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
MTOR	2475	broad.mit.edu	37	1	11217299	11217299	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11217299A>G	uc001asd.2	-	30	4500	c.4379T>C	c.(4378-4380)CTT>CCT	p.L1460P		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	1460	FAT.				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						ATAGGCCACAAGGGCATCCTC	0.547													35	51	---	---	---	---	PASS
CLCNKA	1187	broad.mit.edu	37	1	16360323	16360323	+	3'UTR	SNP	G	T	T	rs61772372		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16360323G>T	uc001axu.2	+	20					CLCNKA_uc001axt.2_RNA|CLCNKA_uc001axv.2_3'UTR|CLCNKA_uc010obw.1_3'UTR|CLCNKB_uc001axw.3_Intron	NM_004070	NP_004061	P51800	CLCKA_HUMAN	chloride channel Ka isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	CTCATCCTGGGTGGGACGATG	0.552													4	26	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16918727	16918727	+	5'UTR	SNP	G	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918727G>C	uc009vos.1	-	6					NBPF1_uc010oce.1_5'UTR	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CGAGGTGCCTGAACTCAGAGC	0.463													3	15	---	---	---	---	PASS
TAS1R2	80834	broad.mit.edu	37	1	19180859	19180859	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19180859C>T	uc001bba.1	-	3	1106	c.1105G>A	c.(1105-1107)GCC>ACC	p.A369T		NM_152232	NP_689418	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2 precursor	369	Extracellular (Potential).				detection of chemical stimulus involved in sensory perception of sweet taste	plasma membrane	protein heterodimerization activity|taste receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	GACAAGGTGGCGTTCAGGCAG	0.622													31	52	---	---	---	---	PASS
ZMYM6	9204	broad.mit.edu	37	1	35484838	35484838	+	Intron	SNP	A	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35484838A>C	uc001byh.2	-						ZMYM6_uc001byf.1_Intron|ZMYM6_uc010oht.1_Intron|ZMYM6_uc009vup.2_Intron|ZMYM6_uc009vuq.1_Intron|ZMYM6_uc009vur.1_Intron|ZMYM6_uc001byj.2_3'UTR|ZMYM6_uc001byi.2_3'UTR|ZMYM6_uc001byk.2_3'UTR	NM_007167	NP_009098	O95789	ZMYM6_HUMAN	zinc finger protein 258						multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				TTAACTAAAAAGTTATTTCTA	0.274													16	38	---	---	---	---	PASS
EIF2C3	192669	broad.mit.edu	37	1	36411321	36411321	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36411321G>A	uc001bzp.2	+	2	304	c.48G>A	c.(46-48)ATG>ATA	p.M16I	EIF2C3_uc001bzn.1_Missense_Mutation_p.M16I|EIF2C3_uc001bzo.2_RNA|EIF2C3_uc001bzq.2_5'UTR	NM_024852	NP_079128	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3	16					mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CCCTACTCATGGTGCCCAGAA	0.488													28	59	---	---	---	---	PASS
INPP5B	3633	broad.mit.edu	37	1	38352672	38352672	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38352672T>C	uc001ccg.1	-	12	1113	c.1019A>G	c.(1018-1020)AAG>AGG	p.K340R	INPP5B_uc009vvk.1_Missense_Mutation_p.K281R|INPP5B_uc001ccf.1_Missense_Mutation_p.K176R|INPP5B_uc010oij.1_RNA	NM_005540	NP_005531	P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	420					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to membrane|microtubule cytoskeleton	GTPase activator activity|inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			urinary_tract(1)	1	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TCGGATAAGCTTCACCTGGAA	0.438													5	156	---	---	---	---	PASS
PTCH2	8643	broad.mit.edu	37	1	45288276	45288276	+	Silent	SNP	A	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45288276A>T	uc010olf.1	-	22	3435	c.3423T>A	c.(3421-3423)CTT>CTA	p.L1141L	PTCH2_uc010olg.1_Silent_p.L839L	NM_003738	NP_003729	Q9Y6C5	PTC2_HUMAN	patched 2	1141	Cytoplasmic (Potential).				protein complex assembly|spermatogenesis	integral to plasma membrane	hedgehog receptor activity			lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1)	18	Acute lymphoblastic leukemia(166;0.155)					CCCCCCACCTAAGCCCGCCTC	0.632									Basal_Cell_Nevus_syndrome				16	27	---	---	---	---	PASS
RAD54L	8438	broad.mit.edu	37	1	46714224	46714224	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46714224C>A	uc009vye.2	+	3	158	c.44C>A	c.(43-45)CCT>CAT	p.P15H	RAD54L_uc001cpl.2_Missense_Mutation_p.P15H	NM_001142548	NP_001136020	Q92698	RAD54_HUMAN	RAD54-like protein	15					meiosis	nucleus	ATP binding|DNA binding|helicase activity			ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)		AAGAGAAAACCTGAAGGCAGG	0.547								Direct_reversal_of_damage|Homologous_recombination					24	65	---	---	---	---	PASS
ARHGAP29	9411	broad.mit.edu	37	1	94697130	94697130	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94697130C>T	uc001dqj.3	-	2	407	c.38G>A	c.(37-39)CGT>CAT	p.R13H	ARHGAP29_uc009wdq.1_RNA|ARHGAP29_uc001dql.2_Missense_Mutation_p.R13H	NM_004815	NP_004806	Q52LW3	RHG29_HUMAN	PTPL1-associated RhoGAP 1	13					Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		TGCCCAAGCACGTTTTTTCTT	0.373													5	398	---	---	---	---	PASS
SASS6	163786	broad.mit.edu	37	1	100572485	100572485	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100572485A>T	uc001dsu.2	-	12	1532	c.1391T>A	c.(1390-1392)CTA>CAA	p.L464Q	SASS6_uc009wdz.2_Missense_Mutation_p.L297Q	NM_194292	NP_919268	Q6UVJ0	SAS6_HUMAN	spindle assembly abnormal protein 6	464	Potential.				centriole replication	centriole				upper_aerodigestive_tract(1)|ovary(1)	2		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		ATTATTTTTTAGAAGTTGTTT	0.214													94	267	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144923791	144923791	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144923791T>G	uc001elw.3	-	6	958	c.667A>C	c.(667-669)AAG>CAG	p.K223Q	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.K289Q|PDE4DIP_uc001emc.1_Missense_Mutation_p.K223Q|PDE4DIP_uc001emd.1_Missense_Mutation_p.K223Q|PDE4DIP_uc001emb.1_Missense_Mutation_p.K386Q|PDE4DIP_uc001eme.1_5'Flank|PDE4DIP_uc001emf.1_Missense_Mutation_p.K10Q	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	223					cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GAATTCAGCTTTTGTTGTTTC	0.428			T	PDGFRB	MPD								42	307	---	---	---	---	PASS
HSD17B7	51478	broad.mit.edu	37	1	162769603	162769603	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162769603G>A	uc001gci.2	+	5	613	c.518G>A	c.(517-519)AGT>AAT	p.S173N	HSD17B7_uc009wuv.2_RNA	NM_016371	NP_057455	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	173	Extracellular (Potential).				cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	3-keto sterol reductase activity|estradiol 17-beta-dehydrogenase activity			ovary(1)	1	all_hematologic(112;0.115)				NADH(DB00157)	TCATCTCGCAGTGCAAGGAAA	0.458													4	130	---	---	---	---	PASS
TSEN15	116461	broad.mit.edu	37	1	184041434	184041434	+	Splice_Site	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184041434T>C	uc001gqt.3	+	4	574	c.495_splice	c.e4+2	p.Q165_splice	TSEN15_uc009wyg.2_Splice_Site|TSEN15_uc001gqu.3_Intron	NM_052965	NP_443197	Q8WW01	SEN15_HUMAN	tRNA splicing endonuclease 15 isoform 1						mRNA processing|tRNA processing	nucleolus	protein binding				0						GACCCTCAGGTCAGTTTTGAG	0.398													6	332	---	---	---	---	PASS
CNIH4	29097	broad.mit.edu	37	1	224553605	224553605	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224553605C>T	uc001hom.1	+	3	195	c.163C>T	c.(163-165)CAT>TAT	p.H55Y	CNIH4_uc001hon.1_RNA	NM_014184	NP_054903	Q9P003	CNIH4_HUMAN	cornichon homolog 4	55					intracellular signal transduction	endoplasmic reticulum|integral to membrane	protein binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.00341)		ATTGATTGGCCATACCATTGT	0.388													54	737	---	---	---	---	PASS
TFB2M	64216	broad.mit.edu	37	1	246707837	246707837	+	Silent	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246707837T>C	uc001ibn.2	-	7	1130	c.1005A>G	c.(1003-1005)GTA>GTG	p.V335V		NM_022366	NP_071761	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	335					positive regulation of transcription, DNA-dependent|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity|transcription cofactor activity			ovary(1)	1	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)			AGTGGTCTATTACAGTGGCGC	0.328													49	204	---	---	---	---	PASS
KIDINS220	57498	broad.mit.edu	37	2	8890360	8890360	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8890360G>T	uc002qzc.2	-	24	3478	c.3296C>A	c.(3295-3297)CCA>CAA	p.P1099Q	KIDINS220_uc010yiv.1_Missense_Mutation_p.P865Q|KIDINS220_uc002qzd.2_Missense_Mutation_p.P1057Q|KIDINS220_uc010yiw.1_Missense_Mutation_p.P1100Q|KIDINS220_uc002qzb.2_5'UTR|KIDINS220_uc002qze.2_Missense_Mutation_p.P104Q	NM_020738	NP_065789	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate of 220 kDa	1099	Cytoplasmic (Potential).				activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GCACACGGATGGGGGCTGGCT	0.622													5	36	---	---	---	---	PASS
LRPPRC	10128	broad.mit.edu	37	2	44176772	44176772	+	Silent	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44176772T>A	uc002rtr.2	-	16	1762	c.1704A>T	c.(1702-1704)GGA>GGT	p.G568G	LRPPRC_uc010yob.1_Silent_p.G468G	NM_133259	NP_573566	P42704	LPPRC_HUMAN	leucine-rich PPR motif-containing protein	568					mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GGCAATAACGTCCATCCTTGT	0.398													35	99	---	---	---	---	PASS
PREPL	9581	broad.mit.edu	37	2	44559712	44559712	+	Silent	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44559712A>G	uc002ruf.2	-	8	1274	c.1239T>C	c.(1237-1239)CGT>CGC	p.R413R	PREPL_uc002rug.2_Intron|PREPL_uc002ruh.2_Silent_p.R351R|PREPL_uc010fax.2_Silent_p.R413R|PREPL_uc002rui.3_Silent_p.R324R|PREPL_uc002ruj.1_Silent_p.R324R|PREPL_uc002ruk.1_Silent_p.R413R	NM_006036	NP_006027	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like isoform C	413					proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				ATTTTGGGGGACGTATTGGAG	0.433													6	434	---	---	---	---	PASS
IWS1	55677	broad.mit.edu	37	2	128238565	128238565	+	3'UTR	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128238565A>G	uc002ton.2	-	14						NM_017969	NP_060439	Q96ST2	IWS1_HUMAN	IWS1 homolog						transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		TTCTTTCTCCAAAGAGTCCAT	0.388													49	132	---	---	---	---	PASS
DARS	1615	broad.mit.edu	37	2	136678057	136678057	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136678057T>C	uc002tux.1	-	10	1109	c.925A>G	c.(925-927)ACC>GCC	p.T309A	DARS_uc010fnj.1_Missense_Mutation_p.T209A	NM_001349	NP_001340	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	309					aspartyl-tRNA aminoacylation|protein complex assembly	cytosol|nuclear membrane|plasma membrane|soluble fraction	aminoacylase activity|aspartate-tRNA ligase activity|ATP binding|nucleic acid binding|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	TGTACCATGGTGTCAGCAATT	0.328													6	319	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152476170	152476170	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152476170T>C	uc010fnx.2	-	69	10129	c.9938A>G	c.(9937-9939)CAG>CGG	p.Q3313R		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	3313	Nebulin 90.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		ACGGTCACTCTGCACTTTGGC	0.478													35	90	---	---	---	---	PASS
GALNT13	114805	broad.mit.edu	37	2	155307077	155307077	+	3'UTR	SNP	C	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155307077C>A	uc002tyr.3	+	13					GALNT13_uc002tyt.3_3'UTR|GALNT13_uc010fod.2_3'UTR|uc002tyu.1_Intron	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						TCATGTCCTCCAAGCCATGAA	0.393													6	27	---	---	---	---	PASS
SCN3A	6328	broad.mit.edu	37	2	165947583	165947583	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165947583T>C	uc002ucx.2	-	28	5572	c.5080A>G	c.(5080-5082)ACC>GCC	p.T1694A	SCN3A_uc010zcy.1_Missense_Mutation_p.T177A|SCN3A_uc002ucy.2_Missense_Mutation_p.T1645A|SCN3A_uc002ucz.2_Missense_Mutation_p.T1645A	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	1694						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)	TTGCCAAAGGTCTCAAAGTTG	0.443													6	255	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179435409	179435409	+	Silent	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179435409C>T	uc010zfg.1	-	275	67970	c.67746G>A	c.(67744-67746)CAG>CAA	p.Q22582Q	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.Q16277Q|TTN_uc010zfi.1_Silent_p.Q16210Q|TTN_uc010zfj.1_Silent_p.Q16085Q	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23509							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTGAAAGCTCCTGATCACCTT	0.413													98	260	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179613662	179613662	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179613662T>C	uc002unb.2	-	46	13689	c.13465A>G	c.(13465-13467)AAG>GAG	p.K4489E	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	619							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCATCAATCTTCTTTTGAGGA	0.323													5	239	---	---	---	---	PASS
ASNSD1	54529	broad.mit.edu	37	2	190532496	190532496	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190532496C>G	uc002uqt.2	+	5	1905	c.1471C>G	c.(1471-1473)CTC>GTC	p.L491V		NM_019048	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1	491	Asparagine synthetase.				asparagine biosynthetic process|glutamine metabolic process		asparagine synthase (glutamine-hydrolyzing) activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)			ATAGGTAGTTCTCACTGGAAT	0.358													90	208	---	---	---	---	PASS
ERBB4	2066	broad.mit.edu	37	2	212426491	212426491	+	Intron	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212426491T>A	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_3'UTR	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		ACCTCTCTGTTATGTATCTTT	0.269										TSP Lung(8;0.080)			7	12	---	---	---	---	PASS
ATG4B	23192	broad.mit.edu	37	2	242606247	242606247	+	Silent	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242606247G>T	uc002wbv.2	+	8	829	c.726G>T	c.(724-726)ACG>ACT	p.T242T	ATG4B_uc002wbu.2_Silent_p.T168T|ATG4B_uc002wbw.2_Silent_p.T242T|ATG4B_uc010zox.1_Silent_p.T228T|ATG4B_uc010zoy.1_Silent_p.T168T|ATG4B_uc010fzp.2_Silent_p.T242T|ATG4B_uc010zoz.1_Silent_p.T168T|ATG4B_uc002wby.2_5'Flank	NM_013325	NP_037457	Q9Y4P1	ATG4B_HUMAN	APG4 autophagy 4 homolog B isoform a	242					autophagic vacuole assembly|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		ACGTGGAGACGCTGAAGGTGG	0.622													7	13	---	---	---	---	PASS
PTH1R	5745	broad.mit.edu	37	3	46939429	46939429	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46939429A>G	uc003cqm.2	+	6	601	c.398A>G	c.(397-399)GAC>GGC	p.D133G	PTH1R_uc003cqn.2_Missense_Mutation_p.D133G	NM_000316	NP_000307	Q03431	PTH1R_HUMAN	parathyroid hormone receptor 1 precursor	133	Extracellular (Potential).					cytoplasm|integral to plasma membrane|nucleus	parathyroid hormone receptor activity|peptide hormone binding|protein self-association			breast(1)	1						CCCTGTCCGGACTACATTTAT	0.612									Ollier_disease_/_Maffuci_syndrome				27	30	---	---	---	---	PASS
ALAS1	211	broad.mit.edu	37	3	52233311	52233311	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52233311T>G	uc003dcy.1	+	3	391	c.54T>G	c.(52-54)TTT>TTG	p.F18L	ALAS1_uc003dcx.1_Missense_Mutation_p.F18L|ALAS1_uc003dcz.1_Missense_Mutation_p.F18L|ALAS1_uc011bec.1_Missense_Mutation_p.F35L	NM_000688	NP_000679	P13196	HEM1_HUMAN	5-aminolevulinate synthase 1 precursor	18					heme biosynthetic process	mitochondrial matrix	5-aminolevulinate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(2)|upper_aerodigestive_tract(1)	3				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	CCCAGGCCTTTCTGCAGAAAG	0.542													8	25	---	---	---	---	PASS
EPHA6	285220	broad.mit.edu	37	3	96533798	96533798	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96533798T>A	uc010how.1	+	1	374	c.331T>A	c.(331-333)TTG>ATG	p.L111M	EPHA6_uc003drp.1_Missense_Mutation_p.L111M	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	17						integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						TGGTTTCTTCTTGCCTCTGCT	0.587													12	23	---	---	---	---	PASS
CPOX	1371	broad.mit.edu	37	3	98299342	98299342	+	3'UTR	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98299342T>A	uc003dsx.2	-	7						NM_000097	NP_000088	P36551	HEM6_HUMAN	coproporphyrinogen oxidase precursor							mitochondrial intermembrane space	coproporphyrinogen oxidase activity|protein homodimerization activity				0						ACTCTGACAATCTGCCATCTC	0.398													6	7	---	---	---	---	PASS
BBX	56987	broad.mit.edu	37	3	107463494	107463494	+	Silent	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107463494C>T	uc010hpr.2	+	8	1014	c.687C>T	c.(685-687)TGC>TGT	p.C229C	BBX_uc003dwk.3_Silent_p.C229C|BBX_uc003dwl.3_Silent_p.C229C|BBX_uc010hps.1_Silent_p.C250C|BBX_uc003dwm.3_Silent_p.C229C	NM_001142568	NP_001136040	Q8WY36	BBX_HUMAN	HMG-BOX transcription factor BBX isoform 1	229					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(3;0.112)			CTGGCACATGCAGGCCTGATG	0.343													37	117	---	---	---	---	PASS
ROPN1B	152015	broad.mit.edu	37	3	125702160	125702160	+	Silent	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125702160G>A	uc003eih.2	+	6	864	c.636G>A	c.(634-636)GAG>GAA	p.E212E	ROPN1B_uc010hsb.2_Silent_p.E212E|ROPN1B_uc010hsc.2_Silent_p.E120E	NM_001012337	NP_001012337	Q9BZX4	ROP1B_HUMAN	ropporin, rhophilin associated protein 1B	212	Interaction with RHPN1 (By similarity).				acrosome reaction|cell-cell adhesion|cytokinesis|fusion of sperm to egg plasma membrane|Rho protein signal transduction|sperm motility|spermatogenesis	cytoplasm|flagellum	cAMP-dependent protein kinase regulator activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling complex scaffold activity				0				GBM - Glioblastoma multiforme(114;0.151)		TTTGGCTGGAGTAACAGCACA	0.373													58	218	---	---	---	---	PASS
PIK3R4	30849	broad.mit.edu	37	3	130463550	130463550	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130463550C>A	uc003enj.2	-	2	1094	c.513G>T	c.(511-513)AAG>AAT	p.K171N		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	171	Protein kinase.				fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12						GATAAGTGGGCTTAAAACTGG	0.423													61	149	---	---	---	---	PASS
IL20RB	53833	broad.mit.edu	37	3	136677034	136677034	+	Silent	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136677034T>C	uc003eri.1	+	1	328	c.79T>C	c.(79-81)TTG>CTG	p.L27L	IL20RB_uc003erj.1_RNA	NM_144717	NP_653318	Q6UXL0	I20RB_HUMAN	interleukin 20 receptor beta precursor	27						integral to membrane	receptor activity			ovary(1)	1						GATTCCATGTTTGCTCACAGG	0.383													6	424	---	---	---	---	PASS
PLSCR4	57088	broad.mit.edu	37	3	145914562	145914562	+	Missense_Mutation	SNP	G	C	C	rs149266233		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145914562G>C	uc010huy.2	-	7	972	c.643C>G	c.(643-645)CCT>GCT	p.P215A	PLSCR4_uc010huz.2_Missense_Mutation_p.P215A|PLSCR4_uc003evt.3_Missense_Mutation_p.P215A|PLSCR4_uc010hva.2_Missense_Mutation_p.P125A|PLSCR4_uc003evu.3_Missense_Mutation_p.P110A	NM_001128305	NP_001121777	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4 isoform a	215	Cytoplasmic (By similarity).				blood coagulation|phospholipid scrambling	integral to membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding				0						GTGACACCAGGAGGACACTGC	0.458													40	103	---	---	---	---	PASS
DHX36	170506	broad.mit.edu	37	3	154002429	154002429	+	Silent	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154002429T>C	uc003ezy.3	-	19	2316	c.2235A>G	c.(2233-2235)AGA>AGG	p.R745R	DHX36_uc010hvq.2_Silent_p.R731R|DHX36_uc003ezz.3_Intron	NM_020865	NP_065916	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	745						cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CCAATTCCTTTCTTCTTGCAT	0.313													13	622	---	---	---	---	PASS
PLCH1	23007	broad.mit.edu	37	3	155212209	155212209	+	Silent	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155212209G>A	uc011bok.1	-	15	2233	c.1956C>T	c.(1954-1956)CTC>CTT	p.L652L	PLCH1_uc011boj.1_Silent_p.L652L|PLCH1_uc011bol.1_Silent_p.L634L	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	652	PI-PLC Y-box.				lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			AAATCCTCGTGAGTTGCTTTT	0.453													118	315	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511214	195511214	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511214G>C	uc011bto.1	-	2	7697	c.7237C>G	c.(7237-7239)CAC>GAC	p.H2413D	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGGGTGGCGTGACCTGTGGAT	0.592													4	56	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511396	195511396	+	Missense_Mutation	SNP	G	A	A	rs147224082	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511396G>A	uc011bto.1	-	2	7515	c.7055C>T	c.(7054-7056)CCT>CTT	p.P2352L	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GACATGAAGAGGGGTGGCGTG	0.582													3	32	---	---	---	---	PASS
SENP5	205564	broad.mit.edu	37	3	196626890	196626890	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196626890A>G	uc003fwz.3	+	4	1964	c.1715A>G	c.(1714-1716)GAC>GGC	p.D572G	SENP5_uc011bty.1_Missense_Mutation_p.D572G	NM_152699	NP_689912	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	572	Protease.				cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		CTGGATATGGACGACCTGGCG	0.388													5	207	---	---	---	---	PASS
RGS12	6002	broad.mit.edu	37	4	3318132	3318132	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3318132G>T	uc003ggw.2	+	2	1139	c.235G>T	c.(235-237)GAT>TAT	p.D79Y	RGS12_uc003ggu.2_Missense_Mutation_p.D79Y|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_RNA|RGS12_uc003ggv.2_Missense_Mutation_p.D79Y|RGS12_uc003ggx.1_Missense_Mutation_p.D79Y	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	79	PDZ.					condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ATCTCATGAAGATGTAGTGAA	0.507													18	53	---	---	---	---	PASS
EPHA5	2044	broad.mit.edu	37	4	66286268	66286268	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66286268G>A	uc003hcy.2	-	6	1611	c.1418C>T	c.(1417-1419)ACC>ATC	p.T473I	EPHA5_uc003hcx.2_Missense_Mutation_p.T404I|EPHA5_uc003hcz.2_Missense_Mutation_p.T473I|EPHA5_uc011cah.1_Missense_Mutation_p.T473I|EPHA5_uc011cai.1_Missense_Mutation_p.T473I|EPHA5_uc003hda.2_Missense_Mutation_p.T473I	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	473	Extracellular (Potential).|Fibronectin type-III 2.				cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity	p.T473T(1)		lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						TTTCACATTGGTGACTGGAGA	0.353										TSP Lung(17;0.13)			5	484	---	---	---	---	PASS
HPSE	10855	broad.mit.edu	37	4	84231973	84231973	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84231973T>A	uc003hoj.3	-	5	843	c.744A>T	c.(742-744)CAA>CAT	p.Q248H	HPSE_uc010ika.2_Missense_Mutation_p.Q190H|HPSE_uc011ccq.1_Intron|HPSE_uc011ccr.1_RNA|HPSE_uc011ccs.1_Intron|HPSE_uc011cct.1_Missense_Mutation_p.Q248H|HPSE_uc003hok.3_Missense_Mutation_p.Q248H	NM_001098540	NP_001092010	Q9Y251	HPSE_HUMAN	heparanase precursor	248					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)	GTTTATGCAATTGAATAAAAT	0.373													65	169	---	---	---	---	PASS
SPP1	6696	broad.mit.edu	37	4	88904007	88904007	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88904007A>G	uc003hra.2	+	7	1069	c.904A>G	c.(904-906)ATT>GTT	p.I302V	SPP1_uc003hrb.2_Missense_Mutation_p.I275V|SPP1_uc003hrc.2_Missense_Mutation_p.I288V|SPP1_uc011cde.1_Missense_Mutation_p.I315V|SPP1_uc003hrd.2_Missense_Mutation_p.I261V	NM_001040058	NP_001035147	P10451	OSTP_HUMAN	secreted phosphoprotein 1 isoform a	302					biomineral tissue development|cell adhesion|decidualization|embryo implantation|ossification|response to vitamin D	extracellular space	cytokine activity			ovary(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		GAAATTTCGTATTTCTCATGA	0.348													39	102	---	---	---	---	PASS
SLC30A5	64924	broad.mit.edu	37	5	68414453	68414453	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68414453A>G	uc003jvh.2	+	12	1768	c.1567A>G	c.(1567-1569)ACA>GCA	p.T523A	SLC30A5_uc003jvj.2_RNA|SLC30A5_uc003jvk.2_Missense_Mutation_p.T252A|SLC30A5_uc003jvi.2_Missense_Mutation_p.T352A	NM_022902	NP_075053	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter),	523	Helical; (Potential).				cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity			central_nervous_system(1)	1		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TCACATGTTAACAGTAAGTCT	0.299													7	552	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75469440	75469440	+	Intron	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75469440A>G	uc003kei.1	+						uc003kej.2_RNA	NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						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)		CAGAGCTACAATGCATTTAGT	0.418													7	197	---	---	---	---	PASS
FAM170A	340069	broad.mit.edu	37	5	118969970	118969970	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118969970T>C	uc003ksm.2	+	3	737	c.527T>C	c.(526-528)GTG>GCG	p.V176A	FAM170A_uc003ksl.2_Intron|FAM170A_uc003ksn.2_Missense_Mutation_p.V176A|FAM170A_uc003kso.2_Missense_Mutation_p.V129A	NM_182761	NP_877438	A1A519	F170A_HUMAN	family with sequence similarity 170, member A	176						intracellular	zinc ion binding			skin(1)	1						CCCTCTGATGTGTCCACCAGA	0.537													18	58	---	---	---	---	PASS
KIF3A	11127	broad.mit.edu	37	5	132039206	132039206	+	Missense_Mutation	SNP	T	C	C	rs35700526		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132039206T>C	uc003kxo.2	-	10	1488	c.1334A>G	c.(1333-1335)AAC>AGC	p.N445S	KIF3A_uc003kxm.2_Missense_Mutation_p.N27S|KIF3A_uc003kxn.2_Missense_Mutation_p.N430S|KIF3A_uc011cxf.1_Missense_Mutation_p.N472S|KIF3A_uc003kxp.2_Missense_Mutation_p.N448S	NM_007054	NP_008985	Q9Y496	KIF3A_HUMAN	kinesin family member 3A	445	Potential.				blood coagulation|organelle organization|plus-end-directed vesicle transport along microtubule	centrosome|cytosol|kinesin II complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|protein binding			pancreas(1)	1		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTAGCCTTGTTTCTTTCTTC	0.348													7	757	---	---	---	---	PASS
