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
NOC2L	26155	broad.mit.edu	37	1	888619	888619	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:888619G>T	uc001abz.3	-	9	997	c.938C>A	c.(937-939)GCT>GAT	p.A313D	NOC2L_uc001aby.3_Missense_Mutation_p.A110D|NOC2L_uc009vjq.2_Missense_Mutation_p.A313D	NM_015658	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog	313						nucleolus	protein binding			ovary(1)|skin(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		GACCAGGAAAGCCAGCACCCG	0.607													18	27	---	---	---	---	PASS
PLCH2	9651	broad.mit.edu	37	1	2435907	2435907	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2435907G>A	uc001aji.1	+	22	3780	c.3506G>A	c.(3505-3507)CGT>CAT	p.R1169H	PLCH2_uc010nyz.1_3'UTR|PLCH2_uc009vle.1_Missense_Mutation_p.R921H|PLCH2_uc001ajj.1_3'UTR|PLCH2_uc001ajk.1_3'UTR|PLCH2_uc001ajl.1_Missense_Mutation_p.R21H	NM_014638	NP_055453	O75038	PLCH2_HUMAN	phospholipase C, eta 2	1169					intracellular signal transduction|lipid catabolic process	cytoplasm|plasma membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			central_nervous_system(3)|ovary(1)|skin(1)	5	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		GGCCGCAGCCGTGAGAACCTC	0.667													5	11	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19446815	19446815	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19446815T>C	uc001bbi.2	-	69	10173	c.10169A>G	c.(10168-10170)CAG>CGG	p.Q3390R	UBR4_uc001bbj.1_5'Flank	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	3390					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TGTGCACAGCTGGTCCTCCTG	0.532													17	30	---	---	---	---	PASS
DNAJC8	22826	broad.mit.edu	37	1	28531794	28531794	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28531794T>C	uc001bpn.2	-	7	571	c.538A>G	c.(538-540)AGA>GGA	p.R180G	DNAJC8_uc001bpo.2_RNA	NM_014280	NP_055095	O75937	DNJC8_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 8	180					nuclear mRNA splicing, via spliceosome|protein folding	nucleoplasm	heat shock protein binding|unfolded protein binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.08e-05)|all_lung(284;4.29e-05)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.0105)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		OV - Ovarian serous cystadenocarcinoma(117;2.81e-22)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00275)|BRCA - Breast invasive adenocarcinoma(304;0.0059)|STAD - Stomach adenocarcinoma(196;0.00671)|READ - Rectum adenocarcinoma(331;0.0649)		TTGGCTTCTCTCTCTTTCCTT	0.318													8	724	---	---	---	---	PASS
OPRD1	4985	broad.mit.edu	37	1	29185683	29185683	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29185683G>A	uc001brf.1	+	2	687	c.445G>A	c.(445-447)GCT>ACT	p.A149T		NM_000911	NP_000902	P41143	OPRD_HUMAN	opioid receptor, delta 1	149	Cytoplasmic (Potential).				immune response|protein import into nucleus, translocation	integral to plasma membrane	delta-opioid receptor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Butorphanol(DB00611)|Codeine(DB00318)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Loperamide(DB00836)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pimozide(DB01100)|Propoxyphene(DB00647)	CCGCTACATCGCTGTCTGCCA	0.577													24	44	---	---	---	---	PASS
PUM1	9698	broad.mit.edu	37	1	31468025	31468025	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31468025T>C	uc001bsi.1	-	6	876	c.763A>G	c.(763-765)AAG>GAG	p.K255E	PUM1_uc001bsf.1_5'Flank|PUM1_uc001bsg.1_Missense_Mutation_p.K67E|PUM1_uc001bsh.1_Missense_Mutation_p.K255E|PUM1_uc001bsj.1_Missense_Mutation_p.K255E|PUM1_uc010oga.1_Missense_Mutation_p.K159E|PUM1_uc001bsk.1_Missense_Mutation_p.K291E|PUM1_uc010ogb.1_Missense_Mutation_p.K195E	NM_014676	NP_055491	Q14671	PUM1_HUMAN	pumilio 1 isoform 2	255					cellular membrane organization|post-Golgi vesicle-mediated transport|regulation of translation	cytosol	RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TTGTTCTTCTTTTCACCTTTG	0.428													9	724	---	---	---	---	PASS
PEF1	553115	broad.mit.edu	37	1	32096480	32096480	+	Intron	SNP	A	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32096480A>C	uc001bth.1	-						HCRTR1_uc010ogl.1_Intron|PEF1_uc001bte.1_3'UTR|PEF1_uc001btf.1_Intron|PEF1_uc001btg.1_Intron	NM_012392	NP_036524	Q9UBV8	PEF1_HUMAN	penta-EF-hand domain containing 1						response to calcium ion	cytoplasm|membrane	calcium ion binding|protein heterodimerization activity				0		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)|all_neural(195;0.186)		STAD - Stomach adenocarcinoma(196;0.0546)		ACACACAAAAACCTGCCATGA	0.527													6	13	---	---	---	---	PASS
INPP5B	3633	broad.mit.edu	37	1	38353034	38353034	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38353034T>G	uc001ccg.1	-	11	1097	c.1003A>C	c.(1003-1005)AAA>CAA	p.K335Q	INPP5B_uc009vvk.1_Missense_Mutation_p.K276Q|INPP5B_uc001ccf.1_Missense_Mutation_p.K171Q|INPP5B_uc010oij.1_RNA	NM_005540	NP_005531	P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	415					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)				TTTGCATATTTGGCATCTGGA	0.428													79	218	---	---	---	---	PASS
RNF220	55182	broad.mit.edu	37	1	44878049	44878049	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44878049C>A	uc001clv.1	+	2	640	c.280C>A	c.(280-282)CAC>AAC	p.H94N	RNF220_uc001clw.1_Missense_Mutation_p.H94N	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220	94					protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						TTCTCTACTACACCTCCACCC	0.527													28	84	---	---	---	---	PASS
PDZK1IP1	10158	broad.mit.edu	37	1	47649487	47649487	+	3'UTR	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47649487C>T	uc001cqw.2	-	4						NM_005764	NP_005755	Q13113	PDZ1I_HUMAN	PDZK1 interacting protein 1							integral to membrane					0						CCAACCTTGGCTGGCTATACT	0.612													3	12	---	---	---	---	PASS
PARS2	25973	broad.mit.edu	37	1	55224781	55224781	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55224781G>T	uc001cxy.2	-	2	137	c.54C>A	c.(52-54)AGC>AGA	p.S18R		NM_152268	NP_689481	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase (mitochondrial)(putative)	18					prolyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|proline-tRNA ligase activity			ovary(2)	2					L-Proline(DB00172)	AGAGCTGGCGGCTGCAGGTGG	0.602													5	13	---	---	---	---	PASS
ACADM	34	broad.mit.edu	37	1	76228484	76228484	+	3'UTR	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76228484C>A	uc001dgw.3	+	12					ACADM_uc009wbp.2_3'UTR|ACADM_uc009wbr.2_3'UTR|ACADM_uc010ore.1_3'UTR|ACADM_uc010orf.1_3'UTR|ACADM_uc001dgx.3_3'UTR|ACADM_uc010org.1_3'UTR	NM_000016	NP_000007	P11310	ACADM_HUMAN	medium-chain acyl-CoA dehydrogenase isoform a						carnitine biosynthetic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|medium-chain fatty acid catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|identical protein binding|medium-chain-acyl-CoA dehydrogenase activity			breast(2)|ovary(1)|skin(1)	4						AACTAGAACACAAGCCACTGT	0.308													10	39	---	---	---	---	PASS
GBP2	2634	broad.mit.edu	37	1	89582840	89582840	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89582840C>T	uc001dmz.1	-	6	974	c.703G>A	c.(703-705)GTC>ATC	p.V235I	GBP2_uc001dmy.1_RNA	NM_004120	NP_004111	P32456	GBP2_HUMAN	guanylate binding protein 2,	235					interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)	1		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		CAATCGAAGACGAAGCACTTC	0.428													61	137	---	---	---	---	PASS
FAM69A	388650	broad.mit.edu	37	1	93308909	93308909	+	3'UTR	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93308909T>G	uc001dpg.2	-	5					FAM69A_uc001dpc.2_Intron|FAM69A_uc010otg.1_3'UTR	NM_001006605	NP_001006606	Q5T7M9	FA69A_HUMAN	family with sequence similarity 69, member A							endoplasmic reticulum membrane|integral to membrane					0		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)		AAGTGGCAGGTTTCTTAAAAT	0.343													10	44	---	---	---	---	PASS
PHTF1	10745	broad.mit.edu	37	1	114267480	114267480	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114267480C>G	uc009wgp.1	-	6	976	c.524G>C	c.(523-525)CGA>CCA	p.R175P	PHTF1_uc001edn.2_Missense_Mutation_p.R175P|PHTF1_uc010own.1_Missense_Mutation_p.R175P	NM_006608	NP_006599	Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	175						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCATTTTCTCGGCTCCCATC	0.343													105	290	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144220807	144220807	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144220807A>C	uc010oxr.1	+	19	2184	c.2180A>C	c.(2179-2181)GAT>GCT	p.D727A	NBPF9_uc010oxn.1_Missense_Mutation_p.D598A|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Missense_Mutation_p.D515A|NBPF9_uc001ekg.1_Missense_Mutation_p.D27A|NBPF9_uc001ekk.1_Missense_Mutation_p.D271A|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Missense_Mutation_p.D27A|uc010oxz.1_Missense_Mutation_p.D515A	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	700	NBPF 5.					cytoplasm					0						GAGCTGCTGGATGAGAAAGAG	0.483													4	23	---	---	---	---	PASS
PDIA3P	171423	broad.mit.edu	37	1	146651135	146651135	+	3'UTR	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146651135C>A	uc001epg.1	+	1						NR_002305				SubName: Full=cDNA FLJ53558, highly similar to Protein disulfide-isomerase A3 (EC 5.3.4.1);												0						CTATCTACAACGAGAAGCTAC	0.393													4	106	---	---	---	---	PASS
APH1A	51107	broad.mit.edu	37	1	150238892	150238892	+	Intron	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150238892T>G	uc001ety.1	-						APH1A_uc010pbx.1_Intron|APH1A_uc001etz.1_3'UTR|APH1A_uc001eua.1_Intron|APH1A_uc010pby.1_3'UTR|APH1A_uc001eub.1_Intron|APH1A_uc010pbz.1_3'UTR	NM_001077628	NP_001071096	Q96BI3	APH1A_HUMAN	anterior pharynx defective 1 homolog A isoform						amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	endoplasmic reticulum membrane|Golgi cisterna membrane|integral to plasma membrane	protein binding			ovary(1)|lung(1)	2	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GACAGGCAGGTGGGATCTGTC	0.607													6	15	---	---	---	---	PASS
S100A14	57402	broad.mit.edu	37	1	153587374	153587374	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153587374A>G	uc001fce.2	-	4	400	c.302T>C	c.(301-303)GTC>GCC	p.V101A	S100A16_uc001fcd.1_5'Flank	NM_020672	NP_065723	Q9HCY8	S10AE_HUMAN	S100 calcium binding protein A14	101					calcium ion homeostasis|defense response to bacterium|positive regulation of granulocyte chemotaxis|positive regulation of monocyte chemotaxis|response to lipopolysaccharide|toll-like receptor 4 signaling pathway	cell junction|microtubule cytoskeleton|perinuclear region of cytoplasm	calcium ion binding|chemokine receptor binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			GTGCCCCCGGACAGGCCTCTC	0.557													8	107	---	---	---	---	PASS
SMG5	23381	broad.mit.edu	37	1	156243168	156243168	+	Silent	SNP	T	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156243168T>A	uc001foc.3	-	6	767	c.618A>T	c.(616-618)TCA>TCT	p.S206S		NM_015327	NP_056142	Q9UPR3	SMG5_HUMAN	SMG5 homolog nonsense mediated mRNA decay	206					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|nucleus	protein phosphatase 2A binding			ovary(2)|skin(2)|pancreas(1)	5	Hepatocellular(266;0.158)					GAGGAGCTACTGACAGGGCTT	0.483													51	120	---	---	---	---	PASS
SMG7	9887	broad.mit.edu	37	1	183495897	183495897	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183495897A>G	uc001gqg.2	+	5	601	c.479A>G	c.(478-480)GAC>GGC	p.D160G	SMG7_uc010pob.1_Missense_Mutation_p.D189G|SMG7_uc001gqf.2_Missense_Mutation_p.D160G|SMG7_uc001gqh.2_Missense_Mutation_p.D160G|SMG7_uc001gqi.2_Missense_Mutation_p.D118G|SMG7_uc010poc.1_Missense_Mutation_p.D118G	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1	160	TPR 1.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						CACCTTGGAGACATTGGTGAG	0.443													5	144	---	---	---	---	PASS
RGS2	5997	broad.mit.edu	37	1	192780790	192780790	+	3'UTR	SNP	A	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192780790A>C	uc001gsl.2	+	5						NM_002923	NP_002914	P41220	RGS2_HUMAN	regulator of G-protein signaling 2						cell cycle|negative regulation of cardiac muscle hypertrophy|negative regulation of G-protein coupled receptor protein signaling pathway|negative regulation of MAP kinase activity|negative regulation of phospholipase activity|positive regulation of cardiac muscle contraction|regulation of adrenergic receptor signaling pathway|regulation of translation|relaxation of cardiac muscle	cytosol|internal side of plasma membrane|mitochondrion|nucleolus	calmodulin binding|GTPase activator activity|signal transducer activity				0						AAGGACTGTGACCTGCCATAA	0.443													5	11	---	---	---	---	PASS
CRB1	23418	broad.mit.edu	37	1	197446956	197446956	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197446956C>T	uc001gtz.2	+	12	4303	c.4168C>T	c.(4168-4170)CGA>TGA	p.R1390*	CRB1_uc010poz.1_Nonsense_Mutation_p.R1366*|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Nonsense_Mutation_p.R1278*|CRB1_uc010ppb.1_Nonsense_Mutation_p.R854*|CRB1_uc010ppd.1_Nonsense_Mutation_p.R871*	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	1390	Cytoplasmic (Potential).				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9						GGAGGGCTCCCGAGTGGAAAT	0.532													26	69	---	---	---	---	PASS
FAM150B	285016	broad.mit.edu	37	2	283163	283163	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:283163C>A	uc002qwi.3	-	5	754	c.401G>T	c.(400-402)TGC>TTC	p.C134F	FAM150B_uc010ewf.1_Missense_Mutation_p.C134F	NM_001002919	NP_001002919	Q6UX46	F150B_HUMAN	hypothetical protein LOC285016 precursor	134						extracellular region					0	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.00091)|Epithelial(75;0.00656)|OV - Ovarian serous cystadenocarcinoma(76;0.00954)|GBM - Glioblastoma multiforme(21;0.128)		AAGCCTGGCGCATCTTTTATA	0.418													58	144	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32640282	32640282	+	Silent	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32640282A>G	uc010ezu.2	+	10	2057	c.1923A>G	c.(1921-1923)AAA>AAG	p.K641K		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	641					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					CTGATGAGAAAGCAGGAAAGA	0.368													5	199	---	---	---	---	PASS
TIA1	7072	broad.mit.edu	37	2	70441538	70441538	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70441538C>G	uc002sgj.3	-	12	1194	c.977G>C	c.(976-978)GGT>GCT	p.G326A	TIA1_uc002sgk.3_Missense_Mutation_p.G315A|TIA1_uc002sgl.3_RNA	NM_022173	NP_071505	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding	326					apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding				0						AACTTGCCAACCATTAGGCAT	0.403													66	140	---	---	---	---	PASS
KIAA1310	55683	broad.mit.edu	37	2	97267383	97267383	+	Silent	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97267383T>C	uc002swn.3	-	20	2759	c.2613A>G	c.(2611-2613)TCA>TCG	p.S871S	KIAA1310_uc002swh.3_Silent_p.S757S|KIAA1310_uc002swi.3_Silent_p.S798S|KIAA1310_uc002swj.3_RNA|KIAA1310_uc002swk.3_Silent_p.S784S|KIAA1310_uc010fhz.2_Silent_p.S691S|KIAA1310_uc002swl.3_Silent_p.S770S|KIAA1310_uc002swm.3_RNA|KIAA1310_uc010yur.1_Silent_p.S665S|KIAA1310_uc002swo.2_Silent_p.S219S	NM_001115016	NP_001108488	Q9P2N6	K1310_HUMAN	hypothetical protein LOC55683 isoform a	897											0						GACTCACCTGTGAGCTGGAGG	0.587													7	54	---	---	---	---	PASS
ZC3H6	376940	broad.mit.edu	37	2	113057575	113057575	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113057575A>G	uc002thq.1	+	2	576	c.182A>G	c.(181-183)AAA>AGA	p.K61R	ZC3H6_uc002thr.1_Missense_Mutation_p.N39D	NM_198581	NP_940983	P61129	ZC3H6_HUMAN	zinc finger CCCH-type domain containing 6	61	Potential.						nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4						gagaagaaaaaATCCAAAAGG	0.114													6	414	---	---	---	---	PASS
ZC3H6	376940	broad.mit.edu	37	2	113060893	113060893	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113060893G>A	uc002thq.1	+	3	695	c.301G>A	c.(301-303)GGT>AGT	p.G101S	ZC3H6_uc002thr.1_Silent_p.L78L	NM_198581	NP_940983	P61129	ZC3H6_HUMAN	zinc finger CCCH-type domain containing 6	101							nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4						AAAAAGAACTGGTTTCTACAG	0.294													4	134	---	---	---	---	PASS
UGGT1	56886	broad.mit.edu	37	2	128878020	128878020	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128878020G>A	uc002tps.2	+	9	1141	c.963G>A	c.(961-963)TGG>TGA	p.W321*	UGGT1_uc010fme.1_Nonsense_Mutation_p.W196*|UGGT1_uc002tpr.2_Nonsense_Mutation_p.W297*	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	321					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						TAAAGGTTTGGCAGTTGCAAG	0.388													65	145	---	---	---	---	PASS
CCNT2	905	broad.mit.edu	37	2	135712152	135712152	+	Silent	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135712152T>C	uc002tuc.1	+	9	2159	c.2127T>C	c.(2125-2127)CAT>CAC	p.H709H	CCNT2_uc002tub.1_3'UTR|CCNT2_uc010zbf.1_3'UTR|CCNT2_uc002tud.1_Silent_p.H372H	NM_058241	NP_490595	O60583	CCNT2_HUMAN	cyclin T2 isoform b	709					cell cycle|cell division|interspecies interaction between organisms|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein kinase binding			ovary(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.107)		GCAGCCAGCATATGGACTACA	0.448													4	106	---	---	---	---	PASS
BBS5	129880	broad.mit.edu	37	2	170361152	170361152	+	3'UTR	SNP	A	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170361152A>C	uc002uet.2	+	12					BBS5_uc010fpw.2_3'UTR|KBTBD10_uc010zdh.1_Intron	NM_152384	NP_689597	Q8N3I7	BBS5_HUMAN	Bardet-Biedl syndrome 5						cilium assembly|flagellum assembly|heart looping|melanosome transport|response to stimulus|visual perception	BBSome|cilium membrane|microtubule basal body	phosphatidylinositol-3-phosphate binding|protein binding				0						GATACTAGTCACCTGCCATAA	0.303									Bardet-Biedl_syndrome				26	20	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179594147	179594147	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179594147T>C	uc010zfg.1	-	61	15228	c.15004A>G	c.(15004-15006)ACA>GCA	p.T5002A	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.T1663A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	5929							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)			TCGGTCAATGTGTATTTTTTG	0.458													6	198	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179634827	179634827	+	Silent	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179634827C>T	uc010zfg.1	-	36	8825	c.8601G>A	c.(8599-8601)GTG>GTA	p.V2867V	TTN_uc010zfh.1_Silent_p.V2821V|TTN_uc010zfi.1_Silent_p.V2821V|TTN_uc010zfj.1_Silent_p.V2821V|TTN_uc002unb.2_Silent_p.V2867V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2867							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)			ATTGCCCGACCACAGCTGTGT	0.473													96	251	---	---	---	---	PASS
CCDC108	255101	broad.mit.edu	37	2	219886632	219886632	+	Silent	SNP	G	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219886632G>C	uc002vjl.1	-	18	3084	c.3000C>G	c.(2998-3000)GCC>GCG	p.A1000A	CCDC108_uc002vjm.3_5'Flank	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	1000						integral to membrane	structural molecule activity			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CATTCCCAAAGGCCAGCTCCT	0.602													14	27	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191570	10191570	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191570T>C	uc003bvc.2	+	3	776	c.563T>C	c.(562-564)CTG>CCG	p.L188P	VHL_uc003bvd.2_Missense_Mutation_p.L147P	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	188			L -> Q (in VHLD; type I).|L -> P (in VHLD; type I-II).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.L188fs*14(2)|p.L188P(2)|p.L188Q(2)|p.D187_L188del(2)|p.L188V(1)|p.D187_N193del(1)|p.E189fs*27(1)|p.Y185fs*11(1)|p.L188R(1)|p.D187fs*14(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TACGAAGATCTGGAAGACCAC	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				25	41	---	---	---	---	PASS
STT3B	201595	broad.mit.edu	37	3	31638323	31638323	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31638323A>G	uc011axe.1	+	4	745	c.745A>G	c.(745-747)ACA>GCA	p.T249A	STT3B_uc010hft.1_Missense_Mutation_p.T249A|STT3B_uc003cer.1_Missense_Mutation_p.T249A|STT3B_uc003cet.2_5'UTR	NM_178862	NP_849193	Q8TCJ2	STT3B_HUMAN	source of immunodominant MHC-associated	249	Helical; (Potential).				protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0						AGTTTTTTGGACAATGTGCTG	0.308													8	611	---	---	---	---	PASS
IMPDH2	3615	broad.mit.edu	37	3	49066862	49066862	+	5'UTR	SNP	A	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49066862A>C	uc003cvt.2	-	1					IMPDH2_uc010hkp.1_Silent_p.G44G	NM_000884	NP_000875	P12268	IMDH2_HUMAN	inosine monophosphate dehydrogenase 2						GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	IMP dehydrogenase activity|metal ion binding|nucleotide binding|protein binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)	GCCAATATAAACCAGCCGATT	0.692													3	0	---	---	---	---	PASS
STXBP5L	9515	broad.mit.edu	37	3	121137382	121137382	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121137382C>T	uc003eec.3	+	27	3637	c.3497C>T	c.(3496-3498)GCA>GTA	p.A1166V	STXBP5L_uc011bji.1_Missense_Mutation_p.A1142V	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	1166	v-SNARE coiled-coil homology.				exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		AGTGCAGAAGCATTTTCCAAA	0.438													25	71	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	3	133910723	133910723	+	IGR	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133910723T>C								RYK (-58863 upstream) : RYK (-34745 downstream)																							AGAGTTATCCTCTCTCTGGAT	0.363													6	324	---	---	---	---	PASS
STAG1	10274	broad.mit.edu	37	3	136221516	136221516	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136221516T>C	uc003era.1	-	8	1074	c.782A>G	c.(781-783)AAG>AGG	p.K261R	STAG1_uc003erb.1_Missense_Mutation_p.K261R|STAG1_uc003erc.1_Missense_Mutation_p.K35R|STAG1_uc010hua.1_Missense_Mutation_p.K124R|STAG1_uc003erd.2_Missense_Mutation_p.K164R	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	261					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						ATTGGCTCTCTTCCCAATCAT	0.378													7	624	---	---	---	---	PASS
HLTF	6596	broad.mit.edu	37	3	148802538	148802538	+	Silent	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148802538T>C	uc003ewq.1	-	2	377	c.159A>G	c.(157-159)GAA>GAG	p.E53E	HLTF_uc003ewr.1_Silent_p.E53E|HLTF_uc003ews.1_Silent_p.E53E|HLTF_uc010hve.1_Silent_p.E53E	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor	53					chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AATCTACTTCTTCATCACTAG	0.368													6	333	---	---	---	---	PASS
PEX5L	51555	broad.mit.edu	37	3	179527284	179527284	+	Silent	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179527284G>T	uc003fki.1	-	12	1457	c.1327C>A	c.(1327-1329)CGG>AGG	p.R443R	PEX5L_uc011bqd.1_Silent_p.R400R|PEX5L_uc011bqe.1_Silent_p.R251R|PEX5L_uc011bqf.1_Silent_p.R335R|PEX5L_uc003fkj.1_Silent_p.R408R|PEX5L_uc010hxd.1_Silent_p.R441R|PEX5L_uc011bqg.1_Silent_p.R419R|PEX5L_uc011bqh.1_Silent_p.R384R	NM_016559	NP_057643	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	443					protein import into peroxisome matrix|regulation of cAMP-mediated signaling	cytosol|peroxisomal membrane	peroxisome matrix targeting signal-1 binding			ovary(3)|large_intestine(1)	4	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			TTAGACATCCGCCGGGTGAGG	0.438													9	221	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506460	195506460	+	Missense_Mutation	SNP	G	C	C	rs113130007		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506460G>C	uc011bto.1	-	3	12067	c.11607C>G	c.(11605-11607)CAC>CAG	p.H3869Q	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.602													4	10	---	---	---	---	PASS
CHRNA9	55584	broad.mit.edu	37	4	40356027	40356027	+	Silent	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40356027C>T	uc003gva.1	+	5	946	c.930C>T	c.(928-930)ATC>ATT	p.I310I		NM_017581	NP_060051	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9	310	Helical; (Potential).				elevation of cytosolic calcium ion concentration|synaptic transmission	cell junction|postsynaptic membrane	calcium channel activity|receptor activity			breast(3)|skin(3)|central_nervous_system(1)	7					Nicotine(DB00184)	TGGCCCTGATCACAGCCTCCA	0.453													39	93	---	---	---	---	PASS
