASS
ZNF700	90592	broad.mit.edu	37	19	12058344	12058344	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12058344A>G	uc002msu.2	+	3	332	c.206A>G	c.(205-207)GAC>GGC	p.D69G	ZNF700_uc010xme.1_Missense_Mutation_p.D87G|ZNF763_uc010xmf.1_Intron	NM_144566	NP_653167	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	69	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AAATGGAGTGACCAGAACATT	0.348													8	385	---	---	---	---	PASS
C19orf62	29086	broad.mit.edu	37	19	17387524	17387524	+	Intron	SNP	T	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17387524T>G	uc002nfu.2	+						C19orf62_uc010xpl.1_3'UTR|C19orf62_uc002nfv.2_Intron|C19orf62_uc010ean.2_Intron|C19orf62_uc002nfw.2_Intron	NM_014173	NP_054892	Q9NWV8	BABA1_HUMAN	mediator of Rap80 interactions and targeting 40						chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of DNA repair|protein K63-linked deubiquitination|response to ionizing radiation	BRCA1-A complex|BRISC complex|cytoplasm	protein binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2						GAGGCTGGGGTGCCTAGAGGT	0.602													12	64	---	---	---	---	PASS
ZNF101	94039	broad.mit.edu	37	19	19791111	19791111	+	3'UTR	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19791111A>G	uc002nni.1	+	4					ZNF101_uc010ecg.1_3'UTR|ZNF101_uc002nnj.1_3'UTR	NM_033204	NP_149981	Q8IZC7	ZN101_HUMAN	zinc finger protein 101						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						ggagtttgagaccagcctggg	0.100													4	92	---	---	---	---	PASS
ZNF90	7643	broad.mit.edu	37	19	20236202	20236202	+	RNA	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20236202G>A	uc002nos.1	+	5		c.878G>A			ZNF90_uc002not.1_RNA			Q03938	ZNF90_HUMAN	Synthetic construct DNA, clone: pF1KB9685, Homo sapiens ZNF90 gene for zinc finger protein 90, without stop codon, in Flexi system.							Golgi apparatus|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2						CAGTATGACCGGACCCTGCTG	0.522													3	44	---	---	---	---	PASS
PLA2G4C	8605	broad.mit.edu	37	19	48608631	48608631	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48608631C>A	uc002phx.2	-	3	477	c.79G>T	c.(79-81)GTG>TTG	p.V27L	PLA2G4C_uc002phw.2_5'UTR|PLA2G4C_uc010elr.2_Missense_Mutation_p.V27L|PLA2G4C_uc010xzd.1_Missense_Mutation_p.V37L|PLA2G4C_uc002phy.3_Missense_Mutation_p.V27L	NM_003706	NP_003697	Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC isoform 1 precursor	27	PLA2c.				arachidonic acid metabolic process|glycerophospholipid catabolic process|inflammatory response|intracellular signal transduction|parturition	cytosol|membrane	calcium-independent phospholipase A2 activity|phospholipid binding			ovary(1)|skin(1)	2		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		GCTTTCAGCACATGAAGTCTT	0.527													19	122	---	---	---	---	PASS
KLK3	354	broad.mit.edu	37	19	51363165	51363165	+	3'UTR	SNP	T	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51363165T>A	uc002pts.1	+	5					KLK3_uc010ycj.1_Intron|KLK3_uc002ptr.1_Intron|KLK3_uc010eof.1_Intron	NM_001030047	NP_001025218	P07288	KLK3_HUMAN	prostate specific antigen isoform 3						negative regulation of angiogenesis|proteolysis	extracellular region	serine-type endopeptidase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		GTCTGAAAGATAGGATTGCCC	0.517													8	115	---	---	---	---	PASS
ZNF577	84765	broad.mit.edu	37	19	52375740	52375740	+	3'UTR	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52375740A>G	uc010yde.1	-	7					ZNF577_uc010ydd.1_Intron|ZNF577_uc002pxx.3_3'UTR|ZNF577_uc002pxv.2_3'UTR|ZNF577_uc002pxw.2_3'UTR	NM_032679	NP_116068	Q9BSK1	ZN577_HUMAN	zinc finger protein 577 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TAATGGCTGGAGGATTCCTAC	0.398													10	30	---	---	---	---	PASS
C20orf186	149954	broad.mit.edu	37	20	31671267	31671267	+	Silent	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31671267T>C	uc010zue.1	+	3	279	c.264T>C	c.(262-264)GGT>GGC	p.G88G		NM_182519	NP_872325	P59827	LPLC4_HUMAN	antimicrobial peptide RY2G5 precursor	88						cytoplasm|extracellular region	lipid binding				0						ACCAGTATGGTCACATTGAGA	0.507													4	68	---	---	---	---	PASS
C20orf114	92747	broad.mit.edu	37	20	31890880	31890880	+	Silent	SNP	C	T	T	rs6088166		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31890880C>T	uc002wyw.1	+	11	1301	c.1140C>T	c.(1138-1140)ATC>ATT	p.I380I	C20orf114_uc002wyx.1_RNA	NM_033197	NP_149974	Q8TDL5	LPLC1_HUMAN	LPLUNC1 protein precursor	380						extracellular space	lipid binding			central_nervous_system(2)|skin(2)	4						CCCTGGGCATCGTGAGTTCAG	0.517													3	54	---	---	---	---	PASS
SAMHD1	25939	broad.mit.edu	37	20	35526278	35526278	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35526278C>T	uc002xgh.1	-	15	1823	c.1693G>A	c.(1693-1695)GCA>ACA	p.A565T	SAMHD1_uc010gft.1_RNA	NM_015474	NP_056289	Q9Y3Z3	SAMH1_HUMAN	SAM domain- and HD domain-containing protein 1	565					defense response to virus|innate immune response|regulation of innate immune response	nucleus	metal ion binding|phosphoric diester hydrolase activity				0		Myeloproliferative disorder(115;0.00878)				TATTGTCTTGCGGCATACAAA	0.383													15	219	---	---	---	---	PASS
PARD6B	84612	broad.mit.edu	37	20	49366295	49366295	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49366295A>G	uc002xvo.2	+	3	632	c.389A>G	c.(388-390)CAT>CGT	p.H130R		NM_032521	NP_115910	Q9BYG5	PAR6B_HUMAN	PAR-6 beta	130	Interaction with PARD3 and CDC42 (By similarity).				axonogenesis|cell cycle|cell division|establishment or maintenance of cell polarity|protein complex assembly|regulation of cell migration|tight junction assembly	cytosol|tight junction	protein binding			kidney(1)	1						AAAAAGCCACATATAGTCATT	0.403													12	101	---	---	---	---	PASS
KRTAP10-10	353333	broad.mit.edu	37	21	46057376	46057376	+	Silent	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46057376T>C	uc002zfq.2	+	1	104	c.42T>C	c.(40-42)ACT>ACC	p.T14T	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_181688	NP_859016	P60014	KR10A_HUMAN	keratin associated protein 10-10	14						keratin filament					0						GCGCCTGCACTGACTCTTGGC	0.582													4	48	---	---	---	---	PASS
CABIN1	23523	broad.mit.edu	37	22	24432627	24432627	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24432627C>G	uc002zzi.1	+	3	221	c.94C>G	c.(94-96)CAG>GAG	p.Q32E	CABIN1_uc002zzj.1_Missense_Mutation_p.Q32E|CABIN1_uc002zzl.1_Missense_Mutation_p.Q32E|CABIN1_uc010guk.1_Missense_Mutation_p.Q32E|CABIN1_uc002zzk.1_Missense_Mutation_p.Q32E	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	32					cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						AAAGGAGGCTCAGGTACGTAA	0.433													17	188	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38119859	38119859	+	Silent	SNP	C	T	T	rs66505048		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38119859C>T	uc003atr.2	+	7	1567	c.1296C>T	c.(1294-1296)TGC>TGT	p.C432C	TRIOBP_uc003atu.2_Silent_p.C260C|TRIOBP_uc003atq.1_Silent_p.C432C|TRIOBP_uc003ats.1_Silent_p.C260C	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	432					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)					GAACATCCTGCGCCCAGCGGG	0.582													5	286	---	---	---	---	PASS
XPNPEP3	63929	broad.mit.edu	37	22	41310325	41310325	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41310325G>A	uc003azh.2	+	7	1144	c.1052G>A	c.(1051-1053)GGC>GAC	p.G351D	XPNPEP3_uc003azi.2_Missense_Mutation_p.G272D|XPNPEP3_uc011aoy.1_RNA	NM_022098	NP_071381	Q9NQH7	XPP3_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 3,	351					cellular process	mitochondrion	aminopeptidase activity|manganese ion binding|metallopeptidase activity				0						CCAGTCAATGGCAGGTAGGGC	0.443													19	149	---	---	---	---	PASS
RBX1	9978	broad.mit.edu	37	22	41368620	41368620	+	3'UTR	SNP	G	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-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													19	101	---	---	---	---	PASS
MOV10L1	54456	broad.mit.edu	37	22	50558941	50558941	+	Nonsense_Mutation	SNP	C	T	T	rs150693045	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50558941C>T	uc003bjj.2	+	10	1548	c.1465C>T	c.(1465-1467)CGA>TGA	p.R489*	MOV10L1_uc003bjk.3_Nonsense_Mutation_p.R489*|MOV10L1_uc011arp.1_Nonsense_Mutation_p.R469*|MOV10L1_uc011arq.1_Nonsense_Mutation_p.R250*|MOV10L1_uc010hao.1_Intron	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1	489					germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GAACTCAAGACGACAACTTCC	0.348													28	160	---	---	---	---	PASS
FRMPD4	9758	broad.mit.edu	37	X	12734955	12734955	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12734955G>A	uc004cuz.1	+	15	2883	c.2377G>A	c.(2377-2379)GAC>AAC	p.D793N	FRMPD4_uc011mij.1_Missense_Mutation_p.D785N	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	793					positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13						AGAAGGTGATGACAATGAGGA	0.557													7	32	---	---	---	---	PASS
MAP7D2	256714	broad.mit.edu	37	X	20074911	20074911	+	Splice_Site	SNP	T	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20074911T>C	uc004czr.1	-	4	392	c.373_splice	c.e4-1	p.E125_splice	MAP7D2_uc004czq.1_Splice_Site|MAP7D2_uc011mji.1_Splice_Site_p.E81_splice|MAP7D2_uc010nfo.1_Splice_Site_p.E125_splice|MAP7D2_uc011mjj.1_Splice_Site_p.E125_splice|MAP7D2_uc004czs.1_Splice_Site_p.E81_splice	NM_152780	NP_689993	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2											ovary(2)|breast(1)	3						CAGCCGTTCCTACACAGTTCG	0.557													3	18	---	---	---	---	PASS
SLC9A7	84679	broad.mit.edu	37	X	46522060	46522060	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46522060A>C	uc004dgu.1	-	6	820	c.812T>G	c.(811-813)TTT>TGT	p.F271C	SLC9A7_uc004dgv.1_Missense_Mutation_p.F271C	NM_032591	NP_115980	Q96T83	SL9A7_HUMAN	solute carrier family 9, member 7	271	Helical; (Potential).				regulation of pH	Golgi membrane|integral to membrane|recycling endosome membrane|trans-Golgi network	potassium:hydrogen antiporter activity|protein homodimerization activity|sodium:hydrogen antiporter activity			ovary(2)	2						CAATTCATTAAATATCGCCAG	0.413													18	63	---	---	---	---	PASS
ACRC	93953	broad.mit.edu	37	X	70824235	70824235	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70824235G>A	uc004eae.2	+	8	1609	c.1108G>A	c.(1108-1110)GCT>ACT	p.A370T	BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	370						nucleus				ovary(3)	3	Renal(35;0.156)					ATCTGATGATGCTGGTGAGCA	0.493													12	31	---	---	---	---	PASS
TCEAL3	85012	broad.mit.edu	37	X	102864047	102864047	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102864047G>C	uc004ekq.2	+	3	317	c.55G>C	c.(55-57)GAA>CAA	p.E19Q	TCEAL3_uc004ekr.2_Missense_Mutation_p.E19Q	NM_001006933	NP_001006934	Q969E4	TCAL3_HUMAN	transcription elongation factor A (SII)-like 3	19	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						gggaaagccagaagatgaagt	0.199													62	188	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	1913	1913	+	5'Flank	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:1913G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		CCCCCGAAACCAGACGAGCTA	0.438													5	63	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11902	11902	+	RNA	SNP	G	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11902G>A	uc004cov.3	+	1		c.1325G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank|uc004coy.2_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		GAACTCTCTGTGCTAGTAACC	0.443													10	70	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	2626472	2626472	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2626472delC								MMEL1 (61991 upstream) : ACTRT2 (311574 downstream)																							GCACCCTGCACCCCCAGGTGA	0.602													4	2	---	---	---	---	
AJAP1	55966	broad.mit.edu	37	1	4826940	4826940	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4826940delA	uc001alm.1	+						AJAP1_uc001aln.2_Intron	NM_001042478	NP_001035943	Q9UKB5	AJAP1_HUMAN	adherens junction associated protein 1						cell adhesion	adherens junction|apical plasma membrane|basolateral plasma membrane|integral to membrane				lung(1)	1	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)		CAGACAGGTTAAAAAAAATGT	0.478													4	2	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15321376	15321376	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15321376delC	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron|KAZ_uc001avo.2_Intron|KAZ_uc001avp.2_Intron|KAZ_uc001avq.2_Intron|KAZ_uc001avr.2_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						AGAGAAGTAGCCCCCCAGCCC	0.393													4	2	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17199371	17199371	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17199371delG	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GTCTCGCTCCGGTGTACACAG	0.622													4	2	---	---	---	---	
SMAP2	64744	broad.mit.edu	37	1	40883191	40883191	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40883191delG	uc001cfj.2	+						SMAP2_uc001cfk.2_Intron|SMAP2_uc010oji.1_Intron|SMAP2_uc010ojj.1_Intron	NM_022733	NP_073570	Q8WU79	SMAP2_HUMAN	small ArfGAP2						regulation of ARF GTPase activity	cytoplasm|nucleus	ARF GTPase activator activity|zinc ion binding				0	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			aagagaagatggagcaggggc	0.169													4	2	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42037692	42037692	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42037692delA	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron|HIVEP3_uc001cgy.2_Intron	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				gtctaactggaaagggggaga	0.209													4	2	---	---	---	---	
EIF2B3	8891	broad.mit.edu	37	1	45320262	45320262	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45320262delT	uc001cmt.1	-						EIF2B3_uc001cmu.1_Intron|EIF2B3_uc001cmv.1_Intron	NM_020365	NP_065098	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B,						negative regulation of translational initiation in response to stress|oligodendrocyte development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	nucleotidyltransferase activity|protein binding|translation initiation factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					GCATTATGtcttttttttttt	0.204													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58536410	58536410	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58536410delA	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						gcatctctagaaggccaatgg	0.000													4	2	---	---	---	---	