CTNNA1	1495	broad.mit.edu	37	5	138163310	138163310	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138163310C>T	uc003ldh.2	+	7	1060	c.965C>T	c.(964-966)TCG>TTG	p.S322L	CTNNA1_uc011cyx.1_Missense_Mutation_p.S219L|CTNNA1_uc011cyy.1_Missense_Mutation_p.S199L|CTNNA1_uc003ldi.2_Missense_Mutation_p.S20L|CTNNA1_uc003ldj.2_Missense_Mutation_p.S322L	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1	322					adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ATGGCCGACTCGTCCTGCACG	0.582													32	120	---	---	---	---	PASS
FLT4	2324	broad.mit.edu	37	5	180036981	180036981	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180036981G>A	uc003mma.3	-	28	3810	c.3731C>T	c.(3730-3732)GCT>GTT	p.A1244V	FLT4_uc003mlz.3_Missense_Mutation_p.A1244V	NM_002020	NP_002011	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 2	1244	Cytoplasmic (Potential).				positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)	ACGGGTCTCAGCCCCTCTGGC	0.572									Congenital_Hereditary_Lymphedema				24	79	---	---	---	---	PASS
TUBB2B	347733	broad.mit.edu	37	6	3225818	3225818	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3225818C>T	uc003mvg.2	-	4	696	c.505G>A	c.(505-507)GTC>ATC	p.V169I	TUBB2B_uc010jnj.2_Missense_Mutation_p.V132I|TUBB2B_uc010jnk.2_Missense_Mutation_p.V97I|TUBB2B_uc003mvh.2_Missense_Mutation_p.V142I|uc011dhu.1_RNA	NM_178012	NP_821080	Q9BVA1	TBB2B_HUMAN	tubulin, beta 2B	169					'de novo' posttranslational protein folding|microtubule-based movement|neuron migration|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			large_intestine(1)	1	Ovarian(93;0.0386)	all_hematologic(90;0.108)				GAGGGCATGACGCTGAAGGTG	0.607													20	57	---	---	---	---	PASS
GMPR	2766	broad.mit.edu	37	6	16250558	16250558	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16250558A>G	uc003nbs.2	+	3	365	c.251A>G	c.(250-252)GAC>GGC	p.D84G		NM_006877	NP_006868	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	84					nucleotide metabolic process|purine base metabolic process|purine-containing compound salvage|response to cold	cytosol	GMP reductase activity|metal ion binding			ovary(1)	1	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				TCCCTGGATGACTGGAAGCTC	0.488													5	202	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38891033	38891033	+	Intron	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38891033T>C	uc003ooe.1	+						uc003oof.1_RNA	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						CATTTCCATGTGTTCATCTCT	0.358													12	25	---	---	---	---	PASS
TAF8	129685	broad.mit.edu	37	6	42025358	42025358	+	Intron	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42025358G>T	uc003ors.2	+						TAF8_uc003orr.2_3'UTR|TAF8_uc003ort.2_Intron|TAF8_uc003oru.1_Intron|TAF8_uc003orv.1_Intron|TAF8_uc011dun.1_Intron	NM_138572	NP_612639	Q7Z7C8	TAF8_HUMAN	TBP-associated factor 8						cell differentiation|maintenance of protein location in nucleus|positive regulation of transcription, DNA-dependent|regulation of fat cell differentiation|transcription, DNA-dependent	perinuclear region of cytoplasm|transcription factor TFIID complex	DNA binding|protein binding			ovary(1)	1	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00179)			TGAAAGAGTGGTTCAAAACTC	0.289													6	14	---	---	---	---	PASS
SLC22A7	10864	broad.mit.edu	37	6	43272209	43272209	+	Intron	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43272209T>C	uc003out.2	+						SLC22A7_uc003ous.2_3'UTR	NM_153320	NP_696961	Q9Y694	S22A7_HUMAN	solute carrier family 22 member 7 isoform b							basolateral plasma membrane|integral to plasma membrane|membrane fraction	anion:anion antiporter activity|sodium-independent organic anion transmembrane transporter activity				0			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			TACATAAGGTTGTTCAGGAAG	0.448													7	9	---	---	---	---	PASS
LIN28B	389421	broad.mit.edu	37	6	105526668	105526668	+	3'UTR	SNP	T	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105526668T>G	uc003pqv.1	+	4					LIN28B_uc010kda.1_3'UTR	NM_001004317	NP_001004317	Q6ZN17	LN28B_HUMAN	lin-28 homolog B						miRNA catabolic process|pre-miRNA processing|regulation of transcription, DNA-dependent|RNA 3'-end processing	cytoplasm|nucleus	DNA binding|protein binding|RNA binding|zinc ion binding				0		all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204)				ACAGGTCTTCTTCATATGTTC	0.418													22	53	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152665354	152665354	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152665354C>A	uc010kiw.2	-	74	12689	c.12087G>T	c.(12085-12087)CAG>CAT	p.Q4029H	SYNE1_uc003qot.3_Missense_Mutation_p.Q3958H|SYNE1_uc003qou.3_Missense_Mutation_p.Q4029H|SYNE1_uc010kja.1_Missense_Mutation_p.Q734H	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4029	Spectrin 10.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GTTCCAAACTCTGGTACATCT	0.453										HNSCC(10;0.0054)			20	71	---	---	---	---	PASS
CPSF4	10898	broad.mit.edu	37	7	99045873	99045873	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99045873A>T	uc003uqj.2	+	3	427	c.284A>T	c.(283-285)GAG>GTG	p.E95V	PTCD1_uc011kiw.1_Intron|CPSF4_uc003uqi.2_Missense_Mutation_p.E95V|CPSF4_uc003uqk.2_Missense_Mutation_p.E95V|CPSF4_uc011kix.1_Missense_Mutation_p.E42V	NM_006693	NP_006684	O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4,	95	C3H1-type 3.				modification by virus of host mRNA processing|mRNA processing|viral infectious cycle	mRNA cleavage and polyadenylation specificity factor complex	RNA binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					AAGATGCCCGAGTGCTACTTC	0.577													24	113	---	---	---	---	PASS
PILRA	29992	broad.mit.edu	37	7	99997510	99997510	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99997510T>A	uc003uuo.1	+	7	1104	c.892T>A	c.(892-894)TAC>AAC	p.Y298N	PILRA_uc011kjo.1_Missense_Mutation_p.V212E|PILRA_uc003uup.1_Missense_Mutation_p.Y225N|PILRA_uc003uuq.1_3'UTR	NM_013439	NP_038467	Q9UKJ1	PILRA_HUMAN	paired immunoglobulin-like type 2 receptor alpha	298	ITIM motif 2.|Cytoplasmic (Potential).				interspecies interaction between organisms	extracellular region|integral to membrane|plasma membrane	protein binding|receptor activity			skin(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CGAGACCCTGTACTCTGTCTT	0.448													37	134	---	---	---	---	PASS
ATXN7L1	222255	broad.mit.edu	37	7	105254533	105254533	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105254533G>T	uc003vde.2	-	10	2275	c.2248C>A	c.(2248-2250)CTT>ATT	p.L750I	ATXN7L1_uc003vdf.2_Missense_Mutation_p.L626I|ATXN7L1_uc003vdg.3_Missense_Mutation_p.L410I|ATXN7L1_uc003vdh.3_Missense_Mutation_p.L534I	NM_020725	NP_065776	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1 isoform 1	750	Ser-rich.										0						TGGAGCGCAAGGGAGGGCACA	0.612													16	49	---	---	---	---	PASS
PRKAR2B	5577	broad.mit.edu	37	7	106781322	106781322	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106781322T>C	uc003vdx.2	+	5	686	c.511T>C	c.(511-513)TTT>CTT	p.F171L		NM_002736	NP_002727	P31323	KAP3_HUMAN	cAMP-dependent protein kinase, regulatory	171	cAMP 1.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G2/M transition of mitotic cell cycle|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|transmembrane transport|water transport	centrosome|cytosol|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity			ovary(1)	1						AGATGCCATGTTTGAAAAATT	0.328													7	470	---	---	---	---	PASS
MCPH1	79648	broad.mit.edu	37	8	6302811	6302811	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6302811A>G	uc003wqi.2	+	8	1636	c.1568A>G	c.(1567-1569)AAT>AGT	p.N523S	MCPH1_uc003wqh.2_Missense_Mutation_p.N523S|MCPH1_uc011kwl.1_Missense_Mutation_p.N475S	NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin	523						microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		CCAGAGGGAAATGGCTTTTCT	0.488													20	45	---	---	---	---	PASS
INTS9	55756	broad.mit.edu	37	8	28625658	28625658	+	3'UTR	SNP	C	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28625658C>G	uc003xha.2	-	17					INTS9_uc011lav.1_3'UTR|INTS9_uc011law.1_3'UTR|INTS9_uc011lax.1_3'UTR|INTS9_uc010lvc.2_RNA	NM_018250	NP_060720	Q9NV88	INT9_HUMAN	integrator complex subunit 9 isoform 1						snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		GCTCAGATGGCCCACTCAGAA	0.517													12	68	---	---	---	---	PASS
PRDM14	63978	broad.mit.edu	37	8	70981476	70981476	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70981476T>C	uc003xym.2	-	2	822	c.620A>G	c.(619-621)TAC>TGC	p.Y207C		NM_024504	NP_078780	Q9GZV8	PRD14_HUMAN	PR domain containing 14	207					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			AGTGACCCCGTACAGAACGAA	0.602													11	37	---	---	---	---	PASS
SLC7A13	157724	broad.mit.edu	37	8	87229856	87229856	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87229856A>G	uc003ydq.1	-	3	1120	c.1022T>C	c.(1021-1023)CTA>CCA	p.L341P	SLC7A13_uc003ydr.1_Missense_Mutation_p.L332P	NM_138817	NP_620172	Q8TCU3	S7A13_HUMAN	solute carrier family 7, (cationic amino acid	341	Helical; Name=9; (Potential).					integral to membrane	amino acid transmembrane transporter activity			central_nervous_system(1)	1						GACAAGTAGTAGCACAGCTGT	0.343													4	82	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113237062	113237062	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113237062A>G	uc003ynu.2	-	71	11221	c.11062T>C	c.(11062-11064)TCA>CCA	p.S3688P	CSMD3_uc003yns.2_Missense_Mutation_p.S2890P|CSMD3_uc003ynt.2_Missense_Mutation_p.S3648P|CSMD3_uc011lhx.1_Missense_Mutation_p.S3519P	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3688	Cytoplasmic (Potential).					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						CCTTCCACTGACTTTGCGTTG	0.443										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			183	452	---	---	---	---	PASS
TOPORS	10210	broad.mit.edu	37	9	32542420	32542420	+	Silent	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32542420T>C	uc003zrb.2	-	3	2270	c.2103A>G	c.(2101-2103)AAA>AAG	p.K701K	TOPORS_uc003zrc.2_Silent_p.K634K	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	701	Interaction with TOP1.|Arg-rich.|Interaction with p53/TP53.				DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TATACTCCCATTTGTATCTGC	0.393													5	216	---	---	---	---	PASS
TMOD1	7111	broad.mit.edu	37	9	100331319	100331319	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100331319G>T	uc004axk.1	+	8	1083	c.870G>T	c.(868-870)CAG>CAT	p.Q290H	TMOD1_uc004axl.1_Missense_Mutation_p.Q290H	NM_003275	NP_003266	P28289	TMOD1_HUMAN	tropomodulin 1	290					muscle filament sliding	cytosol	actin binding				0		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)		TTGACAACCAGGTGAGATGGG	0.498													26	43	---	---	---	---	PASS
OR13C8	138802	broad.mit.edu	37	9	107331603	107331603	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107331603A>G	uc011lvo.1	+	1	155	c.155A>G	c.(154-156)GAT>GGT	p.D52G		NM_001004483	NP_001004483	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C,	52	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						ATCATCTTTGATTCTCACCTG	0.443													162	218	---	---	---	---	PASS
UAP1L1	91373	broad.mit.edu	37	9	139973455	139973455	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139973455T>C	uc010ncb.2	+	4	730	c.698T>C	c.(697-699)CTG>CCG	p.L233P	UAP1L1_uc004cla.3_Missense_Mutation_p.L110P	NM_207309	NP_997192	Q3KQV9	UAP1L_HUMAN	UDP-N-acteylglucosamine pyrophosphorylase 1-like	233							nucleotidyltransferase activity			ovary(1)	1	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		TACTGCGCGCTGGAGGACCAC	0.647													16	35	---	---	---	---	PASS
DIP2C	22982	broad.mit.edu	37	10	323257	323257	+	3'UTR	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:323257A>G	uc001ifp.2	-	37						NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GGAAGCCAAGAGACGAGACTA	0.517													17	35	---	---	---	---	PASS
NET1	10276	broad.mit.edu	37	10	5498060	5498060	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5498060T>C	uc001iia.2	+	11	1346	c.1208T>C	c.(1207-1209)ATT>ACT	p.I403T	NET1_uc010qar.1_Missense_Mutation_p.I222T|NET1_uc001iib.2_Missense_Mutation_p.I349T|NET1_uc010qas.1_Missense_Mutation_p.I222T	NM_001047160	NP_001040625	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming gene 1 isoform	403	PH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell growth|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	Rho guanyl-nucleotide exchange factor activity			breast(1)	1						AAACTTTACATTTTCCTGTTT	0.403													13	39	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	17026201	17026201	+	Silent	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17026201C>T	uc001ioo.2	-	30	4480	c.4428G>A	c.(4426-4428)CAG>CAA	p.Q1476Q		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1476	CUB 9.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGCTGGAGACCTGCATGGGGT	0.498													5	269	---	---	---	---	PASS
SVIL	6840	broad.mit.edu	37	10	29815982	29815982	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29815982T>G	uc001iut.1	-	13	3003	c.2250A>C	c.(2248-2250)GAA>GAC	p.E750D	SVIL_uc001iuu.1_Intron	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	750					cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)				CGGGGATAGGTTCACTTTAAA	0.468													16	38	---	---	---	---	PASS
MARCH8	220972	broad.mit.edu	37	10	45953559	45953559	+	3'UTR	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45953559G>A	uc001jci.1	-	7					MARCH8_uc001jch.2_3'UTR|MARCH8_uc001jcj.1_3'UTR|MARCH8_uc001jck.1_3'UTR|uc001jcf.2_5'Flank|MARCH8_uc001jcg.1_3'UTR	NM_001002266	NP_001002266	Q5T0T0	MARH8_HUMAN	cellular modulator of immune recognition isoform							cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0						TAGAAAAAGAGAAGCCACTAT	0.458													3	7	---	---	---	---	PASS
ANK3	288	broad.mit.edu	37	10	62029966	62029966	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62029966T>C	uc001jky.2	-	5	628	c.436A>G	c.(436-438)ATG>GTG	p.M146V	ANK3_uc010qih.1_Missense_Mutation_p.M129V|ANK3_uc001jkz.3_Missense_Mutation_p.M140V|ANK3_uc001jlb.1_Translation_Start_Site	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	146	ANK 3.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						TGGGCTGCCATATACAATGGC	0.398													4	118	---	---	---	---	PASS
C10orf12	26148	broad.mit.edu	37	10	98743198	98743198	+	Missense_Mutation	SNP	T	G	G	rs149307894		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98743198T>G	uc001kmv.2	+	1	2158	c.2051T>G	c.(2050-2052)GTA>GGA	p.V684G		NM_015652	NP_056467	Q8N655	CJ012_HUMAN	hypothetical protein LOC26148	684										skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		GTGAATGAGGTAGACAACGAA	0.512													20	34	---	---	---	---	PASS
PPRC1	23082	broad.mit.edu	37	10	103901173	103901173	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103901173G>A	uc001kum.2	+	5	2947	c.2908G>A	c.(2908-2910)GTC>ATC	p.V970I	PPRC1_uc001kun.2_Missense_Mutation_p.V850I|PPRC1_uc010qqj.1_Missense_Mutation_p.V970I|PPRC1_uc009xxa.2_RNA	NM_015062	NP_055877	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor	970	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		TCCTGCCCCAGTCTCACCTTA	0.627													12	34	---	---	---	---	PASS
GPR123	84435	broad.mit.edu	37	10	134896159	134896159	+	Silent	SNP	C	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134896159C>A	uc001llw.2	+	6	1245	c.1245C>A	c.(1243-1245)ACC>ACA	p.T415T				Q86SQ6	GP123_HUMAN	RecName: Full=Probable G-protein coupled receptor 123;	Error:Variant_position_missing_in_Q86SQ6_after_alignment						integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CCTACGAGACCCACGGCCTTG	0.612													11	36	---	---	---	---	PASS
IFITM1	8519	broad.mit.edu	37	11	314039	314039	+	5'UTR	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:314039T>C	uc001loy.3	+	1						NM_003641	NP_003632	P13164	IFM1_HUMAN	interferon induced transmembrane protein 1						negative regulation of cell proliferation|regulation of immune response|response to virus|type I interferon-mediated signaling pathway	integral to membrane|plasma membrane	protein binding|receptor signaling protein activity				0		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCTGAGAAACTGAAACGACAG	0.478													3	10	---	---	---	---	PASS
KRTAP5-5	439915	broad.mit.edu	37	11	1651231	1651231	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1651231G>T	uc001lty.2	+	1	199	c.161G>T	c.(160-162)GGC>GTC	p.G54V		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	54						keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ggctgtgcgggctgtggggga	0.229													5	9	---	---	---	---	PASS
OR52W1	120787	broad.mit.edu	37	11	6220794	6220794	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6220794C>A	uc010qzz.1	+	1	341	c.341C>A	c.(340-342)GCC>GAC	p.A114D		NM_001005178	NP_001005178	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W,	114	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCACTGACTGCCATGGAATCA	0.572													17	47	---	---	---	---	PASS
OR52W1	120787	broad.mit.edu	37	11	6220795	6220795	+	Silent	SNP	C	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6220795C>A	uc010qzz.1	+	1	342	c.342C>A	c.(340-342)GCC>GCA	p.A114A		NM_001005178	NP_001005178	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W,	114	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACTGACTGCCATGGAATCAG	0.572													17	48	---	---	---	---	PASS
CCDC73	493860	broad.mit.edu	37	11	32637578	32637578	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32637578T>A	uc001mtv.2	-	15	1327	c.1283A>T	c.(1282-1284)GAA>GTA	p.E428V	CCDC73_uc001mtw.1_Missense_Mutation_p.E418V	NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	428										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)					CATATTTTCTTCCCTTATTTC	0.279													75	196	---	---	---	---	PASS
ALKBH3	221120	broad.mit.edu	37	11	43941471	43941471	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43941471C>T	uc001mxs.2	+	10	1215	c.772C>T	c.(772-774)CGA>TGA	p.R258*	ALKBH3_uc009ykp.2_RNA|ALKBH3_uc001mxt.2_RNA|ALKBH3_uc009ykq.2_Nonsense_Mutation_p.R111*|uc001mxu.1_Intron	NM_139178	NP_631917	Q96Q83	ALKB3_HUMAN	AlkB homolog 3	258	Fe2OG dioxygenase.				DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation	mitochondrion|nucleoplasm	damaged DNA binding|DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0					Vitamin C(DB00126)	CATTTAGCATCGAGTGCCCAA	0.423								Direct_reversal_of_damage					4	197	---	---	---	---	PASS
OR5M1	390168	broad.mit.edu	37	11	56380039	56380039	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56380039C>A	uc001nja.1	-	1	940	c.940G>T	c.(940-942)GCA>TCA	p.A314S		NM_001004740	NP_001004740	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M,	314	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1						GCCTAAACTGCAATTTTATGA	0.378													46	116	---	---	---	---	PASS
CD248	57124	broad.mit.edu	37	11	66082704	66082704	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66082704G>A	uc001ohm.1	-	1	1812	c.1795C>T	c.(1795-1797)CCT>TCT	p.P599S		NM_020404	NP_065137	Q9HCU0	CD248_HUMAN	tumor endothelial marker 1 precursor	599	Pro-rich.|Extracellular (Potential).					integral to membrane|proteinaceous extracellular matrix	calcium ion binding|sugar binding			large_intestine(3)	3					Cefalotin(DB00456)	GGAGACACAGGGGACCTGGAG	0.642													4	204	---	---	---	---	PASS
ARAP1	116985	broad.mit.edu	37	11	72404351	72404351	+	Intron	SNP	A	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72404351A>T	uc001osu.2	-						ARAP1_uc001osv.2_Intron|ARAP1_uc001osr.2_Intron|ARAP1_uc001oss.2_Intron|ARAP1_uc009yth.2_Intron|ARAP1_uc010rre.1_Intron|uc009yti.1_RNA	NM_001040118	NP_001035207	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH						actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding			skin(1)	1						CTGGGGCAGAACCCAGCGGGG	0.592													8	20	---	---	---	---	PASS
GPR83	10888	broad.mit.edu	37	11	94134089	94134089	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94134089A>G	uc001pet.2	-	1	497	c.325T>C	c.(325-327)TTC>CTC	p.F109L		NM_016540	NP_057624	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83 precursor	109	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			central_nervous_system(2)|ovary(1)	3		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TTGACGATGAAGAGGCTGGTG	0.537													5	83	---	---	---	---	PASS
MAML2	84441	broad.mit.edu	37	11	95825407	95825407	+	Silent	SNP	C	T	T	rs60727839		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95825407C>T	uc001pfw.1	-	2	3073	c.1788G>A	c.(1786-1788)CAG>CAA	p.Q596Q		NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2	596					Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgtt	0.189			T	MECT1|CRTC3	salivary gland mucoepidermoid								4	79	---	---	---	---	PASS
TRPC6	7225	broad.mit.edu	37	11	101325815	101325815	+	Silent	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101325815T>C	uc001pgk.3	-	11	2927	c.2502A>G	c.(2500-2502)CAA>CAG	p.Q834Q	TRPC6_uc009ywy.2_Silent_p.Q718Q|TRPC6_uc009ywz.1_Silent_p.Q779Q	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	834	Cytoplasmic (Potential).				axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		TTATACTTGGTTGTTTATTGT	0.294													7	590	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	103058111	103058111	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103058111A>T	uc001pho.2	+	43	7080	c.6936A>T	c.(6934-6936)CAA>CAT	p.Q2312H	DYNC2H1_uc001phn.1_Missense_Mutation_p.Q2312H|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2312	AAA 3 (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GGTCCACTCAAATTGCTACAG	0.413													32	93	---	---	---	---	PASS
SDHD	6392	broad.mit.edu	37	11	111965721	111965721	+	3'UTR	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111965721T>C	uc001pmz.2	+	4						NM_003002	NP_002993	O14521	DHSD_HUMAN	succinate dehydrogenase complex, subunit D						respiratory electron transport chain|transport|tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain complex II	electron carrier activity|heme binding|succinate dehydrogenase activity|ubiquinone binding				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-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;6.13e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;1.05e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0515)	Succinic acid(DB00139)	CTTTGAAGAATTGATGTATGC	0.418			Mis|N|F|S			paraganglioma|pheochromocytoma			Familial_Paragangliomas|Carney-Stratakis_syndrome|Cowden_syndrome				3	11	---	---	---	---	PASS
SDHD	6392	broad.mit.edu	37	11	111965729	111965729	+	3'UTR	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111965729T>A	uc001pmz.2	+	4						NM_003002	NP_002993	O14521	DHSD_HUMAN	succinate dehydrogenase complex, subunit D						respiratory electron transport chain|transport|tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain complex II	electron carrier activity|heme binding|succinate dehydrogenase activity|ubiquinone binding				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-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;6.13e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;1.05e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0515)	Succinic acid(DB00139)	AATTGATGTATGCCTCTTTGC	0.408			Mis|N|F|S			paraganglioma|pheochromocytoma			Familial_Paragangliomas|Carney-Stratakis_syndrome|Cowden_syndrome				3	8	---	---	---	---	PASS
CEP164	22897	broad.mit.edu	37	11	117244472	117244472	+	Silent	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117244472G>A	uc001prc.2	+	10	1305	c.1158G>A	c.(1156-1158)CTG>CTA	p.L386L	CEP164_uc001prb.2_Silent_p.L386L|CEP164_uc010rxk.1_Silent_p.L360L|CEP164_uc001prf.2_RNA|CEP164_uc009yzp.1_RNA	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	386					cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		TCCAGGAACTGGAAATTAGTG	0.478													64	174	---	---	---	---	PASS
AMICA1	120425	broad.mit.edu	37	11	118071315	118071315	+	Missense_Mutation	SNP	G	A	A	rs148107592		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118071315G>A	uc001psk.2	-	7	959	c.785C>T	c.(784-786)CCG>CTG	p.P262L	AMICA1_uc001psg.2_Missense_Mutation_p.P72L|AMICA1_uc001psh.2_Missense_Mutation_p.P223L|AMICA1_uc009yzw.1_RNA|AMICA1_uc001psi.2_Missense_Mutation_p.P252L|AMICA1_uc001psj.2_Missense_Mutation_p.P251L|AMICA1_uc010rxw.1_Missense_Mutation_p.P223L|AMICA1_uc010rxx.1_Missense_Mutation_p.P262L|AMICA1_uc001psl.1_Missense_Mutation_p.P218L	NM_001098526	NP_001091996	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen	262	Extracellular (Potential).				blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	cell junction|integral to membrane				ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CAGGGCTGCCGGGGTCACCAG	0.522													36	122	---	---	---	---	PASS
TECTA	7007	broad.mit.edu	37	11	120989265	120989265	+	Silent	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120989265G>A	uc010rzo.1	+	6	1041	c.1041G>A	c.(1039-1041)TTG>TTA	p.L347L		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	347	VWFD 1.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GTGCCTACTTGCTGGCCCGAC	0.577													25	74	---	---	---	---	PASS
OR10G7	390265	broad.mit.edu	37	11	123909163	123909163	+	Silent	SNP	G	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123909163G>C	uc001pzq.1	-	1	546	c.546C>G	c.(544-546)CCC>CCG	p.P182P		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	182	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		GTTTCAGGATGGGCGGTGCGT	0.532													47	153	---	---	---	---	PASS
PKP2	5318	broad.mit.edu	37	12	32976986	32976986	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32976986T>C	uc001rlj.3	-	8	1914	c.1799A>G	c.(1798-1800)GAT>GGT	p.D600G	PKP2_uc001rlk.3_Missense_Mutation_p.D556G|PKP2_uc010skj.1_Missense_Mutation_p.D556G	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b	600	ARM 4.				cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					TACCTTGTCATCTGGCTGGTA	0.408													5	225	---	---	---	---	PASS
COL2A1	1280	broad.mit.edu	37	12	48376305	48376305	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48376305C>T	uc001rqu.2	-	34	2462	c.2281G>A	c.(2281-2283)GCT>ACT	p.A761T	COL2A1_uc009zkw.2_RNA|COL2A1_uc001rqv.2_Missense_Mutation_p.A692T	NM_001844	NP_001835	P02458	CO2A1_HUMAN	collagen, type II, alpha 1 isoform 1 precursor	761	Triple-helical region.				axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	TTGGGCCCAGCGATACCAGCT	0.632													9	19	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49422725	49422725	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49422725T>A	uc001rta.3	-	45	14268	c.14268A>T	c.(14266-14268)AAA>AAT	p.K4756N		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	4756					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						CCCCATAAGGTTTGGTATCTG	0.552			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			35	50	---	---	---	---	PASS