BMP3	651	broad.mit.edu	37	4	81967318	81967318	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81967318C>T	uc003hmg.3	+	2	1063	c.743C>T	c.(742-744)GCC>GTC	p.A248V		NM_001201	NP_001192	P12645	BMP3_HUMAN	bone morphogenetic protein 3 preproprotein	248					cartilage development|cell differentiation|cell-cell signaling|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity	p.A248A(1)		ovary(4)|central_nervous_system(1)	5						AATGATGCCGCCATTTCTGAG	0.478													31	72	---	---	---	---	PASS
DDX60	55601	broad.mit.edu	37	4	169137918	169137918	+	3'UTR	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169137918T>G	uc003irp.2	-	38					DDX60_uc003iro.2_3'UTR	NM_017631	NP_060101	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		acatggcaggtttgattgcaa	0.075													11	35	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13737365	13737365	+	Silent	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13737365T>C	uc003jfd.2	-	66	11493	c.11451A>G	c.(11449-11451)AGA>AGG	p.R3817R	DNAH5_uc003jfc.2_Intron	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3817	Potential.				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					ACTCACCAGGTCTGTATTCCT	0.413									Kartagener_syndrome				9	433	---	---	---	---	PASS
IL6ST	3572	broad.mit.edu	37	5	55256363	55256363	+	Silent	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55256363G>T	uc003jqq.2	-	8	1095	c.840C>A	c.(838-840)ACC>ACA	p.T280T	IL6ST_uc010iwb.2_Silent_p.T280T|IL6ST_uc010iwc.2_Silent_p.T114T|IL6ST_uc010iwd.2_Intron|IL6ST_uc011cqk.1_5'UTR|IL6ST_uc003jqr.2_Silent_p.T280T	NM_002184	NP_002175	P40189	IL6RB_HUMAN	interleukin 6 signal transducer isoform 1	280	Extracellular (Potential).|Fibronectin type-III 2.				interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production	ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex	ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity			large_intestine(1)|ovary(1)	2		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				ATGAAGATCGGGTGGATGCTG	0.388			O		hepatocellular ca								174	230	---	---	---	---	PASS
MEGF10	84466	broad.mit.edu	37	5	126793028	126793028	+	3'UTR	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126793028G>T	uc003kuh.3	+	26					MEGF10_uc003kui.3_3'UTR	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor						cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		GGACCGCTTGGTAGCCACTGG	0.418													7	43	---	---	---	---	PASS
CYFIP2	26999	broad.mit.edu	37	5	156753229	156753229	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156753229T>C	uc003lwq.2	+	20	2171	c.2033T>C	c.(2032-2034)CTG>CCG	p.L678P	CYFIP2_uc011ddn.1_Missense_Mutation_p.L652P|CYFIP2_uc011ddo.1_Missense_Mutation_p.L482P|CYFIP2_uc003lwr.2_Missense_Mutation_p.L678P|CYFIP2_uc003lws.2_Missense_Mutation_p.L678P|CYFIP2_uc003lwt.2_Missense_Mutation_p.L581P|CYFIP2_uc011ddp.1_Missense_Mutation_p.L412P	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2	703					apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TACTATGCTCTGACCAAGTTT	0.463													63	230	---	---	---	---	PASS
ZNF346	23567	broad.mit.edu	37	5	176471492	176471492	+	Missense_Mutation	SNP	G	A	A	rs139233067		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176471492G>A	uc003mfi.2	+	4	518	c.475G>A	c.(475-477)GCA>ACA	p.A159T	ZNF346_uc011dfr.1_Missense_Mutation_p.A127T|ZNF346_uc011dfs.1_Intron|ZNF346_uc003mfj.2_Intron|ZNF346_uc003mfk.1_Missense_Mutation_p.A184T|ZNF346_uc011dft.1_Intron	NM_012279	NP_036411	Q9UL40	ZN346_HUMAN	zinc finger protein 346	159	Matrin-type 2.					cytoplasm|nucleolus	double-stranded RNA binding|zinc ion binding				0	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAAGACCCACGCAAAGAACTT	0.542													52	160	---	---	---	---	PASS
MXD3	83463	broad.mit.edu	37	5	176733243	176733243	+	3'UTR	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176733243T>C	uc010jkk.2	-	6					RAB24_uc003mfu.2_5'Flank|RAB24_uc003mfv.2_5'Flank|RAB24_uc003mfw.2_5'Flank|PRELID1_uc003mfx.2_Intron|PRELID1_uc003mfy.2_Intron	NM_001142935	NP_001136407	Q9BW11	MAD3_HUMAN	MAX dimerization protein 3 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)			GGGCGTGGAGTCTGGGTTAGT	0.532													101	123	---	---	---	---	PASS
ADAMTS2	9509	broad.mit.edu	37	5	178555036	178555036	+	Silent	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178555036G>A	uc003mjw.2	-	17	2541	c.2541C>T	c.(2539-2541)AAC>AAT	p.N847N		NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	847	Spacer.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		CTTCCAGGACGTTGTTGTCGT	0.587													58	82	---	---	---	---	PASS
MAK	4117	broad.mit.edu	37	6	10804066	10804066	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10804066A>G	uc003mzl.2	-	6	779	c.550T>C	c.(550-552)TGG>CGG	p.W184R	SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jos.1_Intron|MAK_uc010jot.2_RNA|MAK_uc010jou.2_RNA|MAK_uc003mzm.2_Missense_Mutation_p.W184R|MAK_uc010jov.1_RNA	NM_005906	NP_005897	P20794	MAK_HUMAN	male germ cell-associated kinase	184	Protein kinase.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|cyclin-dependent protein kinase activity			breast(2)|skin(1)	3	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				CCAACAGCCCACACATCAATG	0.383													6	258	---	---	---	---	PASS
KIF13A	63971	broad.mit.edu	37	6	17773750	17773750	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17773750T>C	uc003ncg.3	-	36	4388	c.4283A>G	c.(4282-4284)TAT>TGT	p.Y1428C	KIF13A_uc003ncf.2_Missense_Mutation_p.Y1415C|KIF13A_uc003nch.3_Missense_Mutation_p.Y1428C|KIF13A_uc003nci.3_Missense_Mutation_p.Y1415C|KIF13A_uc003nce.1_Missense_Mutation_p.Y14C	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	1428					cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TAAAGTTCCATAACATGCTAC	0.368													5	449	---	---	---	---	PASS
KIF13A	63971	broad.mit.edu	37	6	17831418	17831418	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17831418C>T	uc003ncg.3	-	13	1420	c.1315G>A	c.(1315-1317)GGT>AGT	p.G439S	KIF13A_uc003ncf.2_Missense_Mutation_p.G439S|KIF13A_uc003nch.3_Missense_Mutation_p.G439S|KIF13A_uc003nci.3_Missense_Mutation_p.G439S|KIF13A_uc003ncj.2_Missense_Mutation_p.G115S	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	439					cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			ACCTTGATACCGGACATCTCC	0.408													5	251	---	---	---	---	PASS
VPS52	6293	broad.mit.edu	37	6	33235040	33235040	+	Silent	SNP	G	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33235040G>C	uc003odm.1	-	11	1260	c.1050C>G	c.(1048-1050)CGC>CGG	p.R350R	VPS52_uc003odn.1_Intron	NM_022553	NP_072047	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52	350					protein transport	endosome membrane|Golgi apparatus				ovary(4)|skin(1)	5						TGACAGAGCCGCGGGTTCCTA	0.552													7	115	---	---	---	---	PASS
ITPR3	3710	broad.mit.edu	37	6	33662647	33662647	+	Intron	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33662647A>G	uc011drk.1	+						C6orf125_uc003oez.1_RNA	NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3						activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19						TTTCTAAATGAGGCCTTTCTA	0.522													6	11	---	---	---	---	PASS
ZNF318	24149	broad.mit.edu	37	6	43308012	43308012	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43308012T>A	uc003oux.2	-	10	3802	c.3724A>T	c.(3724-3726)AAC>TAC	p.N1242Y	ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1242	Lys-rich.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			TCAGGGGAGTTCCTACCCTCA	0.398													112	280	---	---	---	---	PASS
CYB5R4	51167	broad.mit.edu	37	6	84603306	84603306	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84603306G>A	uc003pkf.2	+	3	427	c.295G>A	c.(295-297)GCA>ACA	p.A99T		NM_016230	NP_057314	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4	99	Cytochrome b5 heme-binding.				cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process	endoplasmic reticulum|perinuclear region of cytoplasm	cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity			breast(2)	2		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)		ACTAATGAGAGCAGCAGGATC	0.388													5	508	---	---	---	---	PASS
FOXO3	2309	broad.mit.edu	37	6	108985392	108985392	+	Silent	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108985392A>G	uc003psk.2	+	3	1672	c.1356A>G	c.(1354-1356)CAA>CAG	p.Q452Q	FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Silent_p.Q452Q|FOXO3_uc011ean.1_Silent_p.Q232Q|FOXO3_uc010kdj.1_Silent_p.Q232Q	NM_201559	NP_963853	O43524	FOXO3_HUMAN	forkhead box O3A	452					antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding			central_nervous_system(4)|lung(2)	6		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		AGACCATCCAAGAGAACAAGC	0.552													6	10	---	---	---	---	PASS
GPR126	57211	broad.mit.edu	37	6	142623349	142623349	+	5'UTR	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142623349G>A	uc010khc.2	+	1					GPR126_uc010khd.2_5'UTR|GPR126_uc010khe.2_5'UTR|GPR126_uc010khf.2_5'UTR|GPR126_uc003qix.2_5'UTR	NM_020455	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		GGAGGGTCCCGCCGCGGCGCA	0.692													20	44	---	---	---	---	PASS
OPRM1	4988	broad.mit.edu	37	6	154412361	154412361	+	Silent	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154412361C>A	uc003qpr.2	+	3	1155	c.918C>A	c.(916-918)GCC>GCA	p.A306A	OPRM1_uc011efc.1_Silent_p.A225A|OPRM1_uc011efd.1_Silent_p.A206A|OPRM1_uc011efe.1_Silent_p.A399A|OPRM1_uc003qpn.2_Silent_p.A306A|OPRM1_uc003qpo.1_Silent_p.A306A|OPRM1_uc011eff.1_Silent_p.A306A|OPRM1_uc011efg.1_Silent_p.A306A|OPRM1_uc011efh.1_Silent_p.A306A|OPRM1_uc003qpq.1_Silent_p.A306A|OPRM1_uc003qpt.1_Silent_p.A306A|OPRM1_uc011efi.1_Silent_p.A306A|OPRM1_uc003qpp.2_RNA|OPRM1_uc003qps.2_RNA|OPRM1_uc010kjg.2_Silent_p.A206A|OPRM1_uc003qpu.2_Silent_p.A206A	NM_000914	NP_000905	P35372	OPRM_HUMAN	opioid receptor, mu 1 isoform MOR-1	306	Extracellular (Potential).				behavior|negative regulation of cell proliferation|sensory perception	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	mu-opioid receptor activity|protein binding			ovary(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tramadol(DB00193)	TCATTAAAGCCTTGGTTACAA	0.478													80	192	---	---	---	---	PASS
SERAC1	84947	broad.mit.edu	37	6	158569914	158569914	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158569914A>G	uc003qrc.2	-	5	480	c.338T>C	c.(337-339)CTG>CCG	p.L113P	SERAC1_uc003qrb.2_5'UTR	NM_032861	NP_116250	Q96JX3	SRAC1_HUMAN	serine active site containing 1	113					GPI anchor metabolic process|intracellular protein transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	binding|hydrolase activity, acting on ester bonds				0		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)		TGGATTCCGCAGTATCTTGGC	0.338													112	302	---	---	---	---	PASS
BZW2	28969	broad.mit.edu	37	7	16722445	16722445	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16722445A>G	uc003stl.2	+	5	558	c.380A>G	c.(379-381)AAG>AGG	p.K127R	BZW2_uc011jxx.1_5'UTR|BZW2_uc003stm.2_5'UTR|BZW2_uc003stj.2_Missense_Mutation_p.K127R|BZW2_uc003stk.2_Missense_Mutation_p.K51R|BZW2_uc003stn.1_Missense_Mutation_p.K127R|BZW2_uc003sto.1_5'UTR|BZW2_uc003stp.2_5'UTR|BZW2_uc010kua.2_Missense_Mutation_p.K127R	NM_001159767	NP_001153239	Q9Y6E2	BZW2_HUMAN	basic leucine zipper and W2 domains 2	127					cell differentiation|nervous system development|RNA metabolic process		protein binding			ovary(2)	2	Lung NSC(10;0.0367)|all_lung(11;0.0837)			UCEC - Uterine corpus endometrioid carcinoma (126;0.199)		TATTTGGAGAAGGCATTTGAA	0.274													7	434	---	---	---	---	PASS
HIBADH	11112	broad.mit.edu	37	7	27669039	27669039	+	Silent	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27669039T>C	uc003szf.2	-	4	630	c.435A>G	c.(433-435)AAA>AAG	p.K145K	HIBADH_uc003szg.2_Silent_p.K96K|HIBADH_uc003szh.2_Silent_p.K44K|HIBADH_uc003szi.2_Silent_p.K96K	NM_152740	NP_689953	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase precursor	145					branched chain family amino acid catabolic process|pentose-phosphate shunt|valine metabolic process	mitochondrial matrix	3-hydroxyisobutyrate dehydrogenase activity|NAD binding|phosphogluconate dehydrogenase (decarboxylating) activity			ovary(2)	2			GBM - Glioblastoma multiforme(3;0.0368)		NADH(DB00157)	TCTCAACTTCTTTGGCCAATT	0.338													7	571	---	---	---	---	PASS
DNAJC2	27000	broad.mit.edu	37	7	102956266	102956266	+	Silent	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102956266T>C	uc003vbo.2	-	15	1832	c.1581A>G	c.(1579-1581)AAA>AAG	p.K527K	PMPCB_uc011kll.1_Intron|DNAJC2_uc003vbn.2_Silent_p.K152K|DNAJC2_uc010lix.2_Silent_p.K474K|DNAJC2_uc003vbp.2_Silent_p.K152K	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	527					'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1						CTCCATGTTCTTTTTTGAACT	0.323													7	681	---	---	---	---	PASS
ANKRD7	56311	broad.mit.edu	37	7	117876197	117876197	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117876197C>T	uc003vji.2	+	4	744	c.571C>T	c.(571-573)CAA>TAA	p.Q191*		NM_019644	NP_062618	Q92527	ANKR7_HUMAN	ankyrin repeat domain 7	191	ANK 5.				male gonad development						0						AGATAATTATCAAAGGTATAA	0.259													53	157	---	---	---	---	PASS
GCC1	79571	broad.mit.edu	37	7	127222351	127222351	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127222351T>C	uc003vma.2	-	2	2463	c.2045A>G	c.(2044-2046)CAT>CGT	p.H682R		NM_024523	NP_078799	Q96CN9	GCC1_HUMAN	Golgi coiled-coil protein 1	682	Potential.					Golgi membrane|plasma membrane	protein binding			ovary(2)	2						CTGCAGCTGATGCACCTCGAC	0.582													21	50	---	---	---	---	PASS
TTC26	79989	broad.mit.edu	37	7	138865849	138865849	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138865849A>G	uc003vus.2	+	16	1438	c.1324A>G	c.(1324-1326)AAG>GAG	p.K442E	TTC26_uc011kqn.1_Missense_Mutation_p.K442E|TTC26_uc011kqo.1_Missense_Mutation_p.K411E|TTC26_uc011kqp.1_Missense_Mutation_p.K337E|TTC26_uc003vut.2_Missense_Mutation_p.K302E|TTC26_uc011kqq.1_Missense_Mutation_p.K311E	NM_024926	NP_079202	A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26 isoform 1	442							binding			ovary(1)	1						TATTATGAATAAGAAACCAAG	0.358													6	311	---	---	---	---	PASS
NEFM	4741	broad.mit.edu	37	8	24775663	24775663	+	Silent	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24775663G>A	uc003xed.3	+	3	2328	c.2295G>A	c.(2293-2295)GGG>GGA	p.G765G	NEFM_uc011lac.1_Intron|NEFM_uc010lue.2_Silent_p.G389G	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	765	Tail.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		aagaagaggggaagccactgc	0.189													7	62	---	---	---	---	PASS
NCOA2	10499	broad.mit.edu	37	8	71039142	71039142	+	Silent	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71039142T>G	uc003xyn.1	-	19	3984	c.3822A>C	c.(3820-3822)CCA>CCC	p.P1274P	NCOA2_uc011lfb.1_Silent_p.P362P	NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	1274					cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CCACCATGCTTGGTGTCATAT	0.478			T	RUNXBP2	AML								10	303	---	---	---	---	PASS
DPY19L4	286148	broad.mit.edu	37	8	95777480	95777480	+	Missense_Mutation	SNP	G	T	T	rs144794373	byFrequency	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95777480G>T	uc003ygx.2	+	9	1064	c.940G>T	c.(940-942)GCT>TCT	p.A314S		NM_181787	NP_861452	Q7Z388	D19L4_HUMAN	dpy-19-like 4	314						integral to membrane				ovary(2)	2	Breast(36;3.85e-06)					TGAGAATCCAGCTTTGTTGGT	0.284													117	377	---	---	---	---	PASS
DPY19L4	286148	broad.mit.edu	37	8	95777481	95777481	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95777481C>A	uc003ygx.2	+	9	1065	c.941C>A	c.(940-942)GCT>GAT	p.A314D		NM_181787	NP_861452	Q7Z388	D19L4_HUMAN	dpy-19-like 4	314						integral to membrane				ovary(2)	2	Breast(36;3.85e-06)					GAGAATCCAGCTTTGTTGGTA	0.284													118	376	---	---	---	---	PASS
AZIN1	51582	broad.mit.edu	37	8	103851961	103851961	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103851961A>G	uc003ykx.2	-	5	935	c.193T>C	c.(193-195)TTC>CTC	p.F65L	AZIN1_uc003yky.2_Missense_Mutation_p.F65L	NM_015878	NP_056962	O14977	AZIN1_HUMAN	ornithine decarboxylase antizyme inhibitor	65					polyamine biosynthetic process|regulation of cellular amino acid metabolic process	cytosol	catalytic activity|protein binding				0	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)			ACTGTGTAGAATGGCTTTATC	0.398													6	421	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113529433	113529433	+	Missense_Mutation	SNP	C	T	T	rs138068999		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113529433C>T	uc003ynu.2	-	28	4745	c.4586G>A	c.(4585-4587)CGT>CAT	p.R1529H	CSMD3_uc003yns.2_Missense_Mutation_p.R801H|CSMD3_uc003ynt.2_Missense_Mutation_p.R1489H|CSMD3_uc011lhx.1_Missense_Mutation_p.R1425H	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1529	Extracellular (Potential).|Sushi 8.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						CCCTGGGTCACGACACGCAGT	0.413										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			42	97	---	---	---	---	PASS
EIF3H	8667	broad.mit.edu	37	8	117657101	117657101	+	3'UTR	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117657101G>A	uc003yoa.2	-	8					EIF3H_uc003yob.2_3'UTR	NM_003756	NP_003747	O15372	EIF3H_HUMAN	eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(3)	3	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)					ATTATGGCTAGAAAGACACTG	0.328													5	29	---	---	---	---	PASS
NOL6	65083	broad.mit.edu	37	9	33464888	33464888	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33464888T>G	uc003zsz.2	-	21	2869	c.2768A>C	c.(2767-2769)AAT>ACT	p.N923T	SUGT1P1_uc010mjq.1_Intron|NOL6_uc003zsy.2_5'UTR|NOL6_uc003zta.2_Intron|NOL6_uc010mjv.2_Missense_Mutation_p.N920T|NOL6_uc011lob.1_Missense_Mutation_p.N871T|NOL6_uc003ztb.1_Missense_Mutation_p.N923T	NM_022917	NP_075068	Q9H6R4	NOL6_HUMAN	nucleolar protein family 6 alpha isoform	923					rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		AGTGAGCTCATTATTGAGGTT	0.483													45	127	---	---	---	---	PASS
CERCAM	51148	broad.mit.edu	37	9	131193563	131193563	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131193563A>T	uc004buz.3	+	9	1582	c.1184A>T	c.(1183-1185)CAT>CTT	p.H395L	CERCAM_uc004buy.1_Missense_Mutation_p.H317L|CERCAM_uc010mxz.2_Missense_Mutation_p.H317L|CERCAM_uc010mya.1_Missense_Mutation_p.H236L	NM_016174	NP_057258	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule 1	395					cellular component movement|leukocyte cell-cell adhesion|lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen|plasma membrane				pancreas(1)	1						TTCCTCAGCCATTACTCCATC	0.602													23	52	---	---	---	---	PASS
SETX	23064	broad.mit.edu	37	9	135221764	135221764	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135221764T>C	uc004cbk.2	-	4	455	c.272A>G	c.(271-273)GAC>GGC	p.D91G		NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	91					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TCCATTATTGTCTACTATATA	0.353													7	339	---	---	---	---	PASS
USP6NL	9712	broad.mit.edu	37	10	11505441	11505441	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11505441T>C	uc001ikt.3	-	15	1807	c.1486A>G	c.(1486-1488)ACA>GCA	p.T496A	USP6NL_uc001iks.1_Missense_Mutation_p.T513A	NM_014688	NP_055503	Q92738	US6NL_HUMAN	USP6 N-terminal like isoform 1	496						intracellular	Rab GTPase activator activity				0						GTTCTCTCTGTAGCTGAGACG	0.527													4	127	---	---	---	---	PASS
YME1L1	10730	broad.mit.edu	37	10	27434352	27434352	+	Intron	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27434352C>T	uc001iti.2	-						YME1L1_uc001itj.2_Intron|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_Intron|YME1L1_uc001itk.1_3'UTR	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1						protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						AACACATTAACATACCATATT	0.318													51	145	---	---	---	---	PASS
FAM21A	387680	broad.mit.edu	37	10	51826394	51826394	+	5'Flank	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51826394G>A	uc001jjb.2	+						uc001jiz.1_RNA|FAM21A_uc001jja.1_5'Flank|FAM21A_uc010qhi.1_5'Flank|FAM21A_uc010qhj.1_5'Flank	NM_001005751	NP_001005751	Q641Q2	FA21A_HUMAN	hypothetical protein LOC387680						retrograde transport, endosome to Golgi	early endosome membrane|WASH complex				ovary(1)	1						ATAGGAGGGCGTTTCAAGTAT	0.393													3	44	---	---	---	---	PASS
C10orf4	118924	broad.mit.edu	37	10	95459948	95459948	+	Intron	SNP	A	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95459948A>C	uc001kiz.1	-						C10orf4_uc001kiv.1_Intron|C10orf4_uc001kja.1_Intron|C10orf4_uc001kjb.1_5'UTR|C10orf4_uc009xuh.1_Intron	NM_145246	NP_660289	Q70Z53	F10C1_HUMAN	FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)				gttatcttaaacagccacaat	0.149													22	57	---	---	---	---	PASS
TIAL1	7073	broad.mit.edu	37	10	121337217	121337217	+	Silent	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121337217T>C	uc001lei.1	-	8	1152	c.588A>G	c.(586-588)GTA>GTG	p.V196V	TIAL1_uc001leh.1_Silent_p.V174V|TIAL1_uc001lej.1_Silent_p.V213V|TIAL1_uc001lek.1_Silent_p.V73V|TIAL1_uc009xzi.1_Silent_p.V65V|TIAL1_uc010qtb.1_Silent_p.V73V	NM_003252	NP_003243	Q01085	TIAR_HUMAN	TIA-1 related protein isoform 1	196					apoptosis|defense response|induction of apoptosis|regulation of transcription from RNA polymerase II promoter	lysosome|nucleus|stress granule	nucleotide binding|RNA binding			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		ACTGGTTTACTACATCTTCAA	0.363													4	144	---	---	---	---	PASS
HBG1	3047	broad.mit.edu	37	11	5269511	5269511	+	3'UTR	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5269511C>T	uc001mah.1	-	3					HBG2_uc001mai.1_3'UTR	NM_000559	NP_000550	P69891	HBG1_HUMAN	A-gamma globin						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity|protein binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTGATCTCTCAGCAGAATAG	0.368													8	30	---	---	---	---	PASS
RASGRP2	10235	broad.mit.edu	37	11	64508224	64508224	+	Intron	SNP	G	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64508224G>C	uc009ypu.2	-						RASGRP2_uc001oat.2_5'UTR|RASGRP2_uc001oau.2_Intron|RASGRP2_uc009ypv.2_Intron|RASGRP2_uc009ypw.2_Intron	NM_001098671	NP_001092141	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2						platelet activation|Ras protein signal transduction|regulation of cell growth|regulation of small GTPase mediated signal transduction	cell junction|cytosol|ruffle membrane|synapse|synaptosome	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity				0						TGTGGGATGGGTGGTGGCAGT	0.413													5	9	---	---	---	---	PASS
CFL1	1072	broad.mit.edu	37	11	65623211	65623211	+	Intron	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65623211A>G	uc001ofs.2	-						CFL1_uc001oft.2_Intron|CFL1_uc001ofu.2_3'UTR	NM_005507	NP_005498	P23528	COF1_HUMAN	cofilin 1 (non-muscle)						actin cytoskeleton organization|anti-apoptosis|axon guidance|platelet activation|platelet degranulation|response to virus|Rho protein signal transduction	cytoplasm|cytoskeleton|nuclear matrix	actin binding				0				READ - Rectum adenocarcinoma(159;0.169)		CCTGGACAGAAACACGCGTCA	0.552													14	33	---	---	---	---	PASS
ODZ4	26011	broad.mit.edu	37	11	78443572	78443572	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78443572C>T	uc001ozl.3	-	21	3390	c.2927G>A	c.(2926-2928)CGG>CAG	p.R976Q		NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	976	Extracellular (Potential).				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						GAAAGGTGCCCGCTCGAACCG	0.547													4	102	---	---	---	---	PASS
SC5DL	6309	broad.mit.edu	37	11	121177308	121177308	+	Intron	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121177308G>T	uc001pxu.2	+						SC5DL_uc001pxt.2_Missense_Mutation_p.S186I|SC5DL_uc001pxv.2_Intron	NM_006918	NP_008849	O75845	SC5D_HUMAN	sterol-C5-desaturase						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	C-5 sterol desaturase activity|iron ion binding|lathosterol oxidase activity			ovary(1)	1		Breast(109;0.00328)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	OV - Ovarian serous cystadenocarcinoma(1;0.0334)	BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.144)		AAATGTCTAAGTAGCCATAAT	0.333													3	19	---	---	---	---	PASS
OR6T1	219874	broad.mit.edu	37	11	123814182	123814182	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123814182G>T	uc010sab.1	-	1	364	c.364C>A	c.(364-366)CGT>AGT	p.R122S		NM_001005187	NP_001005187	Q8NGN1	OR6T1_HUMAN	olfactory receptor, family 6, subfamily T,	122	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		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;0.0401)		GCCAGGTAACGATCCAGAGAC	0.527													17	59	---	---	---	---	PASS
B4GALNT3	283358	broad.mit.edu	37	12	668484	668484	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:668484G>A	uc001qii.1	+	19	2785	c.2785G>A	c.(2785-2787)GGG>AGG	p.G929R	B4GALNT3_uc001qik.1_Missense_Mutation_p.G478R	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta	929	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			GAATGGGTTCGGGCTGCTTGG	0.607													4	153	---	---	---	---	PASS