TRIM33	51592	broad.mit.edu	37	1	115015553	115015553	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115015553delA	uc001eew.2	-						TRIM33_uc001eex.2_Intron	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform						negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		gagcagaaacaaaaaaaaaaa	0.005			T	RET	papillary thyroid								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116860087	116860087	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116860087delT								C1orf161 (182226 upstream) : ATP1A1 (54917 downstream)																							gctctttccatttttcctctc	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142546060	142546060	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142546060delT								None (None upstream) : None (None downstream)																							ctcactggggttttttcttgg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142792110	142792110	+	Intron	DEL	T	-	-	rs77134205		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142792110delT	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		CTTAATACTATTTTTTTCTAC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144011657	144011658	+	Intron	INS	-	G	G	rs139895110		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144011657_144011658insG	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		GGttcttttttttgttgtttgt	0.228													4	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144528213	144528214	+	Intron	INS	-	CACT	CACT	rs148652392		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144528213_144528214insCACT	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						gcccaatgatacactgatctat	0.000													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145056057	145056058	+	Intron	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145056057_145056058insA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						ttctGAATTAGAAAAAAAATAT	0.114													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145111729	145111729	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145111729delT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						AGCCTAAGGGTCCTCAGAATA	0.388													4	2	---	---	---	---	
CD244	51744	broad.mit.edu	37	1	160805707	160805707	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160805707delA	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)			TGAGTCCCCTAACCAGGTTTC	0.463													4	2	---	---	---	---	
CD247	919	broad.mit.edu	37	1	167411620	167411620	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167411620delG	uc001gei.3	-						CD247_uc001gej.3_Intron|CD247_uc001gek.2_Intron	NM_198053	NP_932170	P20963	CD3Z_HUMAN	T-cell receptor zeta chain isoform 1 precursor						interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)			gaggccatatgtgggagtgct	0.284											OREG0013971	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
METTL13	51603	broad.mit.edu	37	1	171759883	171759883	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171759883delA	uc001ghz.2	+						METTL13_uc001gia.2_Intron|METTL13_uc001gib.2_Intron|METTL13_uc010pml.1_Intron	NM_015935	NP_057019	Q8N6R0	MTL13_HUMAN	CGI-01 protein isoform 1								methyltransferase activity|protein binding			kidney(1)	1						TCTTCATCTCAACCATGTTAT	0.328													4	2	---	---	---	---	
PAPPA2	60676	broad.mit.edu	37	1	176495219	176495219	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176495219delG	uc001gkz.2	+						PAPPA2_uc001gky.1_Intron|PAPPA2_uc009www.2_Intron	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						TGCTGACTGAGGGCTTACAAT	0.463													4	2	---	---	---	---	
FAM5B	57795	broad.mit.edu	37	1	177238743	177238743	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177238743delT	uc001glf.2	+						FAM5B_uc010pna.1_Intron|FAM5B_uc001glg.2_Intron	NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B							extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6						AATTTGCAGCTTTTTAAAGCA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	196826659	196826659	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196826659delA								CFHR1 (25343 upstream) : CFHR4 (30553 downstream)																							ATTCAGTGATAAAAAAATTTA	0.254													4	2	---	---	---	---	
PIK3C2B	5287	broad.mit.edu	37	1	204433942	204433942	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204433942delC	uc001haw.2	-						PIK3C2B_uc010pqv.1_Intron|PIK3C2B_uc001hax.1_Intron|PIK3C2B_uc009xbd.1_Intron	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta						cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CAAAATGTTTCCCACCATTGA	0.408													4	2	---	---	---	---	
RRP15	51018	broad.mit.edu	37	1	218474910	218474910	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218474910delT	uc001hlj.2	+							NM_016052	NP_057136	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog							mitochondrion|nucleolus	protein binding				0				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)		CTGTAGGTGCTTTTTTTGGTG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232293978	232293979	+	IGR	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232293978_232293979insA								DISC1 (116962 upstream) : SIPA1L2 (239735 downstream)																							tgaatttaaacaaattaacaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8215723	8215723	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8215723delA	uc010eww.1	-											Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																		ttcatttcagaaaaaaaaaaa	0.214													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19514551	19514551	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19514551delA								NT5C1B (743713 upstream) : OSR1 (36696 downstream)																							TTTTAATGAGAAGAGTTGGGT	0.378													4	2	---	---	---	---	
GPN1	11321	broad.mit.edu	37	2	27867512	27867512	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27867512delT	uc010ymc.1	+						GPN1_uc010ezf.2_Intron|GPN1_uc010yma.1_Intron|GPN1_uc010ymb.1_Intron|GPN1_uc010ymd.1_Intron|GPN1_uc010yme.1_Intron|GPN1_uc010ezg.1_Intron	NM_007266	NP_009197	Q9HCN4	GPN1_HUMAN	GPN-loop GTPase 1 isoform a							cytoplasm	GTP binding|nucleoside-triphosphatase activity|protein binding				0						gtcggtgttatttttttcata	0.000													4	2	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29478056	29478056	+	Intron	DEL	G	-	-	rs111589309		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29478056delG	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	ctgggggtgtggagtttctga	0.174			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
PRKD3	23683	broad.mit.edu	37	2	37514520	37514520	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37514520delT	uc002rqd.2	-						PRKD3_uc002rqf.1_Intron	NM_005813	NP_005804	O94806	KPCD3_HUMAN	protein kinase D3						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(2)|ovary(1)|central_nervous_system(1)	4		all_hematologic(82;0.21)				ttttcttcccttttttttctt	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42218079	42218080	+	IGR	DEL	CA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42218079_42218080delCA								None (None upstream) : PKDCC (57081 downstream)																							atgcactcaccacacacacaca	0.139													4	2	---	---	---	---	
ABCG8	64241	broad.mit.edu	37	2	44101866	44101866	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44101866delA	uc002rtq.2	+						ABCG8_uc010yoa.1_Intron	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GAAGGAATCTAAAAAAAAGAA	0.383													4	2	---	---	---	---	
MSH2	4436	broad.mit.edu	37	2	47822619	47822619	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47822619delT	uc002rvz.2	+							NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GCAGTTTTTGTTTTTTTTTTC	0.413			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				2	4	---	---	---	---	
PSME4	23198	broad.mit.edu	37	2	54161510	54161510	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54161510delC	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			GTGAATCCCTCAAAACCCTAG	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58687298	58687298	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58687298delT								FANCL (218783 upstream) : None (None downstream)																							TCTGTGTTTCTTTTTTTTTTC	0.313													4	2	---	---	---	---	
KIAA1841	84542	broad.mit.edu	37	2	61312066	61312066	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61312066delC	uc002saw.3	+						KIAA1841_uc002sax.3_Intron|KIAA1841_uc002say.2_Intron|KIAA1841_uc002sav.3_Intron	NM_001129993	NP_001123465	Q6NSI8	K1841_HUMAN	KIAA1841 protein isoform a												0			Epithelial(17;0.193)			agagaggattccaggataatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66484177	66484177	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66484177delT								SPRED2 (824521 upstream) : MEIS1 (178355 downstream)																							TTTGTTGATATTTTTTATGGG	0.308													4	2	---	---	---	---	
AAK1	22848	broad.mit.edu	37	2	69802507	69802507	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69802507delA	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron|AAK1_uc010fdm.1_Intron	NM_014911	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0						gaaaggtgccaaaaaatctca	0.070													4	2	---	---	---	---	
LRRTM4	80059	broad.mit.edu	37	2	77721715	77721715	+	Intron	DEL	T	-	-	rs113837306		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77721715delT	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		GCTTTTCCCATTTTTTTTTTA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132189217	132189219	+	IGR	DEL	TTG	-	-	rs68144813		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132189217_132189219delTTG								LOC150786 (67486 upstream) : LOC401010 (10515 downstream)																							TTGGTGGGACTTGTTGATGGATT	0.266													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134717466	134717466	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134717466delT								NCKAP5 (391435 upstream) : MGAT5 (294364 downstream)																							TCTGAACATATTTTTTTCTGA	0.438													4	2	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	141457487	141457487	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141457487delA	uc002tvj.1	-							NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TGCCCACTGGAAAAAAAAAAT	0.224										TSP Lung(27;0.18)			4	2	---	---	---	---	
DAPL1	92196	broad.mit.edu	37	2	159650683	159650683	+	5'Flank	DEL	C	-	-	rs2356509	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159650683delC	uc002uaf.2	+							NM_001017920	NP_001017920	A0PJW8	DAPL1_HUMAN	death associated protein-like 1						apoptosis|cell differentiation						0						ccttttttttcttgtcttgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	191888083	191888084	+	IGR	DEL	GT	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191888083_191888084delGT								STAT1 (9107 upstream) : STAT4 (6222 downstream)																							GCACACAtgcgtgtgtgtgtgt	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	208041686	208041687	+	IGR	DEL	GT	-	-	rs112498669		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208041686_208041687delGT								KLF7 (10115 upstream) : MIR1302-4 (92312 downstream)																							TTGAGTGAGGgtgtgtgtgtgt	0.351													2	4	---	---	---	---	
MAP2	4133	broad.mit.edu	37	2	210286250	210286250	+	5'Flank	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210286250delA	uc002vdc.1	+						MAP2_uc002vdd.1_5'Flank	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	TTGCTGAGGGAAAAAAAAAAG	0.308													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	224007920	224007921	+	IGR	DEL	TT	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224007920_224007921delTT								KCNE4 (87567 upstream) : SCG2 (453739 downstream)																							TTATTTCTCCTTTACCTGTAGC	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	224815390	224815391	+	IGR	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224815390_224815391insA								WDFY1 (5338 upstream) : MRPL44 (6730 downstream)																							TGCACACTGACAATGAACTGAC	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	231711420	231711420	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231711420delG								CAB39 (25631 upstream) : ITM2C (18201 downstream)																							tgaagggggcgggggggtggc	0.000													4	2	---	---	---	---	
RAD18	56852	broad.mit.edu	37	3	9007319	9007319	+	5'Flank	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9007319delG	uc003brd.2	-						RAD18_uc003bre.2_5'Flank	NM_020165	NP_064550	Q9NS91	RAD18_HUMAN	postreplication repair protein hRAD18p						DNA repair	nucleus|replication fork	damaged DNA binding|ligase activity|ubiquitin protein ligase binding|Y-form DNA binding|zinc ion binding			skin(3)|ovary(2)	5				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		AACTGAGTGTGGGGCCTGCCC	0.358								Rad6_pathway					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	26045051	26045051	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26045051delT								OXSM (209027 upstream) : LRRC3B (619249 downstream)																							TTTGTACTCATTTTTTTTGTA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	43956738	43956738	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43956738delG								ABHD5 (192522 upstream) : MIR138-1 (198966 downstream)																							CTGTCTAGAAGGGGGTTGGGA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	45314954	45314954	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45314954delG								TMEM158 (47140 upstream) : LARS2 (115121 downstream)																							GTAAAGTGTTGGGATTAGCAA	0.478													4	2	---	---	---	---	
LARS2	23395	broad.mit.edu	37	3	45583635	45583636	+	Intron	INS	-	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45583635_45583636insT	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)	TCAGTTTTGTAGGTCACCACAC	0.520													4	2	---	---	---	---	
SCAP	22937	broad.mit.edu	37	3	47516300	47516300	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47516300delA	uc003crh.1	-						SCAP_uc011baz.1_Intron|SCAP_uc003crg.2_Intron	NM_012235	NP_036367	Q12770	SCAP_HUMAN	SREBF chaperone protein						cholesterol metabolic process|negative regulation of cholesterol biosynthetic process|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane	unfolded protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		acaaacaaacaaaaaacaaGT	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	64354097	64354097	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64354097delA								PRICKLE2 (142966 upstream) : ADAMTS9 (147236 downstream)																							gacactgggtaaaataatccc	0.085													4	2	---	---	---	---	
SUCLG2	8801	broad.mit.edu	37	3	67665677	67665677	+	Intron	DEL	A	-	-	rs68073136		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67665677delA	uc003dna.3	-							NM_003848	NP_003839	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming beta subunit						succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	AGCTACACAGAAAAAAAAAAA	0.433													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	80003942	80003942	+	IGR	DEL	G	-	-	rs77429452		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80003942delG								ROBO1 (186883 upstream) : None (None downstream)																							CGTCCTGAAAGATAAGCCCAA	0.403													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90373417	90373418	+	IGR	DEL	GC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90373417_90373418delGC								EPHA3 (842135 upstream) : None (None downstream)																							aggcctcaaagcactccaaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116272518	116272518	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116272518delG								LSAMP (748500 upstream) : LOC285194 (156117 downstream)																							GGAAGTGAATGGGAGCAGATC	0.418													4	2	---	---	---	---	
LOC100125556	100125556	broad.mit.edu	37	3	125647145	125647145	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125647145delA	uc003eif.3	+						LOC100125556_uc003eid.3_Intron|LOC100125556_uc003eie.3_Intron	NR_024251				Homo sapiens family with sequence similarity 86, member A pseudogene, mRNA (cDNA clone IMAGE:4425123).												0						ATTTCTATGCAAAACCAGATT	0.577													4	2	---	---	---	---	