MAP3K12	7786	broad.mit.edu	37	12	53877445	53877445	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53877445A>G	uc001sdm.1	-	10	1420	c.1322T>C	c.(1321-1323)ATG>ACG	p.M441T	MAP3K12_uc001sdn.1_Missense_Mutation_p.M474T	NM_006301	NP_006292	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase	441					histone phosphorylation|JNK cascade|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation	cytosol|membrane fraction|plasma membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			lung(2)|ovary(1)|breast(1)|skin(1)	5						ATTAAGTTCCATATACAGGTT	0.547													31	99	---	---	---	---	PASS
LACRT	90070	broad.mit.edu	37	12	55026135	55026135	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55026135G>A	uc001sgi.1	-	3	181	c.143C>T	c.(142-144)GCA>GTA	p.A48V		NM_033277	NP_150593	Q9GZZ8	LACRT_HUMAN	lacritin precursor	48					calcineurin-NFAT signaling pathway|positive regulation of epithelial cell proliferation|positive regulation of NFAT protein import into nucleus|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of secretion|protein localization in Golgi apparatus|tear secretion	extracellular region|stored secretory granule	collagen binding|fibronectin binding|glycoprotein binding|growth factor activity|laminin-1 binding|protein N-terminus binding			central_nervous_system(1)	1						AGCTGGTTCTGCTGGACCTGA	0.502													83	209	---	---	---	---	PASS
SMARCC2	6601	broad.mit.edu	37	12	56567525	56567525	+	Silent	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56567525A>G	uc001skb.2	-	17	1711	c.1605T>C	c.(1603-1605)GCT>GCC	p.A535A	SMARCC2_uc001skd.2_Silent_p.A535A|SMARCC2_uc001ska.2_Silent_p.A535A|SMARCC2_uc001skc.2_Silent_p.A535A|SMARCC2_uc010sqf.1_Silent_p.A424A	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	535					chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)			ATGGTGTGTCAGCCAAGACAT	0.567													11	35	---	---	---	---	PASS
RAD9B	144715	broad.mit.edu	37	12	110941653	110941653	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110941653A>T	uc001trf.3	+	2	227	c.89A>T	c.(88-90)GAG>GTG	p.E30V	VPS29_uc001tqx.2_5'Flank|VPS29_uc001tqy.2_5'Flank|VPS29_uc001tqz.2_5'Flank|RAD9B_uc001trg.3_Missense_Mutation_p.E30V|RAD9B_uc010sya.1_Missense_Mutation_p.E30V|RAD9B_uc001tre.3_5'UTR|RAD9B_uc001trd.3_5'UTR	NM_152442	NP_689655	Q6WBX8	RAD9B_HUMAN	RAD9 homolog B	27					cell cycle checkpoint|DNA repair|DNA replication	nucleoplasm	protein binding			pancreas(1)|skin(1)	2						ATTAGTGACGAGTTCTGGCTA	0.363													4	232	---	---	---	---	PASS
TRAFD1	10906	broad.mit.edu	37	12	112586091	112586091	+	Missense_Mutation	SNP	G	A	A	rs142954248	byFrequency	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112586091G>A	uc001ttp.2	+	8	1227	c.1141G>A	c.(1141-1143)GTG>ATG	p.V381M	TRAFD1_uc001tto.2_Missense_Mutation_p.V381M|TRAFD1_uc010syj.1_RNA	NM_006700	NP_006691	O14545	TRAD1_HUMAN	TRAF-type zinc finger domain containing 1	381					negative regulation of innate immune response	intracellular	protein binding|zinc ion binding				0						GGAAGAGGAGGTGCTGTTCCA	0.522													40	88	---	---	---	---	PASS
NAA16	79612	broad.mit.edu	37	13	41932575	41932575	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41932575T>C	uc001uyf.2	+	11	1547	c.1223T>C	c.(1222-1224)ATA>ACA	p.I408T	NAA16_uc010tfg.1_RNA|NAA16_uc001uye.3_Missense_Mutation_p.I408T|NAA16_uc001uyd.3_3'UTR	NM_024561	NP_078837	Q6N069	NAA16_HUMAN	NMDA receptor regulated 1-like protein isoform	408					N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1						CCAACTCTAATAGAATTATTC	0.328													5	219	---	---	---	---	PASS
FBXL3	26224	broad.mit.edu	37	13	77581425	77581425	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77581425T>C	uc001vkd.2	-	5	1513	c.1142A>G	c.(1141-1143)AAG>AGG	p.K381R		NM_012158	NP_036290	Q9UKT7	FBXL3_HUMAN	F-box and leucine-rich repeat protein 3	381	LRR 7.				regulation of circadian rhythm|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity				0		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.218)		GBM - Glioblastoma multiforme(99;0.0521)		ACCACACATCTTCACAAACTC	0.413													5	188	---	---	---	---	PASS
CLYBL	171425	broad.mit.edu	37	13	100518550	100518550	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100518550G>A	uc001vok.2	+	6	705	c.691G>A	c.(691-693)GTC>ATC	p.V231I	CLYBL_uc010tix.1_Silent_p.L231L|CLYBL_uc010tiy.1_Missense_Mutation_p.V197I	NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like precursor	231					cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AAAGATTGTTGTCATAGCGAA	0.458													5	168	---	---	---	---	PASS
STRN3	29966	broad.mit.edu	37	14	31416465	31416465	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31416465G>T	uc001wqu.2	-	5	763	c.547C>A	c.(547-549)CTT>ATT	p.L183I	STRN3_uc001wqv.2_Missense_Mutation_p.L183I|STRN3_uc010tpj.1_RNA	NM_001083893	NP_001077362	Q13033	STRN3_HUMAN	nuclear autoantigen isoform 1	183	Calmodulin-binding (Potential).				negative regulation of estrogen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus	cytoplasm|dendrite|Golgi apparatus|neuronal cell body|nucleoplasm|nucleus|plasma membrane|protein complex	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		ACTTCCTGAAGATACCTGTAA	0.328													50	87	---	---	---	---	PASS
C15orf57	90416	broad.mit.edu	37	15	40824381	40824381	+	3'UTR	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40824381A>G	uc001zly.2	-	4					uc001zlx.1_Intron|MRPL42P5_uc010bbq.1_RNA|MRPL42P5_uc001zlz.1_RNA	NM_052849	NP_443081	Q9BV29	CO057_HUMAN	coiled-coil domain containing 32 isoform a											ovary(1)	1						ATTATTATACACAGGATCTGG	0.383													4	8	---	---	---	---	PASS
DUOX1	53905	broad.mit.edu	37	15	45453967	45453967	+	Silent	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45453967G>A	uc001zus.1	+	31	4234	c.3888G>A	c.(3886-3888)CAG>CAA	p.Q1296Q	DUOX1_uc001zut.1_Silent_p.Q1296Q|DUOX1_uc010bee.1_Silent_p.Q676Q	NM_017434	NP_059130	Q9NRD9	DUOX1_HUMAN	dual oxidase 1 precursor	1296	Cytoplasmic (Potential).|FAD-binding FR-type.				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		AGCGGCCCCAGGGCTTTGAGT	0.642													6	24	---	---	---	---	PASS
DUOX1	53905	broad.mit.edu	37	15	45453969	45453969	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45453969G>C	uc001zus.1	+	31	4236	c.3890G>C	c.(3889-3891)GGC>GCC	p.G1297A	DUOX1_uc001zut.1_Missense_Mutation_p.G1297A|DUOX1_uc010bee.1_Missense_Mutation_p.G677A	NM_017434	NP_059130	Q9NRD9	DUOX1_HUMAN	dual oxidase 1 precursor	1297	Cytoplasmic (Potential).|FAD-binding FR-type.				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CGGCCCCAGGGCTTTGAGTAC	0.637													5	26	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	31973467	31973467	+	RNA	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31973467T>A	uc002ect.2	+	1		c.59T>A								Homo sapiens IGH mRNA for immunoglobulin heavy chain VHDJ region, partial cds, clone:H186.																		TCCCTGAGACTCTCCTGTGCA	0.577													3	33	---	---	---	---	PASS
SALL1	6299	broad.mit.edu	37	16	51174807	51174807	+	Silent	SNP	G	C	C	rs143605364		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51174807G>C	uc010vgs.1	-	2	1357	c.1326C>G	c.(1324-1326)TCC>TCG	p.S442S	SALL1_uc010vgr.1_Silent_p.S345S|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	442					adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			ATGCCTCATCGGAAGTACTTT	0.502													16	43	---	---	---	---	PASS
CDH11	1009	broad.mit.edu	37	16	65038638	65038638	+	Silent	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65038638C>T	uc002eoi.2	-	3	569	c.135G>A	c.(133-135)GGG>GGA	p.G45G	CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_Silent_p.G45G|CDH11_uc010vin.1_Intron|CDH11_uc010vio.1_Silent_p.G45G	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	45					adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		GTAGCACCTGCCCCTCCTTGC	0.652			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			7	21	---	---	---	---	PASS
CLEC18B	497190	broad.mit.edu	37	16	74444909	74444909	+	Silent	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74444909C>T	uc002fct.2	-	9	1208	c.1008G>A	c.(1006-1008)CAG>CAA	p.Q336Q	CLEC18B_uc002fcu.2_Silent_p.Q336Q|CLEC18B_uc010vmu.1_3'UTR	NM_001011880	NP_001011880	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	336	C-type lectin.					extracellular region	sugar binding				0						GGCTCTTGATCTGGGCCAGCA	0.612													4	190	---	---	---	---	PASS
NUDT7	283927	broad.mit.edu	37	16	77775769	77775769	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77775769A>C	uc010chd.2	+	4	708	c.639A>C	c.(637-639)CAA>CAC	p.Q213H	NUDT7_uc010vnj.1_Missense_Mutation_p.Q160H	NM_001105663	NP_001099133	P0C024	NUDT7_HUMAN	nudix motif 7	213					nucleoside diphosphate metabolic process	peroxisome	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides|magnesium ion binding|manganese ion binding			ovary(1)|kidney(1)	2						TTGAGGTTCAATTTAATCTTA	0.388													20	71	---	---	---	---	PASS
RABEP1	9135	broad.mit.edu	37	17	5264813	5264813	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5264813C>T	uc002gbm.3	+	9	1630	c.1406C>T	c.(1405-1407)ACC>ATC	p.T469I	RABEP1_uc010clc.1_Missense_Mutation_p.T462I|RABEP1_uc010cld.1_Missense_Mutation_p.T426I|RABEP1_uc010vsw.1_Missense_Mutation_p.T426I|RABEP1_uc002gbl.3_Missense_Mutation_p.T469I|NUP88_uc002gbn.2_RNA	NM_004703	NP_004694	Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	469					apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2						TTTATGTTAACCAAAGATCAG	0.498													57	135	---	---	---	---	PASS
ZNF207	7756	broad.mit.edu	37	17	30694855	30694855	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30694855C>A	uc002hhh.3	+	9	1086	c.938C>A	c.(937-939)ACA>AAA	p.T313K	ZNF207_uc002hhj.3_Missense_Mutation_p.T329K|ZNF207_uc002hhi.3_Missense_Mutation_p.T298K|ZNF207_uc010csz.2_Missense_Mutation_p.T332K|ZNF207_uc002hhk.1_Missense_Mutation_p.T329K|ZNF207_uc002hhl.1_RNA	NM_003457	NP_003448	O43670	ZN207_HUMAN	zinc finger protein 207 isoform a	313						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			ACCCCTGCAACAACTACAGAA	0.428													107	295	---	---	---	---	PASS
KRT26	353288	broad.mit.edu	37	17	38926289	38926289	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38926289A>G	uc002hvf.2	-	4	813	c.767T>C	c.(766-768)TTG>TCG	p.L256S		NM_181539	NP_853517	Q7Z3Y9	K1C26_HUMAN	keratin 26	256	Rod.|Coil 2.					intermediate filament	structural molecule activity				0		Breast(137;0.00526)				CATGTTGTTCAACAGGACAGT	0.493													5	164	---	---	---	---	PASS
GPATCH8	23131	broad.mit.edu	37	17	42477558	42477558	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42477558T>A	uc002igw.1	-	8	1951	c.1887A>T	c.(1885-1887)AGA>AGT	p.R629S	GPATCH8_uc002igv.1_Missense_Mutation_p.R551S|GPATCH8_uc010wiz.1_Missense_Mutation_p.R551S	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	629						intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)|skin(1)	4		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GTGCGTCCATTCTGCCTCCTG	0.552											OREG0024461	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	14	37	---	---	---	---	PASS
TRIM37	4591	broad.mit.edu	37	17	57079057	57079057	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57079057T>G	uc002iwy.3	-	23	3158	c.2714A>C	c.(2713-2715)GAC>GCC	p.D905A	TRIM37_uc002iwz.3_Missense_Mutation_p.D905A|TRIM37_uc002ixa.3_Intron|TRIM37_uc010woc.1_Missense_Mutation_p.D871A	NM_001005207	NP_001005207	O94972	TRI37_HUMAN	tripartite motif-containing 37 protein	905						perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					ACATTCAATGTCACTGTCGCT	0.473									Mulibrey_Nanism				32	105	---	---	---	---	PASS
DDX42	11325	broad.mit.edu	37	17	61886961	61886961	+	Silent	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61886961T>C	uc002jbu.2	+	12	1451	c.1194T>C	c.(1192-1194)CTT>CTC	p.L398L	DDX42_uc002jbv.2_Silent_p.L398L|DDX42_uc002jbw.1_Silent_p.L134L|DDX42_uc002jbx.2_Silent_p.L134L|DDX42_uc002jby.2_5'Flank	NM_007372	NP_031398	Q86XP3	DDX42_HUMAN	DEAD box polypeptide 42 protein	398	Helicase ATP-binding.				protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5						CTACCAATCTTCAAAGAGTCT	0.378													148	361	---	---	---	---	PASS
TEX2	55852	broad.mit.edu	37	17	62291574	62291574	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62291574T>A	uc002jec.2	-	2	177	c.4A>T	c.(4-6)ACA>TCA	p.T2S	TEX2_uc002jed.2_Missense_Mutation_p.T2S|TEX2_uc002jee.2_Missense_Mutation_p.T2S	NM_018469	NP_060939	Q8IWB9	TEX2_HUMAN	testis expressed sequence 2	2					signal transduction|sphingolipid metabolic process	integral to membrane				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TACAGACTTGTCATTGCCGGC	0.527													38	102	---	---	---	---	PASS
HELZ	9931	broad.mit.edu	37	17	65124612	65124612	+	Intron	SNP	T	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65124612T>G	uc010wqk.1	-						HELZ_uc002jfv.3_RNA|HELZ_uc002jfx.3_Intron	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TTCACTTACATGTCCACACTA	0.343													8	19	---	---	---	---	PASS
BPTF	2186	broad.mit.edu	37	17	65955704	65955704	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65955704G>A	uc002jgf.2	+	24	8035	c.7974G>A	c.(7972-7974)ATG>ATA	p.M2658I	BPTF_uc002jge.2_Missense_Mutation_p.M2641I|BPTF_uc002jgg.2_Missense_Mutation_p.M315I|BPTF_uc002jgh.2_Missense_Mutation_p.M117I	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2784					brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAGACCTGATGCAGTTGGCTC	0.393													11	20	---	---	---	---	PASS
BPTF	2186	broad.mit.edu	37	17	65955705	65955705	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65955705C>G	uc002jgf.2	+	24	8036	c.7975C>G	c.(7975-7977)CAG>GAG	p.Q2659E	BPTF_uc002jge.2_Missense_Mutation_p.Q2642E|BPTF_uc002jgg.2_Missense_Mutation_p.Q316E|BPTF_uc002jgh.2_Missense_Mutation_p.Q118E	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2785					brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			AGACCTGATGCAGTTGGCTCA	0.398													11	20	---	---	---	---	PASS
KPNA2	3838	broad.mit.edu	37	17	66042696	66042696	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66042696G>T	uc002jgk.2	+	11	1706	c.1574G>T	c.(1573-1575)GGG>GTG	p.G525V	KPNA2_uc002jgl.2_Missense_Mutation_p.G525V	NM_002266	NP_002257	P52292	IMA2_HUMAN	karyopherin alpha 2	525					DNA metabolic process|G2 phase of mitotic cell cycle|interspecies interaction between organisms|M phase specific microtubule process|NLS-bearing substrate import into nucleus|regulation of DNA recombination	cytoplasm|nuclear pore|nucleoplasm	histone deacetylase binding|nuclear localization sequence binding|protein transporter activity			central_nervous_system(2)	2	all_cancers(12;1.18e-09)		BRCA - Breast invasive adenocarcinoma(8;1.03e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			GGGGCTCCTGGGACCTTTAAC	0.348													32	105	---	---	---	---	PASS
MC2R	4158	broad.mit.edu	37	18	13885108	13885108	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13885108C>T	uc002ksp.1	-	2	587	c.410G>A	c.(409-411)CGG>CAG	p.R137Q		NM_000529	NP_000520	Q01718	ACTHR_HUMAN	melanocortin 2 receptor	137	Cytoplasmic (By similarity).		R -> W (in GCCD1; partial loss of ACTIVITY).|R -> P (found in a glucocorticoid deficiency patient carrying also mutation I-74).		G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	corticotropin receptor activity|protein binding			ovary(4)|skin(1)	5					Corticotropin(DB01285)|Cosyntropin(DB01284)	GCTGTGGTACCGCAGTGCGTG	0.572													10	32	---	---	---	---	PASS
DSC2	1824	broad.mit.edu	37	18	28648279	28648279	+	Intron	SNP	T	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28648279T>G	uc002kwl.3	-						DSC2_uc002kwk.3_Missense_Mutation_p.N847T	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein						homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			CATTGTTTAATTTTTAATCAG	0.279													54	154	---	---	---	---	PASS
KIAA1012	22878	broad.mit.edu	37	18	29435680	29435680	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29435680A>C	uc002kxc.3	-	21	3643	c.3279T>G	c.(3277-3279)AAT>AAG	p.N1093K	KIAA1012_uc002kxb.3_Missense_Mutation_p.N1039K|KIAA1012_uc002kxd.3_RNA	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878	1093					ER to Golgi vesicle-mediated transport	cis-Golgi network					0						TGCCTTCTTCATTTTCAAGAG	0.348													88	225	---	---	---	---	PASS
TICAM1	148022	broad.mit.edu	37	19	4817479	4817479	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4817479C>G	uc002mbi.2	-	2	1162	c.911G>C	c.(910-912)TGC>TCC	p.C304S		NM_182919	NP_891549	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	304	TRAF6-binding.|Pro-rich.				apoptosis|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	protein kinase binding|signal transducer activity			breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		CCCCTCGGTGCACTCCACTGG	0.612													15	30	---	---	---	---	PASS
DENND1C	79958	broad.mit.edu	37	19	6467832	6467832	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6467832C>T	uc002mfe.2	-	23	2181	c.2089G>A	c.(2089-2091)GAA>AAA	p.E697K	DENND1C_uc002mfb.2_Missense_Mutation_p.E247K|DENND1C_uc002mfc.2_Missense_Mutation_p.E247K|DENND1C_uc002mfd.2_Missense_Mutation_p.E247K|DENND1C_uc010xje.1_Missense_Mutation_p.E653K	NM_024898	NP_079174	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	697						clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity			large_intestine(1)	1						GTGGGGTTTTCCTGGGCTGTA	0.577													27	71	---	---	---	---	PASS
GATAD2A	54815	broad.mit.edu	37	19	19609406	19609406	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19609406T>C	uc010xqt.1	+	8	1391	c.1079T>C	c.(1078-1080)CTA>CCA	p.L360P	GATAD2A_uc010xqu.1_5'UTR|GATAD2A_uc010xqv.1_Missense_Mutation_p.L379P|GATAD2A_uc010xqw.1_Missense_Mutation_p.L187P	NM_017660	NP_060130	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	360					DNA methylation|negative regulation of transcription, DNA-dependent	nuclear speck|NuRD complex	protein binding, bridging|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GAGAAGACGCTACTCGAGATC	0.647													5	21	---	---	---	---	PASS
ZNF90	7643	broad.mit.edu	37	19	20229513	20229513	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20229513C>G	uc002nor.2	+	4	1289	c.1150C>G	c.(1150-1152)CTT>GTT	p.L384V	ZNF90_uc002nos.1_Intron|ZNF90_uc002not.1_Intron	NM_007138	NP_009069	Q03938	ZNF90_HUMAN	zinc finger protein 90	384	C2H2-type 8.					Golgi apparatus|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2						ATCCTCACTCCTTTATAAACA	0.383													20	68	---	---	---	---	PASS
ZNF493	284443	broad.mit.edu	37	19	21608478	21608478	+	3'UTR	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21608478G>A	uc002npx.2	+	2					ZNF493_uc002npw.2_3'UTR|ZNF493_uc002npy.2_3'UTR	NM_175910	NP_787106	Q6ZR52	ZN493_HUMAN	zinc finger protein 493 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						AATTCATGCTGGAGAGAAACC	0.328													6	14	---	---	---	---	PASS
MLL4	9757	broad.mit.edu	37	19	36211567	36211567	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36211567C>G	uc010eei.2	+	3	1318	c.1318C>G	c.(1318-1320)CCT>GCT	p.P440A		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	440	Pro-rich.				chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			gtccccaccacctctaccatc	0.249													14	42	---	---	---	---	PASS
WDR87	83889	broad.mit.edu	37	19	38380376	38380376	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38380376G>A	uc010efu.2	-	6	4043	c.3818C>T	c.(3817-3819)GCT>GTT	p.A1273V	WDR87_uc002ohj.2_Missense_Mutation_p.A1312V	NM_031951	NP_114157	Q6ZQQ6	WDR87_HUMAN	NYD-SP11 protein	1273											0						CATCTCCTGAGCAAATGTCAC	0.468													5	317	---	---	---	---	PASS
CAPN12	147968	broad.mit.edu	37	19	39233680	39233680	+	Silent	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39233680C>T	uc002ojd.1	-	2	609	c.300G>A	c.(298-300)GGG>GGA	p.G100G		NM_144691	NP_653292	Q6ZSI9	CAN12_HUMAN	calpain 12	100	Calpain catalytic.				proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			CACCCAGGCTCCCCTGACACA	0.488													14	22	---	---	---	---	PASS
HNRNPL	3191	broad.mit.edu	37	19	39321980	39321980	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39321980T>C	uc002ojj.1	-	6	936	c.856A>G	c.(856-858)AAG>GAG	p.K286E	ECH1_uc002oji.2_Missense_Mutation_p.K77E|ECH1_uc010xuk.1_Missense_Mutation_p.K77E|HNRNPL_uc010ege.1_Intron	NM_001005335	NP_001005335	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	Error:Variant_position_missing_in_P14866_after_alignment					nuclear mRNA splicing, via spliceosome	cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|transcription regulatory region DNA binding				0	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			GCATTCCTCTTGTTGGGCCGG	0.607													27	67	---	---	---	---	PASS
NLRP2	55655	broad.mit.edu	37	19	55485895	55485895	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55485895G>T	uc002qij.2	+	3	394	c.308G>T	c.(307-309)AGG>ATG	p.R103M	NLRP2_uc010yfp.1_Missense_Mutation_p.R80M|NLRP2_uc010esn.2_Missense_Mutation_p.R103M|NLRP2_uc010eso.2_Missense_Mutation_p.R103M|NLRP2_uc010esp.2_Missense_Mutation_p.R103M	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	103					apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TTTAATAAAAGGAAGCCTCTA	0.358													90	228	---	---	---	---	PASS
ZNF584	201514	broad.mit.edu	37	19	58928399	58928399	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58928399T>G	uc002qsp.2	+	4	966	c.514T>G	c.(514-516)TTT>GTT	p.F172V	ZNF584_uc010yia.1_RNA|ZNF584_uc002qsr.2_Missense_Mutation_p.F127V|ZNF584_uc010yib.1_3'UTR	NM_173548	NP_775819	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	172	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0271)		CTTAAAGGCCTTTGCCCTCCT	0.498													22	51	---	---	---	---	PASS
FAM182A	284800	broad.mit.edu	37	20	26063686	26063686	+	RNA	SNP	C	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26063686C>G	uc010gdq.2	+	5		c.1244C>G				NR_026713				Homo sapiens cDNA FLJ38374 fis, clone FEBRA2002552.												0						GCCTGGACATCCACTGGGACA	0.498													9	36	---	---	---	---	PASS
DEFB116	245930	broad.mit.edu	37	20	29891177	29891177	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29891177G>T	uc010ztm.1	-	2	147	c.147C>A	c.(145-147)AAC>AAA	p.N49K		NM_001037731	NP_001032820	Q30KQ4	DB116_HUMAN	beta-defensin 116 precursor	49					defense response to bacterium	extracellular region					0	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			CTCTGCAGGCGTTTCTGCACA	0.453													166	414	---	---	---	---	PASS
ASXL1	171023	broad.mit.edu	37	20	31015950	31015950	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31015950C>G	uc002wxs.2	+	4	698	c.272C>G	c.(271-273)TCT>TGT	p.S91C	ASXL1_uc002wxr.1_RNA|ASXL1_uc010geb.2_Missense_Mutation_p.S33C	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	91					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248						CTGCAGTGGTCTCGCCATCCA	0.502			F|N|Mis		MDS|CMML								68	100	---	---	---	---	PASS
PTPRT	11122	broad.mit.edu	37	20	40864899	40864899	+	Splice_Site	SNP	C	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40864899C>A	uc002xkg.2	-	15	2497	c.2313_splice	c.e15-1	p.R771_splice	PTPRT_uc010ggj.2_Splice_Site_p.R790_splice	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				AGCATTTCTTCTATATATTGA	0.368													5	116	---	---	---	---	PASS
MATN4	8785	broad.mit.edu	37	20	43929999	43929999	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43929999A>G	uc002xnn.2	-	4	915	c.728T>C	c.(727-729)GTT>GCT	p.V243A	MATN4_uc002xno.2_Intron|MATN4_uc002xnp.2_Intron|MATN4_uc010zwr.1_Missense_Mutation_p.V191A|MATN4_uc002xnr.1_Missense_Mutation_p.V243A	NM_003833	NP_003824	O95460	MATN4_HUMAN	matrilin 4 isoform 1 precursor	284	EGF-like 2.					extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)				TACAAAGCCAACTTGGCAGTG	0.582											OREG0025977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	59	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11098827	11098827	+	5'UTR	SNP	C	T	T	rs79274499	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11098827C>T	uc002yit.1	-	1					BAGE_uc002yix.2_RNA	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)		ccatccagagcgagacgagcc	0.000													5	14	---	---	---	---	PASS
COL6A2	1292	broad.mit.edu	37	21	47545941	47545941	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47545941C>T	uc002zia.1	+	26	2294	c.2212C>T	c.(2212-2214)CGG>TGG	p.R738W	COL6A2_uc002zhy.1_Missense_Mutation_p.R738W|COL6A2_uc002zhz.1_Missense_Mutation_p.R738W|COL6A2_uc002zib.1_Missense_Mutation_p.R144W|COL6A2_uc002zic.1_5'Flank	NM_001849	NP_001840	P12110	CO6A2_HUMAN	alpha 2 type VI collagen isoform 2C2 precursor	738	VWFA 2.|Nonhelical region.				axon guidance|cell-cell adhesion|extracellular matrix organization|protein heterotrimerization	collagen|extracellular space|protein complex	extracellular matrix structural constituent|protein binding, bridging			central_nervous_system(7)|ovary(1)	8	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CCACGACCCTCGGGACGATGA	0.622													4	22	---	---	---	---	PASS
HPS4	89781	broad.mit.edu	37	22	26859937	26859937	+	Silent	SNP	C	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26859937C>G	uc003acl.2	-	11	2318	c.1659G>C	c.(1657-1659)CTG>CTC	p.L553L	HPS4_uc003aci.2_Silent_p.L548L|HPS4_uc003acj.2_Silent_p.L417L|HPS4_uc003ack.2_Silent_p.L344L|HPS4_uc003acn.2_Silent_p.L399L|HPS4_uc010gvd.1_Silent_p.L571L|HPS4_uc003ach.2_Silent_p.L288L	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	553					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0						CCAGCAGGGACAGCACCAGCC	0.612									Hermansky-Pudlak_syndrome				7	11	---	---	---	---	PASS
NCAPH2	29781	broad.mit.edu	37	22	50956419	50956419	+	Silent	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50956419C>T	uc003blr.3	+	6	560	c.438C>T	c.(436-438)CCC>CCT	p.P146P	NCAPH2_uc003blq.3_Silent_p.P146P|NCAPH2_uc003blv.2_Silent_p.P146P|NCAPH2_uc010hbb.2_5'UTR|NCAPH2_uc003blu.3_RNA|NCAPH2_uc003bls.3_RNA|NCAPH2_uc003blt.3_RNA|NCAPH2_uc003blw.3_RNA|NCAPH2_uc003blx.3_Silent_p.P146P|NCAPH2_uc003bly.3_RNA	NM_152299	NP_689512	Q6IBW4	CNDH2_HUMAN	kleisin beta isoform 2	146					chromosome condensation	chromosome|nucleus				ovary(1)|skin(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.212)		TCATCATCCCCCTCCTGCCCA	0.617													23	35	---	---	---	---	PASS