C12orf53	196500	broad.mit.edu	37	12	6804739	6804739	+	Silent	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6804739C>T	uc001qqf.1	-	5	760	c.684G>A	c.(682-684)CTG>CTA	p.L228L	C12orf53_uc001qqg.1_Silent_p.L228L	NM_153685	NP_710152	Q8IYJ0	CL053_HUMAN	hypothetical protein LOC196500 precursor	228	Cytoplasmic (Potential).					integral to membrane					0						ACAGGTCTGTCAGTGGCTGCT	0.682													3	5	---	---	---	---	PASS
SLCO1C1	53919	broad.mit.edu	37	12	20893281	20893281	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20893281C>T	uc001rej.3	+	13	2067	c.1712C>T	c.(1711-1713)CCT>CTT	p.P571L	SLCO1C1_uc010sii.1_Missense_Mutation_p.P571L|SLCO1C1_uc010sij.1_Missense_Mutation_p.P522L|SLCO1C1_uc009zip.2_Missense_Mutation_p.P405L|SLCO1C1_uc001rei.2_Missense_Mutation_p.P571L|SLCO1C1_uc010sik.1_Missense_Mutation_p.P453L	NM_017435	NP_059131	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family,	571	Helical; Name=10; (Potential).				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(5)|pancreas(1)|skin(1)	7	Esophageal squamous(101;0.149)					GGTGGCATACCTGGATACATA	0.368													43	278	---	---	---	---	PASS
SLCO1A2	6579	broad.mit.edu	37	12	21471822	21471822	+	Silent	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21471822G>T	uc001rer.2	-	2	347	c.96C>A	c.(94-96)TCC>TCA	p.S32S	SLCO1A2_uc001res.2_Silent_p.S32S|SLCO1A2_uc010siq.1_5'UTR|SLCO1A2_uc010sio.1_5'UTR|SLCO1A2_uc010sip.1_Intron|SLCO1A2_uc001ret.2_Silent_p.S30S|SLCO1A2_uc001reu.2_Silent_p.S12S	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A	32	Helical; Name=1; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						ACAGTGTTTTGGATACAAATG	0.323													107	256	---	---	---	---	PASS
CALCOCO1	57658	broad.mit.edu	37	12	54107576	54107576	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54107576G>C	uc001sef.2	-	13	1844	c.1700C>G	c.(1699-1701)CCT>CGT	p.P567R	CALCOCO1_uc001see.2_Missense_Mutation_p.P68R|CALCOCO1_uc010som.1_Missense_Mutation_p.P482R|CALCOCO1_uc010son.1_Missense_Mutation_p.P444R|CALCOCO1_uc001seh.2_Missense_Mutation_p.P567R|CALCOCO1_uc009znd.2_Missense_Mutation_p.P567R|CALCOCO1_uc001seg.2_Missense_Mutation_p.P392R	NM_020898	NP_065949	Q9P1Z2	CACO1_HUMAN	coiled-coil transcriptional coactivator isoform	567	C-terminal AD (CTNNB1 binding site) (By similarity).				steroid hormone receptor signaling pathway|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm	armadillo repeat domain binding|beta-catenin binding|ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|sequence-specific DNA binding|transcription regulatory region DNA binding			ovary(1)	1						AGCCTCTCGAGGCCCAGCAGG	0.607													12	33	---	---	---	---	PASS
USP15	9958	broad.mit.edu	37	12	62777898	62777898	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62777898A>G	uc001src.1	+	11	1297	c.1288A>G	c.(1288-1290)AAT>GAT	p.N430D	USP15_uc001srb.1_Missense_Mutation_p.N401D	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	430					protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TTTAAAACGAAATGATTCTAT	0.328													6	346	---	---	---	---	PASS
CKAP4	10970	broad.mit.edu	37	12	106633704	106633704	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106633704T>C	uc001tlk.2	-	2	991	c.907A>G	c.(907-909)AGA>GGA	p.R303G		NM_006825	NP_006816	Q07065	CKAP4_HUMAN	cytoskeleton-associated protein 4	303	Potential.					ER-Golgi intermediate compartment membrane|integral to membrane|membrane fraction					0						TCCCACTCTCTGGACTTGGCT	0.537													62	96	---	---	---	---	PASS
ACACB	32	broad.mit.edu	37	12	109678940	109678940	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109678940C>T	uc001tob.2	+	36	4995	c.4876C>T	c.(4876-4878)CGT>TGT	p.R1626C	ACACB_uc001toc.2_Missense_Mutation_p.R1626C|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Missense_Mutation_p.R292C	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	1626					acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	GTGGAAACTCCGTGTGCTACA	0.572													4	51	---	---	---	---	PASS
MRP63	78988	broad.mit.edu	37	13	21751241	21751241	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21751241C>G	uc001unw.2	+	2	676	c.186C>G	c.(184-186)CAC>CAG	p.H62Q	SKA3_uc001unt.2_5'Flank|SKA3_uc001unv.2_5'Flank|SKA3_uc001unu.2_5'Flank	NM_024026	NP_076931	Q9BQC6	RT63_HUMAN	mitochondrial ribosomal protein 63	62											0		all_cancers(29;2.76e-20)|all_epithelial(30;2.97e-18)|all_lung(29;4.58e-16)|Lung SC(185;0.0262)|Breast(139;0.147)		all cancers(112;9.43e-05)|Epithelial(112;0.000285)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|Lung(94;0.0932)		AGCGCGGCCACGCCGCGGTGC	0.642													6	17	---	---	---	---	PASS
UFM1	51569	broad.mit.edu	37	13	38923956	38923956	+	5'UTR	SNP	G	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38923956G>C	uc001uwu.2	+	1					UFM1_uc010abz.2_5'UTR|UFM1_uc010aca.2_5'UTR	NM_016617	NP_057701	P61960	UFM1_HUMAN	ubiquitin-fold modifier 1 precursor						protein ufmylation	cytoplasm|nucleus	protein binding				0		Lung NSC(96;3.18e-06)|Prostate(109;0.00314)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;1.05e-08)|Epithelial(112;1.44e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000855)|BRCA - Breast invasive adenocarcinoma(63;0.00342)|GBM - Glioblastoma multiforme(144;0.0132)		TGCAGAGGGAGACGTGGACGT	0.557													4	73	---	---	---	---	PASS
POTEG	404785	broad.mit.edu	37	14	19563232	19563232	+	Intron	SNP	T	C	C	rs140952576	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19563232T>C	uc001vuz.1	+						POTEG_uc001vva.1_Intron|POTEG_uc010ahc.1_Intron|uc001vvb.2_RNA	NM_001005356	NP_001005356	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G											ovary(1)	1						CCCTTCCTTTTAACCTTGGTG	0.368													6	37	---	---	---	---	PASS
RNF31	55072	broad.mit.edu	37	14	24617487	24617487	+	Silent	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24617487A>G	uc001wmn.1	+	3	609	c.360A>G	c.(358-360)CGA>CGG	p.R120R	PSME2_uc001wmj.2_5'Flank|PSME2_uc001wmk.2_5'Flank|RNF31_uc001wml.1_5'UTR|RNF31_uc001wmm.1_Intron|RNF31_uc010alg.1_5'UTR|RNF31_uc001wmo.1_5'Flank|RNF31_uc001wmp.2_5'Flank	NM_017999	NP_060469	Q96EP0	RNF31_HUMAN	ring finger protein 31	120	Polyubiquitin-binding.				CD40 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein linear polyubiquitination|T cell receptor signaling pathway	CD40 receptor complex|internal side of plasma membrane|LUBAC complex	ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(265;0.00861)		ATGTGCTGCGATTATATGGCT	0.567													18	37	---	---	---	---	PASS
DDHD1	80821	broad.mit.edu	37	14	53527935	53527935	+	Intron	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53527935A>G	uc001xai.2	-						DDHD1_uc001xaj.2_Intron|DDHD1_uc001xah.2_Intron|DDHD1_uc001xag.2_Intron|DDHD1_uc001xak.1_5'UTR	NM_001160148	NP_001153620	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1 isoform c						lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding			ovary(2)	2	Breast(41;0.037)					AAGGGGTATGAGATTATATAC	0.363													7	480	---	---	---	---	PASS
C14orf37	145407	broad.mit.edu	37	14	58471373	58471373	+	3'UTR	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58471373T>G	uc001xdc.2	-	8					C14orf37_uc010tro.1_3'UTR	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						ATGTGGCAGGTTGTTCTTTTT	0.383													15	40	---	---	---	---	PASS
UBR7	55148	broad.mit.edu	37	14	93693406	93693406	+	3'UTR	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93693406C>A	uc001ybm.3	+	11					UBR7_uc001ybn.3_3'UTR|UBR7_uc010auq.2_3'UTR	NM_175748	NP_786924	Q8N806	UBR7_HUMAN	ubiquitin protein ligase E3 component n-recognin								ubiquitin-protein ligase activity|zinc ion binding				0						CTTTCTCATTCAAGCCAATGA	0.463													6	132	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106134510	106134510	+	Intron	SNP	G	C	C	rs10144438	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106134510G>C	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001ysb.1_RNA					Parts of antibodies, mostly variable regions.												0						GAAGTATGTAGACGGGGTACG	0.647													8	34	---	---	---	---	PASS
ZFP106	64397	broad.mit.edu	37	15	42743699	42743699	+	Silent	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42743699A>G	uc001zpw.2	-	2	1037	c.702T>C	c.(700-702)AAT>AAC	p.N234N	ZFP106_uc001zpu.2_5'Flank|ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron|ZFP106_uc010udh.1_Silent_p.N17N|ZFP106_uc001zpy.1_Silent_p.N257N	NM_022473	NP_071918	Q9H2Y7	ZF106_HUMAN	zinc finger protein 106 homolog	234						nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)		TGTAATTCCAATTATTTGTAC	0.403													45	133	---	---	---	---	PASS
ZSCAN29	146050	broad.mit.edu	37	15	43661240	43661240	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43661240T>A	uc001zrk.1	-	2	551	c.404A>T	c.(403-405)CAG>CTG	p.Q135L	ZSCAN29_uc001zrj.1_Missense_Mutation_p.Q15L|ZSCAN29_uc010bdf.1_Missense_Mutation_p.Q134L|ZSCAN29_uc001zrl.1_RNA|ZSCAN29_uc010bdg.1_Missense_Mutation_p.Q134L|ZSCAN29_uc001zrm.2_Missense_Mutation_p.Q134L|TUBGCP4_uc001zrn.2_5'Flank|TUBGCP4_uc001zro.2_5'Flank	NM_152455	NP_689668	Q8IWY8	ZSC29_HUMAN	zinc finger protein 690	135					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		CACTGACTCCTGCCGAACACT	0.547													37	92	---	---	---	---	PASS
TRPM7	54822	broad.mit.edu	37	15	50867287	50867287	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50867287A>G	uc001zyt.3	-	34	5045	c.4781T>C	c.(4780-4782)ATA>ACA	p.I1594T	TRPM7_uc001zyr.2_Missense_Mutation_p.I31T	NM_017672	NP_060142	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel,	1594	Cytoplasmic (Potential).|Alpha-type protein kinase.				cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity			ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1)	10				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		GTTATTTAGTATGTTGGGTGA	0.403													85	169	---	---	---	---	PASS
LACTB	114294	broad.mit.edu	37	15	63421946	63421946	+	Intron	SNP	A	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63421946A>C	uc002alw.2	+						LACTB_uc002alv.2_3'UTR	NM_032857	NP_116246	P83111	LACTB_HUMAN	lactamase, beta isoform a							mitochondrion	hydrolase activity				0						TCCAAAATCAACCTGCCACAT	0.323													12	12	---	---	---	---	PASS
CA12	771	broad.mit.edu	37	15	63632949	63632949	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63632949A>G	uc002amc.2	-	6	715	c.559T>C	c.(559-561)TTC>CTC	p.F187L	CA12_uc002amd.2_Missense_Mutation_p.F187L|CA12_uc002ame.2_Missense_Mutation_p.F127L	NM_001218	NP_001209	O43570	CAH12_HUMAN	carbonic anhydrase XII isoform 1 precursor	187	Extracellular (Potential).				one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)	AGGTGACTGAAGATCTTGTCA	0.488													5	195	---	---	---	---	PASS
ADAMTSL3	57188	broad.mit.edu	37	15	84539634	84539634	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84539634A>G	uc002bjz.3	+	9	1107	c.883A>G	c.(883-885)ACA>GCA	p.T295A	ADAMTSL3_uc010bmt.1_Missense_Mutation_p.T295A|ADAMTSL3_uc010bmu.1_Missense_Mutation_p.T295A	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor	295						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)			AGAAAACACAACAGTGGAATT	0.398													5	219	---	---	---	---	PASS
CLDN6	9074	broad.mit.edu	37	16	3065984	3065984	+	Silent	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3065984C>T	uc002csu.3	-	2	99	c.39G>A	c.(37-39)CTG>CTA	p.L13L		NM_021195	NP_067018	P56747	CLD6_HUMAN	claudin 6	13	Helical; (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity				0						CCAGCAGTGTCAGGACGACTC	0.607													14	22	---	---	---	---	PASS
LOC342346	342346	broad.mit.edu	37	16	4606857	4606857	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4606857C>A	uc010uxn.1	+	1	367	c.367C>A	c.(367-369)CAT>AAT	p.H123N		NM_001145011	NP_001138483	C9JH24	C9JH24_HUMAN	hypothetical protein LOC342346	123											0						GGACCTGTGGCATCTGATCAA	0.622													4	17	---	---	---	---	PASS
A2BP1	54715	broad.mit.edu	37	16	7759121	7759121	+	Silent	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7759121C>T	uc002cys.2	+	15	2047	c.1059C>T	c.(1057-1059)GGC>GGT	p.G353G	A2BP1_uc002cyt.2_Silent_p.G326G|A2BP1_uc010uxz.1_Silent_p.G396G|A2BP1_uc010uya.1_Missense_Mutation_p.A328V|A2BP1_uc010uyb.1_Silent_p.G353G|A2BP1_uc002cyw.2_Missense_Mutation_p.A392V|A2BP1_uc002cyy.2_Silent_p.G374G|A2BP1_uc002cyx.2_Silent_p.G374G|A2BP1_uc010uyc.1_Silent_p.G347G	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4	353					mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		CCACCTACGGCGTTGGTGCCA	0.547													4	170	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	15463933	15463933	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15463933T>C	uc010bvf.1	-	3	236	c.236A>G	c.(235-237)GAT>GGT	p.D79G	uc010uzu.1_Missense_Mutation_p.D79G					RecName: Full=NPIP-like protein 1;																		CGTGGATCCATCATGTCCATT	0.393													6	245	---	---	---	---	PASS
ITGAD	3681	broad.mit.edu	37	16	31424171	31424171	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31424171T>G	uc002ebv.1	+	15	1769	c.1720T>G	c.(1720-1722)TCC>GCC	p.S574A	ITGAD_uc010cap.1_Missense_Mutation_p.S575A	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	574	Extracellular (Potential).|FG-GAP 7.				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1						GATTGCCAGCTCCCAGCTCTC	0.592													7	20	---	---	---	---	PASS
ZNF423	23090	broad.mit.edu	37	16	49670777	49670777	+	Silent	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49670777C>T	uc002efs.2	-	5	2584	c.2286G>A	c.(2284-2286)GAG>GAA	p.E762E	ZNF423_uc010vgn.1_Silent_p.E645E	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	762	C2H2-type 18.				cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)				GCAGGTCAGCCTCCTTGCGGA	0.602													40	104	---	---	---	---	PASS
CHD9	80205	broad.mit.edu	37	16	53340243	53340243	+	Silent	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53340243T>C	uc002ehb.2	+	31	6878	c.6714T>C	c.(6712-6714)AAT>AAC	p.N2238N	CHD9_uc002egy.2_Silent_p.N2238N|CHD9_uc002ehc.2_Silent_p.N2239N|CHD9_uc002ehf.2_Silent_p.N1352N|CHD9_uc010cbw.2_Silent_p.N304N|CHD9_uc002ehg.1_Silent_p.N245N	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2238					cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)				AGATGAACAATGGGACACCAG	0.423													68	155	---	---	---	---	PASS
SLC9A5	6553	broad.mit.edu	37	16	67304703	67304703	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67304703G>T	uc002esm.2	+	16	2344	c.2281G>T	c.(2281-2283)GAG>TAG	p.E761*	SLC9A5_uc010cee.2_Nonsense_Mutation_p.E466*|SLC9A5_uc010vji.1_Nonsense_Mutation_p.E265*	NM_004594	NP_004585	Q14940	SL9A5_HUMAN	solute carrier family 9 (sodium/hydrogen	761					regulation of pH	integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			ovary(1)|pancreas(1)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		TGCAGAAAAGGAGCTCCCCTG	0.567													27	72	---	---	---	---	PASS
SLC9A5	6553	broad.mit.edu	37	16	67304704	67304704	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67304704A>G	uc002esm.2	+	16	2345	c.2282A>G	c.(2281-2283)GAG>GGG	p.E761G	SLC9A5_uc010cee.2_Missense_Mutation_p.E466G|SLC9A5_uc010vji.1_Missense_Mutation_p.E265G	NM_004594	NP_004585	Q14940	SL9A5_HUMAN	solute carrier family 9 (sodium/hydrogen	761					regulation of pH	integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			ovary(1)|pancreas(1)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		GCAGAAAAGGAGCTCCCCTGG	0.567													26	72	---	---	---	---	PASS
ADAMTS18	170692	broad.mit.edu	37	16	77325284	77325284	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77325284C>T	uc002ffc.3	-	21	3700	c.3281G>A	c.(3280-3282)CGA>CAA	p.R1094Q		NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1094	TSP type-1 4.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						ACGGCATCTTCGCTCTGGGAA	0.522													48	154	---	---	---	---	PASS
NCOR1	9611	broad.mit.edu	37	17	16021256	16021256	+	Silent	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16021256A>G	uc002gpo.2	-	18	2241	c.2001T>C	c.(1999-2001)TTT>TTC	p.F667F	NCOR1_uc002gpn.2_Silent_p.F667F|NCOR1_uc002gpp.1_Silent_p.F558F|NCOR1_uc002gpr.2_Silent_p.F558F	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1	667	SANT 2.				cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TTTTATAGTTAAAATAGAAGT	0.363													161	378	---	---	---	---	PASS
SLC5A10	125206	broad.mit.edu	37	17	18923637	18923637	+	Splice_Site	SNP	G	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18923637G>C	uc002guu.1	+	15	1726	c.1685_splice	c.e15-1	p.G562_splice	SLC5A10_uc002gur.1_Splice_Site_p.G532_splice|SLC5A10_uc002gut.1_Splice_Site_p.G578_splice|SLC5A10_uc002guv.1_Splice_Site_p.G535_splice|SLC5A10_uc010vyl.1_Splice_Site_p.G526_splice	NM_001042450	NP_001035915	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/glucose						sodium ion transport|transmembrane transport	integral to membrane	transporter activity			ovary(1)	1						ACCCCCTCCAGGTGATGGCCA	0.552													5	103	---	---	---	---	PASS
STAC2	342667	broad.mit.edu	37	17	37371369	37371369	+	Splice_Site	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37371369A>G	uc002hrs.2	-	5	918	c.699_splice	c.e5+1	p.L233_splice	STAC2_uc010cvt.2_Splice_Site_p.L91_splice	NM_198993	NP_945344	Q6ZMT1	STAC2_HUMAN	SH3 and cysteine rich domain 2						intracellular signal transduction		metal ion binding			pancreas(1)	1						TGCCCACCATACCAGGCTCCT	0.617													8	125	---	---	---	---	PASS
STAT3	6774	broad.mit.edu	37	17	40485988	40485988	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40485988A>T	uc002hzl.1	-	9	1117	c.877T>A	c.(877-879)TAC>AAC	p.Y293N	STAT3_uc002hzk.1_Missense_Mutation_p.Y293N|STAT3_uc002hzm.1_Missense_Mutation_p.Y293N|STAT3_uc010wgh.1_Missense_Mutation_p.Y195N|STAT3_uc002hzn.1_Missense_Mutation_p.Y293N	NM_139276	NP_644805	P40763	STAT3_HUMAN	signal transducer and activator of transcription	293					cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		TCCCCTTTGTAGGAAACTTTT	0.428									Hyperimmunoglobulin_E_Recurrent_Infection_Syndrome				97	212	---	---	---	---	PASS
PSME3	10197	broad.mit.edu	37	17	40986168	40986168	+	Intron	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40986168T>G	uc002ibr.2	+						PSME3_uc002ibp.2_Intron|PSME3_uc002ibq.2_Intron|PSME3_uc002ibs.2_5'UTR|PSME3_uc010whd.1_Intron	NM_005789	NP_005780	P61289	PSME3_HUMAN	proteasome activator subunit 3 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome activator complex	endopeptidase activator activity|identical protein binding|MDM2 binding|p53 binding				0		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		GACAGGCAGGTGCTGTCCTCA	0.468													8	24	---	---	---	---	PASS
GH1	2688	broad.mit.edu	37	17	61994782	61994782	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61994782C>A	uc002jdj.2	-	5	603	c.541G>T	c.(541-543)GCA>TCA	p.A181S	GH1_uc002jdi.2_Missense_Mutation_p.A166S|GH1_uc002jdk.2_Missense_Mutation_p.A141S|GH1_uc002jdl.2_Missense_Mutation_p.A86S|GH1_uc002jdm.2_3'UTR|GH1_uc002jdn.2_Silent_p.T134T	NM_000515	NP_000506	P01241	SOMA_HUMAN	growth hormone 1 isoform 1	181					glucose transport|growth hormone receptor signaling pathway|JAK-STAT cascade|positive regulation of activation of JAK2 kinase activity|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of MAP kinase activity|positive regulation of multicellular organism growth|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|response to estradiol stimulus	extracellular space	growth factor activity|growth hormone receptor binding|hormone activity|metal ion binding|prolactin receptor binding				0						TTGAGTAGTGCGTCATCGTTG	0.552													7	258	---	---	---	---	PASS
NDC80	10403	broad.mit.edu	37	18	2595574	2595574	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2595574A>G	uc002kli.2	+	11	1357	c.1175A>G	c.(1174-1176)CAG>CGG	p.Q392R		NM_006101	NP_006092	O14777	NDC80_HUMAN	kinetochore associated 2	392	Interaction with the N-terminus of CDCA1.|Interaction with PSMC2 and SMC1A.|Potential.|Interaction with NEK2 and ZWINT.|Interaction with SMC1A.				attachment of spindle microtubules to kinetochore|cell division|establishment of mitotic spindle orientation|mitotic prometaphase|mitotic sister chromatid segregation|mitotic spindle organization|phosphatidylinositol-mediated signaling	condensed nuclear chromosome outer kinetochore|cytosol|Ndc80 complex	protein binding			ovary(1)	1						GCTGAACAACAGAAGTTGTGG	0.403													7	274	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	18	14179258	14179258	+	5'UTR	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14179258T>G	uc010xag.1	+	1										RecName: Full=Putative ankyrin repeat domain-containing protein 20A5;																		atcgcggatttggggttggat	0.348													3	11	---	---	---	---	PASS
CELF4	56853	broad.mit.edu	37	18	34833813	34833813	+	Silent	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34833813C>T	uc002lae.2	-	12	1818	c.1422G>A	c.(1420-1422)GTG>GTA	p.V474V	CELF4_uc010dnd.1_Silent_p.V472V|CELF4_uc002lag.2_Silent_p.V436V|CELF4_uc002laf.2_Silent_p.V468V	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1	474	RRM 3.				embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						GCTTCAGCTGCACCTTGAGCC	0.617													13	25	---	---	---	---	PASS
ZNF555	148254	broad.mit.edu	37	19	2853429	2853429	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2853429C>A	uc002lwo.2	+	4	1455	c.1366C>A	c.(1366-1368)CAG>AAG	p.Q456K	ZNF555_uc002lwn.3_Missense_Mutation_p.Q455K	NM_152791	NP_690004	Q8NEP9	ZN555_HUMAN	zinc finger protein 555	456	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				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)		TGAATGTAAGCAGTGTGGGAA	0.418													17	75	---	---	---	---	PASS
SAFB	6294	broad.mit.edu	37	19	5648215	5648215	+	Intron	SNP	A	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5648215A>C	uc002mcf.2	+						SAFB_uc010xiq.1_3'UTR|SAFB_uc002mcg.2_Intron|SAFB_uc002mce.3_Intron|SAFB_uc010xir.1_Intron|SAFB_uc010xis.1_Intron|SAFB_uc010xit.1_Intron|SAFB_uc010xiu.1_Intron	NM_002967	NP_002958	Q15424	SAFB1_HUMAN	scaffold attachment factor B						chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GAGATTGGAAACCCAGCCATA	0.333													5	5	---	---	---	---	PASS
ZNF790	388536	broad.mit.edu	37	19	37310789	37310789	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37310789G>C	uc002oew.2	-	5	576	c.457C>G	c.(457-459)CAG>GAG	p.Q153E	uc002oev.1_Intron	NM_206894	NP_996777	Q6PG37	ZN790_HUMAN	zinc finger protein 790	153					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|skin(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ACTGTATGCTGGTTAAAAGTG	0.398													76	194	---	---	---	---	PASS
EXOSC5	56915	broad.mit.edu	37	19	41895707	41895707	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41895707C>A	uc002oqo.2	-	4	511	c.488G>T	c.(487-489)GGG>GTG	p.G163V	CYP2F1_uc010xvw.1_Intron|BCKDHA_uc002oqm.3_Intron	NM_020158	NP_064543	Q9NQT4	EXOS5_HUMAN	exosome component Rrp46	163					DNA deamination|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5'-exoribonuclease activity|protein binding|RNA binding				0						CACGAGGGTCCCATCAGAGTC	0.612													17	29	---	---	---	---	PASS
PSG1	5669	broad.mit.edu	37	19	43373067	43373067	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43373067C>T	uc002ovb.2	-	4	967	c.829G>A	c.(829-831)GGT>AGT	p.G277S	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Missense_Mutation_p.G277S|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_RNA|PSG1_uc002our.1_Missense_Mutation_p.G277S|PSG1_uc010eio.1_Missense_Mutation_p.G277S|PSG1_uc002oux.1_Missense_Mutation_p.G206S|PSG1_uc002ouy.1_Intron|PSG1_uc002ouz.1_Missense_Mutation_p.G277S|PSG1_uc002ova.1_Missense_Mutation_p.G184S|PSG1_uc002ovc.2_Missense_Mutation_p.G184S|PSG1_uc002ovd.1_Missense_Mutation_p.G277S	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	277	Ig-like C2-type 2.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)				AGGCTCTGACCATTTAGCCAC	0.463													4	188	---	---	---	---	PASS
CD3EAP	10849	broad.mit.edu	37	19	45912825	45912825	+	3'UTR	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45912825A>G	uc002pbq.1	+	3					CD3EAP_uc002pbr.1_3'UTR	NM_012099	NP_036231	O15446	RPA34_HUMAN	CD3E antigen, epsilon polypeptide associated						rRNA transcription|transmembrane receptor protein tyrosine kinase signaling pathway	chromosome|RNA polymerase I transcription factor complex	DNA-directed RNA polymerase activity			large_intestine(2)|ovary(2)	4		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		CCAGAAGGTGACACCCCCAGA	0.592													4	49	---	---	---	---	PASS