PLXND1	23129	broad.mit.edu	37	3	129326090	129326090	+	5'Flank	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129326090delC	uc003emx.2	-							NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1						GGCAGCCCCGCCCCCGGCCCT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139030954	139030955	+	IGR	DEL	TG	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139030954_139030955delTG								PISRT1 (78590 upstream) : MRPS22 (31843 downstream)																							ATtgtgtgcctgtgtgtgtgtg	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	164344812	164344813	+	IGR	INS	-	T	T	rs146169293	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164344812_164344813insT								MIR720 (285574 upstream) : SI (351874 downstream)																							tgacagaaaggtaagaattttt	0.089													2	4	---	---	---	---	
SERPINI1	5274	broad.mit.edu	37	3	167453770	167453770	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167453770delA	uc003ffa.3	+						SERPINI1_uc003ffb.3_5'UTR|PDCD10_uc003fex.2_5'Flank|PDCD10_uc003fez.2_5'Flank|PDCD10_uc003fey.2_5'Flank	NM_001122752	NP_001116224	Q99574	NEUS_HUMAN	neuroserpin precursor						central nervous system development|peripheral nervous system development|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(1)	1						CTTTAAGGGCAAAAAAGCAAA	0.423													4	2	---	---	---	---	
LOC220729	220729	broad.mit.edu	37	3	197355699	197355699	+	5'Flank	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197355699delT	uc011bug.1	-						LOC220729_uc003fxw.2_5'Flank|LOC220729_uc003fxy.2_5'Flank|LOC220729_uc010iao.1_5'Flank					Homo sapiens cDNA FLJ60865 complete cds, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1).												0						tttaggattatttttttagat	0.080													4	2	---	---	---	---	
WHSC1	7468	broad.mit.edu	37	4	1881551	1881552	+	Intron	INS	-	TG	TG	rs140755867	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1881551_1881552insTG	uc003gdz.3	+						WHSC1_uc003gdx.2_Intron|WHSC1_uc003gdy.1_Intron|WHSC1_uc010icd.1_Intron	NM_001042424	NP_001035889	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		CCCATGGCACTtgtgtgtgtgt	0.411			T	IGH@	MM								4	2	---	---	---	---	
C4orf48	401115	broad.mit.edu	37	4	2041767	2041768	+	5'Flank	DEL	AG	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2041767_2041768delAG	uc003geo.3	+						C4orf48_uc003gep.3_5'Flank	NM_001141936	NP_001135408			hypothetical protein LOC401115												0						caagtatgacagagagagagag	0.005													4	2	---	---	---	---	
SH3BP2	6452	broad.mit.edu	37	4	2815396	2815397	+	Intron	DEL	TG	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2815396_2815397delTG	uc003gfi.3	+						SH3BP2_uc010icn.2_Intron|SH3BP2_uc011bvp.1_Intron	NM_001122681	NP_001116153	P78314	3BP2_HUMAN	SH3-domain binding protein 2 isoform a						signal transduction		SH3 domain binding|SH3/SH2 adaptor activity			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		CGTTGGAGGCtgtgtgtgtgtg	0.267									Cherubism				4	2	---	---	---	---	
EVC2	132884	broad.mit.edu	37	4	5667051	5667052	+	Intron	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5667051_5667052insA	uc003gij.2	-						EVC2_uc011bwb.1_Intron|EVC2_uc003gik.2_Intron	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin							integral to membrane				large_intestine(3)|ovary(2)	5						tggctcttaagaaaaaaaaaga	0.015													4	2	---	---	---	---	
ABLIM2	84448	broad.mit.edu	37	4	7978043	7978043	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7978043delA	uc003gko.2	-						ABLIM2_uc003gkk.2_Intron|ABLIM2_uc003gkl.2_Intron|ABLIM2_uc003gkj.3_Intron|ABLIM2_uc003gkm.3_Intron|ABLIM2_uc003gkp.2_Intron|ABLIM2_uc003gkq.2_Intron|ABLIM2_uc003gkr.2_Intron|ABLIM2_uc003gki.2_Intron	NM_001130084	NP_001123556	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2						axon guidance|cytoskeleton organization	actin cytoskeleton|cytoplasm|intermediate filament cytoskeleton|nucleus	actin binding|zinc ion binding			pancreas(3)	3						tctcacactcaccagtccaca	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	9118717	9118718	+	IGR	DEL	CT	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9118717_9118718delCT								LOC650293 (166591 upstream) : USP17 (241391 downstream)																							CTCAGGAAGCCTCTCTCTCTCA	0.396													4	2	---	---	---	---	
CPEB2	132864	broad.mit.edu	37	4	15056232	15056232	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15056232delT	uc003gni.1	+						CPEB2_uc003gnj.1_Intron|CPEB2_uc003gnk.1_Intron|CPEB2_uc003gnl.1_Intron|CPEB2_uc003gnm.1_Intron|CPEB2_uc003gnn.1_Intron	NM_182485	NP_872291	Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding						regulation of translation	cytoplasm	nucleotide binding|RNA binding			skin(1)	1						GTTGGGTCTATTTTTTTTTTC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25056295	25056295	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25056295delG								LGI2 (23881 upstream) : SEPSECS (65333 downstream)																							tttgaggagtggaggtggcac	0.000													4	2	---	---	---	---	
APBB2	323	broad.mit.edu	37	4	40855389	40855392	+	Intron	DEL	CCCA	-	-	rs10602335		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40855389_40855392delCCCA	uc003gvl.2	-						APBB2_uc010ifu.2_Intron|APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron|APBB2_uc003gvk.2_Intron	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						ggatcctgtccccacccacctctt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	42283077	42283077	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42283077delA								BEND4 (128182 upstream) : SHISA3 (116779 downstream)																							ACTTTTTAATAAAAAAAAAGT	0.413											OREG0016173	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	4	49101647	49101651	+	IGR	DEL	CATTC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49101647_49101651delCATTC								CWH43 (37554 upstream) : None (None downstream)																							gattccgttgcattccattccattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49648378	49648379	+	IGR	INS	-	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49648378_49648379insC								CWH43 (584285 upstream) : None (None downstream)																							ggaaaggaatgaatggaatgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	65677389	65677390	+	IGR	DEL	TT	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65677389_65677390delTT								TECRL (402211 upstream) : EPHA5 (507892 downstream)																							TATCCTTTTCTTTTTTTTTTAA	0.347													4	2	---	---	---	---	
HPSE	10855	broad.mit.edu	37	4	84231513	84231514	+	Intron	INS	-	T	T	rs141868874		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84231513_84231514insT	uc003hoj.3	-						HPSE_uc010ika.2_Intron|HPSE_uc011ccq.1_Intron|HPSE_uc011ccr.1_Intron|HPSE_uc011ccs.1_Intron|HPSE_uc011cct.1_Intron|HPSE_uc003hok.3_Intron	NM_001098540	NP_001092010	Q9Y251	HPSE_HUMAN	heparanase precursor						carbohydrate metabolic process|cell adhesion|proteoglycan metabolic process	extracellular region|lysosomal membrane|nucleus	beta-glucuronidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Heparin(DB01109)	CAGAGAGAATCTTTTTTTTTTT	0.203													3	3	---	---	---	---	
GRID2	2895	broad.mit.edu	37	4	94252278	94252278	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94252278delC	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)	tgctatctaacccccccccca	0.000													4	2	---	---	---	---	
DKK2	27123	broad.mit.edu	37	4	107909850	107909850	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107909850delA	uc003hyi.2	-						DKK2_uc010ilw.1_Intron|DKK2_uc003hyj.1_Intron	NM_014421	NP_055236	Q9UBU2	DKK2_HUMAN	dickkopf homolog 2 precursor						multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		AACATCGTTTAAAAACTCCCA	0.353													4	2	---	---	---	---	
MAML3	55534	broad.mit.edu	37	4	140831153	140831154	+	Intron	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140831153_140831154insA	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187	Q96JK9	MAML3_HUMAN	mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)					AGCAAAGAGATAAAAAAAAACA	0.332													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	186462994	186462995	+	IGR	DEL	GT	-	-	rs67049240		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186462994_186462995delGT								PDLIM3 (6282 upstream) : SORBS2 (43604 downstream)																							GTGCATGAGGgtgtgtgtgtgt	0.396													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190598416	190598416	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190598416delG								None (None upstream) : FRG1 (263558 downstream)																							CTATCTACGTGTAATAGCGTG	0.393													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190604520	190604520	+	IGR	DEL	G	-	-	rs73876265		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190604520delG								None (None upstream) : FRG1 (257454 downstream)																							ctctcacagagtcacagccac	0.050													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190804733	190804734	+	Intron	INS	-	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190804733_190804734insT	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		CCTTAGACTGATTTTTTCTTAC	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	191044096	191044096	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:191044096delT								LOC653545 (33920 upstream) : None (None downstream)																							agggttagggtggttagggtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	568503	568503	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:568503delT								SLC9A3 (43954 upstream) : CEP72 (43902 downstream)																							CCTTTCCCCCTTTCCCTATCC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3102808	3102809	+	IGR	INS	-	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3102808_3102809insT								C5orf38 (347296 upstream) : IRX1 (493359 downstream)																							CAACGTTTGTGTCTGCCATTGC	0.540													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4288149	4288149	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4288149delC								IRX1 (686633 upstream) : LOC340094 (746323 downstream)																							CACCTTCACACCCCATTTGGA	0.443													4	2	---	---	---	---	
MARCH11	441061	broad.mit.edu	37	5	16090637	16090638	+	Intron	DEL	CC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16090637_16090638delCC	uc003jfo.2	-						MARCH11_uc010itw.1_Intron	NM_001102562	NP_001096032	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11							cytoplasmic vesicle membrane|integral to membrane	ligase activity|zinc ion binding				0						TTTGCATCAGCCAGGACTTCCC	0.421													4	2	---	---	---	---	
LMBRD2	92255	broad.mit.edu	37	5	36109758	36109759	+	Intron	INS	-	AA	AA			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36109758_36109759insAA	uc003jkb.1	-							NM_001007527	NP_001007528	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2							integral to membrane					0	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATACACAAATTTATGTatttat	0.153													4	2	---	---	---	---	
LMBRD2	92255	broad.mit.edu	37	5	36109760	36109761	+	Intron	INS	-	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36109760_36109761insC	uc003jkb.1	-							NM_001007527	NP_001007528	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2							integral to membrane					0	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACACAAATTTATGTatttattc	0.158													4	2	---	---	---	---	
CCNO	10309	broad.mit.edu	37	5	54527724	54527725	+	Intron	INS	-	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54527724_54527725insT	uc003jpw.2	-						CCNO_uc003jpv.2_Intron	NM_021147	NP_066970	P22674	CCNO_HUMAN	cyclin domain containing						cell cycle|cell division|depyrimidination|regulation of cyclin-dependent protein kinase activity	nucleoplasm	protein kinase binding|uracil DNA N-glycosylase activity				0		Lung NSC(810;4.08e-05)|Breast(144;0.0735)|Prostate(74;0.183)	LUSC - Lung squamous cell carcinoma(15;0.142)|Lung(15;0.161)			CGCTTTGCGGCTTCCCGGGCCC	0.678													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	63926547	63926547	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63926547delA								RGS7BP (18428 upstream) : SFRS12IP1 (87433 downstream)																							gagaagtggtaatagaaagta	0.000													4	2	---	---	---	---	
IQGAP2	10788	broad.mit.edu	37	5	75922855	75922856	+	Intron	INS	-	G	G	rs147069484	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75922855_75922856insG	uc003kek.2	+						IQGAP2_uc010izv.2_Intron|IQGAP2_uc011csv.1_Intron|IQGAP2_uc003kel.2_Intron	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		ttctaactgccgggggaagcct	0.000													3	3	---	---	---	---	
BRD8	10902	broad.mit.edu	37	5	137499257	137499257	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137499257delA	uc003lcf.1	-						BRD8_uc003lcc.1_Intron|BRD8_uc011cyl.1_Intron|BRD8_uc003lcg.2_Intron|BRD8_uc003lci.2_Intron|BRD8_uc003lch.2_Intron|BRD8_uc011cym.1_Intron|BRD8_uc010jer.1_Intron|BRD8_uc011cyn.1_Intron	NM_139199	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8 isoform 2						cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			AAAAAGAAAGAAAAAAAAAAG	0.363													3	3	---	---	---	---	
UBE2D2	7322	broad.mit.edu	37	5	139002761	139002761	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139002761delA	uc003ler.2	+						UBE2D2_uc003leq.2_Intron	NM_003339	NP_003330	P62837	UB2D2_HUMAN	ubiquitin-conjugating enzyme E2D 2 isoform 1						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|protein binding|ubiquitin-protein ligase activity			central_nervous_system(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			caattctgctaaaaaaaaaag	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	143153568	143153568	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143153568delT								NR3C1 (338491 upstream) : HMHB1 (38158 downstream)																							AACAAGAAAATTAGTCTGGAA	0.408													4	2	---	---	---	---	
KCTD16	57528	broad.mit.edu	37	5	143573034	143573034	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143573034delC	uc003lnm.1	+							NM_020768	NP_065819	Q68DU8	KCD16_HUMAN	potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			tggctcccctccccagagtct	0.000													4	2	---	---	---	---	
ARHGEF37	389337	broad.mit.edu	37	5	148992606	148992607	+	Intron	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148992606_148992607insA	uc003lra.1	+							NM_001001669	NP_001001669	A1IGU5	ARH37_HUMAN	hypothetical protein LOC389337						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0						GTGGAAAAGGCGGCCTTGCAGA	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	150195064	150195064	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150195064delA								C5orf62 (18767 upstream) : IRGM (31021 downstream)																							gcatttagggaaaacacatag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157500634	157500634	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157500634delT								CLINT1 (214466 upstream) : EBF1 (622290 downstream)																							TAGTTAACTCTTTTTGGTTTG	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	158105504	158105505	+	IGR	DEL	CC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158105504_158105505delCC								CLINT1 (819336 upstream) : EBF1 (17419 downstream)																							TAACTCTCCTCCTGTCCACAGA	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	160431887	160431888	+	IGR	INS	-	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160431887_160431888insT								LOC285629 (66254 upstream) : GABRB2 (283548 downstream)																							tctttatgtgatttttttttat	0.000													4	2	---	---	---	---	