MED12	9968	broad.mit.edu	37	X	70351933	70351933	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70351933C>T	uc004dyy.2	+	30	4329	c.4130C>T	c.(4129-4131)TCC>TTC	p.S1377F	MED12_uc011mpq.1_Missense_Mutation_p.S1377F|MED12_uc004dyz.2_Missense_Mutation_p.S1377F|MED12_uc004dza.2_Missense_Mutation_p.S1224F|MED12_uc010nla.2_Missense_Mutation_p.S3F	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1377					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)					GAGATGAACTCCCTCTTGGAG	0.507													3	51	---	---	---	---	PASS
DOCK11	139818	broad.mit.edu	37	X	117752678	117752678	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117752678G>T	uc004eqp.2	+	31	3521	c.3458G>T	c.(3457-3459)AGA>ATA	p.R1153I	DOCK11_uc004eqq.2_Missense_Mutation_p.R932I	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1153					blood coagulation	cytosol	GTP binding			ovary(3)	3						TTTGACACAAGATACCAGCAC	0.358													49	42	---	---	---	---	PASS
BCORL1	63035	broad.mit.edu	37	X	129147823	129147823	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129147823A>C	uc004evb.1	+	4	1189	c.1075A>C	c.(1075-1077)ACT>CCT	p.T359P	BCORL1_uc010nrd.1_Missense_Mutation_p.T261P	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	359	Pro-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7						gcccatgcccactccaacccc	0.000													19	12	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3707	3707	+	RNA	SNP	G	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:3707G>A	uc004cos.3	+	2		c.2000G>A			uc011mfh.1_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP47.																		CGGCGCACTGCGAGCAGTAGC	0.468													16	33	---	---	---	---	PASS
SRM	6723	broad.mit.edu	37	1	11116944	11116944	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11116944delT	uc001arz.1	-						SRM_uc001ary.1_5'Flank	NM_003132	NP_003123	P19623	SPEE_HUMAN	spermidine synthase						spermidine biosynthetic process	cytosol	protein homodimerization activity|spermidine synthase activity				0	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.228)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)	S-Adenosylmethionine(DB00118)|Spermine(DB00127)	ttttttattatttttttttga	0.299													4	2	---	---	---	---	
C1QC	714	broad.mit.edu	37	1	22967826	22967827	+	5'Flank	DEL	TC	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22967826_22967827delTC	uc001bgc.3	+						C1QC_uc001bga.3_5'Flank|C1QC_uc001bgb.2_5'Flank	NM_172369	NP_758957	P02747	C1QC_HUMAN	complement component 1, q subcomponent, C chain						complement activation, classical pathway|innate immune response|negative regulation of granulocyte differentiation|negative regulation of macrophage differentiation	collagen					0		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.21e-27)|Colorectal(126;1.5e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.61e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000538)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.196)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CATCGCATATTCTCTCTCTCTT	0.525													4	2	---	---	---	---	
MYOM3	127294	broad.mit.edu	37	1	24385618	24385618	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24385618delT	uc001bin.3	-						MYOM3_uc001bil.3_Intron|MYOM3_uc001bim.3_Intron	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3											skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		cttttttaaatttttttttca	0.100													4	2	---	---	---	---	
ADC	113451	broad.mit.edu	37	1	33583873	33583873	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33583873delG	uc001bwr.2	+						ADC_uc001bws.2_Intron|ADC_uc009vue.2_Intron|ADC_uc001bwt.1_3'UTR|ADC_uc001bwu.2_Intron|ADC_uc001bwv.2_Intron|ADC_uc001bww.2_Intron|ADC_uc001bwx.1_3'UTR|ADC_uc009vug.2_Intron	NM_052998	NP_443724	Q96A70	ADC_HUMAN	ODC antizyme inhibitor-2						polyamine biosynthetic process|spermatogenesis	cytosol	arginine decarboxylase activity			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)			L-Arginine(DB00125)|Pyridoxal Phosphate(DB00114)	ACCTGGCTGTGGCCATAAGTG	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	33605692	33605692	+	IGR	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33605692delG								ADC (19561 upstream) : TRIM62 (5312 downstream)																							GTGTGGCAGAGGGGGGTCCCT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38726290	38726290	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38726290delT								POU3F1 (213840 upstream) : RRAGC (578725 downstream)																							CCTTCCCCCCTTTTTTTCTAG	0.264													4	2	---	---	---	---	
GUCA2A	2980	broad.mit.edu	37	1	42633252	42633253	+	5'Flank	DEL	GT	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42633252_42633253delGT	uc001chd.1	-							NM_033553	NP_291031	Q02747	GUC2A_HUMAN	guanylate cyclase activator 2A precursor						signal transduction	extracellular region	guanylate cyclase activator activity|hormone activity			pancreas(1)	1	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				gagtgctgacgtgtgtgtgtgc	0.059													4	2	---	---	---	---	
YBX1	4904	broad.mit.edu	37	1	43166281	43166281	+	Intron	DEL	C	-	-	rs5773785		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43166281delC	uc001chs.2	+							NM_004559	NP_004550	P67809	YBOX1_HUMAN	nuclease sensitive element binding protein 1						CRD-mediated mRNA stabilization|negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|positive regulation of cell division|transcription from RNA polymerase II promoter	CRD-mediated mRNA stability complex|extracellular region|histone pre-mRNA 3'end processing complex|nucleoplasm|stress granule|U12-type spliceosomal complex	double-stranded DNA binding|protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(4)|upper_aerodigestive_tract(1)	5	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TACTCAGCATCCCCCCCCCCC	0.279													3	3	---	---	---	---	
RNF220	55182	broad.mit.edu	37	1	44907803	44907803	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44907803delT	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						aagacatttctttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48241973	48241973	+	IGR	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48241973delC								FOXD2 (335611 upstream) : SKINTL (325414 downstream)																							cagcccggctccacaacttgc	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	73233373	73233373	+	IGR	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73233373delC								NEGR1 (484968 upstream) : None (None downstream)																							gcacacacatccccatcttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	74329518	74329519	+	IGR	INS	-	T	T	rs143318286	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74329518_74329519insT								None (None upstream) : LRRIQ3 (162185 downstream)																							CATTCATGGTGTTTACCTGGCA	0.426													3	3	---	---	---	---	
FUBP1	8880	broad.mit.edu	37	1	78435530	78435530	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78435530delA	uc001dii.2	-						FUBP1_uc001dih.3_Intron|FUBP1_uc010orm.1_Intron	NM_003902	NP_003893	Q96AE4	FUBP1_HUMAN	far upstream element-binding protein						transcription from RNA polymerase II promoter	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			central_nervous_system(2)|lung(1)	3						ATATCTCAATAAAATAACAGA	0.279													103	48	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88189507	88189507	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88189507delA								LMO4 (374904 upstream) : PKN2 (960415 downstream)																							ATGATCTCAGAAAAAAAAAAT	0.373													5	4	---	---	---	---	
BCAR3	8412	broad.mit.edu	37	1	94123284	94123285	+	Intron	INS	-	A	A	rs35976570		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94123284_94123285insA	uc001dpz.2	-						BCAR3_uc001dqa.2_Intron|BCAR3_uc001dqb.2_Intron	NM_003567	NP_003558	O75815	BCAR3_HUMAN	breast cancer antiestrogen resistance 3						response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		gtatggcccacaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	111759431	111759432	+	IGR	DEL	AC	-	-	rs147367224		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111759431_111759432delAC								DENND2D (12400 upstream) : CHI3L2 (10849 downstream)																							TGTTTTGCTAacacacacacac	0.203													3	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145007452	145007453	+	Intron	INS	-	T	T	rs141963263		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145007452_145007453insT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CATACAttttcttttttttgtt	0.139			T	PDGFRB	MPD								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148848558	148848559	+	IGR	INS	-	TCATT	TCATT	rs149159637	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148848558_148848559insTCATT								NBPF16 (90247 upstream) : LOC645166 (79727 downstream)																							atcatttcatctcatttcatca	0.000													4	2	---	---	---	---	
INTS3	65123	broad.mit.edu	37	1	153699419	153699419	+	5'Flank	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153699419delA	uc009wom.2	+						INTS3_uc001fct.2_5'Flank|INTS3_uc001fcu.2_5'Flank|INTS3_uc001fcv.2_5'Flank	NM_023015	NP_075391	Q68E01	INT3_HUMAN	integrator complex subunit 3						DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AGTGCTCTTGAAAAAAAAATG	0.303													4	2	---	---	---	---	
ATP1A2	477	broad.mit.edu	37	1	160102607	160102607	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160102607delA	uc001fvc.2	+						ATP1A2_uc001fvb.2_Intron|ATP1A2_uc001fvd.2_Intron	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein						ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			ggtgcaaactaaaggcttata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172679093	172679093	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172679093delT								FASLG (43083 upstream) : TNFSF18 (331267 downstream)																							ttttcatttcttttttttttt	0.124													4	2	---	---	---	---	
C1orf125	126859	broad.mit.edu	37	1	179462338	179462339	+	Intron	INS	-	CTAT	CTAT	rs142692537		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179462338_179462339insCTAT	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmp.2_Intron|C1orf125_uc009wxh.2_Intron	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1												0						tgtctgatctactaacaccaaa	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	184602948	184602948	+	IGR	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184602948delG								C1orf21 (4793 upstream) : EDEM3 (56679 downstream)																							TTGGATTCCTGGTAAAAGATC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199438339	199438339	+	IGR	DEL	A	-	-	rs66879226		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199438339delA								MIR181A1 (610057 upstream) : NR5A2 (558431 downstream)																							GGTGAATTACATATTAATCTT	0.239													2	4	---	---	---	---	
NAV1	89796	broad.mit.edu	37	1	201712776	201712776	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201712776delT	uc001gwu.2	+						NAV1_uc001gwv.1_Intron|NAV1_uc001gww.1_Intron|NAV1_uc001gwx.2_Intron	NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1						cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4						ATTCTTTAGATTTTTTTTTTA	0.333													4	2	---	---	---	---	
PPP1R12B	4660	broad.mit.edu	37	1	202349725	202349726	+	Intron	INS	-	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202349725_202349726insC	uc001gya.1	+						PPP1R12B_uc001gxy.2_Intron|PPP1R12B_uc009xad.1_Intron|PPP1R12B_uc009xae.1_Intron|PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			TATATTCTCAACACCCCCCCCA	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	206638895	206638895	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206638895delT								SRGAP2 (1113 upstream) : IKBKE (4901 downstream)																							CAGGCTATGCTTTTTAGGTCC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208609275	208609278	+	IGR	DEL	AGGA	-	-	rs144120608		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208609275_208609278delAGGA								PLXNA2 (191610 upstream) : LOC642587 (992890 downstream)																							ACCTGTAGGTAGGAAGGAAGCAGT	0.348													3	4	---	---	---	---	
CAPN2	824	broad.mit.edu	37	1	223949705	223949705	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223949705delA	uc001hob.3	+						CAPN2_uc010puy.1_Intron|CAPN2_uc001hoc.2_Intron	NM_001748	NP_001739	P17655	CAN2_HUMAN	calpain 2 isoform 1						proteolysis	cytoplasm|plasma membrane				lung(3)|breast(1)|skin(1)	5				GBM - Glioblastoma multiforme(131;0.109)		TTTTAATTAGAAAAAAAAAAC	0.373													7	4	---	---	---	---	
PXDN	7837	broad.mit.edu	37	2	1683373	1683374	+	Intron	DEL	GT	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1683373_1683374delGT	uc002qxa.2	-						PXDN_uc002qxb.1_Intron|PXDN_uc002qxc.1_Intron	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor						extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		gtgtatgtgcgtgtgtgtgtgt	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2513892	2513892	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2513892delA								MYT1L (178847 upstream) : TSSC1 (678849 downstream)																							tcccaacagcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	5229407	5229407	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5229407delA								None (None upstream) : SOX11 (603392 downstream)																							ATGCGTTTCTATTTGTGTGTG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20056789	20056790	+	IGR	DEL	TT	-	-	rs66888956		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20056789_20056790delTT								OSR1 (498417 upstream) : TTC32 (39728 downstream)																							CAAAGGGTAATTTTTTTTTTTT	0.317													4	2	---	---	---	---	
C2orf43	60526	broad.mit.edu	37	2	20892024	20892024	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20892024delG	uc002rec.2	-						C2orf43_uc002rea.1_Intron|C2orf43_uc002reb.1_Intron|C2orf43_uc010yka.1_Intron|C2orf43_uc010ykb.1_Intron|C2orf43_uc010ykc.1_Intron|C2orf43_uc010ykd.1_Intron|C2orf43_uc010yke.1_Intron|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744	Q9H6V9	CB043_HUMAN	hypothetical protein LOC60526												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					aaagccctacgggaccccaaa	0.095													4	2	---	---	---	---	
DTNB	1838	broad.mit.edu	37	2	25769713	25769713	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25769713delT	uc002rgh.2	-						DTNB_uc010yko.1_Intron|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707	O60941	DTNB_HUMAN	dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTTCTAttcttttttttttt	0.194													3	3	---	---	---	---	
XDH	7498	broad.mit.edu	37	2	31600308	31600308	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31600308delA	uc002rnv.1	-							NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase						purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)	CCAGAAGCTGAAAAAAAAAAC	0.458													4	2	---	---	---	---	
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48904065	48904065	+	Intron	DEL	T	-	-	rs71399076		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48904065delT	uc010yol.1	+						STON1-GTF2A1L_uc002rwp.1_Intron|GTF2A1L_uc002rws.1_Intron|GTF2A1L_uc010yom.1_Intron|GTF2A1L_uc002rwt.2_Intron	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			caactttttattttttttttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49841694	49841694	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49841694delA								FSHR (460064 upstream) : NRXN1 (303950 downstream)																							agagagagagaaaaaaaaatg	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	59996494	59996495	+	IGR	DEL	AC	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59996494_59996495delAC								None (None upstream) : BCL11A (681808 downstream)																							AATATGCAATacacacacacac	0.272													4	2	---	---	---	---	
C2orf86	51057	broad.mit.edu	37	2	63607375	63607375	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63607375delT	uc002sch.2	-						C2orf86_uc002sce.2_Intron|C2orf86_uc002scf.2_Intron|C2orf86_uc010ypu.1_Intron|C2orf86_uc002scg.2_Intron|C2orf86_uc002sci.1_Intron	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0						TTTTCTTTCATTTTTTTTTTA	0.254													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	69940315	69940315	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69940315delA								AAK1 (69338 upstream) : ANXA4 (28812 downstream)																							ATTATGAAGTAAAAAAAAAAA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	88272590	88272591	+	IGR	INS	-	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88272590_88272591insC								RMND5A (233824 upstream) : KRCC1 (54133 downstream)																							ACCACCCCCCGCCCCCCGCCTC	0.639													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90417220	90417224	+	Intron	DEL	ATGAA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90417220_90417224delATGAA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		aaatgaaatgatgaaatgaaatggt	0.000													4	2	---	---	---	---	
PAX8	7849	broad.mit.edu	37	2	114017282	114017283	+	Intron	INS	-	ATTA	ATTA	rs150152105	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114017282_114017283insATTA	uc010yxt.1	-						PAX8_uc010yxu.1_Intron|PAX8_uc010yxv.1_Intron|PAX8_uc002tjm.2_Intron|PAX8_uc002tjn.2_Intron|PAX8_uc010fku.1_Intron|LOC654433_uc002tjq.3_Intron|LOC654433_uc010fks.2_Intron|LOC654433_uc010fkt.2_Intron|LOC654433_uc002tjr.3_Intron|LOC654433_uc002tjs.3_Intron	NM_003466	NP_003457	Q06710	PAX8_HUMAN	paired box 8 isoform PAX8A						branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity			ovary(1)|lung(1)	2						TTATCGAAAGCATTAATTGATG	0.332			T	PPARG	follicular thyroid		Thyroid dysgenesis 						5	4	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	116187311	116187312	+	Intron	INS	-	CTC	CTC	rs142863990	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116187311_116187312insCTC	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						AACATAAACTTCTCAGAAGAGG	0.381													1	5	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	125232684	125232684	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125232684delT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		AGAGAATTCATTTTTTTTTTT	0.353													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126325735	126325735	+	IGR	DEL	A	-	-	rs35420703		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126325735delA								CNTNAP5 (652874 upstream) : None (None downstream)																							CGGGTTTATCAAATCATTTGA	0.418													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126552209	126552209	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126552209delA								CNTNAP5 (879348 upstream) : GYPC (861475 downstream)																							caacaacaacaaaaaaaaaac	0.035													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129316486	129316486	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129316486delT								HS6ST1 (240315 upstream) : None (None downstream)																							ATACAAAGGCTTTTTTTTTTT	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132774380	132774380	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132774380delT								C2orf27B (215146 upstream) : NCRNA00164 (130784 downstream)																							TATACCAAGCTTGTGGGATTC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132817202	132817204	+	IGR	DEL	AGA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132817202_132817204delAGA								C2orf27B (257968 upstream) : NCRNA00164 (87960 downstream)																							CTTATCAAGGAGAAGAACTCAAG	0.310													4	2	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	134323798	134323799	+	Intron	DEL	TC	-	-	rs34666668		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134323798_134323799delTC	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002ttt.1_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						AAGAGAAGGTTCCACTGGAGAG	0.465													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146310158	146310158	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146310158delA								None (None upstream) : None (None downstream)																							GAATTATGTGAAAAAAAATCT	0.308													4	2	---	---	---	---	
WIPF1	7456	broad.mit.edu	37	2	175500257	175500257	+	Intron	DEL	G	-	-	rs4972703	byFrequency	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175500257delG	uc010fqt.1	-						uc002uiw.2_Intron|uc002uix.1_Intron|WIPF1_uc002uja.2_Intron|WIPF1_uc002ujc.1_Intron|WIPF1_uc002uiz.2_5'Flank|WIPF1_uc010zep.1_5'Flank	NM_003387	NP_003378	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1						actin polymerization or depolymerization|protein complex assembly	cytoplasmic membrane-bounded vesicle	actin binding|profilin binding			ovary(1)|skin(1)	2						CCTTCTGtttgtttttttttt	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177478390	177478391	+	IGR	INS	-	T	T	rs150626811	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177478390_177478391insT								MIR1246 (12610 upstream) : HNRNPA3 (599031 downstream)																							CTGACCAGCAATTTCTCTCGTG	0.446													4	3	---	---	---	---	
ANKAR	150709	broad.mit.edu	37	2	190605980	190605981	+	Intron	INS	-	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190605980_190605981insT	uc002uqw.1	+						ANKAR_uc002uqu.2_Intron|ANKAR_uc002uqx.1_Intron|ANKAR_uc002uqy.1_Intron	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing							integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			GTGACACAAACTTTTTTCAGTG	0.287													33	15	---	---	---	---	
CCDC150	284992	broad.mit.edu	37	2	197516417	197516417	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197516417delT	uc002utp.1	+						CCDC150_uc002uto.1_Intron|CCDC150_uc010zgq.1_Intron|CCDC150_uc010zgr.1_Intron|CCDC150_uc010zgs.1_Intron	NM_001080539	NP_001074008	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150												0						cccttgatgcttttaaaactc	0.000													4	2	---	---	---	---	
PGAP1	80055	broad.mit.edu	37	2	197780321	197780321	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197780321delT	uc002utw.2	-						PGAP1_uc002utx.2_Intron|PGAP1_uc002uty.1_Intron|PGAP1_uc010zgv.1_Intron|PGAP1_uc010fsj.2_Intron	NM_024989	NP_079265	Q75T13	PGAP1_HUMAN	GPI deacylase						attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4						cactttgcccttccatatctg	0.000													4	2	---	---	---	---	
BOLL	66037	broad.mit.edu	37	2	198642699	198642699	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198642699delT	uc002uus.2	-						BOLL_uc002uur.2_Intron|BOLL_uc002uut.2_Intron|BOLL_uc010zha.1_Intron|BOLL_uc002uuu.1_Intron	NM_033030	NP_149019	Q8N9W6	BOLL_HUMAN	boule isoform 2						cell differentiation|meiosis|multicellular organismal development|positive regulation of translational initiation|spermatogenesis	cytoplasm	nucleotide binding|protein binding|RNA binding|translation activator activity			ovary(2)	2						TTTTACGCTATTTTTTTGGTA	0.289													4	2	---	---	---	---	
NBEAL1	65065	broad.mit.edu	37	2	204066041	204066041	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204066041delT	uc002uzt.3	+						NBEAL1_uc002uzs.3_Intron	NM_001114132	NP_001107604	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1 isoform 3								binding			ovary(1)|skin(1)	2						TGATTTCACCTTTTTTTGTTT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235991318	235991320	+	IGR	DEL	AAT	-	-	rs67478433		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235991318_235991320delAAT								SH3BP4 (26962 upstream) : AGAP1 (411416 downstream)																							ATTTACAGACAATAAAACATTAC	0.241													3	4	---	---	---	---	
SRGAP3	9901	broad.mit.edu	37	3	9135181	9135181	+	Intron	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9135181delC	uc003brf.1	-						SRGAP3_uc003brg.1_Intron|SRGAP3_uc003bri.1_Intron|SRGAP3_uc003brk.2_Intron	NM_014850	NP_055665	O43295	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		acccactcatccactcatcca	0.000			T	RAF1	pilocytic astrocytoma								4	2	---	---	---	---	
RBMS3	27303	broad.mit.edu	37	3	30045605	30045605	+	3'UTR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30045605delA	uc003cel.2	+	15					RBMS3_uc003cem.2_3'UTR|RBMS3_uc010hfr.2_3'UTR	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)				CCAGAAGAGGAAAAAAAAACT	0.269													4	2	---	---	---	---	
C3orf35	339883	broad.mit.edu	37	3	37459335	37459336	+	Intron	DEL	AC	-	-	rs60085343		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37459335_37459336delAC	uc003cha.3	+						C3orf35_uc003chb.2_3'UTR	NM_178339	NP_848029	Q8IVJ8	APRG1_HUMAN	AP20 region protein isoform B							integral to membrane				central_nervous_system(1)	1						ACATACCGATacacacacacac	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	42114058	42114058	+	IGR	DEL	C	-	-	rs7610545	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42114058delC								ULK4 (110398 upstream) : TRAK1 (18688 downstream)																							TTTTTTTTTTCTTTCTCTTTT	0.423													4	2	---	---	---	---	
ACY1	95	broad.mit.edu	37	3	52009472	52009472	+	Intron	DEL	G	-	-	rs111955253		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52009472delG	uc011bea.1	+						ABHD14B_uc010hly.2_5'Flank|ABHD14B_uc003dcm.2_5'Flank|ABHD14B_uc011bdy.1_5'Flank|ABHD14B_uc003dcn.2_Intron|ABHD14B_uc011bdz.1_5'Flank|ABHD14A_uc010hlz.2_Intron|ABHD14A_uc003dco.2_Intron	NM_000666	NP_000657	Q03154	ACY1_HUMAN	aminoacylase 1						cellular amino acid metabolic process|proteolysis	cytosol	aminoacylase activity|metal ion binding|metallopeptidase activity			breast(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	L-Aspartic Acid(DB00128)	TTATATTTTTGGGGGGGGGGT	0.239													4	2	---	---	---	---	