FTL	2512	broad.mit.edu	37	19	49468840	49468840	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49468840C>A	uc002plo.2	+	1	275	c.76C>A	c.(76-78)CAG>AAG	p.Q26K	FTL_uc002pln.1_Missense_Mutation_p.Q26K	NM_000146	NP_000137	P02792	FRIL_HUMAN	ferritin, light polypeptide	26	Ferritin-like diiron.				cell death|cellular iron ion homeostasis|cellular membrane organization|iron ion transport|post-Golgi vesicle-mediated transport	cytosol|intracellular ferritin complex	ferric iron binding|identical protein binding|oxidoreductase activity				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000152)|all cancers(93;0.000435)|GBM - Glioblastoma multiforme(486;0.0171)|Epithelial(262;0.0267)	Iron Dextran(DB00893)	TTTGTACCTGCAGGCCTCCTA	0.597													25	47	---	---	---	---	PASS
CGB7	94027	broad.mit.edu	37	19	49558850	49558850	+	5'UTR	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49558850G>A	uc002pmd.2	-	1					CGB_uc010yad.1_5'UTR|CGB8_uc002pmc.2_5'UTR|CGB7_uc002pme.2_5'UTR|CGB7_uc010emq.1_RNA|CGB7_uc010yah.1_3'UTR	NM_033142	NP_149133	P01233	CGHB_HUMAN	chorionic gonadotropin, beta polypeptide 7						apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)	CGGAGACCACGGTGAAGTGAC	0.612													9	18	---	---	---	---	PASS
RPS11	6205	broad.mit.edu	37	19	50001200	50001200	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50001200A>G	uc002pob.1	+	4	330	c.250A>G	c.(250-252)AGG>GGG	p.R84G		NM_001015	NP_001006	P62280	RS11_HUMAN	ribosomal protein S11	84					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|rRNA binding|structural constituent of ribosome				0		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00206)|GBM - Glioblastoma multiforme(486;0.0245)		GAAGATGCAGAGGACCATTGT	0.567													23	62	---	---	---	---	PASS
SLC27A5	10998	broad.mit.edu	37	19	59010218	59010218	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59010218C>G	uc002qtc.2	-	9	1940	c.1830G>C	c.(1828-1830)GAG>GAC	p.E610D	SLC27A5_uc002qtb.2_RNA	NM_012254	NP_036386	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid	610	Cytoplasmic (Probable).				bile acid and bile salt transport|bile acid biosynthetic process|very long-chain fatty acid metabolic process	endoplasmic reticulum membrane|integral to membrane	ATP binding|cholate-CoA ligase activity|long-chain fatty acid-CoA ligase activity				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		GGTACAACTTCTCCCCGTCGA	0.627													15	24	---	---	---	---	PASS
PLAGL2	5326	broad.mit.edu	37	20	30784297	30784297	+	Silent	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30784297C>T	uc002wxn.2	-	3	1666	c.1449G>A	c.(1447-1449)CTG>CTA	p.L483L		NM_002657	NP_002648	Q9UPG8	PLAL2_HUMAN	pleiomorphic adenoma gene-like 2	483						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TGGTGCTACTCAGGCCAGACG	0.562													31	57	---	---	---	---	PASS
PFDN4	5203	broad.mit.edu	37	20	52835595	52835595	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52835595G>T	uc002xwx.2	+	4	449	c.311G>T	c.(310-312)AGA>ATA	p.R104I		NM_002623	NP_002614	Q9NQP4	PFD4_HUMAN	prefoldin subunit 4	104					'de novo' posttranslational protein folding	prefoldin complex	chaperone binding|unfolded protein binding				0	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		Colorectal(105;0.124)|STAD - Stomach adenocarcinoma(23;0.206)			TTAGAATCCAGAGTGGAATCA	0.328													115	224	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	11020830	11020830	+	RNA	SNP	A	G	G	rs8133131		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11020830A>G	uc002yis.1	-	5		c.1129T>C						P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			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)		CTGACACAGTATGGATGGTAA	0.378													4	79	---	---	---	---	PASS
RBM11	54033	broad.mit.edu	37	21	15599585	15599585	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15599585C>T	uc002yjo.3	+	5	859	c.817C>T	c.(817-819)CGA>TGA	p.R273*	RBM11_uc002yjn.3_Nonsense_Mutation_p.R159*|RBM11_uc002yjp.3_Nonsense_Mutation_p.R159*	NM_144770	NP_658983	P57052	RBM11_HUMAN	RNA binding motif protein 11	273							nucleotide binding|RNA binding				0				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		CCAAAAGTTCCGAAAGTCTAA	0.338													71	153	---	---	---	---	PASS
NRIP1	8204	broad.mit.edu	37	21	16337710	16337710	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16337710A>G	uc002yjx.2	-	4	3402	c.2804T>C	c.(2803-2805)GTT>GCT	p.V935A		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	935					androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		CTGTTTCAGAACATTAAAGCT	0.423													4	72	---	---	---	---	PASS
KRTAP22-1	337979	broad.mit.edu	37	21	31973474	31973474	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31973474G>T	uc011add.1	+	1	35	c.35G>T	c.(34-36)GGC>GTC	p.G12V	KRTAP6-2_uc011adc.1_5'Flank	NM_181620	NP_853651	Q3MIV0	KR221_HUMAN	keratin associated protein 22-1	12						intermediate filament					0						GGTGGCCAGGGCTATGCCAAA	0.443													41	104	---	---	---	---	PASS
B3GALT5	10317	broad.mit.edu	37	21	41032497	41032497	+	Missense_Mutation	SNP	C	T	T	rs146088205	byFrequency	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41032497C>T	uc002yyb.1	+	5	603	c.11C>T	c.(10-12)CCG>CTG	p.P4L	B3GALT5_uc002yye.2_Missense_Mutation_p.P4L|B3GALT5_uc002yyi.1_Missense_Mutation_p.P4L|B3GALT5_uc002yyj.1_Missense_Mutation_p.P4L|B3GALT5_uc002yyk.1_Missense_Mutation_p.P4L|B3GALT5_uc002yyl.1_Missense_Mutation_p.P4L|B3GALT5_uc002yym.1_Missense_Mutation_p.P4L	NM_033173	NP_149363	Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta	4	Cytoplasmic (Potential).				protein glycosylation	endoplasmic reticulum|Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			skin(1)	1		Prostate(19;2.55e-06)				ATGGCTTTCCCGAAGATGAGA	0.418													5	505	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47981523	47981523	+	Intron	SNP	T	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47981523T>G	uc002zjo.2	+						DIP2A_uc011afz.1_Intron|DIP2A_uc002zjs.2_5'UTR|DIP2A_uc002zjt.2_5'Flank	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a						multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TCATGGCAGGTGTGCTGTGGA	0.557													14	11	---	---	---	---	PASS
MYH9	4627	broad.mit.edu	37	22	36694979	36694979	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36694979A>G	uc003apg.2	-	24	3317	c.3086T>C	c.(3085-3087)ATC>ACC	p.I1029T		NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	1029	Potential.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11						CAAGTCAGTGATCATTGCCTC	0.587			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				6	363	---	---	---	---	PASS
CYTH4	27128	broad.mit.edu	37	22	37705485	37705485	+	Intron	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37705485G>T	uc003arf.2	+						CYTH4_uc003are.2_3'UTR|CYTH4_uc011amw.1_Intron|CYTH4_uc010gxe.2_Intron	NM_013385	NP_037517	Q9UIA0	CYH4_HUMAN	cytohesin 4						regulation of ARF protein signal transduction|regulation of cell adhesion	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity			ovary(2)	2						CATGCATCCTGGGGGATGGAG	0.652													6	6	---	---	---	---	PASS
RBX1	9978	broad.mit.edu	37	22	41368620	41368620	+	3'UTR	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41368620G>T	uc003azk.2	+	5						NM_014248	NP_055063	P62877	RBX1_HUMAN	ring-box 1						DNA repair|interspecies interaction between organisms|protein neddylation|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	Cul3-RING ubiquitin ligase complex|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytosol|nucleus|SCF ubiquitin ligase complex	NEDD8 ligase activity|protein binding|zinc ion binding			skin(1)	1						TGCTGTTTCTGTAGCCATATT	0.348													22	199	---	---	---	---	PASS
CHKB	1120	broad.mit.edu	37	22	51018844	51018844	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51018844T>C	uc003bms.2	-	6	897	c.679A>G	c.(679-681)AAG>GAG	p.K227E	CPT1B_uc003bmk.3_5'Flank|CPT1B_uc003bml.2_5'Flank|CPT1B_uc003bmm.2_5'Flank|CPT1B_uc003bmo.2_5'Flank|CPT1B_uc011asa.1_5'Flank|CPT1B_uc003bmn.2_5'Flank|CPT1B_uc011asb.1_5'Flank|CHKB-CPT1B_uc003bmp.2_5'Flank|CHKB-CPT1B_uc003bmt.1_Missense_Mutation_p.K18E|CHKB-CPT1B_uc003bmu.2_Missense_Mutation_p.K106E|CHKB_uc003bmv.2_Missense_Mutation_p.K227E|LOC100144603_uc003bmw.3_5'Flank	NM_005198	NP_005189	Q9Y259	CHKB_HUMAN	choline kinase beta	227					phosphatidylethanolamine biosynthetic process		ATP binding|choline kinase activity|ethanolamine kinase activity				0		all_cancers(38;8.8e-15)|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)		all cancers(3;4.04e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.79e-74)|Epithelial(4;6.17e-70)|GBM - Glioblastoma multiforme(4;5.68e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.205)	Choline(DB00122)	TCTAGTAACTTCCTACAGGGG	0.552													86	218	---	---	---	---	PASS
MOSPD2	158747	broad.mit.edu	37	X	14937818	14937818	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14937818A>G	uc004cwi.2	+	15	1532	c.1444A>G	c.(1444-1446)AGG>GGG	p.R482G	MOSPD2_uc004cwj.2_Missense_Mutation_p.R419G	NM_152581	NP_689794	Q8NHP6	MSPD2_HUMAN	motile sperm domain containing 2	482						integral to membrane	structural molecule activity			lung(1)	1	Hepatocellular(33;0.183)					AGAAAGCAATAGGAAGCTTGA	0.408													6	523	---	---	---	---	PASS
OTC	5009	broad.mit.edu	37	X	38260640	38260640	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38260640T>C	uc004def.3	+	5	713	c.499T>C	c.(499-501)TAC>CAC	p.Y167H		NM_000531	NP_000522	P00480	OTC_HUMAN	ornithine carbamoyltransferase precursor	167					arginine biosynthetic process|urea cycle	mitochondrial matrix|ornithine carbamoyltransferase complex	ornithine carbamoyltransferase activity			ovary(1)|breast(1)	2					L-Citrulline(DB00155)|L-Ornithine(DB00129)	GTCAGATTTGTACCATCCTAT	0.408													5	509	---	---	---	---	PASS
USP9X	8239	broad.mit.edu	37	X	40996073	40996073	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40996073A>G	uc004dfb.2	+	6	1085	c.452A>G	c.(451-453)AAT>AGT	p.N151S	USP9X_uc004dfc.2_Missense_Mutation_p.N151S	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	151				Missing (in Ref. 1; CAA66942).	BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						ATTATTAACAATACTCATCGT	0.388													12	481	---	---	---	---	PASS
IGBP1	3476	broad.mit.edu	37	X	69385728	69385728	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69385728A>G	uc004dxv.2	+	6	1416	c.917A>G	c.(916-918)AAG>AGG	p.K306R	IGBP1_uc004dxw.2_Missense_Mutation_p.K306R	NM_001551	NP_001542	P78318	IGBP1_HUMAN	immunoglobulin binding protein 1	306					B cell activation|negative regulation of caspase activity|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|regulation of microtubule-based movement|response to interleukin-1|response to tumor necrosis factor|signal transduction	cytoplasm	protein phosphatase type 2A regulator activity			kidney(1)|pancreas(1)	2						CAAGAAGAAAAGGAGGAAGAG	0.463													6	400	---	---	---	---	PASS
HDX	139324	broad.mit.edu	37	X	83723772	83723772	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83723772A>G	uc004eek.1	-	3	1068	c.959T>C	c.(958-960)ATA>ACA	p.I320T	HDX_uc011mqv.1_Missense_Mutation_p.I320T|HDX_uc004eel.1_Missense_Mutation_p.I262T	NM_144657	NP_653258	Q7Z353	HDX_HUMAN	highly divergent homeobox	320						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2						ATAGCTTGGTATCTGTGCTCT	0.458													4	154	---	---	---	---	PASS
DIAPH2	1730	broad.mit.edu	37	X	96194327	96194327	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96194327A>G	uc004efu.3	+	12	1667	c.1271A>G	c.(1270-1272)TAC>TGC	p.Y424C	DIAPH2_uc004eft.3_Missense_Mutation_p.Y424C	NM_006729	NP_006720	O60879	DIAP2_HUMAN	diaphanous 2 isoform 156	424	GBD/FH3.				cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4						GCTGAAAATTACTTCTTATCT	0.299													5	365	---	---	---	---	PASS
PRPS1	5631	broad.mit.edu	37	X	106885678	106885678	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106885678G>A	uc004ene.3	+	4	693	c.488G>A	c.(487-489)AGG>AAG	p.R163K	PRPS1_uc010npg.2_Missense_Mutation_p.R130K|PRPS1_uc011msj.1_Intron	NM_002764	NP_002755	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	163					5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process	cytosol	ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			breast(3)|large_intestine(1)	4						TCTGAGTGGAGGAACTGCACT	0.433													112	278	---	---	---	---	PASS
ACSL4	2182	broad.mit.edu	37	X	108904802	108904802	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108904802T>C	uc004eoi.2	-	15	2283	c.1778A>G	c.(1777-1779)AAG>AGG	p.K593R	ACSL4_uc004eoj.2_Missense_Mutation_p.K552R|ACSL4_uc004eok.2_Missense_Mutation_p.K552R	NM_022977	NP_075266	O60488	ACSL4_HUMAN	acyl-CoA synthetase long-chain family member 4	593	Cytoplasmic (Potential).				fatty acid metabolic process|learning or memory|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			large_intestine(1)|lung(1)|ovary(1)	3					Icosapent(DB00159)|Troglitazone(DB00197)	TGGACAATTCTTCAGTGCAGC	0.328													6	388	---	---	---	---	PASS
BCORL1	63035	broad.mit.edu	37	X	129147106	129147106	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129147106G>T	uc004evb.1	+	4	472	c.358G>T	c.(358-360)GAC>TAC	p.D120Y	BCORL1_uc010nrd.1_Missense_Mutation_p.D22Y	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	120					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7						CAGCCCAGGAGACGGGCTCAA	0.597													11	21	---	---	---	---	PASS
ARHGAP36	158763	broad.mit.edu	37	X	130219622	130219622	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130219622G>A	uc004evz.2	+	8	1361	c.1016G>A	c.(1015-1017)TGC>TAC	p.C339Y	ARHGAP36_uc004ewa.2_Missense_Mutation_p.C327Y|ARHGAP36_uc004ewb.2_Missense_Mutation_p.C308Y|ARHGAP36_uc004ewc.2_Missense_Mutation_p.C203Y	NM_144967	NP_659404	Q6ZRI8	RHG36_HUMAN	hypothetical protein LOC158763 precursor	339	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3						ATGCCACCCTGCCACAGTGAT	0.512													7	314	---	---	---	---	PASS
GPC3	2719	broad.mit.edu	37	X	132887952	132887952	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132887952A>T	uc004exe.1	-	3	779	c.589T>A	c.(589-591)TGC>AGC	p.C197S	GPC3_uc004exd.1_Missense_Mutation_p.C69S|GPC3_uc010nrn.1_Missense_Mutation_p.C197S|GPC3_uc011mvh.1_Missense_Mutation_p.C181S|GPC3_uc010nro.1_Missense_Mutation_p.C143S|GPC3_uc010nrp.1_Missense_Mutation_p.C69S	NM_004484	NP_004475	P51654	GPC3_HUMAN	glypican 3 isoform 2 precursor	197						extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)					CCTCGGAGGCACTCATTGATG	0.468			T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				10	844	---	---	---	---	PASS
ZNF75D	7626	broad.mit.edu	37	X	134428150	134428150	+	5'UTR	SNP	G	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134428150G>A	uc004eyp.2	-	3					ZNF75D_uc004eym.2_Intron|ZNF75D_uc004eyn.2_5'Flank|ZNF75D_uc004eyo.2_5'UTR	NM_007131	NP_009062	P51815	ZN75D_HUMAN	zinc finger protein 75						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GCATCAGGTTGGTACCAAATC	0.423													16	58	---	---	---	---	PASS
TKTL1	8277	broad.mit.edu	37	X	153524197	153524197	+	5'UTR	SNP	C	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153524197C>T	uc004fkg.2	+	1					TEX28_uc004fke.2_5'Flank|TEX28_uc004fkf.2_5'Flank|TEX28_uc010nut.1_5'Flank|TKTL1_uc011mzl.1_5'UTR|TKTL1_uc011mzm.1_5'UTR	NM_012253	NP_036385	P51854	TKTL1_HUMAN	transketolase-like 1 isoform a						glucose catabolic process|thiamine metabolic process	cytoplasm|nucleus	metal ion binding|transketolase activity			ovary(3)|skin(1)	4	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTTCAGACTCCAAAGGGGTTG	0.612											OREG0003591	type=REGULATORY REGION|Gene=TKTL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	22	98	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	1437235	1437235	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1437235delT								ATAD3B (5654 upstream) : ATAD3A (10320 downstream)																							TTTGGGTAAgtttttttttgt	0.169													4	2	---	---	---	---	
MEGF6	1953	broad.mit.edu	37	1	3405820	3405822	+	3'UTR	DEL	CTC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3405820_3405822delCTC	uc001akl.2	-	37					MEGF6_uc001akk.2_3'UTR	NM_001409	NP_001400	O75095	MEGF6_HUMAN	EGF-like-domain, multiple 3 precursor							extracellular region	calcium ion binding			large_intestine(1)	1	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GCTCACTGGACTCCTCCTCCTCC	0.567													4	2	---	---	---	---	
DFFA	1676	broad.mit.edu	37	1	10529587	10529587	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10529587delT	uc001arj.2	-						DFFA_uc001ark.2_Intron	NM_004401	NP_004392	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha						DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction|negative regulation of apoptosis	cytosol|mitochondrion|nucleoplasm|plasma membrane	deoxyribonuclease activity|identical protein binding				0	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		tgttcttttctttttttttgt	0.119													4	2	---	---	---	---	
SPEN	23013	broad.mit.edu	37	1	16249125	16249126	+	Intron	INS	-	T	T	rs147564648	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16249125_16249126insT	uc001axk.1	+						SPEN_uc010obp.1_Intron	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator						interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		ACTTTATGTACttttttttttg	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18323817	18323817	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18323817delG								ACTL8 (170261 upstream) : IGSF21 (110423 downstream)																							GTGCAAAGCTGGATGCTCAAC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	19889966	19889967	+	IGR	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19889966_19889967insC								CAPZB (77974 upstream) : C1orf151 (33500 downstream)																							TGGTGTTCTCTCCCCTGGGGAT	0.569													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	23817637	23817638	+	IGR	INS	-	C	C	rs145500078		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23817637_23817638insC								ASAP3 (6580 upstream) : E2F2 (15284 downstream)																							tcactcccttgggattccaccc	0.000													2	4	---	---	---	---	
HMGCL	3155	broad.mit.edu	37	1	24131718	24131718	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24131718delC	uc001bib.2	-						HMGCL_uc010oec.1_Intron|HMGCL_uc009vqr.2_Intron|HMGCL_uc001bic.2_Intron|HMGCL_uc009vqs.1_Intron	NM_000191	NP_000182	P35914	HMGCL_HUMAN	3-hydroxy-3-methylglutaryl CoA lyase isoform 1						acetoacetic acid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA lyase activity|metal ion binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		gaggcccattcccacctgctt	0.000													4	2	---	---	---	---	
SDC3	9672	broad.mit.edu	37	1	31349273	31349273	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31349273delC	uc001bse.2	-						SDC3_uc001bsd.2_Intron	NM_014654	NP_055469	O75056	SDC3_HUMAN	syndecan 3							integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		CTGCCCCTCGCCCCCACTTTG	0.612													4	2	---	---	---	---	
CSMD2	114784	broad.mit.edu	37	1	34612400	34612400	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34612400delG	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				taaagtttctgggggtgggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35705119	35705119	+	IGR	DEL	T	-	-	rs72347875		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35705119delT								SFPQ (46376 upstream) : ZMYM4 (29449 downstream)																							atccagctaattttttttttt	0.000													4	2	---	---	---	---	
GRIK3	2899	broad.mit.edu	37	1	37314754	37314754	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37314754delT	uc001caz.2	-						GRIK3_uc001cba.1_Intron	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3						negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)	GGAAGAATGGTTTTTTCCCCA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	39525533	39525534	+	IGR	INS	-	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39525533_39525534insG								NDUFS5 (25247 upstream) : MACF1 (21584 downstream)																							TGAATGCTGCTGAAAAAAAAAA	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	42549594	42549594	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42549594delG								HIVEP3 (47998 upstream) : GUCA2B (69498 downstream)																							atcctgctctggggttttttg	0.000													4	2	---	---	---	---	
ZSWIM5	57643	broad.mit.edu	37	1	45486714	45486714	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45486714delT	uc001cnd.2	-							NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM domain containing 5								zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)					CTCAGGATCCttttttttttt	0.244													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	46892333	46892333	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46892333delT								FAAH (12813 upstream) : DMBX1 (80335 downstream)																							TTAAATTACATTTTTTTTGTT	0.294													5	3	---	---	---	---	
NFIA	4774	broad.mit.edu	37	1	61657127	61657127	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61657127delT	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145	Q12857	NFIA_HUMAN	nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2						TCTAGCCTGGTTTTTTTTTGC	0.468													4	2	---	---	---	---	
PDE4B	5142	broad.mit.edu	37	1	66714170	66714170	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66714170delG	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron|PDE4B_uc001dcp.2_Intron	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1						signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)	TCTGGTGAAAGGGGGAATTTT	0.408													4	2	---	---	---	---	
PDE4B	5142	broad.mit.edu	37	1	66714192	66714193	+	Intron	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66714192_66714193insA	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron|PDE4B_uc001dcp.2_Intron	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1						signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)	AAGCTACCAGCAAAAAAATATT	0.406													4	2	---	---	---	---	
ANKRD13C	81573	broad.mit.edu	37	1	70740157	70740159	+	Intron	DEL	AAA	-	-	rs71864752		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70740157_70740159delAAA	uc001dex.3	-						ANKRD13C_uc009wbk.2_Intron	NM_030816	NP_110443	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C						protein retention in ER lumen|regulation of anoikis|regulation of receptor biosynthetic process	endoplasmic reticulum membrane|perinuclear region of cytoplasm	receptor binding				0						actccatctcaaaaaaaaaaaaa	0.103													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	71837820	71837820	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71837820delC								ZRANB2 (291075 upstream) : NEGR1 (30806 downstream)																							GGTATGAAAACTTTTTCTATT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	73234571	73234571	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73234571delT								NEGR1 (486166 upstream) : None (None downstream)																							cattgttgcctggatccatca	0.000													4	2	---	---	---	---	
PIGK	10026	broad.mit.edu	37	1	77621198	77621199	+	Intron	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77621198_77621199insA	uc001dhk.2	-						PIGK_uc010orj.1_Intron|PIGK_uc009wbx.2_Intron|PIGK_uc001dhl.1_Intron	NM_005482	NP_005473	Q92643	GPI8_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|protein thiol-disulfide exchange|proteolysis	GPI-anchor transamidase complex	cysteine-type endopeptidase activity|GPI-anchor transamidase activity|protein binding			ovary(2)|pancreas(1)	3						taacaaggtagaaaaaaatgat	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	79657136	79657136	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79657136delT								ELTD1 (184641 upstream) : None (None downstream)																							TCTTCAACTATTTTTATCCCA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	85162970	85162971	+	IGR	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85162970_85162971insT								SSX2IP (6530 upstream) : LPAR3 (116115 downstream)																							aagactgattcttttttttaat	0.079													4	2	---	---	---	---	
ABCA4	24	broad.mit.edu	37	1	94496895	94496896	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94496895_94496896insT	uc001dqh.2	-							NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4						phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TGAAGAATCTGAATGCAGCCCA	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96392082	96392083	+	IGR	DEL	AG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96392082_96392083delAG								RWDD3 (679309 upstream) : PTBP2 (795092 downstream)																							GGTTGTGGGAAGAGAGAGAGAG	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	108596202	108596202	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108596202delA								VAV3 (88657 upstream) : SLC25A24 (81247 downstream)																							gtcaggcgctaaaatgcacaa	0.000													4	2	---	---	---	---	