COL23A1	91522	broad.mit.edu	37	5	177679949	177679949	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177679949delG	uc003mje.2	-						COL23A1_uc010jkt.2_Intron	NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	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)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		atcccctgctggcattcaagg	0.318													4	2	---	---	---	---	
ADAMTS2	9509	broad.mit.edu	37	5	178650684	178650685	+	Intron	DEL	CA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178650684_178650685delCA	uc003mjw.2	-						ADAMTS2_uc011dgm.1_Intron	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		tgaatgcactcacacacacGAA	0.094													3	3	---	---	---	---	
ZKSCAN4	387032	broad.mit.edu	37	6	28219924	28219924	+	5'UTR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28219924delA	uc003nks.1	-	1					ZKSCAN4_uc011dlb.1_Intron	NM_019110	NP_061983	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						GATCTCTCTTATAGTCCGTGC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	32769816	32769817	+	IGR	INS	-	A	A	rs148750371	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32769816_32769817insA								HLA-DQB2 (38486 upstream) : HLA-DOB (10724 downstream)																							taatgggcgagaaaaaaaaaag	0.000													4	3	---	---	---	---	
KCNK16	83795	broad.mit.edu	37	6	39291074	39291075	+	5'Flank	DEL	TA	-	-	rs35044542		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39291074_39291075delTA	uc003ooq.2	-						KCNK16_uc003oor.3_5'Flank|KCNK16_uc010jwy.2_5'Flank|KCNK16_uc011dtz.1_5'Flank	NM_032115	NP_115491	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16							integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|skin(1)	3						AAAAAGAAACTATAAGTATATC	0.411													2	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57415142	57415142	+	Intron	DEL	A	-	-	rs11346545		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57415142delA	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)		CTTTTCATTTAAAAAGTATAA	0.338													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	96387109	96387109	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96387109delA								MANEA (329783 upstream) : FUT9 (76736 downstream)																							AATACTTTTGAAAAAAAAAAG	0.284													4	2	---	---	---	---	
KPNA5	3841	broad.mit.edu	37	6	117004040	117004040	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117004040delT	uc003pxh.2	+						uc003pxg.1_5'Flank	NM_002269	NP_002260	O15131	IMA5_HUMAN	karyopherin alpha 5						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)|skin(1)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		ATGGGGCCCCTTTAGAGATAA	0.373													4	2	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	124154297	124154297	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124154297delT	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010kep.1_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		ctagagtcacttttttttgca	0.000													4	2	---	---	---	---	
NCOA7	135112	broad.mit.edu	37	6	126129405	126129405	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126129405delC	uc010kes.2	+						NCOA7_uc003qae.3_Intron|NCOA7_uc003qah.2_Intron|NCOA7_uc003qai.2_Intron|NCOA7_uc010ket.2_Intron|NCOA7_uc003qaf.2_Intron|NCOA7_uc003qag.2_Intron	NM_181782	NP_861447	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7 isoform 1						cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		gcatctccttcccagcccagc	0.000													4	2	---	---	---	---	
MOXD1	26002	broad.mit.edu	37	6	132637077	132637077	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132637077delA	uc003qdf.2	-						MOXD1_uc003qde.2_Intron	NM_015529	NP_056344	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1 isoform 2						catecholamine metabolic process	endoplasmic reticulum membrane|integral to membrane	copper ion binding|dopamine beta-monooxygenase activity			ovary(1)	1	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		GTAGTGACACAATTAAAAATT	0.279													4	2	---	---	---	---	
KIAA1244	57221	broad.mit.edu	37	6	138528519	138528519	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138528519delT	uc003qhu.2	+							NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		CAGATAGGGATTTTTTTTGTG	0.378													4	2	---	---	---	---	
REPS1	85021	broad.mit.edu	37	6	139234280	139234280	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139234280delA	uc003qii.2	-						REPS1_uc003qig.3_Intron|REPS1_uc011edr.1_Intron|REPS1_uc003qij.2_Intron|REPS1_uc003qik.2_Intron	NM_031922	NP_114128	Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1							coated pit|plasma membrane	calcium ion binding|SH3 domain binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		CTAAGACACTAAAAAAAAAAT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	140863864	140863864	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140863864delT								None (None upstream) : None (None downstream)																							TTCAGAATACTTTTTTTTTTT	0.413													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170762091	170762092	+	IGR	DEL	GA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170762091_170762092delGA								FAM120B (47855 upstream) : PSMB1 (18015 downstream)																							atgtgggagtgagggtgtgagt	0.000													4	2	---	---	---	---	
TBP	6908	broad.mit.edu	37	6	170865462	170865465	+	Intron	DEL	TTTA	-	-	rs74850927		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170865462_170865465delTTTA	uc003qxt.2	+						TBP_uc003qxu.2_Intron|TBP_uc011ehf.1_Intron|TBP_uc011ehg.1_5'Flank	NM_003194	NP_003185	P20226	TBP_HUMAN	TATA box binding protein						cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		CTTTTTTTTTTTTAACAGTTTCAT	0.309													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	3273201	3273201	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3273201delT								CARD11 (189622 upstream) : SDK1 (67879 downstream)																							AGGACCATCATTCCCTCATGG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	21018294	21018294	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21018294delA								RPL23P8 (150855 upstream) : SP4 (449395 downstream)																							AACATGCCAGAAACAGTCTTA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36149685	36149685	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36149685delC								SEPT7 (204770 upstream) : EEPD1 (43151 downstream)																							GTTCTGCCTGCCCAGGTCTTT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	39985949	39985949	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39985949delT								LOC349114 (151728 upstream) : CDK13 (4010 downstream)																							TTCACCATCCTTAGCCTGTGC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52912935	52912935	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52912935delC								None (None upstream) : POM121L12 (190414 downstream)																							ggctagatggccccactcctg	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61675493	61675493	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61675493delA								None (None upstream) : None (None downstream)																							TTTTAAAGATAAAAAAAATTC	0.154													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61825793	61825793	+	IGR	DEL	C	-	-	rs111622361		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61825793delC								None (None upstream) : LOC643955 (925879 downstream)																							cctctgcagacttaaatgtcc	0.000													4	2	---	---	---	---	
GTF2IRD1	9569	broad.mit.edu	37	7	74004418	74004418	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74004418delT	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						TGTATGTTGAttttttttttt	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	81230656	81230656	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81230656delG	uc003uhk.1	-											Homo sapiens mRNA sequence.																		tatgtgcaaaggctcagggga	0.000													4	2	---	---	---	---	
SEMA3A	10371	broad.mit.edu	37	7	83690415	83690415	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83690415delT	uc003uhz.2	-							NM_006080	NP_006071	Q14563	SEM3A_HUMAN	semaphorin 3A precursor						axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4						TTCTTGTGTATTTTTAAGTTA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84906100	84906100	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84906100delG								SEMA3D (89929 upstream) : None (None downstream)																							tagcaagtttgggggaaaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98860645	98860646	+	IGR	DEL	CA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98860645_98860646delCA								KPNA7 (55556 upstream) : MYH16 (10278 downstream)																							AAGAGAAGGTCACACAGCCCAG	0.554													4	2	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122337665	122337666	+	Intron	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122337665_122337666insA	uc010lkp.2	-						CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						CAAAATTGCACAAAAAAAATCC	0.312													4	2	---	---	---	---	
DENND2A	27147	broad.mit.edu	37	7	140264938	140264938	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140264938delC	uc010lnj.2	-						DENND2A_uc011kre.1_Intron|DENND2A_uc010lnk.2_Intron|DENND2A_uc003vvw.2_Intron|DENND2A_uc003vvx.2_Intron	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)					GGAAGGCTGGCCTACAAAAGG	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	145700430	145700430	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145700430delC								None (None upstream) : CNTNAP2 (113023 downstream)																							CATTTAGTGTCCGCCATATTC	0.214													4	2	---	---	---	---	
ZNF398	57541	broad.mit.edu	37	7	148824935	148824936	+	Intron	INS	-	C	C	rs147524589	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148824935_148824936insC	uc011kul.1	+						ZNF425_uc003wfj.2_5'Flank	NM_020781	NP_065832	Q8TD17	ZN398_HUMAN	zinc finger 398 isoform b						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			gccctgtcccaccctgaaactc	0.015													1	5	---	---	---	---	
SLC4A2	6522	broad.mit.edu	37	7	150764744	150764744	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150764744delA	uc003wit.3	+						SLC4A2_uc011kve.1_Intron|SLC4A2_uc003wiu.3_Intron	NM_003040	NP_003031	P04920	B3A2_HUMAN	solute carrier family 4, anion exchanger, member						bicarbonate transport	integral to membrane|membrane fraction	inorganic anion exchanger activity				0			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		tgaggtgggtattattcccat	0.134													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	156692519	156692519	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156692519delG								LMBR1 (6617 upstream) : NOM1 (49898 downstream)																							TAATAGGCTTGGGGAGAGGTT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20523565	20523565	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20523565delA								LZTS1 (410762 upstream) : None (None downstream)																							ttgctcatgtaaggatgggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43761695	43761696	+	IGR	INS	-	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43761695_43761696insG								POTEA (543367 upstream) : None (None downstream)																							taaaaactagacagaagcattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	47097433	47097433	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47097433delG								None (None upstream) : BEYLA (655075 downstream)																							ctttctgctagaaacactagt	0.000													4	2	---	---	---	---	
XKR4	114786	broad.mit.edu	37	8	56427259	56427260	+	Intron	INS	-	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56427259_56427260insT	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)			CATTCAGTGTCTTTTTTTTTAA	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61022810	61022810	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61022810delT								TOX (991043 upstream) : CA8 (78613 downstream)																							gtagagctgattttttttttc	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70887776	70887776	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70887776delC								SLCO5A1 (140477 upstream) : PRDM14 (76249 downstream)																							aaaaaggaGACCCCATCTCTA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	82413917	82413917	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82413917delA								FABP4 (18444 upstream) : FABP12 (23366 downstream)																							CAGAAATAAGAAAAAAAAACC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	84418872	84418872	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84418872delC								None (None upstream) : RALYL (676581 downstream)																							cagtgaacgaccccagcttcc	0.000													4	2	---	---	---	---	
SLC30A8	169026	broad.mit.edu	37	8	118184306	118184306	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118184306delA	uc003yoh.2	+						SLC30A8_uc010mcz.2_Intron|SLC30A8_uc011lia.1_Intron|SLC30A8_uc003yog.2_Intron	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8						insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			TTGGGACAGGAAAAAAATGGC	0.423													4	2	---	---	---	---	
MTSS1	9788	broad.mit.edu	37	8	125697792	125697792	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125697792delA	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ataaccttggaaggtaagtca	0.299													4	2	---	---	---	---	
PVT1	5820	broad.mit.edu	37	8	128933200	128933200	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128933200delA	uc010mdq.2	+						PVT1_uc003ysl.2_Intron|PVT1_uc010mdp.1_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0						tcagcgtgccaaaaaaagatc	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144138674	144138674	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144138674delT								C8orf31 (2954 upstream) : LY6H (100658 downstream)																							attatttttattttttttttt	0.159													4	2	---	---	---	---	
KIFC2	90990	broad.mit.edu	37	8	145693523	145693524	+	Intron	DEL	CT	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145693523_145693524delCT	uc003zcz.2	+						CYHR1_uc003zcw.2_5'Flank|CYHR1_uc003zcx.2_5'Flank|CYHR1_uc003zcy.2_5'Flank	NM_145754	NP_665697	Q96AC6	KIFC2_HUMAN	kinesin family member C2						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			ovary(2)|central_nervous_system(1)	3	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GAAGACCCCCCTCTCCGTGGCC	0.663													4	2	---	---	---	---	
FLJ35024	401491	broad.mit.edu	37	9	2530500	2530500	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2530500delT	uc003zhh.1	-						FLJ35024_uc003zhi.2_Intron					Homo sapiens cDNA FLJ35024 fis, clone OCBBF2015233.												0						ttctcttttcttttttttttg	0.010													3	4	---	---	---	---	
ANKRD20A3	441425	broad.mit.edu	37	9	67934624	67934624	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67934624delA	uc004aeu.2	+						ANKRD20A3_uc010mnn.2_Intron	NM_001012419	NP_001012419	Q5VUR7	A20A3_HUMAN	ankyrin repeat domain 20 family, member A3												0						TCCTTTCTGTATTGTATGTTG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68417875	68417881	+	IGR	DEL	TACAATG	-	-	rs67763802		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68417875_68417881delTACAATG								FAM27B (623686 upstream) : MIR1299 (584358 downstream)																							AACACACACATACAATGAGAGCCATTA	0.217													4	2	---	---	---	---	