SFMBT1	51460	broad.mit.edu	37	3	53052893	53052893	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53052893delT	uc003dgf.2	-						SFMBT1_uc003dgg.2_Intron|SFMBT1_uc003dgh.2_Intron	NM_001005159	NP_001005159	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1						regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)		tcctgtctcctttgctgcctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	98700253	98700253	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98700253delT								DCBLD2 (79720 upstream) : COL8A1 (657201 downstream)																							GGGGAATCAATTTTTTTTGTA	0.403													4	2	---	---	---	---	
DZIP3	9666	broad.mit.edu	37	3	108361006	108361006	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108361006delT	uc003dxd.2	+						DZIP3_uc003dxf.1_Intron|DZIP3_uc011bhm.1_Intron|DZIP3_uc003dxe.1_Intron|DZIP3_uc003dxg.1_Intron	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger						protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						CTTTCTTTCCTTTTTTTTCTG	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116568594	116568594	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116568594delA								LOC285194 (132709 upstream) : None (None downstream)																							tggttcacagaaaaaacaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117298814	117298814	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117298814delT								LOC285194 (862929 upstream) : None (None downstream)																							CCTGACTCCCTGTCTCCTGAT	0.383													4	2	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124172218	124172219	+	Intron	INS	-	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124172218_124172219insT	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron|KALRN_uc003ehh.1_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						GGAGAGCTGGATCCCTGGTCCC	0.574													4	2	---	---	---	---	
COL6A4P2	646300	broad.mit.edu	37	3	129976543	129976543	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129976543delT	uc011blf.1	+							NR_027898				Homo sapiens collagen VI alpha 4 pseudogene 2 (COL6A4P2), non-coding RNA.												0						TTGATGGGACTTTGCAGTAGG	0.408													4	2	---	---	---	---	
FAIM	55179	broad.mit.edu	37	3	138330123	138330123	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138330123delT	uc003esr.2	+						FAIM_uc003eso.1_Intron|FAIM_uc003esp.2_Intron|FAIM_uc003esq.2_Intron|FAIM_uc003ess.2_Intron	NM_001033032	NP_001028204	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule isoform c						apoptosis	cytoplasm					0						TCTTTTTTTGTTTTTtttttt	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139619896	139619896	+	IGR	DEL	C	-	-	rs959555	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139619896delC								NMNAT3 (223056 upstream) : CLSTN2 (34131 downstream)																							tcttttttttCCCACTGCTGG	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152847547	152847548	+	IGR	DEL	AC	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152847547_152847548delAC								P2RY1 (291706 upstream) : RAP2B (32481 downstream)																							TATGTTTTATACACACACACAC	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	156826512	156826512	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156826512delT	uc003fbc.2	-											Homo sapiens cDNA, FLJ18260.																		TTTGTGCCCATTTACTCTTCC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184895721	184895731	+	Intron	DEL	GGAATCATCAG	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184895721_184895731delGGAATCATCAG	uc003fpe.2	+											Homo sapiens hypothetical LOC339926, mRNA (cDNA clone IMAGE:4838153).																		ctgttgatacggaatcatcagagaaagccct	0.000													3	4	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188166799	188166799	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188166799delA	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		CTAAGATAGCAAAAAATAGAA	0.244			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
NOP14	8602	broad.mit.edu	37	4	2958218	2958218	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2958218delA	uc003ggj.1	-						C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_5'Flank|NOP14_uc003ggk.3_Intron|NOP14_uc003ggl.2_Intron|NOP14_uc010icq.1_Intron	NM_003703	NP_003694	P78316	NOP14_HUMAN	probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1						CTGAAAACTTAAAAAAAAAAC	0.229													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3607512	3607513	+	IGR	INS	-	C	C	rs144084479	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3607512_3607513insC								LRPAP1 (73288 upstream) : ADRA2C (160562 downstream)																							GGAATGGCAGGAGGCTGCGTGC	0.629													4	2	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7641150	7641153	+	Intron	DEL	TGTA	-	-	rs146029796	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7641150_7641153delTGTA	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						Agtgtgtgtgtgtatgcacacttg	0.127													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13966513	13966513	+	IGR	DEL	A	-	-	rs112998189		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13966513delA								BOD1L (337185 upstream) : None (None downstream)																							CAATGTCAAGAAAAAAAAAAA	0.363													3	3	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20597097	20597098	+	Intron	INS	-	ATC	ATC	rs142662998	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20597097_20597098insATC	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						GGATGTTCACTATCAAGGAGAT	0.431													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58986283	58986283	+	IGR	DEL	T	-	-	rs34721582		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58986283delT								None (None upstream) : None (None downstream)																							CAAACAAGAATTTTTAACGAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	60489942	60489942	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60489942delA								None (None upstream) : None (None downstream)																							gaagtgacagaaaaaaaatta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	68025224	68025225	+	IGR	DEL	CA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68025224_68025225delCA								MIR1269 (882578 upstream) : CENPC1 (312764 downstream)																							TACTCTCTCTCACACACACACA	0.317													4	2	---	---	---	---	
ART3	419	broad.mit.edu	37	4	76976661	76976661	+	Intron	DEL	A	-	-	rs4543147	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76976661delA	uc003hjk.2	+						ART3_uc003hji.2_Intron|ART3_uc003hjj.2_Intron	NM_001130017	NP_001123489	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3 isoform c						protein ADP-ribosylation	anchored to membrane|integral to plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity			ovary(2)	2			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			gcggggtcagAGGACAGCAGC	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82316641	82316641	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82316641delT								PRKG2 (180423 upstream) : RASGEF1B (31578 downstream)																							ACAGCCACTGTCCTGACTTGC	0.488													4	2	---	---	---	---	
COQ2	27235	broad.mit.edu	37	4	84208912	84208912	+	5'Flank	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84208912delT	uc003hog.2	-						COQ2_uc011ccp.1_5'Flank|COQ2_uc003hoh.1_5'Flank	NM_015697	NP_056512	Q96H96	COQ2_HUMAN	para-hydroxybenzoate-polyprenyltransferase,						glycerol metabolic process|isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrial membrane	4-hydroxybenzoate decaprenyltransferase activity|4-hydroxybenzoate nonaprenyltransferase activity			ovary(1)|central_nervous_system(1)	2		Hepatocellular(203;0.114)				gcttgaagtgttttcttaata	0.000													4	2	---	---	---	---	
BANK1	55024	broad.mit.edu	37	4	102508320	102508324	+	Intron	DEL	AAAAG	-	-	rs74949529		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102508320_102508324delAAAAG	uc003hvx.3	+							NM_001083907	NP_001077376	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		gagaaaaaaaaaaagaagaagaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	129173444	129173445	+	IGR	INS	-	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129173444_129173445insA								LARP1B (29364 upstream) : PGRMC2 (17853 downstream)																							ctcaaaacatgaggtgatcagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	136049773	136049774	+	IGR	INS	-	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136049773_136049774insA								PABPC4L (926870 upstream) : None (None downstream)																							TCCCAAATAAGAAAAAAAAAGA	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	144524863	144524863	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144524863delA								LOC441046 (35550 upstream) : GYPE (267157 downstream)																							agaggcatttaaaatgtaaca	0.025													4	2	---	---	---	---	
RXFP1	59350	broad.mit.edu	37	4	159558946	159558946	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159558946delA	uc003ipz.2	+						RXFP1_uc010iqj.1_Intron|RXFP1_uc011cja.1_Intron|RXFP1_uc010iqo.2_Intron|RXFP1_uc011cjb.1_Intron|RXFP1_uc010iqk.2_Intron|RXFP1_uc011cjc.1_Intron|RXFP1_uc011cjd.1_Intron|RXFP1_uc010iql.2_Intron|RXFP1_uc011cje.1_Intron|RXFP1_uc010iqm.2_Intron|RXFP1_uc011cjf.1_Intron|RXFP1_uc010iqn.2_Intron	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1							integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		ggcaatatccaaaaaaatcat	0.000													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164464105	164464105	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164464105delG	uc003iqs.1	-						MARCH1_uc003iqr.1_Intron	NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GAGTGTGTGTGGTGGTGGTGG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190825682	190825683	+	Intron	INS	-	T	T	rs138468383		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190825682_190825683insT	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		AACTACTGTGATATTTTTTAGA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	11744	11745	+	IGR	INS	-	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11744_11745insC								None (None upstream) : PLEKHG4B (128628 downstream)																							cctaaccctaaccctaacccta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2493465	2493466	+	IGR	DEL	TG	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2493465_2493466delTG								IRX4 (610585 upstream) : IRX2 (252815 downstream)																							AGTGCTCATATGTGTGTGTGCA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5588923	5588924	+	IGR	INS	-	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5588923_5588924insT								KIAA0947 (98586 upstream) : FLJ33360 (721630 downstream)																							TCACCTGACCCTTTTCTTTTTG	0.391													4	2	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21529460	21529461	+	Intron	DEL	AT	-	-	rs149556493		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21529460_21529461delAT	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						cttaaacgtcattttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	25684937	25684938	+	IGR	DEL	GT	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25684937_25684938delGT								None (None upstream) : None (None downstream)																							gtgtgtgtgcgtgtgtgtgtgt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38126980	38126982	+	IGR	DEL	ATG	-	-	rs4019480		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38126980_38126982delATG								GDNF (287198 upstream) : EGFLAM (131551 downstream)																							aatctctcatatgatgagtattg	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38751523	38751523	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38751523delT								LIFR (156016 upstream) : OSMR (94605 downstream)																							tgtttgttgattttttttttt	0.174													3	3	---	---	---	---	
DAB2	1601	broad.mit.edu	37	5	39389739	39389739	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39389739delA	uc003jlx.2	-						DAB2_uc003jlw.2_Intron	NM_001343	NP_001334	P98082	DAB2_HUMAN	disabled homolog 2						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)			tcagacgcccaagtagctggg	0.000													4	2	---	---	---	---	
OXCT1	5019	broad.mit.edu	37	5	41853423	41853423	+	Intron	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41853423delC	uc003jmn.2	-							NM_000436	NP_000427	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1 precursor						cellular lipid metabolic process|ketone body catabolic process	mitochondrial matrix	3-oxoacid CoA-transferase activity|protein homodimerization activity			ovary(2)|large_intestine(1)	3					Succinic acid(DB00139)	AAGTACTATTCCTTCTGCCTT	0.328													22	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43799956	43799957	+	IGR	INS	-	T	T	rs138006838	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43799956_43799957insT								NNT (94289 upstream) : FGF10 (505140 downstream)																							ttttctggttgttttttttttg	0.000													3	4	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59324459	59324459	+	Intron	DEL	C	-	-	rs16890447	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59324459delC	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.1_Intron	NM_006203	NP_006194	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	CCATGAAATGCCCCTGATCCA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	71736375	71736375	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71736375delT								PTCD2 (80339 upstream) : ZNF366 (2859 downstream)																							GCTTCATCCCTTAGTTCTCTG	0.463													4	2	---	---	---	---	
CMYA5	202333	broad.mit.edu	37	5	79038584	79038584	+	Intron	DEL	A	-	-	rs111610940		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79038584delA	uc003kgc.2	+							NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5							perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		attgagagtgaaaaaaaaaaa	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	88740508	88740508	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88740508delA								MEF2C (540639 upstream) : CETN3 (949023 downstream)																							AGAATGCTTGAAAAAAAAAAC	0.323													4	2	---	---	---	---	
C5orf36	285600	broad.mit.edu	37	5	93622526	93622526	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93622526delG	uc011cuk.1	-						C5orf36_uc003kkn.2_Intron	NM_001145678	NP_001139150	Q8IV33	K0825_HUMAN	hypothetical protein LOC285600 isoform 1												0		all_cancers(142;2.12e-08)|all_epithelial(76;5.95e-11)|all_lung(232;0.000996)|Lung NSC(167;0.0108)|Ovarian(174;0.0218)|Colorectal(57;0.0329)|Breast(839;0.214)|Lung SC(612;0.236)		all cancers(79;3.96e-19)		CTTCACCTATGGGGGACTGTG	0.413													4	2	---	---	---	---	
GLRX	2745	broad.mit.edu	37	5	95157176	95157177	+	Intron	DEL	GA	-	-	rs147644496		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95157176_95157177delGA	uc003klo.3	-						GLRX_uc003kln.3_Intron	NM_001118890	NP_001112362	P35754	GLRX1_HUMAN	glutaredoxin (thioltransferase)						cell redox homeostasis|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|transport	cytosol	electron carrier activity|glutathione disulfide oxidoreductase activity|protein disulfide oxidoreductase activity|protein N-terminus binding				0		all_cancers(142;3.38e-06)|all_epithelial(76;5.66e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;2.62e-16)	Glutathione(DB00143)	GAGAGAAGGGGAGAGAAACAAC	0.441													5	3	---	---	---	---	
ERAP1	51752	broad.mit.edu	37	5	96107036	96107036	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96107036delG	uc003kml.2	-						CAST_uc003klt.2_Intron|CAST_uc003klu.2_Intron|CAST_uc003klv.2_Intron|CAST_uc003klw.2_Intron|CAST_uc003klx.2_Intron|CAST_uc003kly.2_Intron|CAST_uc011cuo.1_Intron|CAST_uc003klz.1_Intron|CAST_uc011cur.1_Intron|CAST_uc011cus.1_Intron|CAST_uc003kma.1_Intron|CAST_uc011cut.1_Intron|CAST_uc003kmb.2_Intron|CAST_uc003kmc.2_Intron|CAST_uc003kmd.2_Intron|CAST_uc003kme.2_Intron|CAST_uc003kmf.2_Intron|CAST_uc003kmh.2_Intron|CAST_uc010jbj.2_Intron|CAST_uc010jbk.2_Intron|CAST_uc010jbl.1_Intron|CAST_uc003kmi.2_Intron|CAST_uc003kmj.2_Intron|CAST_uc003kmk.2_Intron|ERAP1_uc010jbm.1_Intron	NM_016442	NP_057526	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding						angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		GTACAGGAAAGGAAGGATCAC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116414593	116414593	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116414593delT								SEMA6A (504042 upstream) : None (None downstream)																							tttgtttttgtttttttcatc	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	140099222	140099222	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140099222delT								VTRNA1-2 (624 upstream) : VTRNA1-3 (6522 downstream)																							aagagatatcttttttttttt	0.055													2	4	---	---	---	---	
PCDHGA1	56114	broad.mit.edu	37	5	140714433	140714433	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140714433delA	uc003lji.1	+							NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACTGAACCCAGGAGGGAAGG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	152627120	152627120	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152627120delT								NMUR2 (842280 upstream) : GRIA1 (242055 downstream)																							ctcttttgtattttttgtttg	0.000													4	2	---	---	---	---	
GEMIN5	25929	broad.mit.edu	37	5	154285261	154285261	+	Intron	DEL	T	-	-	rs112942279		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154285261delT	uc003lvx.3	-						GEMIN5_uc011ddk.1_Intron	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5						ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			ATTACTTTGGttttttttttt	0.199													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164916629	164916629	+	IGR	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164916629delG								None (None upstream) : None (None downstream)																							TTAGTGGTCTGGAGAGCAGGG	0.393													4	2	---	---	---	---	
FGF18	8817	broad.mit.edu	37	5	170876364	170876365	+	Intron	INS	-	GTGTGT	GTGTGT			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170876364_170876365insGTGTGT	uc003mbk.2	+							NM_003862	NP_003853	O76093	FGF18_HUMAN	fibroblast growth factor 18 precursor						cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of cell proliferation	extracellular space|nucleolus	growth factor activity|type 1 fibroblast growth factor receptor binding|type 2 fibroblast growth factor receptor binding				0	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GAAAACAGGCCgtgtgtgtgtg	0.322													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	175606963	175606963	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175606963delT	uc003mdn.2	-						uc003mdo.1_Intron|uc003mdq.2_5'Flank					Homo sapiens cDNA clone IMAGE:5171181.																		GGTGTTGCAATTTTTTTTTTA	0.428													5	3	---	---	---	---	
ZNF354B	117608	broad.mit.edu	37	5	178293705	178293706	+	Intron	DEL	TC	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178293705_178293706delTC	uc003mjl.2	+						ZNF354B_uc003mjm.2_Intron	NM_058230	NP_478137	Q96LW1	Z354B_HUMAN	zinc finger protein 354B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	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)			TCATCCTTCTTCATCGACCTAC	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180555192	180555193	+	IGR	INS	-	CA	CA	rs148645196	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180555192_180555193insCA								BTNL9 (66670 upstream) : OR2V2 (26750 downstream)																							tgtcctctcctcacacacacac	0.000													4	2	---	---	---	---	
BMP6	654	broad.mit.edu	37	6	7748294	7748294	+	Intron	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7748294delC	uc003mxu.3	+							NM_001718	NP_001709	P22004	BMP6_HUMAN	bone morphogenetic protein 6 preproprotein						BMP signaling pathway|cartilage development|growth|immune response|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|SMAD protein signal transduction	extracellular space	BMP receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity			large_intestine(2)|ovary(1)	3	Ovarian(93;0.0721)					GGGCTTTGTTCCCTTGGAACC	0.154													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8228601	8228601	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8228601delT								EEF1E1 (125773 upstream) : SLC35B3 (183132 downstream)																							ttttctttccttttttttttt	0.134													2	5	---	---	---	---	
SYCP2L	221711	broad.mit.edu	37	6	10899389	10899389	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10899389delA	uc003mzo.2	+						SYCP2L_uc011din.1_Intron|SYCP2L_uc010jow.2_Intron	NM_001040274	NP_001035364	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			TTTAACTTGGAGCTGATTCAG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	15146798	15146798	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15146798delA								None (None upstream) : JARID2 (98936 downstream)																							acaccatctcaaaaaaaaaaa	0.134													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	25733107	25733108	+	IGR	INS	-	AAACAA	AAACAA	rs147896608	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25733107_25733108insAAACAA								HIST1H2BA (5535 upstream) : SLC17A4 (21819 downstream)																							ATGTCTAGAAGaaacaaaaaca	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28430362	28430363	+	IGR	DEL	CA	-	-	rs72457417		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28430362_28430363delCA								ZSCAN23 (19083 upstream) : GPX6 (40710 downstream)																							cacacacacccacacacacaca	0.238													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	34125888	34125889	+	IGR	INS	-	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34125888_34125889insT								GRM4 (12019 upstream) : HMGA1 (78688 downstream)																							cccgaaaggggaaggtgtccct	0.000													3	6	---	---	---	---	
ZFAND3	60685	broad.mit.edu	37	6	38112481	38112481	+	Intron	DEL	A	-	-	rs13195333	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38112481delA	uc003onx.2	+							NM_021943	NP_068762	Q9H8U3	ZFAN3_HUMAN	zinc finger, AN1-type domain 3								DNA binding|zinc ion binding			ovary(1)	1						CAAATGAGGTAAAAACACCTG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50467646	50467646	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50467646delA	uc003pae.1	+											full-length cDNA clone CS0DD007YH13 of Neuroblastoma Cot 50-normalized of Homo sapiens (human).																		cttagtacccaaagagttgtc	0.000													4	2	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51948206	51948209	+	Intron	DEL	TCCG	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51948206_51948209delTCCG	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					agtttctggttccgtaggtctggg	0.078													9	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57499442	57499442	+	Intron	DEL	A	-	-	rs11360933		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57499442delA	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)		tatgcaaatgaacaggtatga	0.020													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57527818	57527818	+	IGR	DEL	G	-	-	rs67858073		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57527818delG								PRIM2 (14443 upstream) : GUSBL2 (718341 downstream)																							AACCAGAACTGGGGGCTGACA	0.348													6	3	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65987344	65987346	+	Intron	DEL	ATT	-	-	rs145692139		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65987344_65987346delATT	uc011dxu.1	-							NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						aagttaattaattaaaaaaaaaa	0.000													4	2	---	---	---	---	
ANKRD6	22881	broad.mit.edu	37	6	90158155	90158156	+	Intron	INS	-	AA	AA	rs79076059		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90158155_90158156insAA	uc003pni.3	+						ANKRD6_uc003pne.3_Intron|ANKRD6_uc003pnf.3_Intron	NM_014942	NP_055757	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6								protein binding			ovary(2)|pancreas(1)	3		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		tgtcaaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
HS3ST5	222537	broad.mit.edu	37	6	114462027	114462028	+	Intron	INS	-	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114462027_114462028insT	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840	Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		tagttatgtaatttttttttag	0.040													4	2	---	---	---	---	
ZUFSP	221302	broad.mit.edu	37	6	116978183	116978183	+	Intron	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116978183delC	uc003pxf.1	-						ZUFSP_uc010kef.1_Intron	NM_145062	NP_659499	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain							intracellular	zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		cacacacacacacacaAAAAA	0.254													5	3	---	---	---	---	
MAP3K5	4217	broad.mit.edu	37	6	136977762	136977762	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136977762delT	uc003qhc.2	-						MAP3K5_uc011edj.1_5'Flank|MAP3K5_uc011edk.1_Intron|MAP3K5_uc010kgw.1_Intron	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GTTTTCACACttttttttttt	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	143030183	143030183	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143030183delT								LOC153910 (71157 upstream) : HIVEP2 (42422 downstream)																							aaaaaactgaTTTtttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	150733079	150733080	+	IGR	INS	-	A	A	rs139338880	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150733079_150733080insA								IYD (7315 upstream) : PLEKHG1 (187919 downstream)																							TCTCTGAAAATAAAAAAAAAGC	0.327													4	2	---	---	---	---	
AGPAT4	56895	broad.mit.edu	37	6	161557384	161557384	+	3'UTR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161557384delA	uc003qtr.1	-	9					AGPAT4_uc003qts.1_3'UTR|AGPAT4_uc011egb.1_3'UTR	NM_020133	NP_064518	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4						phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		GCACATGGGGAAAAAAAGATT	0.517													4	2	---	---	---	---	
PACRG	135138	broad.mit.edu	37	6	163184430	163184431	+	Intron	INS	-	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163184430_163184431insA	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		TAATTTACAGTTGAAGAAGCAC	0.391													4	2	---	---	---	---	