SLC16A4	9122	broad.mit.edu	37	1	110929901	110929902	+	Intron	DEL	AC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110929901_110929902delAC	uc001dzo.1	-						SLC16A4_uc009wfs.1_Intron|SLC16A4_uc001dzp.1_Intron|SLC16A4_uc010ovy.1_Intron|SLC16A4_uc001dzq.1_Intron|SLC16A4_uc010ovz.1_Intron	NM_004696	NP_004687	O15374	MOT5_HUMAN	solute carrier family 16, member 4							integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			ovary(3)	3		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	gtctagtaagacagactgaata	0.084													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	118252630	118252630	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118252630delC								FAM46C (81620 upstream) : GDAP2 (153478 downstream)																							CAGGTGGGCTCCAGAAGTAAC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120149764	120149764	+	IGR	DEL	A	-	-	rs79524356		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120149764delA								HSD3B1 (92083 upstream) : ZNF697 (12236 downstream)																							GCACCATCTCAAAAAAAAAAA	0.428													5	4	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120540271	120540274	+	Intron	DEL	CTCA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120540271_120540274delCTCA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCTCTCAGAGCTCACTGTCTTTGC	0.348			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				2	4	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144675428	144675428	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144675428delC	uc009wig.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF9_uc009wii.1_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						tattgcaaagcttcttaaatg	0.080													5	4	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144929756	144929756	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144929756delT	uc001elw.3	-						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_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_Intron|PDE4DIP_uc001emf.1_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)		ATTTAAAAGGTTGGTACAGAA	0.338			T	PDGFRB	MPD								4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145012806	145012806	+	Intron	DEL	T	-	-	rs58323921		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145012806delT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron|uc001emj.2_5'Flank	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)		CCAACATAAATGATAATTGTC	0.343			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145087540	145087540	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145087540delA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						gtggaacattaaaaaaaatta	0.000													4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145481022	145481023	+	Intron	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145481022_145481023insC	uc001emp.3	+						LIX1L_uc001enr.2_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		tttttttttttttaagaaatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148898510	148898510	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148898510delG	uc009wkv.1	+											Homo sapiens cDNA, FLJ17483.																		tttaccccatgttttttttat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152933594	152933595	+	IGR	DEL	AC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152933594_152933595delAC								IVL (49233 upstream) : SPRR4 (9533 downstream)																							acacacacaaacacacacacac	0.450													4	2	---	---	---	---	
SPRR2D	6703	broad.mit.edu	37	1	153047323	153047323	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153047323delT	uc009wnz.2	-						SPRR2A_uc001fbf.2_Intron|SPRR2A_uc009woa.2_Intron			P22532	SPR2D_HUMAN	Homo sapiens cDNA FLJ76407 complete cds, highly similar to Homo sapiens small proline-rich protein 2D (SPRR2D), mRNA.						keratinization	cornified envelope|cytoplasm					0	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GATAATGGTCTTTTTTATTTT	0.348													4	2	---	---	---	---	
C1orf77	26097	broad.mit.edu	37	1	153616229	153616230	+	Intron	DEL	AG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153616229_153616230delAG	uc001fcm.1	+						C1orf77_uc001fcn.1_Intron|C1orf77_uc001fco.1_Intron|C1orf77_uc001fcp.2_RNA	NM_015607	NP_056422	Q9Y3Y2	CHTOP_HUMAN	small protein rich in arginine and glycine						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	protein binding|RNA binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGAATATAGAAGAGAGAGAGAG	0.455													4	2	---	---	---	---	
ARHGEF2	9181	broad.mit.edu	37	1	155933136	155933137	+	Intron	DEL	TT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155933136_155933137delTT	uc001fmt.2	-						ARHGEF2_uc001fmr.2_Intron|ARHGEF2_uc001fms.2_Intron|ARHGEF2_uc001fmu.2_Intron|ARHGEF2_uc010pgt.1_Intron|ARHGEF2_uc010pgu.1_Intron	NM_001162383	NP_001155855	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor 2						actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CAtttttatctttttttttttt	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	156413173	156413173	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156413173delT								C1orf61 (12680 upstream) : MEF2D (20347 downstream)																							CACTGATGCCTGCTAAAATAG	0.468													4	2	---	---	---	---	
COPA	1314	broad.mit.edu	37	1	160281537	160281537	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160281537delA	uc009wti.2	-						COPA_uc001fvv.3_Intron|COPA_uc009wtj.1_Intron	NM_004371	NP_004362	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha isoform						COPI coating of Golgi vesicle|intracellular protein transport|pancreatic juice secretion|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|extracellular space|microsome|soluble fraction	hormone activity|structural molecule activity			ovary(1)|skin(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			actccgtctcaaaaaaaaatt	0.149													5	3	---	---	---	---	
FCGR2A	2212	broad.mit.edu	37	1	161491291	161491292	+	Intron	INS	-	TA	TA	rs146780320	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161491291_161491292insTA	uc001gao.2	+						HSPA6_uc001gap.2_5'Flank|HSPA6_uc001gaq.2_5'Flank			P12318	FCG2A_HUMAN	Homo sapiens mRNA for Low affinity immunoglobulin gamma Fc region receptor II-a precursor variant, clone: HRT01864.							integral to membrane|plasma membrane	IgG binding|receptor activity			ovary(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		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)	tcaCTGACTTTTATATATATAT	0.054													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165118627	165118627	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165118627delA								PBX1 (264327 upstream) : LMX1A (52478 downstream)																							attacctgctaagggctattt	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168363172	168363172	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168363172delA								MIR557 (18313 upstream) : XCL2 (146833 downstream)																							TGAGAGCTGGAGAGAGGCAGA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	173306025	173306025	+	Intron	DEL	A	-	-	rs35057866		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173306025delA	uc001gix.1	-											Homo sapiens cDNA FLJ45305 fis, clone BRHIP3004193.																		tcctaccaccaaaaaaaaagg	0.000													3	4	---	---	---	---	
ASTN1	460	broad.mit.edu	37	1	177002844	177002844	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177002844delG	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron|ASTN1_uc009wwx.1_Intron|ASTN1_uc001gle.3_5'Flank	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15						CCCAAGTCCTGGAGTCAGGCT	0.507													4	2	---	---	---	---	
KIAA1614	57710	broad.mit.edu	37	1	180911094	180911094	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180911094delC	uc001gok.2	+						KIAA1614_uc001gol.1_Intron|KIAA1614_uc001gom.1_Intron	NM_020950	NP_066001	Q5VZ46	K1614_HUMAN	hypothetical protein LOC57710											ovary(3)|skin(1)	4						ctcccaccttccccacctgca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181105874	181105875	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181105874_181105875delCA								IER5 (45897 upstream) : CACNA1E (346841 downstream)																							agacatacgccacacacacaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	201539658	201539658	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201539658delG								RPS10P7 (40056 upstream) : NAV1 (77792 downstream)																							CCTCAGGGCTGGGTGTGGTGA	0.537													4	2	---	---	---	---	
PPP1R12B	4660	broad.mit.edu	37	1	202436349	202436349	+	Intron	DEL	T	-	-	rs76794254		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202436349delT	uc001gya.1	+						PPP1R12B_uc001gxz.1_Intron|PPP1R12B_uc001gyb.1_Intron|PPP1R12B_uc001gyc.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)			TGTCTCTCTCTTTtttttttt	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	203842788	203842788	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203842788delC								SNRPE (2510 upstream) : C1orf157 (158787 downstream)																							TTCTTGAAGTCCTCCAGCAGC	0.473													4	2	---	---	---	---	
FAIM3	9214	broad.mit.edu	37	1	207097689	207097690	+	5'Flank	INS	-	GT	GT	rs141836464		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207097689_207097690insGT	uc001hey.2	-						FAIM3_uc010prz.1_5'Flank|FAIM3_uc010psa.1_5'Flank|FAIM3_uc010psb.1_5'Flank	NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)					tgtggctatgagtgtgtgtgct	0.000													4	2	---	---	---	---	
TRAF5	7188	broad.mit.edu	37	1	211509321	211509321	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211509321delT	uc001hih.2	+						TRAF5_uc001hii.2_Intron|TRAF5_uc010psx.1_Intron|TRAF5_uc010psy.1_Intron	NM_004619	NP_004610	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis	CD40 receptor complex|centrosome|internal side of plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(2)|ovary(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		atgatctctgtttttttttgc	0.060													4	2	---	---	---	---	
TRAF5	7188	broad.mit.edu	37	1	211543164	211543165	+	Intron	INS	-	TG	TG	rs139123011	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211543164_211543165insTG	uc001hih.2	+						TRAF5_uc001hii.2_Intron|TRAF5_uc010psx.1_Intron|TRAF5_uc010psy.1_Intron|TRAF5_uc001hij.2_Intron	NM_004619	NP_004610	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis	CD40 receptor complex|centrosome|internal side of plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(2)|ovary(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		cccgacgtgtatgtgtgtgtgt	0.000													3	3	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	215861094	215861094	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215861094delG	uc001hku.1	-							NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		tggaaatagtggcaaaactgt	0.085										HNSCC(13;0.011)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228967705	228967705	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228967705delA								RHOU (85296 upstream) : RAB4A (439174 downstream)																							AACTGAGGGTATTTGAACCCT	0.438													4	2	---	---	---	---	
GALNT2	2590	broad.mit.edu	37	1	230259034	230259035	+	Intron	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230259034_230259035insC	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				gttagctgtttccaaaaaacaa	0.000													4	2	---	---	---	---	
CAPN9	10753	broad.mit.edu	37	1	230936746	230936746	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230936746delA	uc001htz.1	+						CAPN9_uc009xfg.1_Intron|CAPN9_uc001hua.1_Intron	NM_006615	NP_006606	O14815	CAN9_HUMAN	calpain 9 isoform 1						digestion|proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				GAGAAGGGAGAAAAAAACCAT	0.463													4	2	---	---	---	---	
C1orf131	128061	broad.mit.edu	37	1	231370632	231370632	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231370632delC	uc001hun.1	-						C1orf131_uc001hul.2_Intron|C1orf131_uc001hum.2_Intron|C1orf131_uc010pwd.1_Intron	NM_152379	NP_689592	Q8NDD1	CA131_HUMAN	hypothetical protein LOC128061											central_nervous_system(1)|skin(1)	2	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				ctcttccctgccccattcacc	0.000													4	2	---	---	---	---	
NID1	4811	broad.mit.edu	37	1	236177521	236177522	+	Intron	DEL	CT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236177521_236177522delCT	uc001hxo.2	-						NID1_uc009xgd.2_Intron|NID1_uc009xgc.2_5'Flank	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor						cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	ACCCCCTCAACTCTCTCTCTCT	0.455													4	2	---	---	---	---	
GPR137B	7107	broad.mit.edu	37	1	236317683	236317683	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236317683delC	uc001hxq.2	+							NM_003272	NP_003263	O60478	G137B_HUMAN	G protein-coupled receptor 137B							integral to plasma membrane|membrane fraction					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			attgtgtcttccccgagttct	0.035													4	2	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237560202	237560202	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237560202delA	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			gttttaagggaaaaaaaatca	0.000													4	2	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237741601	237741601	+	Intron	DEL	A	-	-	rs80110961		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237741601delA	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TTTAGCACAGAAAAAAAAATG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238226680	238226680	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238226680delT								LOC100130331 (135063 upstream) : LOC339535 (417006 downstream)																							GAGACTGGCCTTTACTGGTGC	0.512													4	2	---	---	---	---	
CHRM3	1131	broad.mit.edu	37	1	239620181	239620181	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239620181delA	uc001hyo.1	+									P20309	ACM3_HUMAN	Homo sapiens clone N10 NTera2D1 teratocarcinoma, m3 muscarinic acetylcholine receptor mRNA, partial cds.						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)	GTACTGACCCAAGTATAAAAA	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	242855484	242855485	+	IGR	INS	-	AC	AC	rs147261190	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242855484_242855485insAC								PLD5 (167486 upstream) : CEP170 (432246 downstream)																							GCTCTGTTTAGacacacacaca	0.361													3	3	---	---	---	---	
TSSC1	7260	broad.mit.edu	37	2	3365246	3365246	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3365246delA	uc002qxj.2	-							NM_003310	NP_003301	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		TTCTCCTTGGAaaaaaaaaaa	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6342389	6342389	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6342389delT								LOC400940 (214025 upstream) : CMPK2 (638114 downstream)																							TTTTTCTCTGTTTTTAATTAT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	13069785	13069786	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13069785_13069786insA								TRIB2 (186929 upstream) : None (None downstream)																							taaaagtacttaaaaaaaaaca	0.094													4	2	---	---	---	---	
MATN3	4148	broad.mit.edu	37	2	20207632	20207633	+	Intron	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20207632_20207633insC	uc002rdl.2	-						MATN3_uc010exu.1_Intron	NM_002381	NP_002372	O15232	MATN3_HUMAN	matrilin 3 precursor						skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTTCCTGTTTCCCCCAACCCC	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23535054	23535054	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23535054delC								None (None upstream) : KLHL29 (220401 downstream)																							aaggccatgtccccaggagga	0.000													4	2	---	---	---	---	
LCLAT1	253558	broad.mit.edu	37	2	30812681	30812681	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30812681delT	uc002rnj.2	+						LCLAT1_uc010ymp.1_Intron|LCLAT1_uc002rnk.1_Intron|LCLAT1_uc002rnl.2_Intron|LCLAT1_uc010ymq.1_Intron	NM_182551	NP_872357	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1 isoform 1						multicellular organismal development|phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity			ovary(2)	2						AATCTTTTAGTTCGTTTTCTT	0.338													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35120508	35120508	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35120508delG								None (None upstream) : None (None downstream)																							TGGCTAATATGACATCACAAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35945233	35945238	+	IGR	DEL	AACAGT	-	-	rs146327237		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35945233_35945238delAACAGT								None (None upstream) : CRIM1 (638159 downstream)																							GATGAGAGTAAACAGTAAGTTCTGAG	0.398													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	36204827	36204828	+	IGR	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36204827_36204828insT								None (None upstream) : CRIM1 (378569 downstream)																							agccatagcggttttttttttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	41559554	41559554	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41559554delT								SLC8A1 (819979 upstream) : PKDCC (715607 downstream)																							AGGAAATTAGTTTTTACTACA	0.328													4	2	---	---	---	---	
NRXN1	9378	broad.mit.edu	37	2	50264378	50264378	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50264378delT	uc010fbp.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TCCTTTGTTCTTTTTTTTAAG	0.249													4	2	---	---	---	---	
NRXN1	9378	broad.mit.edu	37	2	50960546	50960547	+	Intron	DEL	GA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50960546_50960547delGA	uc010fbq.2	-						NRXN1_uc002rxe.3_Intron	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TAGCAAATGGGAGAAAACAAAA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	52807610	52807612	+	IGR	DEL	GCT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:52807610_52807612delGCT								None (None upstream) : None (None downstream)																							aagcagagtagctgctgctgcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	56251249	56251249	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56251249delT	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																		ctttgtagcatttttttgcta	0.000													4	2	---	---	---	---	
COMMD1	150684	broad.mit.edu	37	2	62147630	62147630	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62147630delA	uc002sbp.2	+							NM_152516	NP_689729	Q8N668	COMD1_HUMAN	MURR1						copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			GTGTTCCTCTAAAAAAGGCTA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64714272	64714272	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64714272delG								HSPC159 (25761 upstream) : AFTPH (37193 downstream)																							GGGTGACTGTGGACAGTAGCA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65368667	65368668	+	IGR	DEL	AG	-	-	rs145512482	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65368667_65368668delAG								RAB1A (11232 upstream) : ACTR2 (86161 downstream)																							tctcaaaaaaagaaaaaaagaa	0.149													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65405346	65405346	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65405346delC								RAB1A (47911 upstream) : ACTR2 (49483 downstream)																							agtgtatttgcccacgaaacc	0.224													4	2	---	---	---	---	
ANTXR1	84168	broad.mit.edu	37	2	69459115	69459117	+	Intron	DEL	ACC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69459115_69459117delACC	uc002sfg.2	+							NM_032208	NP_115584	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1 isoform 1 precursor						actin cytoskeleton reorganization|substrate adhesion-dependent cell spreading	filopodium membrane|integral to membrane|lamellipodium membrane	actin filament binding|collagen binding|metal ion binding|protein binding|transmembrane receptor activity			ovary(2)|skin(2)	4						cagataagctaccacCACCACAA	0.246									Familial_Infantile_Hemangioma				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82993989	82993989	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82993989delA								None (None upstream) : None (None downstream)																							cacaagtcttaaaaaaaaaat	0.000													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87906045	87906046	+	Intron	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87906045_87906046insC	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						CATCGATAGTACTTTTTCTGCT	0.312													4	2	---	---	---	---	
KIAA1310	55683	broad.mit.edu	37	2	97266544	97266544	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97266544delA	uc002swn.3	-						KIAA1310_uc002swh.3_Intron|KIAA1310_uc002swi.3_Intron|KIAA1310_uc002swj.3_Intron|KIAA1310_uc002swk.3_Intron|KIAA1310_uc010fhz.2_Intron|KIAA1310_uc002swl.3_Intron|KIAA1310_uc002swm.3_Intron|KIAA1310_uc010yur.1_Intron|KIAA1310_uc002swo.2_3'UTR	NM_001115016	NP_001108488	Q9P2N6	K1310_HUMAN	hypothetical protein LOC55683 isoform a												0						TGAGACCTATAAAAACCTAGC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108183532	108183532	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108183532delG								ST6GAL2 (679969 upstream) : LOC729121 (255988 downstream)																							agtgttgagaggaagcaccaa	0.000													4	2	---	---	---	---	
ACOXL	55289	broad.mit.edu	37	2	111846439	111846439	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111846439delA	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0						AAATTCTACGAAAGACTATTC	0.254													4	2	---	---	---	---	
CKAP2L	150468	broad.mit.edu	37	2	113519126	113519127	+	Intron	INS	-	AA	AA			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113519126_113519127insAA	uc002tie.2	-						CKAP2L_uc002tif.2_Intron|CKAP2L_uc010yxp.1_Intron|CKAP2L_uc010yxq.1_Intron	NM_152515	NP_689728	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like							centrosome					0						AAAGAAATATTAAAAAAAAAAA	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114073499	114073501	+	IGR	DEL	GAA	-	-	rs148115547		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114073499_114073501delGAA								PAX8 (37001 upstream) : CBWD2 (121767 downstream)																							ggcaaagagggaagaaggacaag	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119511962	119511963	+	IGR	DEL	AG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119511962_119511963delAG								INSIG2 (644366 upstream) : EN1 (87785 downstream)																							AACATTCCTTAGAACAGCTCTC	0.520													4	2	---	---	---	---	
STEAP3	55240	broad.mit.edu	37	2	120011044	120011045	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120011044_120011045insT	uc002tlp.2	+						STEAP3_uc002tlq.2_Intron|STEAP3_uc002tlr.2_Intron|STEAP3_uc010fle.2_Intron	NM_018234	NP_060704	Q658P3	STEA3_HUMAN	dudulin 2 isoform b						apoptosis|cell cycle|cellular iron ion homeostasis|protein secretion|transferrin transport|transmembrane transport	endosome membrane|integral to membrane|multivesicular body	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			central_nervous_system(2)|skin(1)	3						CTGAGCTCGTGTTTTTTTTTTT	0.287													3	3	---	---	---	---	