TLE4	7091	broad.mit.edu	37	9	82271874	82271874	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82271874delT	uc004ald.2	+						TLE4_uc004alc.2_Intron|TLE4_uc010mpr.2_Intron|TLE4_uc004ale.2_Intron|TLE4_uc011lsq.1_Intron|TLE4_uc010mps.2_Intron|TLE4_uc004alf.2_Intron	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4											lung(2)|ovary(1)|breast(1)|skin(1)	5						TATTGATCTCTTTTTCTATAG	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93793875	93793875	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93793875delT								SYK (133042 upstream) : AUH (182224 downstream)																							gtttttgccatttttttaaaa	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	94737707	94737707	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94737707delA								ROR2 (25263 upstream) : SPTLC1 (55713 downstream)																							aaaacaaaacaaaaAaagacc	0.010													4	2	---	---	---	---	
GPR144	347088	broad.mit.edu	37	9	127220643	127220644	+	Intron	DEL	AC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127220643_127220644delAC	uc010mwn.2	+						GPR144_uc004bom.1_Intron	NM_001161808	NP_001155280	Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity				0						CCCCTGCCCAACACACACACAC	0.614													6	3	---	---	---	---	
GOLGA1	2800	broad.mit.edu	37	9	127685120	127685120	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127685120delT	uc004bpc.2	-						GOLGA1_uc010mws.2_Intron|GOLGA1_uc010mwt.1_Intron	NM_002077	NP_002068	Q92805	GOGA1_HUMAN	golgin 97							Golgi cisterna membrane				ovary(1)	1						TATAAGAGAATTTATATACCC	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	135248413	135248414	+	IGR	DEL	TT	-	-	rs111292974		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135248413_135248414delTT								SETX (18041 upstream) : TTF1 (2525 downstream)																							ttgttttttgtttttttttttt	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	764217	764217	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:764217delT								DIP2C (28609 upstream) : LARP4B (91267 downstream)																							TCTCTAGCCCTTCTGTGTCCA	0.597													4	2	---	---	---	---	
GTPBP4	23560	broad.mit.edu	37	10	1061586	1061592	+	Intron	DEL	CTGAGCA	-	-	rs72135483		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1061586_1061592delCTGAGCA	uc001ift.2	+						GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		gtcctgagcgctgagcactgagcctgg	0.101													6	5	---	---	---	---	
LOC100216001	100216001	broad.mit.edu	37	10	4686226	4686226	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4686226delC	uc001ihe.3	-											Homo sapiens, clone IMAGE:4450067, mRNA.												0						ccacactcttcccccacattc	0.000													4	2	---	---	---	---	
CACNB2	783	broad.mit.edu	37	10	18462787	18462787	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18462787delT	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc010qcl.1_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron	NM_201596	NP_963890	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	CTTTTAAATGTTTAGATTTTA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30574710	30574710	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30574710delA								KIAA1462 (170290 upstream) : MTPAP (24021 downstream)																							tggtagagggaaaaaaaacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38945072	38945073	+	IGR	INS	-	G	G	rs138710510		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38945072_38945073insG								LOC399744 (203992 upstream) : None (None downstream)																							aaagaaaaaaaaaGACCAAGTG	0.198													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45114108	45114108	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45114108delT								CXCL12 (233566 upstream) : TMEM72 (292656 downstream)																							TAATCCAGCCTTTTTTTGTCC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	61505656	61505656	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61505656delA	uc001jkr.2	-											Homo sapiens mRNA of muscle specific gene M1.																		GTCCCCTGGcaaaaaaaacca	0.318													4	2	---	---	---	---	
C10orf107	219621	broad.mit.edu	37	10	63444576	63444577	+	Intron	DEL	GT	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63444576_63444577delGT	uc010qik.1	+							NM_173554	NP_775825	Q8IVU9	CJ107_HUMAN	hypothetical protein LOC219621												0	Prostate(12;0.016)					AGGGTGGATAGTGTGTGTGTGG	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80108611	80108612	+	Intron	DEL	CA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80108611_80108612delCA	uc010qlp.1	+						uc001jzw.1_Intron					SubName: Full=cDNA FLJ57363;																		AAATGGGATGCACACACACACA	0.515													4	2	---	---	---	---	
SLIT1	6585	broad.mit.edu	37	10	98943752	98943753	+	Intron	INS	-	CA	CA			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98943752_98943753insCA	uc001kmw.2	-						SLIT1_uc009xvh.1_Intron|ARHGAP19_uc001kmy.2_Intron|SLIT1_uc001kmz.2_Intron	NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		acacaagcattcacacacacac	0.307													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	112926356	112926356	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112926356delG								ADRA2A (85696 upstream) : GPAM (983266 downstream)																							TAGAATAAGCGGAAGGTGAGA	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113853447	113853448	+	IGR	DEL	TC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113853447_113853448delTC								None (None upstream) : GPAM (56174 downstream)																							GGCCACATTGTCTCTCTCTCTC	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	120567950	120567951	+	IGR	INS	-	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120567950_120567951insG								C10orf46 (53192 upstream) : NANOS1 (221277 downstream)																							TGGAATTCACAGGGGGACTCTG	0.535													4	2	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126843972	126843973	+	Intron	INS	-	TT	TT			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126843972_126843973insTT	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		TGAATCCCCCCTTTTTTTTTTT	0.416													4	2	---	---	---	---	
PTPRE	5791	broad.mit.edu	37	10	129817136	129817137	+	Intron	INS	-	CA	CA	rs137995109	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129817136_129817137insCA	uc001lkb.2	+						PTPRE_uc009yat.2_Intron|PTPRE_uc010qup.1_Intron|PTPRE_uc009yau.2_Intron|PTPRE_uc001lkc.1_Intron	NM_006504	NP_006495	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway|protein phosphorylation	cytoplasm|integral to membrane|intermediate filament cytoskeleton|nucleus|plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(1)	1		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)				TCTCTCTCTCTcacacacacac	0.391													1	5	---	---	---	---	
ADM	133	broad.mit.edu	37	11	10323747	10323747	+	5'Flank	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10323747delT	uc001mik.1	+						ADM_uc001mil.1_5'Flank|ADM_uc001mim.1_5'Flank	NM_001124	NP_001115	P35318	ADML_HUMAN	adrenomedullin precursor						blood circulation|cAMP biosynthetic process|female pregnancy|negative regulation of vasoconstriction|progesterone biosynthetic process|response to wounding	cytoplasm|extracellular space|soluble fraction	hormone activity			central_nervous_system(1)	1				all cancers(16;3.51e-65)|Epithelial(150;1.52e-62)|BRCA - Breast invasive adenocarcinoma(625;0.0257)		ATTCTAGTGATTTTTTTTTGT	0.353													4	2	---	---	---	---	
LDHAL6A	160287	broad.mit.edu	37	11	18477953	18477954	+	Intron	INS	-	CT	CT	rs138754091	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18477953_18477954insCT	uc001mop.1	+						LDHAL6A_uc001moq.2_5'UTR	NM_001144071	NP_001137543	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A						glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)	CTGTTCCTTTCCTCTCTCTCTC	0.554													2	4	---	---	---	---	
NAV2	89797	broad.mit.edu	37	11	19884318	19884318	+	Intron	DEL	A	-	-	rs75590756		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19884318delA	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						ACAGGTGGACAAAAAAAAGAA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	22618614	22618614	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22618614delC								SLC17A6 (217570 upstream) : FANCF (25465 downstream)																							gcaacacacaccccaccagca	0.000													4	2	---	---	---	---	
C11orf41	25758	broad.mit.edu	37	11	33643345	33643346	+	Intron	INS	-	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33643345_33643346insC	uc001mup.3	+							NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758							integral to membrane				ovary(2)	2						CATTAAATCATCCCCCAGAAAG	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	34623012	34623013	+	IGR	DEL	CA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34623012_34623013delCA								ELF5 (87682 upstream) : EHF (19655 downstream)																							AGGAGCTGTTCAAGGGTGGTCT	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93932944	93932947	+	IGR	DEL	TGAT	-	-	rs137910271		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93932944_93932947delTGAT								PANX1 (17809 upstream) : FOLR4 (105856 downstream)																							GTTGATTAACTGATTGATTGATTC	0.407													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	110367871	110367871	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110367871delA								FDX1 (32267 upstream) : ARHGAP20 (79895 downstream)																							CTTCATGGAGAAGGTGGGGCT	0.453													4	2	---	---	---	---	
PKNOX2	63876	broad.mit.edu	37	11	125271114	125271115	+	Intron	DEL	AG	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125271114_125271115delAG	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron	NM_022062	NP_071345	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		GAAAAGAGCAAGAGAGAGAGAC	0.490													4	2	---	---	---	---	
GLB1L2	89944	broad.mit.edu	37	11	134242023	134242023	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134242023delG	uc001qhp.2	+						GLB1L2_uc009zdg.1_Intron	NM_138342	NP_612351	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2 precursor						carbohydrate metabolic process	extracellular region	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(1)|pancreas(1)|skin(1)	3	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		ATGTCTGCTTGGGGGGGCGGC	0.552													4	2	---	---	---	---	
GPRC5A	9052	broad.mit.edu	37	12	13065680	13065680	+	3'UTR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13065680delT	uc001rba.2	+	4					uc001rbb.3_5'Flank	NM_003979	NP_003970	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, family C, group 5,							cytoplasmic vesicle membrane|Golgi apparatus|integral to plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)	CGCTGTAGTATTTTTTTTTTT	0.398													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	28137531	28137532	+	IGR	INS	-	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28137531_28137532insG								PTHLH (12615 upstream) : CCDC91 (194678 downstream)																							GTCATAGGAAAGGGGGAAAAAA	0.401													4	2	---	---	---	---	
IPO8	10526	broad.mit.edu	37	12	30836988	30836988	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30836988delT	uc001rjd.2	-							NM_006390	NP_006381	O15397	IPO8_HUMAN	importin 8						intracellular protein transport|signal transduction	cytoplasm|nucleus	protein transporter activity|Ran GTPase binding			skin(2)|central_nervous_system(1)	3	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					TTAAGTATCATTTTTTTTAAA	0.294													4	2	---	---	---	---	
PCBP2	5094	broad.mit.edu	37	12	53848896	53848896	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53848896delT	uc001sdl.3	+						PCBP2_uc001sdc.3_Intron|PCBP2_uc001sdb.3_Intron|PCBP2_uc001sde.3_Intron|PCBP2_uc001sdi.3_Intron|PCBP2_uc001sdd.3_Intron|PCBP2_uc001sdf.3_Intron|PCBP2_uc009zna.2_Intron|PCBP2_uc010soh.1_Intron|PCBP2_uc009zmz.1_Intron	NM_001128911	NP_001122383	Q15366	PCBP2_HUMAN	poly(rC) binding protein 2 isoform d						innate immune response|negative regulation of defense response to virus|negative regulation of type I interferon production|nuclear mRNA splicing, via spliceosome|proteasomal ubiquitin-dependent protein catabolic process|response to virus	cytosol|nucleoplasm|ribonucleoprotein complex	DNA binding|RNA binding|ubiquitin protein ligase binding				0						GATGGTAAGGTTTTTCTCATG	0.423													4	2	---	---	---	---	
HSD17B6	8630	broad.mit.edu	37	12	57168091	57168091	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57168091delA	uc001smg.1	+							NM_003725	NP_003716	O14756	H17B6_HUMAN	hydroxysteroid (17-beta) dehydrogenase 6						androgen biosynthetic process|androgen catabolic process	early endosome membrane|endoplasmic reticulum|microsome	binding|electron carrier activity|estradiol 17-beta-dehydrogenase activity|retinol dehydrogenase activity|testosterone 17-beta-dehydrogenase (NAD+) activity			upper_aerodigestive_tract(1)|pancreas(1)	2					Succinic acid(DB00139)	tcccttatataaaatagtgca	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	74260817	74260817	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74260817delT								None (None upstream) : ATXN7L3B (670734 downstream)																							caaaatatgcttttacatgca	0.075													4	2	---	---	---	---	
MGAT4C	25834	broad.mit.edu	37	12	86738495	86738496	+	Intron	DEL	GG	-	-	rs35983368		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86738495_86738496delGG	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						ATCTCTTCTCGgtgtgtgtgtg	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92596576	92596576	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92596576delT								BTG1 (56903 upstream) : CLLU1OS (217294 downstream)																							cttctatcccttttctctctt	0.254													4	2	---	---	---	---	
CLLU1OS	574016	broad.mit.edu	37	12	92819004	92819005	+	Intron	DEL	TG	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92819004_92819005delTG	uc001tcb.1	-						CLLU1_uc001tcc.2_Intron|CLLU1_uc001tcd.2_Intron|CLLU1_uc001tce.1_Intron|CLLU1_uc001tcf.2_RNA	NM_001025232	NP_001020403	Q5K130	CLU1O_HUMAN	chronic lymphocytic leukemia up-regulated 1												0						tgtgtgtgtatgtgtgtgtgtg	0.292													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	100213663	100213663	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100213663delA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		ggagaacaagaaaaaaaggga	0.095													4	2	---	---	---	---	
ANO4	121601	broad.mit.edu	37	12	101199562	101199563	+	Intron	INS	-	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101199562_101199563insT	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.2_Intron	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						AGGGATCTCACTTTTTTTTTAT	0.248										HNSCC(74;0.22)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	101818527	101818528	+	IGR	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101818527_101818528insA								ARL1 (16955 upstream) : SPIC (50671 downstream)																							CATTTTGGATTaaaaaaaaaat	0.203													2	4	---	---	---	---	
NUAK1	9891	broad.mit.edu	37	12	106503934	106503934	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106503934delC	uc001tlj.1	-							NM_014840	NP_055655	O60285	NUAK1_HUMAN	AMPK-related protein kinase 5								ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2						AAAAAGCAATCCCAGGAGCAT	0.463													4	2	---	---	---	---	