PRKAR1B	5575	broad.mit.edu	37	7	648019	648019	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:648019delG	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CTGACTCCCAGGGATGGGGGC	0.527													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	9129888	9129889	+	IGR	INS	-	A	A	rs150182469	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9129888_9129889insA								NXPH1 (337296 upstream) : PER4 (544011 downstream)																							gaaaagtggccagactctcttc	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	9676824	9676825	+	IGR	INS	-	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9676824_9676825insT								PER4 (1377 upstream) : None (None downstream)																							aaagctgaaggttttttttttc	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	20646220	20646220	+	IGR	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20646220delC								ITGB8 (190842 upstream) : ABCB5 (9025 downstream)																							ctcaagttttccccatttcct	0.055													4	2	---	---	---	---	
CHN2	1124	broad.mit.edu	37	7	29511197	29511197	+	Intron	DEL	A	-	-	rs3842624		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29511197delA	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058	P52757	CHIO_HUMAN	beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2						TGAATGAGGCAAAATTGTATT	0.468													5	5	---	---	---	---	
LOC646762	646762	broad.mit.edu	37	7	29712202	29712202	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29712202delA	uc003tad.3	-							NR_024278				Homo sapiens cDNA: FLJ23070 fis, clone LNG05629.												0						aaaatggcagaaaaaaaatca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	29757892	29757893	+	Intron	INS	-	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29757892_29757893insA	uc003tai.2	+											Homo sapiens DPY-19-like 2 pseudogene 3 (DPY19L2P3) pseudogene mRNA, complete sequence.																		GGACTTTTAGGAAAAAAAAAAA	0.149													3	3	---	---	---	---	
CCDC129	223075	broad.mit.edu	37	7	31624151	31624151	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31624151delA	uc003tcj.1	+						CCDC129_uc011kad.1_Intron|CCDC129_uc003tci.1_Intron|CCDC129_uc011kae.1_Intron|CCDC129_uc003tck.1_Intron	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129												0						CAATCATTCCAAAAAATTATT	0.368													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	34193010	34193011	+	3'UTR	INS	-	TA	TA	rs140714031	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34193010_34193011insTA	uc011kap.1	+	15						NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						Gtatatatgtgtatatatatat	0.307													3	3	---	---	---	---	
HECW1	23072	broad.mit.edu	37	7	43573219	43573220	+	Intron	INS	-	TGGT	TGGT	rs145535536	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43573219_43573220insTGGT	uc003tid.1	+						HECW1_uc011kbi.1_Intron	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						AGATGCCATAGTGGTTAGAAGA	0.500													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57620087	57620088	+	IGR	INS	-	AA	AA	rs151053678	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57620087_57620088insAA								ZNF716 (86822 upstream) : None (None downstream)																							TTCATAGGGATCTTTTTCAAAC	0.233													2	7	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78004164	78004164	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78004164delT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				ATTGTGTTGAttttttttttt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84598134	84598134	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84598134delT								SEMA3A (773917 upstream) : SEMA3D (26740 downstream)																							agcctctgtcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	89048699	89048699	+	IGR	DEL	T	-	-	rs112345378		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89048699delT								ZNF804B (82355 upstream) : DPY19L2P4 (700015 downstream)																							ggaggaaaccttttttttttt	0.000													3	3	---	---	---	---	
COL1A2	1278	broad.mit.edu	37	7	94051508	94051508	+	Intron	DEL	A	-	-	rs11312537		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94051508delA	uc003ung.1	+						COL1A2_uc011kib.1_Intron|COL1A2_uc010lfi.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor						axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GGTCTTTTTGAAAAAAAAAAA	0.313										HNSCC(75;0.22)			6	3	---	---	---	---	
AP4M1	9179	broad.mit.edu	37	7	99700053	99700054	+	Intron	INS	-	C	C	rs72592400		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99700053_99700054insC	uc003utb.3	+						MCM7_uc003usv.1_5'Flank|MCM7_uc003usw.1_5'Flank|MCM7_uc003usx.1_5'Flank|AP4M1_uc011kjg.1_Intron|AP4M1_uc010lgl.1_Intron|AP4M1_uc003utc.3_Intron|AP4M1_uc010lgm.2_Intron|AP4M1_uc003utd.2_Intron|AP4M1_uc011kjh.1_Intron|AP4M1_uc003ute.3_Intron|AP4M1_uc003utf.3_Intron	NM_004722	NP_004713	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|coated pit|Golgi trans cisterna	transporter activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AAAGAGTCAATGGGCGCCAGCA	0.238													10	6	---	---	---	---	
NAMPT	10135	broad.mit.edu	37	7	105924293	105924294	+	Intron	INS	-	A	A	rs115201749	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105924293_105924294insA	uc003vdq.2	-						NAMPT_uc003vdr.1_Intron|NAMPT_uc011klu.1_Intron	NM_005746	NP_005737	P43490	NAMPT_HUMAN	nicotinamide phosphoribosyltransferase						cell-cell signaling|NAD biosynthetic process|nicotinamide metabolic process|positive regulation of cell proliferation|positive regulation of nitric-oxide synthase biosynthetic process|signal transduction|water-soluble vitamin metabolic process	cytosol	cytokine activity|nicotinamide phosphoribosyltransferase activity|nicotinate phosphoribosyltransferase activity|nicotinate-nucleotide diphosphorylase (carboxylating) activity			large_intestine(1)	1						AAAAACAAAGGAAAAAAAAAGA	0.322													4	2	---	---	---	---	
IMMP2L	83943	broad.mit.edu	37	7	110603840	110603840	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110603840delA	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		AAGCCATGTTAAAACTTTACA	0.279													7	4	---	---	---	---	
TES	26136	broad.mit.edu	37	7	115893920	115893921	+	Intron	DEL	GT	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115893920_115893921delGT	uc003vho.2	+						TES_uc011kmy.1_Intron|TES_uc003vhp.2_Intron|uc003vhq.1_RNA	NM_015641	NP_056456	Q9UGI8	TES_HUMAN	testin isoform 1						negative regulation of cell proliferation	cytoplasm|focal adhesion|nucleus|protein complex	zinc ion binding				0	Lung NSC(10;0.0137)|all_lung(10;0.0148)	Breast(660;0.0602)	STAD - Stomach adenocarcinoma(10;0.00878)			gtgtgtgggggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	120572007	120572007	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120572007delA								TSPAN12 (73830 upstream) : ING3 (18810 downstream)																							CAAAGAACTTAAAAAAAGGGG	0.328													4	2	---	---	---	---	
C7orf58	79974	broad.mit.edu	37	7	120836856	120836857	+	Intron	INS	-	T	T	rs143605756	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120836856_120836857insT	uc003vjq.3	+						C7orf58_uc003vjs.3_Intron|C7orf58_uc003vjt.3_Intron	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1							endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)					ACTAAAGTTTCTTTTTTTTTTT	0.361													6	4	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126447398	126447398	+	Intron	DEL	A	-	-	rs149299768		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126447398delA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	gtgccttaggaaaaaaaagga	0.000										HNSCC(24;0.065)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	127058649	127058650	+	IGR	DEL	CA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127058649_127058650delCA								ZNF800 (25882 upstream) : GCC1 (162033 downstream)																							ttgccactatcactaccatcgc	0.059													4	2	---	---	---	---	
LOC100124692	100124692	broad.mit.edu	37	7	141885945	141885945	+	Intron	DEL	T	-	-	rs111646116		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141885945delT	uc003vxa.2	+							NR_003717				Homo sapiens cDNA FLJ16351 fis, clone TESTI2039060, moderately similar to Maltase-glucoamylase, intestinal.												0						CTTGGTTGTCTTTTTTTTTTT	0.229													5	4	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146076949	146076949	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146076949delA	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TTTGTAAAAGAAAAAAAAAGA	0.333										HNSCC(39;0.1)			4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146594676	146594676	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146594676delT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			AGTACGCAGATTTTTTTTTTT	0.348										HNSCC(39;0.1)			4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154035170	154035170	+	Intron	DEL	T	-	-	rs118022102	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154035170delT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron|DPP6_uc010lqh.1_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TGGATTCACATTTTTTTTTTC	0.413													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157342017	157342018	+	Intron	DEL	TT	-	-	rs137882305		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157342017_157342018delTT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron|PTPRN2_uc003wnn.2_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		ctttcttttctttttttttttt	0.337													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158069802	158069803	+	Intron	DEL	CA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158069802_158069803delCA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		cacacacgtgcacacacacaca	0.391													4	2	---	---	---	---	
ERICH1	157697	broad.mit.edu	37	8	614910	614910	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:614910delG	uc003wph.2	-						ERICH1_uc011kwh.1_Intron|ERICH1_uc003wpe.1_Intron	NM_207332	NP_997215	Q86X53	ERIC1_HUMAN	glutamate-rich 1											large_intestine(2)	2		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		GTATTTCACTGGGGTGTGAAC	0.368													4	2	---	---	---	---	
LOC340357	340357	broad.mit.edu	37	8	12653621	12653621	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12653621delG	uc003wwf.3	-						LOC340357_uc003wwe.3_Intron	NR_015383				Homo sapiens cDNA clone IMAGE:3922201.												0						CAACCTGTCTGGGTTCACGCC	0.284													4	2	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	26085277	26085277	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26085277delA	uc003xek.2	+							NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		GTTCATACTTAAAAAAACCTC	0.428													4	2	---	---	---	---	
BEYLA	497634	broad.mit.edu	37	8	47751806	47751806	+	5'Flank	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47751806delG	uc010lxr.1	+						BEYLA_uc003xqb.1_5'Flank	NR_027013				Homo sapiens cDNA FLJ40156 fis, clone TESTI2014385.												0						attttcaagtgggattggggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54335627	54335627	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54335627delA								OPRK1 (171433 upstream) : ATP6V1H (292489 downstream)																							CCAGAAGTTGAAAAAAAAAGA	0.289													4	2	---	---	---	---	
XKR4	114786	broad.mit.edu	37	8	56429459	56429459	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56429459delA	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)			ggattggattaaaaaaaatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58200344	58200344	+	IGR	DEL	T	-	-	rs79518077		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58200344delT								C8orf71 (3056 upstream) : FAM110B (706769 downstream)																							GGGACATGAATTTTTTTTTTG	0.398													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61545578	61545578	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61545578delA								RAB2A (11949 upstream) : CHD7 (45761 downstream)																							TTTGCTGAAGAAAAAAAAAAT	0.164													5	3	---	---	---	---	
CPA6	57094	broad.mit.edu	37	8	68482335	68482335	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68482335delT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			AAACAAGAACTTTTTTTTTTC	0.313													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	75425635	75425638	+	IGR	DEL	AGTT	-	-	rs112258711		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75425635_75425638delAGTT								GDAP1 (146302 upstream) : MIR2052 (192290 downstream)																							gttgagaaacagttaggcaagcta	0.098													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81508156	81508156	+	IGR	DEL	T	-	-	rs112489078		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81508156delT								ZBTB10 (73548 upstream) : ZNF704 (42613 downstream)																							TTCACACCCATTTTTTTCTTT	0.294													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98566133	98566136	+	IGR	DEL	CTTT	-	-	rs111948244		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98566133_98566136delCTTT								TSPYL5 (275957 upstream) : MTDH (90271 downstream)																							GGCAGGTATGCTTTGGTTTGTAGG	0.564											OREG0018885	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98612481	98612481	+	IGR	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98612481delG								TSPYL5 (322305 upstream) : MTDH (43926 downstream)																							TTGACAGAGTGGAGTTCATCA	0.328													4	2	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	113568791	113568791	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113568791delG	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							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						AGAAGATTATGGGAGGAATAA	0.299										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	2	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	113950091	113950091	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113950091delT	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							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						CATCTAAACATTTTTTGGAGA	0.299										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	2	---	---	---	---	
LOC157381	157381	broad.mit.edu	37	8	125952111	125952111	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125952111delT	uc003yro.1	+						LOC157381_uc003yrp.2_5'Flank|uc011lip.1_5'Flank					Homo sapiens cDNA FLJ32337 fis, clone PROST2005880.												0						TGAAGTCCTATTTTTTTTTTT	0.348													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129921943	129921943	+	IGR	DEL	C	-	-	rs112425192		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129921943delC								MIR1208 (759509 upstream) : GSDMC (838500 downstream)																							aaaaaaatctcaaggttaata	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134161911	134161911	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134161911delT								TG (14770 upstream) : WISP1 (41401 downstream)																							TTTGACCTCCTCATTGAGAAC	0.378													4	2	---	---	---	---	
ZNF696	79943	broad.mit.edu	37	8	144380753	144380753	+	3'UTR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144380753delA	uc003yxy.3	+	3						NM_030895	NP_112157	Q9H7X3	ZN696_HUMAN	zinc finger protein 696						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			actgagggccaacagaaacag	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	43840606	43840606	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43840606delT	uc004acz.1	+											Homo sapiens cDNA FLJ30083 fis, clone BGGI12001097, weakly similar to Homo sapiens contactin associated protein (Caspr) mRNA.																		TTGTCCATTCTTTTTTTTCTG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66455543	66455543	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66455543delG	uc010mng.1	-						uc004aec.2_5'Flank					Homo sapiens cDNA, FLJ98602.																		GGGCCCCTTTGGCCAGGGTAG	0.478													4	2	---	---	---	---	
LOC442421	442421	broad.mit.edu	37	9	66499823	66499824	+	Frame_Shift_Ins	INS	-	TC	TC			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66499823_66499824insTC	uc004aee.1	+	1	633_634	c.633_634insTC	c.(631-636)TATACAfs	p.Y211fs	LOC442421_uc004aed.1_RNA					Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).												0						CCACCTTCTATACAGTTATGCG	0.599													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68424476	68424476	+	IGR	DEL	A	-	-	rs141661264		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68424476delA								FAM27B (630287 upstream) : MIR1299 (577763 downstream)																							TCATCACGGGAATCTTGTACA	0.338													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68430746	68430746	+	IGR	DEL	T	-	-	rs113456947		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68430746delT								FAM27B (636557 upstream) : MIR1299 (571493 downstream)																							TTTTACTAGCTTCTTATATCC	0.313													4	2	---	---	---	---	
SMC5	23137	broad.mit.edu	37	9	72900877	72900878	+	Intron	INS	-	A	A			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72900877_72900878insA	uc004ahr.2	+							NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3						aataaGACAGGAAGATAAATGT	0.158													4	2	---	---	---	---	
TDRD7	23424	broad.mit.edu	37	9	100248454	100248454	+	Intron	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100248454delC	uc004axj.2	+						TDRD7_uc011lux.1_Intron|TDRD7_uc011luy.1_Intron	NM_014290	NP_055105	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7						lens fiber cell differentiation|lens morphogenesis in camera-type eye|posttranscriptional regulation of gene expression|spermatogenesis	chromatoid body	mRNA binding			ovary(2)|pancreas(1)	3		Acute lymphoblastic leukemia(62;0.158)				GAATGACTGACCATGCCACCT	0.512													4	2	---	---	---	---	
ZNF462	58499	broad.mit.edu	37	9	109694520	109694521	+	Intron	DEL	TG	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109694520_109694521delTG	uc004bcz.2	+						ZNF462_uc010mto.2_Intron|ZNF462_uc004bda.2_Intron|ZNF462_uc011lvz.1_5'Flank	NM_021224	NP_067047	Q96JM2	ZN462_HUMAN	zinc finger protein 462						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5						TGGTGGGGCATGTGTGTGTGTG	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	121660080	121660080	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121660080delA								None (None upstream) : DBC1 (268828 downstream)																							aatgatagccaaaaactcaca	0.114													4	2	---	---	---	---	
COL5A1	1289	broad.mit.edu	37	9	137676796	137676797	+	Intron	INS	-	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137676796_137676797insT	uc004cfe.2	+							NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GTGTGTGTGCGGGGGGTGGTCT	0.624													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8526448	8526448	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8526448delA								GATA3 (409286 upstream) : None (None downstream)																							GTCTGTAAGGaaaaaaaaaca	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30761549	30761550	+	IGR	INS	-	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30761549_30761550insG								MAP3K8 (10788 upstream) : LYZL2 (139159 downstream)																							agcccattgaaggggaaaaggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30801783	30801783	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30801783delT								MAP3K8 (51022 upstream) : LYZL2 (98926 downstream)																							aattagtcccttttcccctgg	0.025													4	2	---	---	---	---	
CCNY	219771	broad.mit.edu	37	10	35639329	35639329	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35639329delT	uc001iyw.3	+						CCNY_uc001iyu.3_Intron|CCNY_uc001iyv.3_Intron|CCNY_uc001iyx.3_Intron|CCNY_uc009xmb.2_Intron|CCNY_uc010qet.1_Intron	NM_145012	NP_659449	Q8ND76	CCNY_HUMAN	cyclin Y isoform 1						cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein kinase binding				0						CACAGTGGACTTTTTTTTTGA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42653350	42653350	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42653350delT								None (None upstream) : LOC441666 (173965 downstream)																							TGAGAAAATGTTTCCCCCAAA	0.338													6	3	---	---	---	---	
RASGEF1A	221002	broad.mit.edu	37	10	43691513	43691513	+	3'UTR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43691513delA	uc001jap.1	-	13					RASGEF1A_uc001jao.1_3'UTR	NM_145313	NP_660356	Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A						cell migration|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0						TAAAATAAACAAAAAAAACTT	0.393													3	3	---	---	---	---	
ZNF365	22891	broad.mit.edu	37	10	64323088	64323089	+	Intron	DEL	CA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64323088_64323089delCA	uc001jmd.1	+						ZNF365_uc001jmc.2_Intron	NM_199452	NP_955524	Q70YC4	TALAN_HUMAN	zinc finger protein 365 isoform D											ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					TTATTATGCGcacacacacaca	0.421													5	4	---	---	---	---	
CBARA1	10367	broad.mit.edu	37	10	74294576	74294576	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74294576delA	uc001jtb.1	-						CBARA1_uc009xqo.1_Intron	NM_006077	NP_006068	Q9BPX6	MICU1_HUMAN	calcium binding atopy-related autoantigen 1						calcium ion import|defense response|elevation of mitochondrial calcium ion concentration	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			ovary(1)	1						CACTGACTGTAAAAGAAACAG	0.318													4	2	---	---	---	---	
ZMYND17	118490	broad.mit.edu	37	10	75182782	75182783	+	3'UTR	INS	-	GA	GA			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75182782_75182783insGA	uc001juc.2	-	6								Q4VC12	ZMY17_HUMAN	RecName: Full=Zinc finger MYND domain-containing protein 17;								zinc ion binding			ovary(1)	1	Prostate(51;0.0119)					AATATGTGTGTGAGAGACAGTC	0.332													4	2	---	---	---	---	
DLG5	9231	broad.mit.edu	37	10	79569163	79569165	+	Intron	DEL	CAA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79569163_79569165delCAA	uc001jzk.2	-						DLG5_uc001jzi.2_Intron|DLG5_uc001jzj.2_Intron|DLG5_uc009xru.1_Intron	NM_004747	NP_004738	Q8TDM6	DLG5_HUMAN	discs large homolog 5						cell-cell adhesion|intracellular signal transduction|negative regulation of cell proliferation|regulation of apoptosis	cell junction|cytoplasm	beta-catenin binding|cytoskeletal protein binding|receptor signaling complex scaffold activity			ovary(5)|breast(3)	8	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			gactctgcctcaacaacaacaac	0.256													4	2	---	---	---	---	
LOC650623	650623	broad.mit.edu	37	10	81442721	81442721	+	5'Flank	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81442721delA	uc010qlu.1	+							NR_027512				Homo sapiens BEN domain containing 3 pseudogene (LOC650623), non-coding RNA.												0						aaccatctccaaaaaaaaTTG	0.219													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	86866905	86866906	+	IGR	INS	-	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86866905_86866906insG								FAM190B (588629 upstream) : GRID1 (492406 downstream)																							gttctgtggctggcttgctgga	0.000													4	2	---	---	---	---	
STAMBPL1	57559	broad.mit.edu	37	10	90660808	90660808	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90660808delG	uc001kfk.2	+						STAMBPL1_uc010qmx.1_Intron|STAMBPL1_uc009xto.2_Intron|STAMBPL1_uc001kfl.2_5'Flank	NM_020799	NP_065850	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		aacattattagggggattctt	0.000													4	2	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100401358	100401359	+	Intron	INS	-	A	A	rs149789116	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100401358_100401359insA	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600	Q8WWQ2	HPSE2_HUMAN	heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		aaaaattaattaaaaaaaaaaT	0.178													4	3	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100948771	100948771	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100948771delG	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600	Q8WWQ2	HPSE2_HUMAN	heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		CTGGCACCAAGGCAAACCAAA	0.418													4	2	---	---	---	---	
SFXN2	118980	broad.mit.edu	37	10	104478586	104478586	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104478586delG	uc001kwb.2	+						SFXN2_uc001kwc.2_Intron|SFXN2_uc001kwd.2_Intron	NM_178858	NP_849189	Q96NB2	SFXN2_HUMAN	sideroflexin 2						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity				0		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		ccaaagtgctgggattacagg	0.353													4	2	---	---	---	---	
PNLIPRP1	5407	broad.mit.edu	37	10	118351098	118351099	+	Intron	INS	-	TAC	TAC	rs148419179	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118351098_118351099insTAC	uc001lco.1	+						PNLIPRP1_uc001lcp.2_Intron|PNLIPRP1_uc001lcn.2_Intron|PNLIPRP1_uc009xys.1_Intron	NM_006229	NP_006220	P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1 precursor						lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)		AATGGGACTGATACTACTACCG	0.485													2	7	---	---	---	---	
PTPRE	5791	broad.mit.edu	37	10	129871913	129871913	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129871913delT	uc001lkb.2	+						PTPRE_uc009yat.2_Intron|PTPRE_uc009yau.2_Intron|PTPRE_uc001lkd.2_Intron|PTPRE_uc010quq.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)				ACCCTTTCCCTTTTTGGGAGT	0.468													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130417471	130417471	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130417471delT								MKI67 (493003 upstream) : MGMT (847983 downstream)																							AGAGTCGCACTTTTTTTTTTG	0.478													4	3	---	---	---	---	
SIRT3	23410	broad.mit.edu	37	11	219242	219243	+	Intron	DEL	CT	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:219242_219243delCT	uc001lok.3	-						SIRT3_uc001loj.3_Intron|SIRT3_uc010qvm.1_Intron|SIRT3_uc010qvn.1_Intron|SIRT3_uc010qvo.1_Intron|SIRT3_uc010qvp.1_Intron|SIRT3_uc010qvq.1_Intron	NM_012239	NP_036371	Q9NTG7	SIRT3_HUMAN	sirtuin 3 isoform a						chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding			urinary_tract(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		TCCCCTCCGCCTCTCTCTCTCT	0.554													4	2	---	---	---	---	