EPB41L5	57669	broad.mit.edu	37	2	120793504	120793505	+	Intron	DEL	GT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120793504_120793505delGT	uc002tmg.2	+						EPB41L5_uc010flk.2_Intron|EPB41L5_uc010fll.2_Intron|EPB41L5_uc002tmh.3_Intron	NM_020909	NP_065960	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1						TGATACTGGAGTGTGTGTGTGG	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126247658	126247658	+	IGR	DEL	A	-	-	rs11303468		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126247658delA								CNTNAP5 (574797 upstream) : None (None downstream)																							agataaagtgaaaaaaaaaaa	0.219													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	127649652	127649653	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127649652_127649653insA								GYPC (195407 upstream) : BIN1 (155954 downstream)																							ACAGCAGCCCCACCTGTCACAG	0.554													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130893081	130893081	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130893081delA								POTEF (6286 upstream) : CCDC74B (3781 downstream)																							actccatctcaaaaaaaaaaa	0.259													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133021070	133021071	+	IGR	INS	-	A	A	rs148734070		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133021070_133021071insA								NCRNA00164 (5528 upstream) : GPR39 (153076 downstream)																							TTGGATAATAGAAAAAAACACT	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134625398	134625398	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134625398delT								NCKAP5 (299367 upstream) : MGAT5 (386432 downstream)																							aactaaaggctcaagtaagtt	0.030													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	137195307	137195308	+	IGR	DEL	CC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137195307_137195308delCC								CXCR4 (319582 upstream) : THSD7B (327807 downstream)																							GGCTAGCTTTCCCTCAGGGTCT	0.550													4	2	---	---	---	---	
ARHGAP15	55843	broad.mit.edu	37	2	143910478	143910479	+	Intron	INS	-	AG	AG			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143910478_143910479insAG	uc002tvm.3	+						ARHGAP15_uc010zbl.1_Intron	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)		AACATTGTGGTAGAGAGAGAGA	0.431													4	2	---	---	---	---	
KIF5C	3800	broad.mit.edu	37	2	149864251	149864252	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149864251_149864252insT	uc010zbu.1	+						KIF5C_uc002tws.1_Intron|KIF5C_uc002twu.1_Intron	NM_004522	NP_004513	O60282	KIF5C_HUMAN	kinesin family member 5C						microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)		ATTTGAAGGAGTTTTTTTTTTT	0.302													4	2	---	---	---	---	
FMNL2	114793	broad.mit.edu	37	2	153481699	153481699	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153481699delA	uc002tye.2	+						FMNL2_uc010fob.2_Intron|FMNL2_uc002tyf.2_Intron	NM_052905	NP_443137	Q96PY5	FMNL2_HUMAN	formin-like 2						actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3						GAGTTAAAAGAAAAAAAAAAA	0.368													6	3	---	---	---	---	
KCNH7	90134	broad.mit.edu	37	2	163601892	163601893	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163601892_163601893insT	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	TACCTGAAGGCTTTTTTTTTAA	0.332													4	2	---	---	---	---	
ABCB11	8647	broad.mit.edu	37	2	169852273	169852274	+	Intron	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169852273_169852274insC	uc002ueo.1	-							NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),						bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)	agcttcactttccccatgtgtg	0.173													4	2	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171210781	171210781	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171210781delT	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002uga.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						TTCTGGTTCCTTTTTTTTGTT	0.388													4	2	---	---	---	---	
DCAF17	80067	broad.mit.edu	37	2	172305520	172305520	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172305520delT	uc002ugx.2	+						DCAF17_uc010zdq.1_Intron|DCAF17_uc010fqf.1_Intron|DCAF17_uc010zdr.1_Intron	NM_025000	NP_079276	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17 isoform 1							CUL4 RING ubiquitin ligase complex|integral to membrane|nucleolus					0						ATCAtttgtcttttttttttc	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174894714	174894715	+	IGR	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174894714_174894715insT								SP3 (64651 upstream) : OLA1 (42461 downstream)																							AAGTCGTGGTCTTTTTTTTGGT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	176526767	176526767	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176526767delA								ATP5G3 (480277 upstream) : KIAA1715 (263643 downstream)																							TTTTCCACCTAAAAAGCAGGT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	184352213	184352213	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184352213delA								NUP35 (325806 upstream) : None (None downstream)																							AAGTATGCCTAAAATAGAGTG	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	186218702	186218703	+	IGR	DEL	CT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186218702_186218703delCT								ZNF804A (414490 upstream) : None (None downstream)																							cacacacacactctctctctct	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	187724106	187724106	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187724106delT								ZSWIM2 (10209 upstream) : CALCRL (483745 downstream)																							AGAAACGGAGTTAAGATTTGA	0.249													4	2	---	---	---	---	
GULP1	51454	broad.mit.edu	37	2	189235595	189235596	+	Intron	DEL	TG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189235595_189235596delTG	uc010fru.2	+						GULP1_uc002uqc.3_Intron|GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqe.2_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron	NM_016315	NP_057399	Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			CATGTGTGTATGTGTGTGTGTG	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	193979185	193979185	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193979185delA								PCGEM1 (337564 upstream) : None (None downstream)																							tatttacaagaaaaaaaaaca	0.005													4	2	---	---	---	---	
ANKRD44	91526	broad.mit.edu	37	2	197888297	197888297	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197888297delA	uc002uua.1	-						ANKRD44_uc002utz.3_Intron	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TACACTGTGGAAAAAAAAAAG	0.408													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	200691870	200691870	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200691870delA	uc002uvg.2	-											Homo sapiens hypothetical protein LOC348751, mRNA (cDNA clone IMAGE:5311172).																		aattcctgccaaaaaaattaa	0.025													4	2	---	---	---	---	
MAP2	4133	broad.mit.edu	37	2	210574397	210574397	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210574397delA	uc002vde.1	+						MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Intron	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	AACAAATCAGAAAAAAAAAAT	0.209													5	3	---	---	---	---	
ACADL	33	broad.mit.edu	37	2	211053947	211053948	+	Intron	INS	-	A	A	rs141418871	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211053947_211053948insA	uc002vdz.3	-							NM_001608	NP_001599	P28330	ACADL_HUMAN	long-chain acyl-CoA dehydrogenase precursor						carnitine catabolic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|negative regulation of fatty acid biosynthetic process|negative regulation of fatty acid oxidation|regulation of cholesterol metabolic process|temperature homeostasis	mitochondrial matrix	long-chain-acyl-CoA dehydrogenase activity|palmitoyl-CoA oxidase activity				0		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		GGAATAATAGTAAAAAAAACTA	0.213													4	4	---	---	---	---	
ERBB4	2066	broad.mit.edu	37	2	212904564	212904564	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212904564delA	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	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)		CTACCACCACaaaaaaaagaa	0.199										TSP Lung(8;0.080)			4	2	---	---	---	---	
ERBB4	2066	broad.mit.edu	37	2	213333661	213333661	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213333661delA	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	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)		CCTTATTAGGAAAAAAATTAT	0.294										TSP Lung(8;0.080)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	216801387	216801387	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216801387delA								FN1 (500596 upstream) : MREG (5928 downstream)																							TATTGCCATCAAATGCCTCTG	0.358													4	2	---	---	---	---	
TNS1	7145	broad.mit.edu	37	2	218696424	218696424	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218696424delT	uc002vgt.2	-						TNS1_uc002vgr.2_Intron|TNS1_uc002vgs.2_Intron|TNS1_uc010zjv.1_Intron	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TCCACTGCCCTTTCCCGCCTC	0.582													4	2	---	---	---	---	
WNT10A	80326	broad.mit.edu	37	2	219750132	219750132	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219750132delC	uc002vjd.1	+							NM_025216	NP_079492	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family,						anterior/posterior pattern formation|axis specification|canonical Wnt receptor signaling pathway|cellular response to transforming growth factor beta stimulus|female gonad development|hair follicle morphogenesis|odontogenesis|regulation of odontogenesis of dentine-containing tooth|sebaceous gland development|skin development|tongue development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	G-protein-coupled receptor binding|signal transducer activity			lung(1)|skin(1)	2		Renal(207;0.0474)		Epithelial(149;4.26e-07)|all cancers(144;8.8e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTACAGAGAACCCCTTCTCTC	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	222275924	222275925	+	IGR	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222275924_222275925insC								None (None upstream) : EPHA4 (6824 downstream)																							tggtttgttttccctaaagtga	0.059													4	2	---	---	---	---	
DIS3L2	129563	broad.mit.edu	37	2	232982832	232982832	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232982832delC	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron|DIS3L2_uc002vsn.1_Intron|DIS3L2_uc002vso.2_Intron	NM_152383	NP_689596	Q8IYB7	DI3L2_HUMAN	DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		gctgcctgctccatgggcctc	0.000													4	2	---	---	---	---	
RAMP1	10267	broad.mit.edu	37	2	238816152	238816153	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238816152_238816153insT	uc002vxj.2	+							NM_005855	NP_005846	O60894	RAMP1_HUMAN	receptor activity-modifying protein 1 precursor						intracellular protein transport|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane	protein transporter activity				0		Breast(86;0.000596)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;9.56e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.49e-11)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.49e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00013)|Lung(119;0.0119)|LUSC - Lung squamous cell carcinoma(224;0.0288)	Pramlintide(DB01278)	ttttccctcacttttttttctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239482340	239482341	+	IGR	DEL	CC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239482340_239482341delCC								ASB1 (121450 upstream) : TWIST2 (274332 downstream)																							GGCTCTGGATCCCAGCTCCCAA	0.624											OREG0015339	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	242523790	242523790	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242523790delA								BOK (10239 upstream) : THAP4 (31 downstream)																							ATCAGCAGATAAAAAAAAAAT	0.249													4	3	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2476071	2476071	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2476071delA	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		GAgtaaagggaagggcatgtg	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	5389923	5389924	+	IGR	INS	-	T	T	rs147621547	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5389923_5389924insT								EDEM1 (128274 upstream) : None (None downstream)																							CAGTGCTAAGCCAGAAGAGAGC	0.455													4	2	---	---	---	---	
LOC285375	285375	broad.mit.edu	37	3	13702037	13702038	+	Intron	DEL	TC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13702037_13702038delTC	uc003byd.1	+							NR_027103				Homo sapiens, clone IMAGE:5742174, mRNA.												0						aggagaaatttctatctcattc	0.104													4	2	---	---	---	---	
FGD5	152273	broad.mit.edu	37	3	14963752	14963753	+	Intron	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14963752_14963753insA	uc003bzc.2	+						FGD5_uc011avk.1_Intron|FGD5_uc003bzd.2_Intron	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5						GTTTCCCAACCAAGGGTGAGCA	0.609													4	2	---	---	---	---	
GADL1	339896	broad.mit.edu	37	3	30769514	30769515	+	3'UTR	INS	-	T	T	rs9879502	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30769514_30769515insT	uc003cep.2	-	15						NM_207359	NP_997242	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)	TGAGAAAATCATTTTTTTTTTT	0.381													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	34594248	34594249	+	IGR	INS	-	GTGT	GTGT	rs9879692	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34594248_34594249insGTGT								PDCD6IP (683054 upstream) : None (None downstream)																							TTAGGgtgtgcgtgtgtgtgtg	0.317													3	5	---	---	---	---	
GOLGA4	2803	broad.mit.edu	37	3	37308569	37308569	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37308569delA	uc003cgv.2	+						GOLGA4_uc010hgr.1_Intron|GOLGA4_uc003cgw.2_Intron|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgu.1_Intron	NM_002078	NP_002069	Q13439	GOGA4_HUMAN	golgi autoantigen, golgin subfamily a, 4						Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4						ACCCTGCTCTAAAAAAATCAG	0.388													4	2	---	---	---	---	
OXSR1	9943	broad.mit.edu	37	3	38207457	38207458	+	Intron	INS	-	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38207457_38207458insG	uc003chy.2	+						OXSR1_uc010hhb.2_Intron|OXSR1_uc010hha.1_Intron	NM_005109	NP_005100	O95747	OXSR1_HUMAN	oxidative-stress responsive 1						intracellular protein kinase cascade|response to oxidative stress		ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity			skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GGCGCTGCGGAGGGGGGAGGCG	0.703													4	2	---	---	---	---	
NKTR	4820	broad.mit.edu	37	3	42681445	42681446	+	Intron	INS	-	CT	CT	rs150466796	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42681445_42681446insCT	uc003clo.2	+						NKTR_uc003clp.2_Intron|NKTR_uc011azp.1_Intron|NKTR_uc003cls.2_Intron	NM_005385	NP_005376	P30414	NKTR_HUMAN	natural killer-tumor recognition sequence						protein folding	membrane	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.24)		ggtttacaaaactattactatc	0.000													2	6	---	---	---	---	
ZNF662	389114	broad.mit.edu	37	3	42948676	42948677	+	Intron	DEL	GA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42948676_42948677delGA	uc003cmi.2	+						ZNF662_uc003cmk.2_Intron|ZNF662_uc003cmj.2_Intron	NM_207404	NP_997287	Q6ZS27	ZN662_HUMAN	zinc finger protein 662 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.217)		TTAAGAGGATGAGAGAAAGAAG	0.505													5	3	---	---	---	---	
ANO10	55129	broad.mit.edu	37	3	43474436	43474436	+	Intron	DEL	C	-	-	rs10663117		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43474436delC	uc003cmv.2	-						ANO10_uc011azs.1_Intron|ANO10_uc003cmw.2_Intron|ANO10_uc010hil.2_Intron|ANO10_uc011azt.1_Intron	NM_018075	NP_060545	Q9NW15	ANO10_HUMAN	transmembrane protein 16K						cell death	chloride channel complex	chloride channel activity			ovary(2)	2						TTGCTTAATTCtttttttttt	0.219													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	43901257	43901258	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43901257_43901258delCA								ABHD5 (137041 upstream) : MIR138-1 (254446 downstream)																							aaggcatattcacacaaatcct	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	43905654	43905655	+	IGR	INS	-	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43905654_43905655insG								ABHD5 (141438 upstream) : MIR138-1 (250049 downstream)																							TTGGAAGGGATGGGACTCCAAT	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	46898103	46898104	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46898103_46898104delCA								PRSS42 (22518 upstream) : MYL3 (1253 downstream)																							AGCCCCCATCCACACACACTCA	0.510													4	2	---	---	---	---	
SHISA5	51246	broad.mit.edu	37	3	48545080	48545080	+	5'Flank	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48545080delT	uc003ctr.1	-						SHISA5_uc003cts.1_5'Flank	NM_016479	NP_057563	Q8N114	SHSA5_HUMAN	scotin precursor						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade	endoplasmic reticulum membrane|integral to membrane|nuclear membrane	signal transducer activity|WW domain binding				0						GGGCAAGAGCTTTTGCCCAGC	0.527													4	2	---	---	---	---	
ACY1	95	broad.mit.edu	37	3	52009472	52009472	+	Intron	DEL	G	-	-	rs111955253		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-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	3	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54716189	54716192	+	Intron	DEL	CACA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54716189_54716192delCACA	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		AACAGAACAGcacacacacacaca	0.142													4	2	---	---	---	---	
RPP14	11102	broad.mit.edu	37	3	58290024	58290025	+	5'Flank	DEL	TG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58290024_58290025delTG	uc010hnh.2	+						RPP14_uc010hni.2_5'Flank|RPP14_uc003dju.3_5'Flank|RPP14_uc003djv.3_5'Flank|RPP14_uc003djw.3_5'Flank	NM_001098783	NP_001092253	O95059	RPP14_HUMAN	ribonuclease P 14kDa subunit						tRNA processing	nucleus	identical protein binding|ribonuclease P activity|RNA binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000187)|KIRC - Kidney renal clear cell carcinoma(10;0.0102)|Kidney(10;0.0118)|OV - Ovarian serous cystadenocarcinoma(275;0.191)		GAACAAGCCCTGTCTCCTCTGA	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75510803	75510804	+	IGR	DEL	AG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75510803_75510804delAG								FAM86D (26537 upstream) : MIR1324 (169110 downstream)																							AACCCCTCGCAGAGAGAGAGAG	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	78252135	78252135	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78252135delC								ROBO2 (555474 upstream) : ROBO1 (394253 downstream)																							AGGATGAAGTCAAAGTTTCTT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	83050280	83050281	+	IGR	INS	-	AG	AG			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83050280_83050281insAG								None (None upstream) : None (None downstream)																							gagatagagaaagagagagaga	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	97902014	97902014	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97902014delT								OR5H15 (13531 upstream) : OR5H6 (81115 downstream)																							ATTGACTAGATTTTTTTTTAT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	103383830	103383830	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103383830delA								None (None upstream) : None (None downstream)																							CATCTAAATTAAAAAAAAAAT	0.358													5	3	---	---	---	---	
DZIP3	9666	broad.mit.edu	37	3	108380487	108380487	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108380487delA	uc003dxd.2	+						DZIP3_uc003dxf.1_Intron|DZIP3_uc011bhm.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						tataataattaaaaaaaaaGA	0.214													4	2	---	---	---	---	
PHLDB2	90102	broad.mit.edu	37	3	111651486	111651486	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111651486delT	uc010hqa.2	+						PHLDB2_uc003dyc.2_Intron|PHLDB2_uc003dyd.2_Intron|PHLDB2_uc003dyg.2_Intron|PHLDB2_uc003dyh.2_Intron|PHLDB2_uc003dyi.2_Intron	NM_001134438	NP_001127910	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,							cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6						TCTGGAGTCATTTTTTTTTGT	0.318													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116547915	116547916	+	IGR	INS	-	A	A	rs149627036		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116547915_116547916insA								LOC285194 (112030 upstream) : None (None downstream)																							taccaaactttaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117588593	117588593	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117588593delA								None (None upstream) : None (None downstream)																							TTAGGTCACCAAGACACGAAG	0.413													4	2	---	---	---	---	
GSK3B	2932	broad.mit.edu	37	3	119748921	119748921	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119748921delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	ATCTAGTTGGAAAAAAAAAAT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127181455	127181455	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127181455delA								PLXNA1 (425227 upstream) : TPRA1 (110453 downstream)																							TAGTAAAAGGAAGCTGGTAGC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127206028	127206029	+	Intron	DEL	AC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127206028_127206029delAC	uc003ejk.2	-											Homo sapiens cDNA FLJ25806 fis, clone TST07194.																		tctctcacaaacacacacacac	0.000													3	3	---	---	---	---	
PODXL2	50512	broad.mit.edu	37	3	127352316	127352317	+	Intron	DEL	TG	-	-	rs145346367		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127352316_127352317delTG	uc003ejq.2	+							NM_015720	NP_056535	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2 precursor						leukocyte tethering or rolling	integral to plasma membrane	glycosaminoglycan binding|protein binding			ovary(1)|central_nervous_system(1)	2						ttaCAAATTTtgtgtgtgtgtg	0.050													6	3	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131726470	131726470	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131726470delT	uc003eok.2	-						CPNE4_uc011blq.1_Intron|CPNE4_uc003eol.2_Intron|CPNE4_uc003eom.2_Intron	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						acagcagccctTTTTTTTTTT	0.169													3	3	---	---	---	---	
RAB6B	51560	broad.mit.edu	37	3	133604315	133604315	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133604315delC	uc003epy.2	-						RAB6B_uc011blu.1_Intron	NM_016577	NP_057661	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family						protein transport|retrograde vesicle-mediated transport, Golgi to ER|small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle|Golgi membrane	GTP binding|GTPase activity|protein binding			pancreas(1)	1						GACTTACACACCCAATGACCA	0.532													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137549670	137549670	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137549670delT								SOX14 (65274 upstream) : CLDN18 (167988 downstream)																							AATATCTAGGTGGAGAGCTGA	0.269													4	2	---	---	---	---	
FAIM	55179	broad.mit.edu	37	3	138348258	138348259	+	Intron	INS	-	TAGCAAGTAAAATACC	TAGCAAGTAAAATACC	rs144618719	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138348258_138348259insTAGCAAGTAAAATACC	uc003esr.2	+						FAIM_uc003eso.1_3'UTR|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						AGGCTCCAGCATAGCAAGTAAA	0.446													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139452582	139452582	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139452582delG								NMNAT3 (55742 upstream) : CLSTN2 (201445 downstream)																							GGTGAGCAGTGGTGAAATGGC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	140870586	140870587	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140870586_140870587delCA								SPSB4 (3134 upstream) : ACPL2 (80095 downstream)																							cacacgcgtgcacacacacaca	0.401													4	2	---	---	---	---	
RASA2	5922	broad.mit.edu	37	3	141277533	141277533	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141277533delT	uc003etz.1	+						RASA2_uc010huq.1_Intron|RASA2_uc003eua.1_Intron|RASA2_uc011bnc.1_Intron	NM_006506	NP_006497	Q15283	RASA2_HUMAN	RAS p21 protein activator 2						intracellular signal transduction|negative regulation of Ras protein signal transduction	intracellular membrane-bounded organelle|intrinsic to internal side of plasma membrane|perinuclear region of cytoplasm	metal ion binding|Ras GTPase activator activity			ovary(2)|lung(2)|breast(1)|skin(1)	6						ATTATTTTGATTTTTTTTTTA	0.303													4	3	---	---	---	---	
PAQR9	344838	broad.mit.edu	37	3	142684280	142684280	+	5'Flank	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142684280delT	uc003evg.2	-						PAQR9_uc003evf.1_5'Flank	NM_198504	NP_940906	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX							integral to membrane	receptor activity				0						gtctagtggaTTTTTTTTTTT	0.154													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	155812148	155812148	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155812148delT								GMPS (156630 upstream) : KCNAB1 (26189 downstream)																							GCATTTGCAATTTTTTTTTTC	0.393													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	167868939	167868939	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167868939delT								GOLIM4 (55522 upstream) : MIR551B (400703 downstream)																							tttttctttcttttttttttg	0.000													1	5	---	---	---	---	