RIC8B	55188	broad.mit.edu	37	12	107236159	107236159	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107236159delT	uc001tlx.2	+						RIC8B_uc001tlw.2_Intron|RIC8B_uc001tly.2_Intron|RIC8B_uc001tlz.2_Intron|RIC8B_uc009zur.2_Intron	NM_018157	NP_060627	Q9NVN3	RIC8B_HUMAN	resistance to inhibitors of cholinesterase 8						regulation of G-protein coupled receptor protein signaling pathway	cell cortex|cytosol|plasma membrane	G-protein alpha-subunit binding|guanyl-nucleotide exchange factor activity			ovary(1)	1						TCAACATTTGTTTTTTTTCTA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127915576	127915576	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127915576delT								LOC100128554 (958246 upstream) : TMEM132C (983715 downstream)																							AAGGCTCCCATTTTTTTGCCT	0.438													4	2	---	---	---	---	
TMEM132C	92293	broad.mit.edu	37	12	128932662	128932664	+	Intron	DEL	TTG	-	-	rs6486643	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128932662_128932664delTTG	uc001uhs.3	+							NM_001136103	NP_001129575	Q8N3T6	T132C_HUMAN	transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1						ACAATTTTTTTTGTTGTTGTTGT	0.227													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131379900	131379901	+	IGR	DEL	GT	-	-	rs67224987		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131379900_131379901delGT								RAN (19076 upstream) : GPR133 (58551 downstream)																							TGGTGCTTACgtgtgtgtgtgt	0.292													5	3	---	---	---	---	
GPR133	283383	broad.mit.edu	37	12	131538655	131538655	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131538655delA	uc001uit.3	+						GPR133_uc010tbm.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)		TACAAACAATAAAAAAAACaa	0.259													4	2	---	---	---	---	
UBL3	5412	broad.mit.edu	37	13	30356462	30356463	+	Intron	INS	-	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30356462_30356463insC	uc001usp.2	-							NM_007106	NP_009037	O95164	UBL3_HUMAN	ubiquitin-like 3 precursor							intracellular|plasma membrane					0		Lung SC(185;0.0281)		all cancers(112;0.0598)|GBM - Glioblastoma multiforme(144;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.147)		TTAACTGGGTTCCTGCCACAAA	0.282													4	2	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	49033658	49033658	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49033658delC	uc001vcb.2	+							NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(6)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	tcataataaaccagtaaacat	0.124		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			14	12	---	---	---	---	
FNDC3A	22862	broad.mit.edu	37	13	49748887	49748888	+	Intron	INS	-	AT	AT			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49748887_49748888insAT	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		CACAGGAAACATTAAACTTACA	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	50446372	50446372	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50446372delG								KPNA3 (79315 upstream) : LOC220429 (18173 downstream)																							GTGGTGGCTTGGAGCTCTGGT	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85092840	85092841	+	IGR	INS	-	T	T	rs148018828	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85092840_85092841insT								SLITRK1 (636312 upstream) : None (None downstream)																							ttagggcatggttagagtagca	0.074													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	100228579	100228580	+	IGR	INS	-	G	G	rs141509022	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100228579_100228580insG								TM9SF2 (13303 upstream) : CLYBL (30356 downstream)																							TGATTGGGGGAGGGGGAGCCTA	0.520													3	3	---	---	---	---	
TMCO3	55002	broad.mit.edu	37	13	114192428	114192429	+	Intron	INS	-	TTC	TTC			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114192428_114192429insTTC	uc001vtu.3	+							NM_017905	NP_060375	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3							integral to membrane	solute:hydrogen antiporter activity				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			gcatgtatgtgtttgtgcatgc	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	44211241	44211241	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44211241delT								None (None upstream) : FSCB (762114 downstream)																							ctgctacaccttttttttttc	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	54260812	54260812	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54260812delG								DDHD1 (640766 upstream) : BMP4 (155645 downstream)																							ACATAGAAATGGAGACTTAGA	0.338													4	2	---	---	---	---	
SIPA1L1	26037	broad.mit.edu	37	14	72072787	72072788	+	Intron	INS	-	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72072787_72072788insG	uc001xms.2	+						SIPA1L1_uc001xmt.2_Intron|SIPA1L1_uc001xmu.2_Intron|SIPA1L1_uc001xmv.2_Intron|SIPA1L1_uc010ttm.1_Intron	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like						actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		ctggctatggtgggcaggggct	0.000													4	2	---	---	---	---	
YLPM1	56252	broad.mit.edu	37	14	75288138	75288138	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75288138delA	uc001xqj.3	+						YLPM1_uc001xql.3_Intron|YLPM1_uc001xqm.1_3'UTR	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		ATTACATATGAAAGGGCATTC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	78520068	78520068	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78520068delT								ADCK1 (119772 upstream) : NRXN3 (116860 downstream)																							AAGGAAAGCCTTTGGCTGTAT	0.562													4	2	---	---	---	---	
GTF2A1	2957	broad.mit.edu	37	14	81676222	81676222	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81676222delG	uc001xvf.1	-						GTF2A1_uc010atb.1_5'UTR|GTF2A1_uc001xvg.1_Intron|GTF2A1_uc001xvh.1_Intron	NM_015859	NP_056943	P52655	TF2AA_HUMAN	TFIIA alpha, p55 isoform 1						regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|transcription factor TFIIA complex	DNA binding|protein binding|protein heterodimerization activity|TBP-class protein binding|transcription coactivator activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0287)		ACCACACAAAGTCTACCATTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	89528558	89528559	+	IGR	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89528558_89528559insA								TTC8 (184224 upstream) : FOXN3 (93958 downstream)																							catctcacatgaaaaaagggac	0.040													4	2	---	---	---	---	
C14orf159	80017	broad.mit.edu	37	14	91624669	91624669	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91624669delT	uc001xzb.2	+						C14orf159_uc010atu.1_Intron|C14orf159_uc010atv.1_Intron|C14orf159_uc001xyy.2_Intron|C14orf159_uc001xyx.2_Intron|C14orf159_uc001xyw.2_Intron|C14orf159_uc001xzc.2_Intron|C14orf159_uc001xza.2_Intron|C14orf159_uc001xyv.2_Intron|C14orf159_uc001xyz.2_Intron|C14orf159_uc010twj.1_Intron|C14orf159_uc001xze.2_Intron	NM_001102366	NP_001095836	Q7Z3D6	CN159_HUMAN	hypothetical protein LOC80017 isoform a							mitochondrion				central_nervous_system(2)|ovary(1)	3		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CAGCACCCCCTCCCACTAGCC	0.542													4	2	---	---	---	---	
SERPINA1	5265	broad.mit.edu	37	14	94845675	94845675	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94845675delG	uc001ycx.3	-						SERPINA1_uc001ycw.3_Intron|SERPINA1_uc010auw.2_Intron|SERPINA1_uc010aux.2_Intron|SERPINA1_uc001ycy.3_Intron|SERPINA1_uc010auy.2_Intron|SERPINA1_uc001ycz.3_Intron|SERPINA1_uc010auz.2_Intron|SERPINA1_uc010ava.2_Intron|SERPINA1_uc001ydb.3_Intron|SERPINA1_uc010avb.2_Intron|SERPINA1_uc001ydc.3_Intron|SERPINA1_uc001yda.1_3'UTR	NM_000295	NP_000286	P01009	A1AT_HUMAN	serine proteinase inhibitor, clade A, member 1						acute-phase response|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen|proteinaceous extracellular matrix	protease binding|serine-type endopeptidase inhibitor activity			skin(1)	1		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)	Alpha-1-proteinase inhibitor(DB00058)	GGCATCTTCAGGAGCTCAGCC	0.592									Alpha-1-Antitrypsin_Deficiency				4	2	---	---	---	---	
NF1P1	440225	broad.mit.edu	37	15	22147571	22147571	+	5'Flank	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22147571delA	uc010tzs.1	-											Human NF1-related locus DNA in A9 mouse DNA background.												0						TCTATCAGTCAAAAAAAAGTA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	29064371	29064372	+	IGR	DEL	CA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29064371_29064372delCA								WHAMML2 (40086 upstream) : APBA2 (66796 downstream)																							ACAGTGAGGTCACAGAAATGAT	0.381													4	2	---	---	---	---	
NDNL2	56160	broad.mit.edu	37	15	29560840	29560840	+	3'UTR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29560840delA	uc001zco.2	-	1					FAM189A1_uc010azk.1_Intron	NM_138704	NP_619649	Q96MG7	MAGG1_HUMAN	necdin-like 2						regulation of growth	cytoplasm|nucleus					0		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		ACACAACATTAAAAAAACAAA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	29930138	29930139	+	IGR	INS	-	T	T	rs144450446	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29930138_29930139insT								FAM189A1 (67211 upstream) : TJP1 (62220 downstream)																							tgaagatggtcggagttattgt	0.188													3	3	---	---	---	---	
C15orf41	84529	broad.mit.edu	37	15	37029621	37029622	+	Intron	DEL	TG	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37029621_37029622delTG	uc001zje.3	+						C15orf41_uc001zjd.2_Intron|C15orf41_uc010bbb.1_Intron|C15orf41_uc001zjf.2_Intron|C15orf41_uc010uci.1_Intron	NM_001130010	NP_001123482	Q9Y2V0	CO041_HUMAN	hypothetical protein LOC84529 isoform 1								protein binding			pancreas(1)	1		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		GCCACCGTAATGTGACATGATA	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62534752	62534753	+	RNA	INS	-	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62534752_62534753insT	uc002ain.1	-	11		c.2894_2895insA			uc002aio.2_5'Flank|uc002aip.2_5'Flank|uc002air.1_5'Flank|uc002ais.2_5'Flank|uc002ait.2_5'Flank|uc002aiu.2_5'Flank|uc002aiv.2_5'Flank|uc002aix.1_5'Flank|uc002aiy.2_5'Flank|uc002aiz.1_5'Flank|uc002aja.2_5'Flank|uc002ajb.2_5'Flank|uc002ajc.2_5'Flank|uc002ajd.2_5'Flank|uc002aje.2_5'Flank|uc002ajf.2_5'Flank|uc010uhn.1_5'Flank|uc002ajg.1_5'Flank					Homo sapiens cDNA FLJ38723 fis, clone KIDNE2010137, weakly similar to GOLGIN-95.																		TTTCCCATAACTTTTTTTTTTT	0.322													4	2	---	---	---	---	
CLPX	10845	broad.mit.edu	37	15	65442904	65442904	+	3'UTR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65442904delT	uc002aom.2	-	14					CLPX_uc010uiu.1_RNA	NM_006660	NP_006651	O76031	CLPX_HUMAN	ClpX caseinolytic protease X homolog precursor						protein folding|proteolysis involved in cellular protein catabolic process	mitochondrial endopeptidase Clp complex|mitochondrial inner membrane|mitochondrial nucleoid	ATP binding|ATPase activity|metal ion binding|peptidase activator activity|unfolded protein binding				0						TTAAAGCATATTTTTTTTAAA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	71069140	71069140	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71069140delT								UACA (13290 upstream) : LARP6 (54751 downstream)																							agtcccctaattttttttcca	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78164774	78164775	+	IGR	DEL	GT	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78164774_78164775delGT								LINGO1 (176299 upstream) : LOC645752 (41784 downstream)																							GTGGTACCAGGTGTGTGTGTGT	0.559													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	89608542	89608542	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89608542delC								MFGE8 (151879 upstream) : ABHD2 (22839 downstream)																							GAATCATTGTCCATAGCACAT	0.438													4	2	---	---	---	---	
ABHD2	11057	broad.mit.edu	37	15	89714979	89714979	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89714979delA	uc002bnj.2	+						ABHD2_uc002bnk.2_Intron	NM_007011	NP_008942	P08910	ABHD2_HUMAN	alpha/beta hydrolase domain containing protein							integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)					AGAGTGCTTCAAAAAAATGCC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95953183	95953183	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95953183delT								MCTP2 (926003 upstream) : LOC145820 (23139 downstream)																							TTTCACTCTGTTTTTTTTTTC	0.363													4	2	---	---	---	---	
ADAMTS17	170691	broad.mit.edu	37	15	100641443	100641443	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100641443delC	uc002bvv.1	-						ADAMTS17_uc002bvx.1_Intron	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		tcctcctcagccacagtcccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102036091	102036092	+	IGR	INS	-	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102036091_102036092insC								PCSK6 (5904 upstream) : TM2D3 (137088 downstream)																							ACTCTGACTTTCCCCACCTTCC	0.455													4	2	---	---	---	---	
NPRL3	8131	broad.mit.edu	37	16	187993	187993	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:187993delT	uc002cfr.2	-						NPRL3_uc010uua.1_Intron|NPRL3_uc002cfp.1_Intron|NPRL3_uc002cfq.2_Intron|NPRL3_uc010uub.1_Intron|NPRL3_uc002cfs.1_Intron	NM_001077350	NP_001070818	Q12980	NPRL3_HUMAN	conserved gene telomeric to alpha globin cluster								protein binding			ovary(1)	1						ATGATTTTAATTTTTTTTTTC	0.373													4	2	---	---	---	---	
CACNA1H	8912	broad.mit.edu	37	16	1215081	1215081	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1215081delA	uc002cks.2	+						CACNA1H_uc002ckt.2_Intron	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,						aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	CGGGGCAAGGAGGGGGCTGAT	0.677													4	2	---	---	---	---	
GRIN2A	2903	broad.mit.edu	37	16	10221528	10221528	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10221528delG	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)	cacagagcctggcacctagct	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	13865411	13865411	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13865411delA								SHISA9 (531139 upstream) : ERCC4 (148603 downstream)																							TTGCAAATGTAAAATTTTCTC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	14387845	14387845	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14387845delC								MKL2 (27216 upstream) : MIR193B (9979 downstream)																							gggttgcctgccccaggggat	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17743850	17743850	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17743850delC								XYLT1 (179112 upstream) : NOMO2 (767333 downstream)																							TCCTCAGCATCCCCCAGAGAA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	19949108	19949109	+	IGR	DEL	CC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19949108_19949109delCC								GPRC5B (52276 upstream) : GPR139 (93934 downstream)																							gtggtgccttccctgatcgagc	0.000													4	2	---	---	---	---	
HS3ST4	9951	broad.mit.edu	37	16	26112537	26112537	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26112537delC	uc002dof.2	+							NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)		catctccaatccatttcaccc	0.000													2	5	---	---	---	---	