EPS8L2	64787	broad.mit.edu	37	11	722342	722342	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:722342delG	uc001lqt.2	+						EPS8L2_uc001lqu.2_Intron|EPS8L2_uc010qwk.1_Intron|EPS8L2_uc001lqv.2_Intron|EPS8L2_uc001lqw.2_Intron|EPS8L2_uc001lqx.2_5'UTR|EPS8L2_uc001lqy.2_5'Flank	NM_022772	NP_073609	Q9H6S3	ES8L2_HUMAN	epidermal growth factor receptor pathway							cytoplasm				pancreas(1)	1		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTGGAGCTACGGGGGTGCTGG	0.677													11	7	---	---	---	---	
ZNF143	7702	broad.mit.edu	37	11	9534311	9534312	+	Intron	DEL	GA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9534311_9534312delGA	uc001mhr.2	+						ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Intron	NM_003442	NP_003433	P52747	ZN143_HUMAN	zinc finger protein 143						regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|zinc ion binding				0				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		GAGAGATTAGGAGAGAGAGAAG	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	13779766	13779766	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13779766delA								FAR1 (25875 upstream) : SPON1 (204148 downstream)																							AGTAGCTTCTAAAATATAAgc	0.264													126	67	---	---	---	---	
PLEKHA7	144100	broad.mit.edu	37	11	17037368	17037368	+	5'Flank	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17037368delA	uc001mmo.2	-						PLEKHA7_uc010rcu.1_5'Flank	NM_175058	NP_778228	Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3						gactcagtctaaaaaaaaaaa	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	29772573	29772573	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29772573delA								None (None upstream) : KCNA4 (259193 downstream)																							TGCCTCTCCCAAAGAGTATGT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42926783	42926783	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42926783delA								None (None upstream) : API5 (406722 downstream)																							TTCAAGAATTAAAAAAAAATG	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42969148	42969150	+	IGR	DEL	GAC	-	-	rs147756906		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42969148_42969150delGAC								None (None upstream) : API5 (364355 downstream)																							tgatgatgatgacgatgatggtg	0.044													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	60578565	60578566	+	IGR	INS	-	C	C	rs138090625	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60578565_60578566insC								MS4A10 (9787 upstream) : CCDC86 (30863 downstream)																							TCTTCCCCAGGCCTCATTGCCA	0.604													4	2	---	---	---	---	
ASRGL1	80150	broad.mit.edu	37	11	62103893	62103894	+	5'Flank	INS	-	AG	AG	rs142567555	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62103893_62103894insAG	uc001nte.3	+						ASRGL1_uc001ntf.3_5'Flank|ASRGL1_uc001ntg.3_5'Flank	NM_025080	NP_079356	Q7L266	ASGL1_HUMAN	asparaginase-like 1						asparagine catabolic process via L-aspartate|protein maturation	cytoplasm|microtubule cytoskeleton|nucleus	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0					L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)	gcagcagaaacaggccagaggg	0.000													4	4	---	---	---	---	
MACROD1	28992	broad.mit.edu	37	11	63770508	63770508	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63770508delG	uc001nyh.2	-							NM_014067	NP_054786	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1												0						CAGAAAACCTGGGGTCTTTCC	0.592													4	2	---	---	---	---	
MACROD1	28992	broad.mit.edu	37	11	63839896	63839896	+	Intron	DEL	A	-	-	rs34047031		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63839896delA	uc001nyh.2	-							NM_014067	NP_054786	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1												0						CGGCTCatttaaaaaaaaaaa	0.284													7	5	---	---	---	---	
SYT12	91683	broad.mit.edu	37	11	66788214	66788214	+	5'Flank	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66788214delT	uc009yrl.2	+						SYT12_uc001oju.2_5'Flank	NM_177963	NP_808878	Q8IV01	SYT12_HUMAN	synaptotagmin XII							cell junction|integral to membrane|synaptic vesicle membrane				ovary(1)	1						tcacccaccatttttttttag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76308238	76308239	+	IGR	DEL	AG	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76308238_76308239delAG								C11orf30 (45650 upstream) : LRRC32 (60330 downstream)																							caaacaagcaagcaagcaaaca	0.257													4	2	---	---	---	---	
CLNS1A	1207	broad.mit.edu	37	11	77341833	77341833	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77341833delA	uc001oyk.2	-						CLNS1A_uc001oyl.2_Intron	NM_001293	NP_001284	P54105	ICLN_HUMAN	chloride channel, nucleotide-sensitive, 1A						blood circulation|cell volume homeostasis|chloride transport|ncRNA metabolic process|spliceosomal snRNP assembly	cytoskeleton|cytosol|nucleus|plasma membrane	protein binding			ovary(1)	1	all_cancers(14;5.43e-17)|all_epithelial(13;1.78e-19)		Epithelial(5;1.02e-48)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			tgaagaagtcaaaaaaaaaat	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	83060109	83060110	+	Intron	DEL	CA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83060109_83060110delCA	uc001pag.2	+											Homo sapiens cDNA clone IMAGE:5296561.																		CTGTACACACCACACACACACA	0.257													5	3	---	---	---	---	
ATM	472	broad.mit.edu	37	11	108191996	108191996	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108191996delT	uc001pkb.1	+						ATM_uc009yxr.1_Intron|C11orf65_uc010rvx.1_Intron|ATM_uc001pke.1_Intron|ATM_uc001pkg.1_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		CTCTTCTTTATTTTCAGAGTG	0.353			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			130	58	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	108843168	108843169	+	IGR	INS	-	TG	TG	rs148425444	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108843168_108843169insTG								DDX10 (31522 upstream) : C11orf87 (449706 downstream)																							GAATTTGAGTCtgtgtgtgtgt	0.356													2	6	---	---	---	---	
FDX1	2230	broad.mit.edu	37	11	110316130	110316130	+	Intron	DEL	T	-	-	rs144690643		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110316130delT	uc001pkx.2	+							NM_004109	NP_004100	P10109	ADX_HUMAN	ferredoxin 1 precursor						electron transport chain|transport	mitochondrial matrix	2 iron, 2 sulfur cluster binding|electron carrier activity|iron ion binding				0		all_cancers(61;1.59e-12)|all_epithelial(67;8.38e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;5.27e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0384)|Colorectal(284;0.228)	Mitotane(DB00648)	TACAGTAcagttttttttaaa	0.095													4	2	---	---	---	---	
PCSK7	9159	broad.mit.edu	37	11	117099870	117099870	+	Intron	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117099870delC	uc001pqr.2	-							NM_004716	NP_004707	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7						peptide hormone processing	integral to Golgi membrane	serine-type endopeptidase activity				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		ggaccatgagcccaggcagcc	0.119			T	IGH@	MLCLS								4	2	---	---	---	---	
HMBS	3145	broad.mit.edu	37	11	118964143	118964143	+	3'UTR	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118964143delG	uc001puz.1	+	14					HMBS_uc001pvc.1_3'UTR|HMBS_uc009zap.1_3'UTR|HMBS_uc001pva.1_3'UTR|HMBS_uc001pvb.1_3'UTR|HMBS_uc001pvd.1_3'UTR|HMBS_uc001pve.1_3'UTR|HMBS_uc001pvf.1_3'UTR	NM_000190	NP_000181	P08397	HEM3_HUMAN	hydroxymethylbilane synthase isoform 1						peptidyl-pyrromethane cofactor linkage	cytosol	hydroxymethylbilane synthase activity				0	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		GCCTCACCTTGGGGCCTTGAT	0.522									Porphyria_Acute_Intermittent				4	2	---	---	---	---	
TMEM136	219902	broad.mit.edu	37	11	120199654	120199655	+	Intron	INS	-	G	G	rs76673086		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120199654_120199655insG	uc001pxh.1	+						TMEM136_uc001pxg.2_Intron|TMEM136_uc010rzm.1_Intron|TMEM136_uc001pxj.2_Intron|TMEM136_uc009zas.1_Intron|TMEM136_uc001pxi.1_Intron	NM_174926	NP_777586	Q6ZRR5	TM136_HUMAN	transmembrane protein 136							integral to membrane				ovary(1)	1		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Hepatocellular(160;0.206)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.07e-06)		tgtgtgtgtgtttgtgtatgtT	0.050													4	2	---	---	---	---	
TMEM136	219902	broad.mit.edu	37	11	120199655	120199656	+	Intron	INS	-	G	G	rs76673086		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120199655_120199656insG	uc001pxh.1	+						TMEM136_uc001pxg.2_Intron|TMEM136_uc010rzm.1_Intron|TMEM136_uc001pxj.2_Intron|TMEM136_uc009zas.1_Intron|TMEM136_uc001pxi.1_Intron	NM_174926	NP_777586	Q6ZRR5	TM136_HUMAN	transmembrane protein 136							integral to membrane				ovary(1)	1		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Hepatocellular(160;0.206)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.07e-06)		gtgtgtgtgtttgtgtatgtTT	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	125991444	125991444	+	IGR	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125991444delG								CDON (58257 upstream) : RPUSD4 (80546 downstream)																							agctggaagtggggagtgtgc	0.000													4	2	---	---	---	---	
SNX19	399979	broad.mit.edu	37	11	130776249	130776249	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130776249delT	uc001qgk.3	-						SNX19_uc009zcw.2_Intron|SNX19_uc010sce.1_Intron|SNX19_uc010scf.1_Intron|SNX19_uc010scg.1_Intron|SNX19_uc001qgl.3_Intron|SNX19_uc009zcx.1_Intron	NM_014758	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|lung(2)	4	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		TGGTCATCCATTTTTTTTTCC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134671646	134671646	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134671646delA								B3GAT1 (389834 upstream) : None (None downstream)																							gacaggaagcaaaaaaaagag	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	27288204	27288204	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27288204delT								C12orf71 (52749 upstream) : STK38L (108874 downstream)																							AAAGTGTTTATGTAATTAGAA	0.313													10	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38926471	38926471	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38926471delT								ALG10B (202944 upstream) : CPNE8 (119531 downstream)																							GGTTCTATTATTTTTTTGGCC	0.353													4	2	---	---	---	---	
COL2A1	1280	broad.mit.edu	37	12	48380331	48380332	+	Intron	INS	-	G	G	rs144941834	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48380331_48380332insG	uc001rqu.2	-						COL2A1_uc009zkw.2_Intron|COL2A1_uc001rqv.2_Intron	NM_001844	NP_001835	P02458	CO2A1_HUMAN	collagen, type II, alpha 1 isoform 1 precursor						axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	GTTTCAGGGCTGGGGGGGGGCT	0.550													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	49591369	49591369	+	IGR	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49591369delC								TUBA1A (8508 upstream) : TUBA1C (30340 downstream)																							TAGAGTTCAGCCCAGGAGCTG	0.483													4	2	---	---	---	---	
R3HDM2	22864	broad.mit.edu	37	12	57664009	57664009	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57664009delT	uc009zpm.1	-						R3HDM2_uc010srn.1_Intron|R3HDM2_uc001snu.2_Intron|R3HDM2_uc001snr.2_Intron|R3HDM2_uc001sns.2_Intron|R3HDM2_uc001snt.2_Intron|R3HDM2_uc009zpn.1_Intron	NM_014925	NP_055740	Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2							nucleus	nucleic acid binding			ovary(2)	2						TAATTGTGTGtttttttgttt	0.209													4	2	---	---	---	---	
SRGAP1	57522	broad.mit.edu	37	12	64521186	64521186	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64521186delA	uc010ssp.1	+						SRGAP1_uc001srv.2_Intron	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		ttgtacctgtaatgaaattgt	0.090													4	2	---	---	---	---	
CNOT2	4848	broad.mit.edu	37	12	70747896	70747896	+	3'UTR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70747896delT	uc001svv.2	+	16					CNOT2_uc009zro.2_3'UTR|CNOT2_uc009zrp.2_3'UTR|CNOT2_uc009zrq.2_3'UTR	NM_014515	NP_055330	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	protein binding|RNA polymerase II transcription cofactor activity				0	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			ACTAAATTTGTAATTTGTTTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77675358	77675359	+	IGR	DEL	TC	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77675358_77675359delTC								E2F7 (215998 upstream) : NAV3 (549710 downstream)																							ATATACTCAttctctctctccc	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77887360	77887360	+	IGR	DEL	G	-	-	rs35295859		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77887360delG								E2F7 (428000 upstream) : NAV3 (337709 downstream)																							cattcccaaaggcagcaaaat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80359201	80359201	+	IGR	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80359201delC								PPP1R12A (29966 upstream) : PTPRQ (478925 downstream)																							tttttgtattctcaatatctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97291801	97291801	+	IGR	DEL	G	-	-	rs112793656		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97291801delG								C12orf63 (132753 upstream) : NEDD1 (9200 downstream)																							gcctgggggcggggggggggc	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	105775060	105775060	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105775060delT								C12orf75 (9765 upstream) : NUAK1 (682065 downstream)																							ctgattttgctttacctcgaa	0.000													4	2	---	---	---	---	
TMEM119	338773	broad.mit.edu	37	12	108993720	108993720	+	5'Flank	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108993720delA	uc001tng.2	-						TMEM119_uc001tnf.2_5'Flank	NM_181724	NP_859075	Q4V9L6	TM119_HUMAN	transmembrane protein 119 precursor							integral to membrane				ovary(1)	1						GAGGGGTAGTAAGTGTTGGAG	0.577													4	2	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124952858	124952859	+	Intron	INS	-	TCC	TCC			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124952858_124952859insTCC	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		caccctcatcatcctcatcacc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	48321865	48321865	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48321865delA								HTR2A (850815 upstream) : SUCLA2 (194927 downstream)																							TTCTCACTTTAAAAAAATACA	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	56413056	56413056	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56413056delT								None (None upstream) : None (None downstream)																							CTCCTCCTTGTTCTGAGCATG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73065411	73065411	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73065411delA								DACH1 (624081 upstream) : C13orf37 (217084 downstream)																							TCAGAGGCAGAAAAAAAAAAA	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	76724528	76724528	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76724528delT								LMO7 (290524 upstream) : KCTD12 (729776 downstream)																							TTTCCCCTCCTTTTTTTTTTT	0.269													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85852159	85852159	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85852159delA								None (None upstream) : SLITRK6 (514763 downstream)																							GTGTTAAAGGAAAAAAAAAAG	0.299													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	88574753	88574753	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88574753delT								SLITRK5 (242885 upstream) : None (None downstream)																							caagcttcccttttaaagtcc	0.000													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102555589	102555590	+	Intron	DEL	GT	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102555589_102555590delGT	uc001vpe.2	-						FGF14_uc001vpf.2_Intron	NM_004115	NP_004106	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1A						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TCTAATTGTGgtgtgtgtgtgt	0.307													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	103935190	103935191	+	IGR	INS	-	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103935190_103935191insT								SLC10A2 (215994 upstream) : None (None downstream)																							GTTGGTTTCTCTTTTTTTTCCA	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	109186898	109186898	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109186898delT								TNFSF13B (227534 upstream) : MYO16 (61602 downstream)																							AAAATTGCAGTTTTTTTTTTC	0.388													8	4	---	---	---	---	
NOVA1	4857	broad.mit.edu	37	14	27066695	27066695	+	5'UTR	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27066695delC	uc001wpy.2	-	1					NOVA1_uc001wpz.2_5'UTR|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_5'UTR	NM_002515	NP_002506	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1 isoform 1						locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)		TTTGTTTTGGCtttttctttt	0.383													4	2	---	---	---	---	
DCAF4	26094	broad.mit.edu	37	14	73418334	73418334	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73418334delA	uc001xng.2	+						DCAF4_uc001xnj.2_Intron|DCAF4_uc010ttr.1_Intron|DCAF4_uc001xnh.2_Intron|DCAF4_uc010tts.1_Intron|DCAF4_uc010ttt.1_Intron|DCAF4_uc001xni.2_Intron|DCAF4_uc001xnk.2_Intron	NM_015604	NP_056419	Q8WV16	DCAF4_HUMAN	DDB1 and CUL4 associated factor 4 isoform 1							CUL4 RING ubiquitin ligase complex				ovary(1)|central_nervous_system(1)|skin(1)	3						acaaacaaacaaaaaaaaaaC	0.224													7	4	---	---	---	---	
ADCK1	57143	broad.mit.edu	37	14	78397896	78397896	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78397896delC	uc001xui.2	+	10	1341	c.1242delC	c.(1240-1242)CTCfs	p.L414fs	ADCK1_uc001xuj.2_Frame_Shift_Del_p.L346fs|ADCK1_uc001xul.2_Frame_Shift_Del_p.L121fs	NM_020421	NP_065154	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1 isoform a	421	Protein kinase.					extracellular region	ATP binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		CCAACTACCTCCCCCAGATCA	0.607													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	87351315	87351316	+	IGR	DEL	AC	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87351315_87351316delAC								None (None upstream) : GALC (952848 downstream)																							acacccccgtacacacacacac	0.178													4	2	---	---	---	---	
CPSF2	53981	broad.mit.edu	37	14	92597127	92597127	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92597127delA	uc001yah.1	+							NM_017437	NP_059133	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		GCTTTCACTTAAAAAAAAAAA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97193861	97193864	+	IGR	DEL	AGAG	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97193861_97193864delAGAG								PAPOLA (160415 upstream) : VRK1 (69820 downstream)																							gagaggagtcagagaggctattag	0.010													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21918463	21918464	+	IGR	DEL	CA	-	-	rs150921370		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21918463_21918464delCA								NF1P1 (783838 upstream) : LOC646214 (14050 downstream)																							tttatttactcacagttccaga	0.074													4	2	---	---	---	---	
CYFIP1	23191	broad.mit.edu	37	15	22919705	22919708	+	Intron	DEL	GACG	-	-	rs150466291		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22919705_22919708delGACG	uc001yus.2	+						CYFIP1_uc001yut.2_Intron|CYFIP1_uc010aya.1_5'Flank	NM_014608	NP_055423	Q7L576	CYFP1_HUMAN	cytoplasmic FMR1 interacting protein 1 isoform						axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		GGCAGTTAGAGACGGAGCAAAGTA	0.539													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	28948447	28948448	+	5'Flank	INS	-	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28948447_28948448insG	uc001zcd.2	+											DQ593033																		AAATGGGTGCAGGGGGAGTCAG	0.594													3	3	---	---	---	---	
FAM189A1	23359	broad.mit.edu	37	15	29552955	29552956	+	Intron	INS	-	AT	AT	rs151296870	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29552955_29552956insAT	uc010azk.1	-							NM_015307	NP_056122	O60320	F1891_HUMAN	hypothetical protein LOC23359							integral to membrane					0						TCTACTTTCACGTTTGaaattt	0.302													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30454994	30454995	+	IGR	INS	-	CATTCATT	CATTCATT			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30454994_30454995insCATTCATT								FAM7A3 (31048 upstream) : DKFZP434L187 (33244 downstream)																							TGTGAGAGACAcattcattcat	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	31712255	31712256	+	IGR	INS	-	A	A	rs140237940	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31712255_31712256insA								KLF13 (42154 upstream) : OTUD7A (63074 downstream)																							agtgctggaagaaaaaaacctt	0.104													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	38328685	38328686	+	Intron	DEL	TC	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38328685_38328686delTC	uc001zjx.1	+											Homo sapiens, clone IMAGE:5755094, mRNA.																		tctgtttttgtctctctctctc	0.203													4	2	---	---	---	---	
EIF2AK4	440275	broad.mit.edu	37	15	40326997	40326997	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40326997delA	uc001zkm.1	+						EIF2AK4_uc010bbj.1_Intron|EIF2AK4_uc001zkn.1_Intron|EIF2AK4_uc001zko.1_Intron|EIF2AK4_uc010bbk.1_Intron	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha						translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		TCATACACTTAAAAGGCAACA	0.348													4	2	---	---	---	---	
SPG11	80208	broad.mit.edu	37	15	44861363	44861363	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44861363delA	uc001ztx.2	-						SPG11_uc010bdw.2_Intron|SPG11_uc010ueh.1_Intron|SPG11_uc010uei.1_Intron	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1						cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		actccgtctcaaaaaaaaaaa	0.154													3	3	---	---	---	---	
SLC28A2	9153	broad.mit.edu	37	15	45545881	45545881	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45545881delA	uc001zva.2	+							NM_004212	NP_004203	O43868	S28A2_HUMAN	solute carrier family 28 (sodium-coupled						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity			ovary(4)	4		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)		TAAACTCCATAAAAAAAAAGG	0.308													4	5	---	---	---	---	
FBN1	2200	broad.mit.edu	37	15	48782414	48782414	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48782414delA	uc001zwx.1	-							NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor						heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TTTATTCCTCAAAAAAAACCC	0.413													4	2	---	---	---	---	
COPS2	9318	broad.mit.edu	37	15	49436170	49436170	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49436170delG	uc001zxf.2	-						COPS2_uc001zxh.2_Intron|COPS2_uc010ufa.1_Intron	NM_004236	NP_004227	P61201	CSN2_HUMAN	COP9 constitutive photomorphogenic homolog						cullin deneddylation|transcription from RNA polymerase II promoter	cytoplasm|signalosome	protein binding|signal transducer activity			lung(1)	1		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		gtgacagagcgggGGAAAAAA	0.119													4	2	---	---	---	---	
GLDN	342035	broad.mit.edu	37	15	51696228	51696229	+	Intron	INS	-	TCTT	TCTT	rs149014390	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51696228_51696229insTCTT	uc002aba.2	+						GLDN_uc002abb.2_Intron	NM_181789	NP_861454	Q6ZMI3	GLDN_HUMAN	gliomedin						cell differentiation|nervous system development	collagen|integral to membrane|plasma membrane				ovary(2)	2				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)		GGTGATTATTCTGACACCACAC	0.381													4	2	---	---	---	---	
TEX9	374618	broad.mit.edu	37	15	56680976	56680976	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56680976delT	uc002adp.2	+						TEX9_uc002ado.1_Intron|TEX9_uc010ugl.1_Intron|TEX9_uc002adq.1_Intron	NM_198524	NP_940926	Q8N6V9	TEX9_HUMAN	testis expressed 9												0				all cancers(107;0.0394)|GBM - Glioblastoma multiforme(80;0.056)		CTGAGGCTTATTTTTTTTTCC	0.294													4	2	---	---	---	---	
HERC1	8925	broad.mit.edu	37	15	63927233	63927233	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63927233delT	uc002amp.2	-							NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						CTTTTAAAAAttttttttttt	0.129													6	3	---	---	---	---	
HERC1	8925	broad.mit.edu	37	15	63955573	63955573	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63955573delA	uc002amp.2	-							NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						cctctcttgcaaaaggggata	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	72625057	72625057	+	Intron	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72625057delG	uc002aug.2	+						CELF6_uc002auk.3_Intron					Homo sapiens hexosaminidase A (alpha polypeptide), mRNA (cDNA clone IMAGE:4823589).																		tcatagagatgggggggtctc	0.000													4	2	---	---	---	---	
SEMA7A	8482	broad.mit.edu	37	15	74708660	74708661	+	Intron	DEL	AC	-	-	rs56284721		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74708660_74708661delAC	uc002axv.2	-						SEMA7A_uc010ulk.1_Intron|SEMA7A_uc010ull.1_Intron	NM_003612	NP_003603	O75326	SEM7A_HUMAN	semaphorin 7A isoform 1 preproprotein						axon guidance|immune response|inflammatory response|integrin-mediated signaling pathway|positive regulation of axon extension|positive regulation of ERK1 and ERK2 cascade|positive regulation of macrophage cytokine production|regulation of inflammatory response	anchored to membrane|external side of plasma membrane	receptor activity			breast(1)|central_nervous_system(1)	2						cacaggcaaaacacacacacac	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79774645	79774645	+	IGR	DEL	T	-	-	rs67595543		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79774645delT								KIAA1024 (10003 upstream) : MTHFS (362675 downstream)																							cttcagcacattttttttttt	0.000													9	5	---	---	---	---	