GNB4	59345	broad.mit.edu	37	3	179144775	179144776	+	Intron	DEL	CC	-	-	rs6443650	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179144775_179144776delCC	uc003fjv.3	-							NM_021629	NP_067642	Q9HAV0	GBB4_HUMAN	guanine nucleotide-binding protein, beta-4						cellular response to glucagon stimulus|energy reserve metabolic process	plasma membrane	signal transducer activity			skin(2)	2	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			cacacacacacccccctctgac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181723083	181723083	+	RNA	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181723083delA	uc003fkz.2	+	1		c.287delA								Homo sapiens mRNA; cDNA DKFZp686I1925 (from clone DKFZp686I1925).																		CTCAAAATGGAAAATTAAAAA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186405116	186405117	+	IGR	INS	-	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186405116_186405117insG								HRG (9094 upstream) : KNG1 (30003 downstream)																							TGCATTCCCCAGGAAAATGCAA	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194535188	194535188	+	IGR	DEL	A	-	-	rs11328673		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194535188delA								FAM43A (125424 upstream) : C3orf21 (253827 downstream)																							GTAAGTCAGGAAAGGAGTTGT	0.428													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195737231	195737231	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195737231delA								SDHAP1 (20081 upstream) : TFRC (38925 downstream)																							CTGCCACTggaggggcaggtg	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18831	18831	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18831delC								None (None upstream) : ZNF595 (34396 downstream)																							ttataaagttctttccaacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	415851	415851	+	IGR	DEL	T	-	-	rs146931675		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:415851delT								ZNF141 (38092 upstream) : ABCA11P (3373 downstream)																							CACACCCTACttttttttttt	0.109													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3600248	3600248	+	IGR	DEL	G	-	-	rs66494629		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3600248delG								LRPAP1 (66024 upstream) : ADRA2C (167827 downstream)																							tgtgtgagcaggtgtggacat	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4617530	4617533	+	Intron	DEL	AGGC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4617530_4617533delAGGC	uc003gid.2	+											Homo sapiens, clone IMAGE:5204729, mRNA.																		cagatgatggaggcaggcaggccg	0.211													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6206267	6206267	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6206267delA	uc003giw.1	+											Homo sapiens cDNA FLJ33698 fis, clone BRAWH2004779.																		cggcatagggaaagagacaga	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6766145	6766145	+	IGR	DEL	A	-	-	rs34965563		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6766145delA								CNO (46758 upstream) : KIAA0232 (18314 downstream)																							GAAGTGCTGGAAAAAAAAATA	0.249													4	2	---	---	---	---	
HMX1	3166	broad.mit.edu	37	4	8868823	8868823	+	3'UTR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8868823delA	uc003izz.1	-	2						NM_018942	NP_061815	Q9NP08	HMX1_HUMAN	homeo box (H6 family) 1						multicellular organismal development|negative regulation of transcription, DNA-dependent		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						AGATTCATTTAAAAAAACAAC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14961115	14961115	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14961115delA	uc003gng.3	-											Homo sapiens cDNA FLJ35938 fis, clone TESTI2011549.																		tgctcaagccaaaaaaaaaat	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18117941	18117941	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18117941delT								LCORL (94556 upstream) : None (None downstream)																							GCATTGGTAATTTTTTTTAAT	0.348													4	2	---	---	---	---	
ATP8A1	10396	broad.mit.edu	37	4	42507944	42507944	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42507944delT	uc003gwr.2	-						ATP8A1_uc003gwq.2_Intron|ATP8A1_uc003gws.2_Intron	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	GTGAAAAAACTTTTTTTTTCT	0.343													4	2	---	---	---	---	
ATP10D	57205	broad.mit.edu	37	4	47535218	47535218	+	Intron	DEL	A	-	-	rs139979863		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47535218delA	uc003gxk.1	+						ATP10D_uc003gxj.3_Intron	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D						ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3						TAGGGATAAGAAAAAAAAAAT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49534603	49534604	+	IGR	INS	-	T	T	rs143333563		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49534603_49534604insT								CWH43 (470510 upstream) : None (None downstream)																							ATACTAAGTAATTAAAAAAAAA	0.129													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	61199973	61199973	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61199973delA								None (None upstream) : LPHN3 (867001 downstream)																							gagttatgagaaaagggccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	67722450	67722452	+	IGR	DEL	ATG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67722450_67722452delATG								MIR1269 (579804 upstream) : CENPC1 (615537 downstream)																							tttcaaacttatgatgctctaag	0.000													4	2	---	---	---	---	
FAM13A	10144	broad.mit.edu	37	4	89679647	89679648	+	Intron	INS	-	A	A	rs113524788		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89679647_89679648insA	uc003hse.1	-						FAM13A_uc003hsa.1_Intron|FAM13A_uc003hsb.1_Intron|FAM13A_uc003hsd.1_Intron|FAM13A_uc003hsc.1_Intron|FAM13A_uc011cdq.1_Intron|FAM13A_uc003hsf.1_Intron|FAM13A_uc003hsg.1_Intron|FAM13A_uc010ikr.1_Intron	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2						GAGTCACAAAGGAAAAAAAAAG	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	113688722	113688723	+	IGR	INS	-	AATA	AATA	rs139226825	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113688722_113688723insAATA								LARP7 (109981 upstream) : ANK2 (50516 downstream)																							gaccctgtctcaataaataaat	0.178													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	118841661	118841661	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118841661delT								TRAM1L1 (834925 upstream) : NDST3 (113112 downstream)																							attctcttactttcttgcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	120375150	120375151	+	Intron	DEL	AA	-	-	rs71595387		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120375150_120375151delAA	uc003idd.2	-											Homo sapiens cDNA clone IMAGE:4671554, partial cds.																		ccatctctagaaaaaaaaaaTA	0.020													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	124377193	124377193	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124377193delT								SPRY1 (52286 upstream) : LOC285419 (194229 downstream)																							GTAAGtttccttttttttttg	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	126862801	126862801	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126862801delA								MIR2054 (434339 upstream) : None (None downstream)																							caccagcagcaaagttttatg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	129438844	129438844	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129438844delA	uc003igh.1	+											Homo sapiens cDNA FLJ36097 fis, clone TESTI2020956.																		AAAACAATGTAAGAAAGAGGC	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	131496734	131496734	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131496734delT								None (None upstream) : None (None downstream)																							ACATGAATGGTTATGCTCTCA	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	141305787	141305787	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141305787delT								SCOC (2077 upstream) : CLGN (3822 downstream)																							tttctttcccttattgggtga	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	142940726	142940726	+	IGR	DEL	T	-	-	rs139464041		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142940726delT								IL15 (286115 upstream) : INPP4B (8458 downstream)																							CCCTCTTACCTTTTTTTTTtg	0.055													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	152993397	152993397	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152993397delG								PET112L (311251 upstream) : FBXW7 (249014 downstream)														p.?(1)									TTGGGAGCCAGGGGCCACTCC	0.587													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164675881	164675881	+	Intron	DEL	T	-	-	rs5863625		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164675881delT	uc003iqs.1	-							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)				TTAAAGACTCTTTTTTTTTTA	0.308													2	4	---	---	---	---	
NEK1	4750	broad.mit.edu	37	4	170321966	170321966	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170321966delA	uc003isb.1	-						NEK1_uc003isc.1_Intron|NEK1_uc003isd.1_Intron|NEK1_uc003ise.1_Intron|NEK1_uc003isf.1_Intron	NM_012224	NP_036356	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1						cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		TTTATTTGGCAAAAAAAATGT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	177257014	177257014	+	IGR	DEL	G	-	-	rs67050840		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177257014delG								SPCS3 (3620 upstream) : VEGFC (347677 downstream)																							ttgtaatatagtcatccatag	0.000													4	2	---	---	---	---	
VEGFC	7424	broad.mit.edu	37	4	177688119	177688120	+	Intron	INS	-	A	A	rs148555855	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177688119_177688120insA	uc003ius.1	-							NM_005429	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C						angiogenesis|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of mast cell chemotaxis|substrate-dependent cell migration|vascular endothelial growth factor receptor signaling pathway	membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity			lung(5)	5		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		ggaaaaacaagaaaaaatcacc	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	182093415	182093415	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182093415delT								None (None upstream) : MGC45800 (966744 downstream)																							GACAAACTCCTTTTTTTTCTC	0.373													4	2	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183627236	183627236	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183627236delT	uc003ivd.1	+						ODZ3_uc003ive.1_Intron	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		TTTAGTCTGATTTTTTTTATT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	183731632	183731633	+	IGR	DEL	AA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183731632_183731633delAA								ODZ3 (7455 upstream) : DCTD (79612 downstream)																							caccacacacaaatacactcac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	183991077	183991077	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183991077delG								FAM92A3 (29806 upstream) : C4orf38 (27097 downstream)																							tgttggtccaggttctacaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188534594	188534594	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188534594delT								FAT1 (886744 upstream) : ZFP42 (382331 downstream)																							tttcttccacttttttttaac	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190201125	190201126	+	IGR	INS	-	CT	CT	rs142468040		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190201125_190201126insCT								None (None upstream) : FRG1 (660848 downstream)																							agtgtctggaactctgcagggg	0.000													5	3	---	---	---	---	
FRG1	2483	broad.mit.edu	37	4	190875086	190875086	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190875086delG	uc003izs.2	+							NM_004477	NP_004468	Q14331	FRG1_HUMAN	FSHD region gene 1						rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TGACAAATGAGGAAAATATTT	0.294													7	6	---	---	---	---	
SDHAP3	728609	broad.mit.edu	37	5	1587435	1587438	+	Intron	DEL	AAAC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1587435_1587438delAAAC	uc011cme.1	-							NR_003263				Homo sapiens cDNA FLJ58919 complete cds, moderately similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC1.3.5.1).												0						aaaaGTTGAAaaacaaacaaacaa	0.010													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1943836	1943837	+	IGR	DEL	TC	-	-	rs137933189		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1943836_1943837delTC								IRX4 (60956 upstream) : IRX2 (802444 downstream)																							tcacatattttctgtttgtctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2206053	2206053	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2206053delT								IRX4 (323173 upstream) : IRX2 (540228 downstream)																							CCTGTTGTCCTTTTTTTTAAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4143324	4143324	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4143324delT								IRX1 (541808 upstream) : LOC340094 (891148 downstream)																							ATTAAACTCATTTTTTTTTTC	0.443													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4263289	4263289	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4263289delT								IRX1 (661773 upstream) : LOC340094 (771183 downstream)																							GGCACCGGCCTTTTTTGAGGT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5096924	5096924	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5096924delA								LOC340094 (26815 upstream) : ADAMTS16 (43519 downstream)																							AAAATCTGCCAAAACAATGCT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5669021	5669021	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5669021delT								KIAA0947 (178684 upstream) : FLJ33360 (641533 downstream)																							AGGAAAGTACTAAGTTGTTAA	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5692499	5692500	+	IGR	DEL	AG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5692499_5692500delAG								KIAA0947 (202162 upstream) : FLJ33360 (618054 downstream)																							GGCCCTTATTAGAAGGGCACAC	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5941483	5941486	+	IGR	DEL	TTTT	-	-	rs5865630		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5941483_5941486delTTTT								KIAA0947 (451146 upstream) : FLJ33360 (369068 downstream)																							AATAGTGGGCTTTTTTTTAGAGAA	0.417													4	3	---	---	---	---	
NSUN2	54888	broad.mit.edu	37	5	6600499	6600499	+	Intron	DEL	A	-	-	rs11325322		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6600499delA	uc003jdu.2	-						NSUN2_uc003jds.2_Intron|NSUN2_uc003jdt.2_Intron|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1						TCTGGATCCGAGGGGTAGGTT	0.443													3	4	---	---	---	---	
TAS2R1	50834	broad.mit.edu	37	5	9632998	9632998	+	5'Flank	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9632998delT	uc003jem.1	-							NM_019599	NP_062545	Q9NYW7	TA2R1_HUMAN	taste receptor T2R1						chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity			ovary(3)	3						attgttggtgtttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17382975	17382975	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17382975delA	uc003jga.2	-											Homo sapiens hypothetical gene supported by BC052942, mRNA (cDNA clone IMAGE:5268622).																		ttcaggtgagaaaaaaatgca	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17614595	17614595	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17614595delT								BASP1 (337660 upstream) : None (None downstream)																							TACTTGACTATTTTCTATCAT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27491960	27491962	+	Intron	DEL	CTA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27491960_27491962delCTA	uc003jgw.1	+						uc003jgx.1_Intron|uc010iuh.1_Intron|uc003jgy.2_Intron					Homo sapiens hypothetical protein LOC340109, mRNA (cDNA clone IMAGE:5578073), partial cds.																		agatctcaccctactaaccaagg	0.000													4	2	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33786566	33786567	+	Intron	INS	-	T	T	rs35812060		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33786566_33786567insT	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron|ADAMTS12_uc003jib.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						atctaagaagcttttTTTTTTT	0.327										HNSCC(64;0.19)			5	3	---	---	---	---	
PRLR	5618	broad.mit.edu	37	5	35088868	35088869	+	Intron	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35088868_35088869delCA	uc003jjm.2	-						PRLR_uc003jjg.1_Intron|PRLR_uc003jjh.1_Intron|PRLR_uc003jji.1_Intron|PRLR_uc003jjj.1_Intron|PRLR_uc003jjk.1_Intron|PRLR_uc003jjl.3_Intron|PRLR_uc010iuw.1_5'Flank	NM_000949	NP_000940	P16471	PRLR_HUMAN	prolactin receptor precursor						activation of JAK2 kinase activity|activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|embryo implantation|lactation|steroid biosynthetic process|T cell activation	cell surface|extracellular region|integral to membrane	metal ion binding|ornithine decarboxylase activator activity|peptide hormone binding|prolactin receptor activity|protein homodimerization activity			ovary(2)|skin(1)	3	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Dromostanolone(DB00858)|Fluoxymesterone(DB01185)|Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	GTacacacaccacacacacaca	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38736754	38736754	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38736754delA								LIFR (141247 upstream) : OSMR (109374 downstream)																							taaaattcttaaaaaaaagaa	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	39539568	39539568	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39539568delT								DAB2 (114233 upstream) : None (None downstream)																							TTCCTAGGGCTTTTTTTTTTC	0.139													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	39966378	39966378	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39966378delT								DAB2 (541043 upstream) : PTGER4 (713654 downstream)																							AATCTTCTAGTTTATTCAGCC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	50889057	50889057	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50889057delA								ISL1 (198500 upstream) : None (None downstream)																							CAGTTTaaagaggcactatgg	0.159													4	2	---	---	---	---	
ARL15	54622	broad.mit.edu	37	5	53266919	53266920	+	Intron	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53266919_53266920insA	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)				GGCTGGCatttaaaaaaaaatt	0.277													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	55827982	55827982	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55827982delT								ANKRD55 (298796 upstream) : MAP3K1 (282918 downstream)																							CAAGGCTCCCTTTTTTATACA	0.388													4	2	---	---	---	---	
GPBP1	65056	broad.mit.edu	37	5	56542533	56542533	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56542533delT	uc003jrh.3	+						GPBP1_uc010iwg.2_Intron|GPBP1_uc003jri.3_Intron|GPBP1_uc003jrj.3_Intron|GPBP1_uc003jrk.3_Intron|GPBP1_uc003jrl.3_Intron	NM_022913	NP_075064	Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			large_intestine(1)|central_nervous_system(1)	2		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		AACTTAAAAATTTTTTTTTTT	0.328													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	63416141	63416141	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63416141delC								HTR1A (158595 upstream) : RNF180 (45530 downstream)																							ttccttctttccatttccact	0.045													4	2	---	---	---	---	
NLN	57486	broad.mit.edu	37	5	65118554	65118555	+	Intron	INS	-	TT	TT			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65118554_65118555insTT	uc003juf.2	+						NLN_uc003jug.2_Intron|NLN_uc010iww.2_Intron	NM_020726	NP_065777	Q9BYT8	NEUL_HUMAN	neurolysin precursor						proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		GCATCTAGAGATTTGGAAAATT	0.376													118	98	---	---	---	---	
MAST4	375449	broad.mit.edu	37	5	66194811	66194812	+	Intron	INS	-	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66194811_66194812insG	uc003jut.1	+						MAST4_uc003jur.3_Intron|MAST4_uc010iwz.2_Intron|MAST4_uc003jus.2_Intron	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TTGAAGCTGATGGGGAAATACC	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	67941097	67941098	+	IGR	DEL	GT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67941097_67941098delGT								PIK3R1 (343450 upstream) : SLC30A5 (448720 downstream)																							GAGGAAGTGGGTGAAGGCTCTG	0.525													4	2	---	---	---	---	
CDK7	1022	broad.mit.edu	37	5	68551654	68551654	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68551654delT	uc003jvs.3	+						CDK7_uc010ixd.1_3'UTR|CDK7_uc003jvt.3_Intron|CDK7_uc003jvu.3_Intron	NM_001799	NP_001790	P50613	CDK7_HUMAN	cyclin-dependent kinase 7						androgen receptor signaling pathway|cell division|cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex|mitochondrion	androgen receptor binding|ATP binding|cyclin-dependent protein kinase activity|DNA-dependent ATPase activity|protein C-terminus binding|RNA polymerase II carboxy-terminal domain kinase activity|transcription coactivator activity			lung(1)	1		Lung NSC(167;7.26e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.98e-56)|Epithelial(20;3.54e-52)|all cancers(19;9.11e-48)|Lung(70;0.0185)		Atttgtttgcttttttttttt	0.164								NER					4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	70717996	70717997	+	Intron	INS	-	TATA	TATA			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70717996_70717997insTATA	uc010iyu.1	-						uc003kbl.1_Intron					Homo sapiens cDNA FLJ41874 fis, clone OCBBF2019327.																		AAGCATTTATTTATATATTTTC	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	74900944	74900947	+	IGR	DEL	ACAC	-	-	rs141723230		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74900944_74900947delACAC								POLK (5300 upstream) : POC5 (69086 downstream)																							GTATacacatacacacacacacac	0.309													3	4	---	---	---	---	
JMY	133746	broad.mit.edu	37	5	78597124	78597124	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78597124delA	uc003kfx.3	+						JMY_uc003kfw.1_Intron	NM_152405	NP_689618	Q8N9B5	JMY_HUMAN	junction-mediating and regulatory protein						'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		CCTGTGTCTTAAAAAATGTTT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87432315	87432315	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87432315delT								CCNH (723479 upstream) : TMEM161B (58709 downstream)																							GTGTCTCTTCTTTTTTTTTTT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	89137245	89137245	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89137245delT								MEF2C (937376 upstream) : CETN3 (552286 downstream)																							AGAGTCCTGATTTTTTTTCCC	0.343													4	2	---	---	---	---	
NR2F1	7025	broad.mit.edu	37	5	92919011	92919012	+	5'Flank	DEL	TC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92919011_92919012delTC	uc003kkj.2	+						FLJ42709_uc011cue.1_5'Flank|FLJ42709_uc010jbb.1_5'Flank|FLJ42709_uc003kkf.2_5'Flank|FLJ42709_uc003kkg.2_5'Flank|FLJ42709_uc010jbc.2_5'Flank|FLJ42709_uc003kki.2_5'Flank|FLJ42709_uc003kkh.2_5'Flank	NM_005654	NP_005645	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1						negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding			urinary_tract(1)|ovary(1)|lung(1)	3		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)		cttcttctcttctctctctctc	0.168													3	3	---	---	---	---	
CHD1	1105	broad.mit.edu	37	5	98194994	98194994	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98194994delA	uc003knf.2	-						CHD1_uc010jbn.2_Intron	NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	agcttctcctaatgttaatat	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	104984152	104984152	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104984152delA								RAB9BP1 (548354 upstream) : None (None downstream)																							aagaaaacataaaaaaaaatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	107136818	107136818	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107136818delA								EFNA5 (130222 upstream) : FBXL17 (57922 downstream)																							CACAATCAAGAAAAAAATATA	0.299													4	2	---	---	---	---	