IL4R	3566	broad.mit.edu	37	16	27336137	27336137	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27336137delC	uc002don.2	+						IL4R_uc002dom.2_Intron|IL4R_uc002dop.3_Intron|IL4R_uc010bxy.2_Intron|IL4R_uc002doo.2_Intron	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a						immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2						GCGTGGTCTTCCCCAGCAAAT	0.607													4	2	---	---	---	---	
GSG1L	146395	broad.mit.edu	37	16	27803419	27803419	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27803419delA	uc002doz.2	-						GSG1L_uc010bya.1_Intron|GSG1L_uc010bxz.1_Intron|GSG1L_uc002doy.2_Intron	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						TGCAGCCATCATCCACCACCA	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33976598	33976598	+	IGR	DEL	A	-	-	rs112123079		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33976598delA								MIR1826 (11006 upstream) : UBE2MP1 (427204 downstream)																							atatcttcacaaaaaaagtag	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54826327	54826327	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54826327delA								IRX3 (505949 upstream) : IRX5 (138784 downstream)																							ATGTTGTTCCAAAAAAAATGA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	67458645	67458646	+	IGR	INS	-	T	T			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67458645_67458646insT								ZDHHC1 (8306 upstream) : HSD11B2 (6390 downstream)																							GCAGGAGTGGCTTGGGCCCCTT	0.554													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	72627962	72627962	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72627962delT								PMFBP1 (421613 upstream) : ZFHX3 (188826 downstream)																							GACACTGGCATTTTTTTGTGG	0.373													3	3	---	---	---	---	
WFDC1	58189	broad.mit.edu	37	16	84344647	84344648	+	Intron	DEL	TG	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84344647_84344648delTG	uc002fhw.2	+						WFDC1_uc002fhv.2_Intron	NM_021197	NP_067020	Q9HC57	WFDC1_HUMAN	WAP four-disulfide core domain 1 precursor						negative regulation of cell growth	extracellular space	serine-type endopeptidase inhibitor activity			breast(1)	1						TATCTAACTCTGTGTGTGTGTG	0.480													4	2	---	---	---	---	
ZCCHC14	23174	broad.mit.edu	37	16	87455537	87455537	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87455537delA	uc002fjz.1	-						ZCCHC14_uc002fka.1_Intron|ZCCHC14_uc002fkb.2_Intron	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14						cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)		aagacataccaaaaaaaaaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88229645	88229645	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88229645delT								BANP (118722 upstream) : ZNF469 (264234 downstream)																							TAATGTTCTGTTTTTCCTGGA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88322765	88322767	+	IGR	DEL	ATG	-	-	rs111501348	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88322765_88322767delATG								BANP (211842 upstream) : ZNF469 (171112 downstream)																							ggtgatggcaatgatgatgatga	0.000													4	2	---	---	---	---	
PIK3R6	146850	broad.mit.edu	37	17	8752288	8752288	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8752288delG	uc002glq.1	-						PIK3R6_uc002glr.1_Intron|PIK3R6_uc002gls.1_Intron	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6						platelet activation	cytosol					0						GTCTCAGCGTGGTGGCCTAAG	0.512													4	2	---	---	---	---	
GAS7	8522	broad.mit.edu	37	17	10069929	10069930	+	Intron	DEL	CA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10069929_10069930delCA	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						cttttatgtgcacacacacatt	0.045			T	MLL	AML*								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25299747	25299747	+	IGR	DEL	T	-	-	rs111243274		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25299747delT								None (None upstream) : WSB1 (321359 downstream)																							agaatttgaatttttttgtga	0.144													5	3	---	---	---	---	
PIGS	94005	broad.mit.edu	37	17	26886007	26886007	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26886007delT	uc002hbo.2	-						PIGS_uc002hbn.2_Intron|PIGS_uc010wap.1_Intron	NM_033198	NP_149975	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			breast(2)|urinary_tract(1)|kidney(1)	4	Lung NSC(42;0.00431)					tcttcacatcttttttttttg	0.000													5	3	---	---	---	---	
RHOT1	55288	broad.mit.edu	37	17	30469850	30469851	+	Intron	INS	-	TC	TC			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30469850_30469851insTC	uc002hgz.2	+						RHOT1_uc002hgw.2_Intron|RHOT1_uc002hgy.2_Intron|RHOT1_uc002hha.2_Intron|RHOT1_uc010csv.2_Intron|RHOT1_uc002hgx.2_Intron|RHOT1_uc010wby.1_Intron|RHOT1_uc002hhb.2_Intron|RHOT1_uc002hgv.2_Intron	NM_018307	NP_060777	Q8IXI2	MIRO1_HUMAN	ras homolog gene family, member T1 isoform 3						apoptosis|cellular homeostasis|mitochondrion transport along microtubule|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to mitochondrial outer membrane|plasma membrane	calcium ion binding|GTP binding|GTPase activity|protein binding			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				TTGCAGCCCCGGCCCTTCTCGC	0.574													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31784573	31784574	+	Intron	INS	-	G	G	rs58194488		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31784573_31784574insG	uc002hhu.2	-							NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	aggcataaaaatgaacaagaca	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	32728633	32728634	+	IGR	DEL	CC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32728633_32728634delCC								CCL1 (38381 upstream) : C17orf102 (172508 downstream)																							aaccccttctccccaggcagtc	0.114													4	2	---	---	---	---	
MLLT6	4302	broad.mit.edu	37	17	36884257	36884257	+	3'UTR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36884257delA	uc002hqi.3	+	20					MLLT6_uc002hqk.3_3'UTR|MLLT6_uc010cvn.1_RNA|CISD3_uc010wds.1_5'Flank	NM_005937	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent	nucleus	protein binding|zinc ion binding			breast(3)|prostate(1)|lung(1)|skin(1)	6	Breast(7;4.43e-21)					CCCCACCCAGAACACTTCTTC	0.527			T	MLL	AL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	38761738	38761738	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38761738delA								CCR7 (40014 upstream) : SMARCE1 (22238 downstream)																							TTGTCAGACGAGTGCATGACA	0.333													4	2	---	---	---	---	
KAT2A	2648	broad.mit.edu	37	17	40270157	40270158	+	Intron	DEL	GA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40270157_40270158delGA	uc002hyx.2	-							NM_021078	NP_066564	Q92830	KAT2A_HUMAN	general control of amino acid synthesis 5-like						chromatin remodeling|histone deubiquitination|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex	H3 histone acetyltransferase activity|histone deacetylase binding|protein binding|transcription coactivator activity			upper_aerodigestive_tract(1)|lung(1)	2						TGAAGCTGAGGAGAGAGAGAGA	0.649													4	2	---	---	---	---	
KCNH4	23415	broad.mit.edu	37	17	40315894	40315894	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40315894delC	uc002hzb.2	-	13	2540	c.2207delG	c.(2206-2208)GGTfs	p.G736fs		NM_012285	NP_036417	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H,	736	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	two-component sensor activity|voltage-gated potassium channel activity			large_intestine(1)	1		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		CCTGGGACCACCCCCAGGCTC	0.706													4	2	---	---	---	---	
STAT5B	6777	broad.mit.edu	37	17	40371125	40371125	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40371125delC	uc002hzh.2	-						STAT5B_uc002hzi.3_Intron	NM_012448	NP_036580	P51692	STA5B_HUMAN	signal transducer and activator of transcription						2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|skin(1)	6		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)	CGAACCCTGTCCCATCTCCAG	0.612													4	2	---	---	---	---	
MPP2	4355	broad.mit.edu	37	17	41957507	41957507	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41957507delC	uc010wip.1	-						MPP2_uc002ien.1_Intron|MPP2_uc010wim.1_Intron|MPP2_uc002ieo.1_Intron|MPP2_uc010win.1_Intron|MPP2_uc010wio.1_Intron	NM_005374	NP_005365	Q14168	MPP2_HUMAN	palmitoylated membrane protein 2						signal transduction	cell surface|integral to plasma membrane|membrane fraction	guanylate kinase activity				0		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		CACACACCTGCCCCCCACTCT	0.587											OREG0024443	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	17	47567765	47567765	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47567765delT								PHB (75523 upstream) : NGFR (4890 downstream)																							CAGAACCCCCTTGCAGCCCAG	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48403509	48403509	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48403509delA								TMEM92 (44665 upstream) : XYLT2 (19884 downstream)																							cagattagggaaaagcaagtc	0.045													4	2	---	---	---	---	
TRIM25	7706	broad.mit.edu	37	17	54990556	54990556	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54990556delA	uc002iut.2	-						TRIM25_uc010dcj.2_Intron	NM_005082	NP_005073	Q14258	TRI25_HUMAN	tripartite motif-containing 25						innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|response to virus	cell junction|cytosol|nucleus	sequence-specific DNA binding transcription factor activity|ubiquitin-protein ligase activity|zinc ion binding			lung(1)|breast(1)|skin(1)	3	Breast(9;6.15e-08)					CAAGCAACCTAACCTGTCTTC	0.239													4	2	---	---	---	---	
MSI2	124540	broad.mit.edu	37	17	55693643	55693644	+	Intron	DEL	TG	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55693643_55693644delTG	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)		tgtgcatgcatgtgtgtgtgtg	0.134			T	HOXA9	CML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	55853294	55853294	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55853294delA								MSI2 (95995 upstream) : MRPS23 (63550 downstream)																							TGCCGACTGGAAAAAAAATCT	0.448													4	2	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71629593	71629593	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71629593delT	uc010dfm.2	-							NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						TACCTTCCCATTTTTTTCCCA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75869018	75869019	+	IGR	DEL	AC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75869018_75869019delAC								SEPT9 (372342 upstream) : FLJ45079 (6090 downstream)																							GAATGACCATAcacacacacac	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	9543150	9543152	+	IGR	DEL	CCC	-	-	rs113967673		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9543150_9543152delCCC								RALBP1 (5045 upstream) : PPP4R1 (3640 downstream)																							ccacaccacgccccccaccacac	0.153													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14145018	14145019	+	IGR	DEL	TA	-	-	rs34266186	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14145018_14145019delTA								ZNF519 (12589 upstream) : LOC284233 (192403 downstream)																							GGAGGCAGCGTACCCCCCCCAC	0.639													4	3	---	---	---	---	
KLHL14	57565	broad.mit.edu	37	18	30321605	30321605	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30321605delG	uc002kxm.1	-						KLHL14_uc010dmd.1_Intron	NM_020805	NP_065856	Q9P2G3	KLH14_HUMAN	kelch-like 14							cytosol|endoplasmic reticulum membrane				ovary(1)	1						GAAGAATTTTGGGGGGAAGAT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	59659741	59659741	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59659741delA								RNF152 (99437 upstream) : PIGN (51719 downstream)																							AAGGCTGAGTAATATGGAAGG	0.428													4	2	---	---	---	---	
DOK6	220164	broad.mit.edu	37	18	67445852	67445852	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67445852delA	uc002lkl.2	+							NM_152721	NP_689934	Q6PKX4	DOK6_HUMAN	docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				actgcttttgaaatgtactta	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	70001180	70001181	+	IGR	DEL	GG	-	-	rs34664081		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70001180_70001181delGG								None (None upstream) : CBLN2 (202734 downstream)																							CAGCACTGGTGGAAAATGTGAC	0.233													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71579528	71579528	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71579528delC								None (None upstream) : FBXO15 (161060 downstream)																							TCACAATCCTCCCCCTACTCT	0.557													4	2	---	---	---	---	
GALR1	2587	broad.mit.edu	37	18	74971649	74971650	+	Intron	INS	-	GTG	GTG	rs149681298	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74971649_74971650insGTG	uc002lms.3	+							NM_001480	NP_001471	P47211	GALR1_HUMAN	galanin receptor 1						digestion|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity			lung(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		tggtggcaattgtggtgatggt	0.054													4	3	---	---	---	---	
ATP9B	374868	broad.mit.edu	37	18	76965482	76965482	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76965482delT	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933	O43861	ATP9B_HUMAN	ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		ATTTGATTTCTTTTTTTTTTT	0.308													4	2	---	---	---	---	
TXNL4A	10907	broad.mit.edu	37	18	77734058	77734058	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77734058delC	uc002lnp.2	-						TXNL4A_uc002lnr.2_Intron|TXNL4A_uc002lnq.2_Intron|TXNL4A_uc010drf.2_Intron|TXNL4A_uc010drg.2_Intron	NM_006701	NP_006692	P83876	TXN4A_HUMAN	thioredoxin-like 4A						cell division|mitosis|spliceosome assembly	nucleoplasm|spliceosomal complex	protein binding				0		all_cancers(4;1.15e-12)|all_epithelial(4;8.61e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0646)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;7.36e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0249)		GCATTGTCCACCATGCTCTTT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	1705592	1705593	+	IGR	INS	-	TGGA	TGGA			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1705592_1705593insTGGA								TCF3 (53266 upstream) : ONECUT3 (48069 downstream)																							agatgagtgggtggatggatgg	0.000													6	3	---	---	---	---	
PIP5K1C	23396	broad.mit.edu	37	19	3651534	3651535	+	Intron	DEL	TC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3651534_3651535delTC	uc002lyj.1	-						PIP5K1C_uc010xhq.1_Intron|PIP5K1C_uc010xhr.1_Intron	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type						axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		GGAAACGCTATCTCTCTCTCAT	0.639													4	2	---	---	---	---	
KDM4B	23030	broad.mit.edu	37	19	4997568	4997568	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4997568delG	uc002mbq.3	+						KDM4B_uc010xil.1_Intron	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1						gtgtgatctagggtaggccac	0.294													4	2	---	---	---	---	