BCL2A1	597	broad.mit.edu	37	15	80260273	80260273	+	Intron	DEL	A	-	-	rs8025803		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80260273delA	uc002bfc.3	-						BCL2A1_uc002bfd.3_Intron	NM_004049	NP_004040	Q16548	B2LA1_HUMAN	BCL2-related protein A1 isoform 1						anti-apoptosis|apoptosis	cytoplasm	protein binding			pancreas(1)	1						TGTTTTTTTTAAAAAAAAAAA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	81828265	81828265	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81828265delA								TMC3 (161847 upstream) : MEX3B (505863 downstream)																							caggaaaaagaaaaaaagaaa	0.000													4	2	---	---	---	---	
IQGAP1	8826	broad.mit.edu	37	15	91009834	91009834	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91009834delT	uc002bpl.1	+							NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1						energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			GAAAATATCCTTCCCCCCCCC	0.368													4	4	---	---	---	---	
DECR2	26063	broad.mit.edu	37	16	460794	460794	+	Intron	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:460794delC	uc002chb.2	+						DECR2_uc002chc.2_Intron|DECR2_uc010bqv.2_Intron|DECR2_uc002chd.2_Intron|DECR2_uc002che.1_Intron	NM_020664	NP_065715	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2							peroxisome	2,4-dienoyl-CoA reductase (NADPH) activity|binding				0		Hepatocellular(16;0.00015)				GGTATGACCACCCCCCCCCGC	0.677													9	6	---	---	---	---	
IFT140	9742	broad.mit.edu	37	16	1569647	1569647	+	Intron	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1569647delC	uc002cmb.2	-						IFT140_uc002clz.2_Intron	NM_014714	NP_055529	Q96RY7	IF140_HUMAN	intraflagellar transport 140											ovary(3)|pancreas(1)|skin(1)	5		Hepatocellular(780;0.219)				TCCTCCCACTCCCCCACCAGG	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8537670	8537671	+	IGR	INS	-	A	A	rs149579746	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8537670_8537671insA								A2BP1 (774330 upstream) : TMEM114 (81832 downstream)																							CATAATAAACTGGGGGCAATGG	0.446													2	4	---	---	---	---	
METTL9	51108	broad.mit.edu	37	16	21636063	21636063	+	Intron	DEL	A	-	-	rs42747	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21636063delA	uc002dje.2	+						uc002diq.3_Intron|METTL9_uc002djf.2_Intron	NM_016025	NP_057109	Q9H1A3	METL9_HUMAN	methyltransferase like 9 isoform 1											ovary(1)	1				GBM - Glioblastoma multiforme(48;0.0759)		agaaaaaattaaaaaaaaaaa	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32828004	32828004	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32828004delA								TP53TG3B (139126 upstream) : SLC6A10P (60793 downstream)																							caaatacaagaaaaacaaaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32833097	32833097	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32833097delA								TP53TG3B (144219 upstream) : SLC6A10P (55700 downstream)																							ttagaaatggaaagactaggc	0.055													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33046739	33046739	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33046739delT								SLC6A10P (150276 upstream) : MIR1826 (918769 downstream)																							atgttatgactctatttagta	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33046741	33046741	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33046741delT								SLC6A10P (150278 upstream) : MIR1826 (918767 downstream)																							gttatgactctatttagtacc	0.025													4	2	---	---	---	---	
TOX3	27324	broad.mit.edu	37	16	52517026	52517026	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52517026delA	uc002egw.2	-						TOX3_uc010vgt.1_Intron|TOX3_uc010vgu.1_Intron	NM_001080430	NP_001073899	O15405	TOX3_HUMAN	TOX high mobility group box family member 3						apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity				0						ACTCCAGACCAAAAATATGCC	0.458													4	2	---	---	---	---	
NLRC5	84166	broad.mit.edu	37	16	57111993	57111994	+	Intron	INS	-	G	G	rs142860883	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57111993_57111994insG	uc002ekk.1	+						NLRC5_uc010ccr.1_Intron|NLRC5_uc010ccs.1_Intron|NLRC5_uc002eko.1_Intron|NLRC5_uc002ekq.1_Intron|NLRC5_uc002ekr.1_Intron	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27						defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)				TCGGGAGCAGTGGGGGGGTCCA	0.649													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64395091	64395092	+	IGR	INS	-	T	T	rs140371169	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64395091_64395092insT								None (None upstream) : CDH11 (585593 downstream)																							AACCCTTTACATACAGTGCACT	0.351													2	4	---	---	---	---	
TAT	6898	broad.mit.edu	37	16	71606720	71606720	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71606720delA	uc002fap.2	-							NM_000353	NP_000344	P17735	ATTY_HUMAN	tyrosine aminotransferase						2-oxoglutarate metabolic process|glutamate metabolic process|L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	1-aminocyclopropane-1-carboxylate synthase activity|L-tyrosine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(2)	2		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Glutamic Acid(DB00142)|L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Pyridoxal Phosphate(DB00114)	TAGGAAATGTACTAAGCCAAA	0.373													6	3	---	---	---	---	
VAT1L	57687	broad.mit.edu	37	16	77926387	77926387	+	Intron	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77926387delC	uc002ffg.1	+							NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.								oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1						CTCCTTTGAGCTGTTTGCAGA	0.483													4	2	---	---	---	---	
TAF1C	9013	broad.mit.edu	37	16	84216549	84216551	+	Intron	DEL	AAA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84216549_84216551delAAA	uc002fhn.2	-						TAF1C_uc002fhm.2_Intron|TAF1C_uc010vnx.1_Intron|TAF1C_uc010vny.1_Intron|TAF1C_uc010vnz.1_Intron|TAF1C_uc002fho.2_Intron|TAF1C_uc010voa.1_Intron|TAF1C_uc002fhp.1_Intron|TAF1C_uc010vob.1_Intron	NM_005679	NP_005670	Q15572	TAF1C_HUMAN	TBP-associated factor 1C isoform 1						regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding			ovary(1)	1						CTGGTATAAGAAAGTACAGCTCA	0.404													33	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86759444	86759444	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86759444delA								FOXL1 (144141 upstream) : FBXO31 (603500 downstream)																							gagaagtcttaacattgccta	0.204													4	2	---	---	---	---	
SREBF1	6720	broad.mit.edu	37	17	17727903	17727904	+	Intron	DEL	AC	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17727903_17727904delAC	uc002gru.1	-						SREBF1_uc002grs.1_5'Flank|SREBF1_uc002grt.1_Intron|SREBF1_uc010cpp.1_5'Flank|SREBF1_uc010cpq.1_Intron	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription						cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1						GGTAAAAGTTACACACACACAC	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21225034	21225035	+	IGR	INS	-	AG	AG	rs77521218		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21225034_21225035insAG								MAP2K3 (6485 upstream) : KCNJ12 (54664 downstream)																							TGGTTCCCCACAGTCTGAGGTC	0.505													6	3	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21310735	21310735	+	Intron	DEL	T	-	-	rs111420634		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21310735delT	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	atccacccactcaaccatata	0.000										Prostate(3;0.18)			4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21548662	21548662	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21548662delT								C17orf51 (70931 upstream) : FAM27L (276708 downstream)																							AGAAGGCATCTTCTTAGATTA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21548665	21548666	+	IGR	DEL	TT	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21548665_21548666delTT								C17orf51 (70934 upstream) : FAM27L (276704 downstream)																							AGGCATCTTCTTAGATTAGGCT	0.406													4	2	---	---	---	---	
TMEM97	27346	broad.mit.edu	37	17	26653991	26653991	+	3'UTR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26653991delT	uc002hat.2	+	3						NM_014573	NP_055388	Q5BJF2	TMM97_HUMAN	transmembrane protein 97						cholesterol homeostasis|regulation of cell growth	integral to membrane|lysosome|nuclear membrane|plasma membrane|rough endoplasmic reticulum	protein binding				0	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		CCTTCTTCCAttttttttttt	0.249													4	2	---	---	---	---	
CCDC55	84081	broad.mit.edu	37	17	28499865	28499865	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28499865delA	uc002heu.2	+						CCDC55_uc002hev.2_Intron|CCDC55_uc010wbl.1_Intron|CCDC55_uc010wbm.1_Intron|CCDC55_uc002hex.2_Intron	NM_032141	NP_115517	Q9H0G5	NSRP1_HUMAN	coiled-coil domain containing 55 isoform 1						developmental process|nucleocytoplasmic transport|regulation of alternative nuclear mRNA splicing, via spliceosome	nuclear speck|ribonucleoprotein complex	mRNA binding|protein binding				0						ACTTGCAGGGAAAAAAAAAAC	0.313													4	2	---	---	---	---	
UBE2Z	65264	broad.mit.edu	37	17	46993227	46993228	+	Intron	INS	-	CC	CC	rs139516659	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46993227_46993228insCC	uc002ioi.2	+							NM_023079	NP_075567	Q9H832	UBE2Z_HUMAN	ubiquitin-conjugating enzyme E2Z						apoptosis	cytoplasm|nucleus	ATP binding|ubiquitin-protein ligase activity				0						CTGTTCTTTTGCCCCCCCCCCT	0.376													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66673726	66673727	+	IGR	INS	-	C	C	rs147126198	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66673726_66673727insC								FAM20A (76631 upstream) : ABCA8 (189706 downstream)																							CATTGTGTGTTCCCAGGCCTCG	0.421													6	5	---	---	---	---	
EXOC7	23265	broad.mit.edu	37	17	74099171	74099171	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74099171delT	uc002jqs.2	-						EXOC7_uc010dgv.1_5'Flank|EXOC7_uc002jqq.2_Intron|EXOC7_uc010wsw.1_Intron|EXOC7_uc010wsx.1_Intron|EXOC7_uc002jqr.2_Intron|EXOC7_uc010wsv.1_Intron|EXOC7_uc002jqu.2_Intron|EXOC7_uc002jqv.2_Intron	NM_001145297	NP_001138769	Q9UPT5	EXOC7_HUMAN	exocyst complex component 7 isoform 4						exocytosis|protein transport	centriolar satellite|cytosol|exocyst|plasma membrane	protein binding				0			LUSC - Lung squamous cell carcinoma(166;0.187)			TCACTGAGTGTTTGCAGAAGG	0.542													4	2	---	---	---	---	
SLC38A10	124565	broad.mit.edu	37	17	79255817	79255817	+	Intron	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79255817delC	uc002jzz.1	-						SLC38A10_uc002jzy.1_Intron|SLC38A10_uc002kab.2_Intron	NM_001037984	NP_001033073	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10 isoform a						amino acid transport|sodium ion transport	integral to membrane				pancreas(1)|skin(1)	2	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCCCATGGTGCCCAGGGACCA	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10150	10151	+	IGR	INS	-	C	C			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10150_10151insC								None (None upstream) : USP14 (148332 downstream)																							ctaacccttaaccctaaccctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	20676663	20676663	+	IGR	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20676663delC								RBBP8 (70218 upstream) : CABLES1 (37865 downstream)																							GGTTCACCTTccctagggccc	0.274													4	2	---	---	---	---	
LAMA3	3909	broad.mit.edu	37	18	21461891	21461891	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21461891delT	uc002kuq.2	+						LAMA3_uc002kur.2_Intron|LAMA3_uc002kus.3_Intron|LAMA3_uc002kut.3_Intron	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1						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)	GCTGTTCACCTGTCCCCAGAA	0.532													29	14	---	---	---	---	
CHST9	83539	broad.mit.edu	37	18	24717843	24717844	+	Intron	INS	-	G	G			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24717843_24717844insG	uc002kwd.2	-						C18orf16_uc010xbm.1_Intron|CHST9_uc002kwe.2_Intron	NM_031422	NP_113610	Q7L1S5	CHST9_HUMAN	GalNAc-4-sulfotransferase 2						carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)					AAACAGTAGCTGGGGGAAAAAA	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53498105	53498106	+	IGR	DEL	CA	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53498105_53498106delCA								TCF4 (194920 upstream) : TXNL1 (771949 downstream)																							CACACACCCGCACACACACACA	0.416													4	2	---	---	---	---	
CCBE1	147372	broad.mit.edu	37	18	57332413	57332414	+	Intron	INS	-	T	T	rs150497924	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57332413_57332414insT	uc002lib.2	-							NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)				AGAGTCCCCCCGAGACAAAAGC	0.470													3	5	---	---	---	---	
SOCS6	9306	broad.mit.edu	37	18	67976713	67976713	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67976713delT	uc002lkr.1	+							NM_004232	NP_004223	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6						defense response|JAK-STAT cascade|negative regulation of signal transduction|regulation of growth	cytoplasm				large_intestine(1)|lung(1)	2		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				taagtgcatattttttggtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	72057056	72057057	+	IGR	INS	-	T	T	rs142828698		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72057056_72057057insT								CYB5A (97835 upstream) : FAM69C (45907 downstream)																							ttttattattatttttttttGA	0.168													2	6	---	---	---	---	
MED16	10025	broad.mit.edu	37	19	874243	874243	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:874243delA	uc002lqd.1	-						MED16_uc010drw.1_Intron|MED16_uc002lqe.2_Intron|MED16_uc002lqf.2_Intron|MED16_uc010xfv.1_Intron|MED16_uc010xfw.1_Intron|MED16_uc010xfx.1_Intron|MED16_uc010xfy.1_Intron|MED16_uc010xfz.1_5'Flank	NM_005481	NP_005472	Q9Y2X0	MED16_HUMAN	mediator complex subunit 16						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		cctcccgagtagctgggacta	0.000													3	3	---	---	---	---	
TMPRSS9	360200	broad.mit.edu	37	19	2405705	2405705	+	Intron	DEL	T	-	-	rs113589749		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2405705delT	uc010xgx.1	+						TMPRSS9_uc002lvv.1_Intron	NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9						proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2				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)		GAGGGCAttcttttttttttt	0.214													4	2	---	---	---	---	
ZNF177	7730	broad.mit.edu	37	19	9463227	9463227	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9463227delT	uc002mli.2	+						ZNF177_uc002mlj.2_Intron	NM_003451	NP_003442	Q13360	ZN177_HUMAN	zinc finger protein 177						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						cgaagttcccttccactgctt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	9498618	9498619	+	IGR	INS	-	A	A	rs145098434	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9498618_9498619insA								ZNF177 (5754 upstream) : ZNF266 (24653 downstream)																							gtatgctttgcaaaaaaaatct	0.000													2	4	---	---	---	---	
ASF1B	55723	broad.mit.edu	37	19	14232643	14232643	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14232643delT	uc002mye.2	-							NM_018154	NP_060624	Q9NVP2	ASF1B_HUMAN	anti-silencing function 1B						cell differentiation|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus					0						CTCAGTTTTCTTTTTTTTact	0.219													4	2	---	---	---	---	
TECR	9524	broad.mit.edu	37	19	14665599	14665599	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14665599delT	uc002mza.2	+						TECR_uc002mzb.2_Intron|TECR_uc010xns.1_Intron|TECR_uc002mzc.2_Intron|TECR_uc002mzd.2_Intron	NM_138501	NP_612510	Q9NZ01	TECR_HUMAN	glycoprotein, synaptic 2						fatty acid elongation|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	integral to endoplasmic reticulum membrane	trans-2-enoyl-CoA reductase (NADPH) activity|very long-chain-acyl-CoA dehydrogenase activity				0						TGCCTTGTGCttttttttttt	0.279													5	4	---	---	---	---	
CYP4F22	126410	broad.mit.edu	37	19	15627797	15627798	+	Intron	INS	-	T	T	rs35179917		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15627797_15627798insT	uc002nbh.3	+							NM_173483	NP_775754	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F,							endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen			ovary(1)|pancreas(1)	2						cgcatggctgattttttgtatt	0.000													4	3	---	---	---	---	
LGALS7B	653499	broad.mit.edu	37	19	39282041	39282041	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39282041delA	uc002ojf.3	+							NM_001042507	NP_001035972	P47929	LEG7_HUMAN	galectin-7B						apoptosis|heterophilic cell-cell adhesion	cytoplasm|extracellular space|nucleus	sugar binding				0						TACCAGCACTAAAAAAGCCGC	0.313													4	2	---	---	---	---	
CYP2F1	1572	broad.mit.edu	37	19	41949685	41949686	+	Intron	DEL	AG	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41949685_41949686delAG	uc010xvw.1	+						C19orf69_uc010xwc.1_Intron			P24903	CP2F1_HUMAN	SubName: Full=cDNA FLJ51986, highly similar to Homo sapiens cytochrome P450, family 2, subfamily F, polypeptide 1 (CYP2F1), mRNA;						naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0						gggaggagacagagagagagaA	0.213													4	2	---	---	---	---	
DMRTC2	63946	broad.mit.edu	37	19	42352414	42352414	+	Intron	DEL	A	-	-	rs79959130		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42352414delA	uc002ors.2	+						DMRTC2_uc002orr.1_Intron|DMRTC2_uc010xwe.1_Intron	NM_001040283	NP_001035373	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2						cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0						actccatctcaaaaaaaaaaa	0.244													4	3	---	---	---	---	
PSG9	5678	broad.mit.edu	37	19	43759258	43759258	+	Intron	DEL	A	-	-	rs35986995		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43759258delA	uc002owd.3	-						PSG9_uc002owe.3_Intron|PSG9_uc010xwm.1_Intron|PSG9_uc002owf.3_Intron	NM_002784	NP_002775	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)				tctctcttccaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	50223427	50223427	+	IGR	DEL	T	-	-	rs12979136		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50223427delT								CPT1C (6439 upstream) : TSKS (19585 downstream)																							tttccttttcttttttttttt	0.229													6	4	---	---	---	---	
ProSAPiP1	9762	broad.mit.edu	37	20	3150110	3150110	+	5'Flank	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3150110delG	uc002wia.1	-						ProSAPiP1_uc002wib.1_Intron	NM_014731	NP_055546	O60299	PRIP1_HUMAN	ProSAPiP1 protein							cell junction|cytoplasm|postsynaptic density|postsynaptic membrane				pancreas(1)	1						GTCAGGTGGTGGGGACAAGGG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	11656711	11656712	+	IGR	INS	-	T	T	rs138067514	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11656711_11656712insT								None (None upstream) : BTBD3 (214765 downstream)																							GTGGAGCGCTCTTCTCTCTCTC	0.470													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	11716791	11716791	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11716791delT								None (None upstream) : BTBD3 (154686 downstream)																							TCCCCACTTCTTTCTTCACCT	0.279													4	2	---	---	---	---	
DSTN	11034	broad.mit.edu	37	20	17553964	17553964	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17553964delT	uc002wpr.2	+						DSTN_uc002wpq.2_Intron	NM_006870	NP_006861	P60981	DEST_HUMAN	destrin isoform a						actin filament severing|actin polymerization or depolymerization		actin binding			large_intestine(1)|skin(1)	2						GTGGGGGTGGTTTTTTTTTTC	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23319081	23319081	+	IGR	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23319081delA								CD93 (252104 upstream) : NXT1 (12292 downstream)																							ggaaagccataaaaaaaatag	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	34664142	34664142	+	IGR	DEL	T	-	-	rs113482157		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34664142delT								LOC647979 (25260 upstream) : EPB41L1 (15284 downstream)																							TTCACCCAACTTTTTTTTTTC	0.418													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49822357	49822357	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49822357delT								KCNG1 (182682 upstream) : NFATC2 (185409 downstream)																							TACCACAGCCTTTGCTGCCCC	0.219													4	2	---	---	---	---	
OSBPL2	9885	broad.mit.edu	37	20	60859431	60859431	+	Intron	DEL	T	-	-	rs112769454		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60859431delT	uc002yck.1	+						OSBPL2_uc002ycl.1_Intron|OSBPL2_uc011aah.1_Intron|OSBPL2_uc002ycm.1_3'UTR	NM_144498	NP_653081	Q9H1P3	OSBL2_HUMAN	oxysterol-binding protein-like protein 2 isoform						lipid transport		lipid binding			ovary(1)|central_nervous_system(1)	2	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)			tttctttccattttttttttt	0.204													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10086217	10086221	+	IGR	DEL	TGGAG	-	-	rs143059597	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10086217_10086221delTGGAG								None (None upstream) : TPTE (820522 downstream)																							tggactggaatggagtggagtggag	0.000													5	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11084479	11084479	+	Intron	DEL	A	-	-	rs112755619		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11084479delA	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)		AGGGGGTCATAAAACCAGAAA	0.269													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14777757	14777757	+	IGR	DEL	T	-	-	rs140129927		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14777757delT								C21orf99 (287188 upstream) : POTED (204741 downstream)																							Gtttttgttgttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	18313707	18313708	+	IGR	DEL	TG	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18313707_18313708delTG								C21orf34 (331613 upstream) : CXADR (571622 downstream)																							tagttttgtatgtgtgtgtgtg	0.000													4	3	---	---	---	---	
BACE2	25825	broad.mit.edu	37	21	42640890	42640890	+	Intron	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42640890delT	uc002yyw.2	+						BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron|BACE2_uc010goo.2_Intron	NM_012105	NP_036237	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2 isoform A						membrane protein ectodomain proteolysis|negative regulation of amyloid precursor protein biosynthetic process|peptide hormone processing	cell surface|endoplasmic reticulum|endosome|Golgi apparatus|integral to membrane	aspartic-type endopeptidase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				ttctcttttctttttttttga	0.154													6	3	---	---	---	---	
AGPAT3	56894	broad.mit.edu	37	21	45390356	45390357	+	Intron	DEL	TG	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45390356_45390357delTG	uc002zdv.2	+						AGPAT3_uc002zdw.2_Intron|AGPAT3_uc002zdx.2_Intron|AGPAT3_uc002zdy.2_Intron	NM_020132	NP_064517	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		GAGTGCAGACTGTGGCCCTAGA	0.480													5	6	---	---	---	---	
ADARB1	104	broad.mit.edu	37	21	46575975	46575976	+	Intron	INS	-	CCATCAT	CCATCAT	rs143597101	by1000genomes	TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46575975_46575976insCCATCAT	uc002zgy.2	+						ADARB1_uc002zgr.2_Intron|ADARB1_uc002zgs.2_Intron|ADARB1_uc002zgw.2_Intron|ADARB1_uc002zgv.2_Intron|ADARB1_uc002zgt.2_Intron|ADARB1_uc010gpx.2_Intron|ADARB1_uc002zgq.2_Intron|ADARB1_uc002zgu.2_Intron|ADARB1_uc011afo.1_Intron	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2						adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)		cccaccatcacccatcatccat	0.000													3	3	---	---	---	---	
UPK3A	7380	broad.mit.edu	37	22	45685866	45685866	+	Intron	DEL	A	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45685866delA	uc003bfy.2	+						UPK3A_uc010gzy.2_Intron	NM_006953	NP_008884	O75631	UPK3A_HUMAN	uroplakin 3A precursor						epithelial cell differentiation	endoplasmic reticulum membrane|integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CCCCTTTGCTAAATCCTCATA	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	229389	229390	+	5'Flank	INS	-	TACCCC	TACCCC			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:229389_229390insTACCCC	uc004cpd.1	-						uc004cpe.1_Intron|uc011mgy.1_In_Frame_Ins_p.71_72insGY	NM_012227	NP_036359			pseudoautosomal GTP-binding protein-like																		CCTCACCGGTGACACGGAGACC	0.713													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	6815512	6815512	+	IGR	DEL	G	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6815512delG								VCX3A (362353 upstream) : HDHD1A (151449 downstream)																							TTCTCTTGTAGGATGCAGTTT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	8081683	8081683	+	IGR	DEL	T	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8081683delT								PNPLA4 (185903 upstream) : MIR651 (13323 downstream)																							AATGCTCCGGTTTTTTTTTTT	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9936789	9936789	+	IGR	DEL	C	-	-			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9936789delC								TTTY22 (285935 upstream) : None (None downstream)																							CTTTAATCTTCAATTCATCAT	0.269													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9960883	9960883	+	IGR	DEL	A	-	-	rs146746526		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9960883delA								TTTY22 (310029 upstream) : None (None downstream)																							TTGGCTAAACAAGATGTTTGC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	27583214	27583215	+	IGR	INS	-	T	T			TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:27583214_27583215insT								DAZ4 (530034 upstream) : None (None downstream)																							AAAATATTTAGTTTTTTTTTTT	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59002466	59002470	+	IGR	DEL	TTCTT	-	-	rs147645278		TCGA-B0-5701-01A-11D-1534-10	TCGA-B0-5701-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59002466_59002470delTTCTT								None (None upstream) : None (None downstream)																							TGATAAAGTCTTCTTTTCTTCACGT	0.307													3	3	---	---	---	---	