ACTL9	284382	broad.mit.edu	37	19	8810506	8810506	+	5'Flank	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8810506delG	uc002mkl.2	-							NM_178525	NP_848620	Q8TC94	ACTL9_HUMAN	actin-like 9							cytoplasm|cytoskeleton				large_intestine(2)|pancreas(1)	3						GATGAGGGATGGGGGAAGTCT	0.333													4	2	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	9080249	9080250	+	Intron	INS	-	AA	AA	rs3079082		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9080249_9080250insAA	uc002mkp.2	-							NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						aagaaagaaagagaaagaaaga	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	34106619	34106619	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34106619delG								PEPD (93818 upstream) : CHST8 (6242 downstream)																							TGCTGAGCCTGGACAATTTGA	0.443													4	2	---	---	---	---	
CEACAM21	90273	broad.mit.edu	37	19	42092496	42092496	+	Intron	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42092496delC	uc002ore.3	+						CEACAM21_uc002ord.1_Intron|CEACAM21_uc002org.3_Intron	NM_001098506	NP_001091976	Q3KPI0	CEA21_HUMAN	carcinoembryonic antigen-related cell adhesion							integral to membrane				ovary(1)	1						ACCCCTCTCTCCCCTGCCCAG	0.617													4	2	---	---	---	---	
ARHGEF1	9138	broad.mit.edu	37	19	42420955	42420956	+	Intron	DEL	CA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42420955_42420956delCA	uc002osc.2	+									Q92888	ARHG1_HUMAN	SubName: Full=ARHGEF1 protein; SubName: Full=Rho guanine nucleotide exchange factor (GEF) 1, isoform CRA_g;						cell proliferation|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol|plasma membrane	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(3)|large_intestine(1)	4		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		cagtcacaatcacacacacaca	0.272													4	2	---	---	---	---	
PSG1	5669	broad.mit.edu	37	19	43380449	43380450	+	Intron	INS	-	C	C			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43380449_43380450insC	uc002ovb.2	-						PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_Intron|PSG1_uc002our.1_Intron|PSG1_uc010eio.1_Intron|PSG1_uc002oux.1_Intron|PSG1_uc002ouy.1_Intron|PSG1_uc002ouz.1_Intron|PSG1_uc002ova.1_Intron|PSG1_uc002ovc.2_Intron|PSG1_uc002ovd.1_Intron	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1						female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)				GGGACCAGGTGCCCCCAGTTCC	0.564													4	2	---	---	---	---	
PSG6	5675	broad.mit.edu	37	19	43414386	43414387	+	Intron	DEL	TG	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43414386_43414387delTG	uc002ovj.1	-						PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG6_uc002ove.1_Intron|PSG6_uc002ovf.1_Intron|PSG6_uc002ovg.1_Intron	NM_002782	NP_002773	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6 isoform						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)				AATCCTGGTCTGTGGAAGGGAC	0.520													4	2	---	---	---	---	
A1BG	1	broad.mit.edu	37	19	58870088	58870088	+	Intron	DEL	G	-	-	rs11332731		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58870088delG	uc002qsf.1	-						ZNF497_uc002qsh.1_Intron|ZNF497_uc002qsi.1_Intron|uc002qsk.1_Frame_Shift_Del_p.G20fs			P04217	A1BG_HUMAN	Homo sapiens primary hepatoblastoma mRNA for alpha-1-B glycoprotein precursor, partial cds, clone:HYST2477.							extracellular region					0		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)		ACACAGGTGTGGACTGGAGAT	0.577													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	936059	936059	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:936059delA								ANGPT4 (39099 upstream) : RSPO4 (3039 downstream)																							ggagctccctaacccctgtat	0.000													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15498059	15498060	+	Intron	DEL	CA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15498059_15498060delCA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.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)				tccctcacttcaccatttgatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	17471757	17471757	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17471757delC								PCSK2 (6537 upstream) : BFSP1 (2794 downstream)																							agcatgaactccccaggacaa	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25903695	25903695	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25903695delA								FAM182B (54909 upstream) : LOC100134868 (86740 downstream)																							TTAAGATGACAAAAAAACACC	0.428													4	4	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29617844	29617844	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29617844delT	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0						tggttcagggttttttttttt	0.000													4	2	---	---	---	---	
DEFB115	245929	broad.mit.edu	37	20	29844195	29844195	+	5'Flank	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29844195delT	uc002wvp.1	+							NM_001037730	NP_001032819	Q30KQ5	DB115_HUMAN	beta-defensin 115 precursor						defense response to bacterium	extracellular region				ovary(1)	1			Colorectal(19;0.00445)|COAD - Colon adenocarcinoma(19;0.0347)			tgtttactgcttttcaagtta	0.055													4	2	---	---	---	---	
DEFB118	117285	broad.mit.edu	37	20	29959188	29959188	+	Intron	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29959188delT	uc002wvr.2	+							NM_054112	NP_473453	Q96PH6	DB118_HUMAN	beta-defensin 118 precursor						cell-matrix adhesion|defense response to bacterium|innate immune response|spermatogenesis	extracellular region				ovary(3)|pancreas(1)	4	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			aatgcttatcTTTTTTTTGTA	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	39120725	39120725	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39120725delA								None (None upstream) : MAFB (193794 downstream)																							ACCCCCTGACATCAAGCAAAC	0.328													4	2	---	---	---	---	
JPH2	57158	broad.mit.edu	37	20	42787811	42787811	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42787811delG	uc002xli.1	-							NM_020433	NP_065166	Q9BR39	JPH2_HUMAN	junctophilin 2 isoform 1						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane					0		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			GACTGGAGGTGGGTGTGTGGG	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	47088037	47088037	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47088037delT								LOC284749 (88656 upstream) : PREX1 (152756 downstream)																							cgcacatccatttacacagaa	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50472437	50472438	+	IGR	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50472437_50472438insA								SALL4 (53389 upstream) : ZFP64 (228113 downstream)																							tacagagtggtaaaaaaaaatc	0.010													4	2	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51774810	51774810	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51774810delA	uc002xwo.2	+							NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			gggacttcataaggactttgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55292358	55292359	+	IGR	DEL	TT	-	-	rs67280754		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55292358_55292359delTT								TFAP2C (78022 upstream) : BMP7 (451450 downstream)																							AAGGGCTGCGTTTCAGGCATGA	0.559													1	5	---	---	---	---	
SPO11	23626	broad.mit.edu	37	20	55903657	55903658	+	5'Flank	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55903657_55903658insA	uc002xye.2	+						SPO11_uc002xyf.2_5'Flank	NM_012444	NP_036576	Q9Y5K1	SPO11_HUMAN	meiotic recombination protein SPO11 isoform a						female gamete generation|reciprocal meiotic recombination	chromosome|nucleus	ATP binding|DNA binding|hydrolase activity			breast(2)|skin(1)	3	Lung NSC(12;0.0066)|all_lung(29;0.0188)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.73e-14)|Epithelial(14;9.02e-10)|all cancers(14;9.31e-09)			GAAACAAAAGCAAAATCGTCCC	0.441								Editing_and_processing_nucleases					4	2	---	---	---	---	
PHACTR3	116154	broad.mit.edu	37	20	58391820	58391820	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58391820delG	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron|PHACTR3_uc002yaw.2_Intron|PHACTR3_uc002yax.2_Intron	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			gtgggtggttgggtagttaga	0.169													4	2	---	---	---	---	
CDH26	60437	broad.mit.edu	37	20	58582788	58582788	+	Intron	DEL	T	-	-	rs113480441		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58582788delT	uc002ybe.2	+						CDH26_uc002ybf.1_Intron|CDH26_uc010zzy.1_Intron|CDH26_uc002ybg.2_Intron|CDH26_uc002ybh.2_Intron|CDH26_uc002ybi.2_Intron	NM_177980	NP_817089	Q8IXH8	CAD26_HUMAN	cadherin-like 26 isoform a						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			tttctgctggttttttttttt	0.010													4	2	---	---	---	---	
COL20A1	57642	broad.mit.edu	37	20	61944079	61944079	+	Intron	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61944079delG	uc011aau.1	+						COL20A1_uc011aav.1_Intron	NM_020882	NP_065933	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1						cell adhesion	collagen|extracellular space	structural molecule activity			central_nervous_system(1)	1	all_cancers(38;1.39e-10)					GGGTGTGGCTGCCCCTCCTCT	0.647													5	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11061508	11061510	+	Intron	DEL	CAC	-	-	rs60979732		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11061508_11061510delCAC	uc002yit.1	-						BAGE_uc002yiw.1_5'Flank|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)		ATCTATAAAACACAACAGAATGA	0.236													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11083781	11083781	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11083781delA	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)		cttgtccaataaaaaaagact	0.055													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14367406	14367407	+	IGR	INS	-	C	C	rs140142693	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14367406_14367407insC								None (None upstream) : C21orf99 (43080 downstream)																							ttccttttacaccataggcctc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	33895878	33895878	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33895878delG								C21orf63 (8181 upstream) : TCP10L (51274 downstream)																							CCTGTGTCCTGGCTGTAAGAA	0.502													4	2	---	---	---	---	
SYNJ1	8867	broad.mit.edu	37	21	34031525	34031526	+	Intron	INS	-	A	A			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34031525_34031526insA	uc002yqh.2	-						SYNJ1_uc011ads.1_Intron|SYNJ1_uc002yqf.2_Intron|SYNJ1_uc002yqg.2_Intron|SYNJ1_uc002yqi.2_Intron	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a								inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5						GGACTTAACCCAAAAAAAAAAC	0.287													3	3	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45824752	45824753	+	Intron	INS	-	TGA	TGA			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-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													1	7	---	---	---	---	
COL18A1	80781	broad.mit.edu	37	21	46933460	46933461	+	3'UTR	INS	-	CA	CA	rs151123689	by1000genomes	TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46933460_46933461insCA	uc011afs.1	+	42					COL18A1_uc002zhg.2_3'UTR|COL18A1_uc002zhi.2_3'UTR|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_3'UTR|COL18A1_uc002zhk.2_3'UTR	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		AACATCAACCCGAGTCATTCGT	0.624													4	3	---	---	---	---	
MCM3AP	8888	broad.mit.edu	37	21	47680521	47680521	+	Intron	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47680521delA	uc002zir.1	-						MCM3AP_uc002zip.1_5'Flank|MCM3AP_uc002ziq.1_Intron	NM_003906	NP_003897	O60318	MCM3A_HUMAN	minichromosome maintenance complex component 3						DNA replication|protein import into nucleus	cytosol|nucleus	DNA binding|nucleotide binding			large_intestine(2)|lung(1)|ovary(1)|skin(1)	5	Breast(49;0.112)					AGAATTTTTTATAATAAAATT	0.368													4	2	---	---	---	---	
SYN3	8224	broad.mit.edu	37	22	32928918	32928919	+	Intron	INS	-	G	G			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32928918_32928919insG	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron|SYN3_uc011amc.1_5'Flank	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						CTGAGGCCAGAGGGGCTTTTCA	0.639													4	2	---	---	---	---	
MFNG	4242	broad.mit.edu	37	22	37877128	37877129	+	Intron	DEL	CA	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37877128_37877129delCA	uc003ass.1	-						MFNG_uc011ani.1_Intron|MFNG_uc011anj.1_Intron|CARD10_uc003ast.1_Intron	NM_002405	NP_002396	O00587	MFNG_HUMAN	O-fucosylpeptide						pattern specification process	extracellular space|integral to Golgi membrane	O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity			lung(1)	1	Melanoma(58;0.0574)					cacacacaatcacacacacaca	0.421													4	2	---	---	---	---	
SCUBE1	80274	broad.mit.edu	37	22	43601963	43601964	+	Intron	DEL	CA	-	-	rs145676151		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43601963_43601964delCA	uc003bdt.1	-							NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1						adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)				acccactcaccacactcacCCC	0.030													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	46256406	46256406	+	IGR	DEL	T	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46256406delT								ATXN10 (15577 upstream) : WNT7B (59842 downstream)																							TCAGTGCCCCTTTGTGAGATT	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48564090	48564090	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48564090delG								TBC1D22A (994368 upstream) : FAM19A5 (321198 downstream)																							CCCTGTCCTTGCAGCCCTTAG	0.493													4	2	---	---	---	---	
TTLL8	164714	broad.mit.edu	37	22	50467835	50467836	+	Intron	INS	-	C	C	rs34192325		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50467835_50467836insC	uc011ark.1	-							NM_001080447	NP_001073916			tubulin tyrosine ligase-like family, member 8											ovary(2)	2		all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		READ - Rectum adenocarcinoma(2;0.000882)|Colorectal(2;0.00311)|BRCA - Breast invasive adenocarcinoma(115;0.226)		CATCCTGAAGACCCCACACACA	0.426													4	2	---	---	---	---	
ZNF157	7712	broad.mit.edu	37	X	47250199	47250200	+	Intron	DEL	TC	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47250199_47250200delTC	uc004dhr.1	+							NM_003446	NP_003437	P51786	ZN157_HUMAN	zinc finger protein 157						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						tctgtctctgtctctctctctc	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	71492424	71492424	+	IGR	DEL	A	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71492424delA								PIN4 (7612 upstream) : RPS4X (30 downstream)																							AAACTGAATTAAAAAAAAAAA	0.383													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	88908012	88908012	+	IGR	DEL	C	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:88908012delC								CPXCR1 (898229 upstream) : TGIF2LX (268928 downstream)																							ctttgatatacccccatcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9944638	9944638	+	IGR	DEL	G	-	-			TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9944638delG								TTTY22 (293784 upstream) : None (None downstream)																							gccaagtagtggttgcagtgg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28588050	28588052	+	IGR	DEL	CAT	-	-	rs111989825		TCGA-B0-5702-01A-11D-1534-10	TCGA-B0-5702-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28588050_28588052delCAT								None (None upstream) : None (None downstream)																							tcttcttttacatcattctgtcA	0.182													4	2	---	---	---	---	