C5orf13	9315	broad.mit.edu	37	5	111058597	111058597	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111058597delA	uc003kpk.2	-									Q16612	NP311_HUMAN	Homo sapiens cDNA FLJ55239 complete cds, moderately similar to Neuronal protein 3.1.							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)		CTGGAGAAATAAAAAAAAAGT	0.373													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	111401338	111401339	+	IGR	INS	-	CA	CA	rs144411228	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111401338_111401339insCA								C5orf13 (88710 upstream) : EPB41L4A (76799 downstream)																							gtgcgtgcgcgcacacacacac	0.248													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	114360943	114360943	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114360943delA								KCNN2 (528747 upstream) : TRIM36 (99524 downstream)																							gaagagtaggaaagggtctgg	0.000													4	2	---	---	---	---	
SNX24	28966	broad.mit.edu	37	5	122180110	122180111	+	5'Flank	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122180110_122180111delCA	uc011cwo.1	+						SNX24_uc003ktf.2_5'Flank|SNX24_uc010jcy.2_5'Flank	NM_014035	NP_054754	Q9Y343	SNX24_HUMAN	SBBI31 protein						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)		GGTGTGTAGTCACAGGGCACAG	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	122971793	122971793	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122971793delC								CSNK1G3 (19331 upstream) : None (None downstream)																							TCGGCTTCCTCCCCGGACAGC	0.458													4	2	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127797192	127797192	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127797192delG	uc003kuu.2	-						FBN2_uc003kuv.2_Intron|FBN2_uc003kuw.3_Intron|FBN2_uc003kux.1_Intron	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		tcccattagtgggtgtatacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129660800	129660800	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129660800delC								CHSY3 (138474 upstream) : HINT1 (834075 downstream)																							gagcaggtgtcccacagagct	0.139													4	2	---	---	---	---	
GDF9	2661	broad.mit.edu	37	5	132198374	132198374	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132198374delA	uc003kxz.1	-						GDF9_uc011cxj.1_Intron	NM_005260	NP_005251	O60383	GDF9_HUMAN	growth differentiation factor 9 precursor						female gamete generation|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			skin(1)	1		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTCAAGCCTCAAAAAAAAAAA	0.363													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134831175	134831175	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134831175delA								TIFAB (43086 upstream) : NEUROG1 (38805 downstream)																							cccccaaagcaagtgttccaa	0.000													4	2	---	---	---	---	
WNT8A	7478	broad.mit.edu	37	5	137425682	137425682	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137425682delG	uc003lcd.1	+						BRD8_uc003lcc.1_Intron|WNT8A_uc011cyj.1_Intron|WNT8A_uc011cyk.1_Intron	NM_058244	NP_490645	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family,						brain segmentation|canonical Wnt receptor signaling pathway involved in neural crest cell differentiation|cell migration involved in gastrulation|dorsal/ventral pattern formation|ectoderm development|endoderm development|eye development|hindbrain development|mesodermal cell fate commitment|negative regulation of Wnt receptor signaling pathway|neural crest cell fate commitment|neural plate pattern specification|notochord development|palate development|polarity specification of anterior/posterior axis|polarity specification of proximal/distal axis|positive regulation of fibroblast growth factor receptor signaling pathway|regulation of transcription involved in anterior/posterior axis specification|response to retinoic acid|somitogenesis|spinal cord anterior/posterior patterning|tail morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled binding|signal transducer activity			ovary(1)|lung(1)|breast(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GTACAACCATGGGTAATTCAT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139535360	139535361	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139535360_139535361insA								C5orf53 (26969 upstream) : C5orf32 (19292 downstream)																							CTATCACAGTTAAAAAAAAATG	0.317													4	2	---	---	---	---	
FGF1	2246	broad.mit.edu	37	5	142045217	142045218	+	Intron	DEL	GA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142045217_142045218delGA	uc003lmn.3	-						FGF1_uc003lmp.3_Intron|FGF1_uc003lmq.2_Intron|FGF1_uc010jgj.2_Intron|FGF1_uc003lmr.2_Intron|FGF1_uc003lms.3_Intron	NM_000800	NP_000791	P05230	FGF1_HUMAN	fibroblast growth factor 1 (acidic) isoform 1						angiogenesis|cellular response to heat|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of angiogenesis|positive regulation of cell division|positive regulation of cell migration|positive regulation of cholesterol biosynthetic process|positive regulation of intracellular protein kinase cascade|positive regulation of transcription from RNA polymerase II promoter	cell cortex|cytosol|extracellular space	fibroblast growth factor receptor binding|growth factor activity|heparin binding|S100 alpha binding				0		all_neural(839;0.0416)|Ovarian(839;0.0955)|all_hematologic(541;0.1)|Prostate(461;0.157)|Lung NSC(810;0.21)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00032)	Pentosan Polysulfate(DB00686)	TCTACCCATTGAGTCCTGTCTA	0.485													4	2	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142189637	142189637	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142189637delT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAACTCACCCTTAGCTGCCCT	0.458													4	2	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142606708	142606708	+	3'UTR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142606708delG	uc011dbj.1	+	23					ARHGAP26_uc003lmt.2_3'UTR|ARHGAP26_uc003lmw.2_3'UTR	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACTGAGTTTTGTGGACATGGC	0.512													4	2	---	---	---	---	
TCERG1	10915	broad.mit.edu	37	5	145849095	145849097	+	Intron	DEL	TTC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145849095_145849097delTTC	uc003lob.2	+						TCERG1_uc003loc.2_Intron|TCERG1_uc011dbt.1_Intron	NM_006706	NP_006697	O14776	TCRG1_HUMAN	transcription elongation regulator 1 isoform 1						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTTTTTATTATTCTTTTTTTAGG	0.360													272	167	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148196323	148196324	+	Intron	DEL	GT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148196323_148196324delGT	uc003lpp.1	-							NM_024577		Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			gtgtgtgtgagtgtgtgtgtgt	0.257													3	3	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148389117	148389117	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148389117delG	uc003lpu.2	-						SH3TC2_uc003lpp.1_Intron|SH3TC2_uc010jgw.2_Intron|SH3TC2_uc003lps.2_Intron|SH3TC2_uc003lpt.2_Intron|SH3TC2_uc010jgx.2_Intron	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ggcacagactgggtatttgct	0.139													4	2	---	---	---	---	
SLC36A1	206358	broad.mit.edu	37	5	150836656	150836657	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150836656_150836657insT	uc003luc.2	+						GM2A_uc011dcs.1_Intron|SLC36A1_uc003lub.1_Intron|SLC36A1_uc010jhw.1_Intron	NM_078483	NP_510968	Q7Z2H8	S36A1_HUMAN	solute carrier family 36 member 1						cellular nitrogen compound metabolic process|ion transport	endoplasmic reticulum|integral to membrane|lysosomal membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			skin(1)	1		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glycine(DB00145)|L-Alanine(DB00160)	TTAATGTACCCTTTTTTTGTCA	0.455													4	2	---	---	---	---	
GRIA1	2890	broad.mit.edu	37	5	152871788	152871789	+	Intron	INS	-	C	C	rs145997536	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152871788_152871789insC	uc003lva.3	+						GRIA1_uc003luy.3_Intron|GRIA1_uc003luz.3_Intron|GRIA1_uc011dcv.1_Intron|GRIA1_uc011dcw.1_Intron|GRIA1_uc011dcx.1_Intron|GRIA1_uc011dcy.1_Frame_Shift_Ins_p.P10fs|GRIA1_uc011dcz.1_Frame_Shift_Ins_p.P10fs|GRIA1_uc010jia.1_Intron	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	TCTTTCAGCCTCTCCAGCTAGC	0.485													0	6	---	---	---	---	
GRIA1	2890	broad.mit.edu	37	5	153078159	153078159	+	Intron	DEL	A	-	-	rs5872335		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153078159delA	uc003lva.3	+						GRIA1_uc003luy.3_Intron|GRIA1_uc003luz.3_Intron|GRIA1_uc011dcv.1_Intron|GRIA1_uc011dcw.1_Intron|GRIA1_uc011dcx.1_Intron|GRIA1_uc011dcy.1_Intron|GRIA1_uc011dcz.1_Intron|GRIA1_uc010jia.1_Intron	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AGGTATTTCCAAAAAAAATAC	0.348													3	3	---	---	---	---	
LARP1	23367	broad.mit.edu	37	5	154166111	154166111	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154166111delT	uc003lvp.2	+						LARP1_uc003lvo.2_Intron|LARP1_uc010jie.1_Intron	NM_033551	NP_291029	Q6PKG0	LARP1_HUMAN	la related protein isoform 2								protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCCACCCTGCTACAGTCTGGG	0.502													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155384124	155384125	+	Intron	INS	-	G	G	rs149764635	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155384124_155384125insG	uc003lwa.1	+							NM_172244	NP_758447	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 2						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ttcactgagaatgacatttgat	0.035													3	4	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155661813	155661813	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155661813delG	uc003lwa.1	+							NM_172244	NP_758447	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 2						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			actactgcatgggatctgagt	0.000													4	2	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156820216	156820216	+	3'UTR	DEL	A	-	-	rs33954943		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156820216delA	uc003lwq.2	+	33					CYFIP2_uc011ddn.1_3'UTR|CYFIP2_uc011ddo.1_3'UTR|CYFIP2_uc003lwr.2_3'UTR|CYFIP2_uc003lws.2_3'UTR|CYFIP2_uc003lwt.2_3'UTR|CYFIP2_uc011ddp.1_3'UTR|CYFIP2_uc003lwv.2_3'UTR	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AGCATAAATGAAAAAAAAAAA	0.453													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	161021199	161021199	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161021199delG								GABRB2 (46069 upstream) : GABRA6 (91459 downstream)																							tattttaGGAGGGTGCCTTCT	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162242502	162242502	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162242502delT								GABRG2 (659958 upstream) : CCNG1 (622075 downstream)																							ATTCTGTCCATTTTTTTTTAT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162722726	162722727	+	IGR	DEL	TT	-	-	rs71885601		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162722726_162722727delTT								None (None upstream) : CCNG1 (141850 downstream)																							ggaaaagggctttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165753356	165753356	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165753356delA								None (None upstream) : ODZ2 (958487 downstream)																							aataaaaaataaaaaaaataa	0.284													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167182418	167182419	+	Intron	INS	-	T	T	rs138368489	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167182418_167182419insT	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		GTTGATCTGAATTTTTTTTTTG	0.287													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	175339696	175339696	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175339696delG								CPLX2 (28673 upstream) : THOC3 (46840 downstream)																							ATTTGCTCAAGTCAGGAGCCT	0.259													4	2	---	---	---	---	
ZNF346	23567	broad.mit.edu	37	5	176465082	176465083	+	Intron	DEL	TT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176465082_176465083delTT	uc003mfi.2	+						ZNF346_uc011dfr.1_Intron|ZNF346_uc011dfs.1_Intron|ZNF346_uc003mfj.2_Intron|ZNF346_uc003mfk.1_Intron|ZNF346_uc011dft.1_Intron	NM_012279	NP_036411	Q9UL40	ZN346_HUMAN	zinc finger protein 346							cytoplasm|nucleolus	double-stranded RNA binding|zinc ion binding				0	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			cccatgatgatttttttttttt	0.000													4	2	---	---	---	---	
PRR7	80758	broad.mit.edu	37	5	176877464	176877464	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176877464delT	uc003mgu.1	+						uc003mgt.2_5'Flank|PRR7_uc003mgv.1_Intron|PRR7_uc003mgw.1_Intron	NM_030567	NP_085044	Q8TB68	PRR7_HUMAN	proline rich 7 (synaptic)							cell junction|integral to membrane|postsynaptic membrane					0	all_cancers(89;1.51e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)			ATGGCTGACATTTCCCAGGAA	0.557													4	2	---	---	---	---	
LOC728554	728554	broad.mit.edu	37	5	177306168	177306168	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177306168delT	uc010jkr.2	+							NR_003615				Homo sapiens cDNA, FLJ17316.												0						TCATACTCCCtttttttttgt	0.144													9	4	---	---	---	---	
BTNL8	79908	broad.mit.edu	37	5	180342536	180342536	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180342536delA	uc003mmp.2	+						BTNL8_uc003mmq.2_Intron|BTNL8_uc011dhg.1_Intron|BTNL8_uc010jll.2_Intron|BTNL8_uc010jlm.2_Intron|BTNL8_uc011dhh.1_Intron	NM_001040462	NP_001035552	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8 isoform 2 precursor							integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			gtacatccataaaaaagatct	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	4550171	4550171	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4550171delC								PECI (414340 upstream) : CDYL (156222 downstream)																							CAGCCTTGTGCAGTCCAGAAA	0.572													4	2	---	---	---	---	
CDYL	9425	broad.mit.edu	37	6	4881320	4881321	+	Intron	INS	-	TG	TG			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4881320_4881321insTG	uc003mwi.2	+						CDYL_uc003mwj.2_Intron|CDYL_uc003mwk.2_Intron|CDYL_uc011dhx.1_Intron	NM_001143971	NP_001137443	Q9Y232	CDYL1_HUMAN	chromodomain protein, Y chromosome-like isoform						regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	histone acetyltransferase activity				0	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		tacttgggttctgtgtgtgtgt	0.000													4	2	---	---	---	---	
RREB1	6239	broad.mit.edu	37	6	7164388	7164388	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7164388delA	uc003mxc.2	+						RREB1_uc010jnw.2_Intron|RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron|RREB1_uc003mxd.2_Intron	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				AAAAGATCCTAAAAAATACTG	0.468													4	2	---	---	---	---	
RREB1	6239	broad.mit.edu	37	6	7211594	7211595	+	Intron	INS	-	GGATGGAT	GGATGGAT			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7211594_7211595insGGATGGAT	uc003mxc.2	+						RREB1_uc010jnw.2_Intron|RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron|RREB1_uc003mxd.2_Intron	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				gatggatggatggatggatgga	0.069													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8361671	8361671	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8361671delT								EEF1E1 (258843 upstream) : SLC35B3 (50062 downstream)																							ttttgaaatattaccccctga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9516635	9516635	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9516635delT								HULC (862558 upstream) : TFAP2A (880282 downstream)																							CCCCTTGCTCTTTCTCCTGTG	0.567													4	2	---	---	---	---	
CAP2	10486	broad.mit.edu	37	6	17453169	17453169	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17453169delA	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357	P40123	CAP2_HUMAN	adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			TTCTAGTTTTAAAAAAAAGTG	0.418													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	22660900	22660900	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22660900delC								HDGFL1 (90151 upstream) : None (None downstream)																							CCTGTCTCCTCCACCCCCTGC	0.438													4	2	---	---	---	---	
BTN2A2	10385	broad.mit.edu	37	6	26386987	26386988	+	Intron	DEL	AA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26386987_26386988delAA	uc003nhq.2	+						BTN2A2_uc011dkf.1_Intron|BTN2A2_uc011dkg.1_Intron|BTN2A2_uc003nhr.2_Intron|BTN2A2_uc011dkh.1_Intron|BTN2A2_uc003nhs.2_Intron|BTN2A2_uc003nht.2_Intron	NM_006995	NP_008926	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2 isoform a						negative regulation of activated T cell proliferation|negative regulation of cellular metabolic process|negative regulation of cytokine secretion	integral to membrane					0						TTTTTCCCTTAAATCTATTGTG	0.386													4	2	---	---	---	---	
VARS2	57176	broad.mit.edu	37	6	30885840	30885843	+	Intron	DEL	TTTG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30885840_30885843delTTTG	uc003nsc.1	+						VARS2_uc011dmx.1_Intron|VARS2_uc011dmy.1_Intron|VARS2_uc011dmz.1_Intron|VARS2_uc011dna.1_Intron|VARS2_uc011dnb.1_Intron|VARS2_uc011dnc.1_Intron|VARS2_uc011dnd.1_5'Flank|VARS2_uc010jsg.1_5'Flank	NM_020442	NP_065175	Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial						valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4						TAtgttttgttttgtttgtttgtt	0.211													5	3	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32522507	32522526	+	Intron	DEL	CACTTGGCAGGTGTAAACCT	-	-	rs72118746		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32522507_32522526delCACTTGGCAGGTGTAAACCT	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obm.1_RNA|HLA-DRB6_uc003obn.1_RNA|HLA-DRB6_uc003obo.1_RNA	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						TTGGATGCTCCACTTGGCAGGTGTAAACCTCTCCACTCCG	0.527													4	2	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34077711	34077712	+	Intron	INS	-	C	C	rs142555568	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34077711_34077712insC	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc010jvk.1_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	CATGTACACCACCCCCCAGCAG	0.441													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	40318613	40318614	+	Intron	INS	-	A	A	rs146697002		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40318613_40318614insA	uc003opf.1	-											Homo sapiens cDNA FLJ41649 fis, clone FEBRA2024343.																		ctgacacacatatgcatatgca	0.069													4	2	---	---	---	---	
MDFI	4188	broad.mit.edu	37	6	41605627	41605628	+	Intron	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41605627_41605628insA	uc003oqp.3	+						MDFI_uc003oqq.3_5'Flank|MDFI_uc010jxn.2_5'Flank	NM_005586	NP_005577	Q99750	MDFI_HUMAN	MyoD family inhibitor						cytoplasmic sequestering of transcription factor|dorsal/ventral axis specification|negative regulation of DNA binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of Wnt receptor signaling pathway	cytoplasm|nucleus					0	Ovarian(28;0.0327)|Colorectal(47;0.121)		Colorectal(64;0.0123)|COAD - Colon adenocarcinoma(64;0.0264)|KIRC - Kidney renal clear cell carcinoma(1;0.138)			GGGCTGCTGCGGCACAGGGCAG	0.624													4	2	---	---	---	---	
MRPS10	55173	broad.mit.edu	37	6	42182256	42182256	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42182256delA	uc003osa.3	-						MRPS10_uc011dup.1_Intron	NM_018141	NP_060611	P82664	RT10_HUMAN	mitochondrial ribosomal protein S10						translation	actin cytoskeleton|mitochondrion|ribosome	structural constituent of ribosome				0	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00528)			AGCTGATGATAAAAAAAAAAG	0.274													6	3	---	---	---	---	
C6orf153	88745	broad.mit.edu	37	6	42992401	42992401	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42992401delA	uc003otp.1	+							NM_033112	NP_149103	Q96EU6	RRP36_HUMAN	hypothetical protein LOC88745						ribosomal small subunit biogenesis|rRNA processing	nucleolus					0			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			gTAACTGAGCAAGGGAGGCAG	0.184													4	2	---	---	---	---	
GTPBP2	54676	broad.mit.edu	37	6	43590115	43590115	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43590115delT	uc003ovs.2	-						GTPBP2_uc010jyv.2_Intron|GTPBP2_uc003ovt.1_Intron	NM_019096	NP_061969	Q9BX10	GTPB2_HUMAN	GTP binding protein 2								GTP binding|GTPase activity			liver(1)|skin(1)	2	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			ACGCTTCACATTTTTAGGGTC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	48195859	48195859	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48195859delA								C6orf138 (116916 upstream) : None (None downstream)																							taaaaccagtaaaaaacagcc	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50465449	50465449	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50465449delT	uc003pae.1	+											full-length cDNA clone CS0DD007YH13 of Neuroblastoma Cot 50-normalized of Homo sapiens (human).																		TAGGCAAAAGTTTACACCTGT	0.338													4	2	---	---	---	---	
DST	667	broad.mit.edu	37	6	56392019	56392019	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56392019delT	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ATCATTTTCCTTTTTTTTTTC	0.313													2	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57375666	57375667	+	Intron	INS	-	T	T	rs11384142		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57375666_57375667insT	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)		AAGTAACCTTGTATAACGCCTT	0.332													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57415028	57415029	+	Intron	INS	-	T	T	rs145113134		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57415028_57415029insT	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)		GAAAATGGACCTAAGTGTGTTA	0.347													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	63064181	63064181	+	IGR	DEL	A	-	-	rs67114933		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63064181delA								KHDRBS2 (68081 upstream) : LGSN (921676 downstream)																							CTGGAATTCCAAAAAAAAAAA	0.343													1	5	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65537151	65537151	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65537151delT	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						TTGCAGCCTGTTTTTTTATTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	69216279	69216280	+	IGR	INS	-	A	A	rs144629846	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69216279_69216280insA								None (None upstream) : BAI3 (129352 downstream)																							atggaaacagtaaaaaaaaaat	0.005													4	2	---	---	---	---	
LMBRD1	55788	broad.mit.edu	37	6	70478742	70478742	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70478742delT	uc003pfa.2	-						LMBRD1_uc003pez.2_Intron|LMBRD1_uc010kal.2_Intron|LMBRD1_uc003pfb.2_Intron	NM_018368	NP_060838	Q9NUN5	LMBD1_HUMAN	liver regeneration p-53 related protein						interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1						gaaatctttattttttttttc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	74572334	74572334	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74572334delA								CD109 (34294 upstream) : None (None downstream)																							CATGAGCAAGAAATGTGAGGA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	80678119	80678120	+	IGR	DEL	AA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80678119_80678120delAA								ELOVL4 (20804 upstream) : TTK (36239 downstream)																							ctagactaataaaaaaaaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	81678238	81678239	+	IGR	INS	-	TGTC	TGTC	rs142757117	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81678238_81678239insTGTC								BCKDHB (622251 upstream) : FAM46A (777209 downstream)																							tcctcttactttgtctcaccat	0.040													1	5	---	---	---	---	
UBE2CBP	90025	broad.mit.edu	37	6	83734915	83734915	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83734915delT	uc003pjp.2	-						UBE2CBP_uc011dyx.1_Intron|UBE2CBP_uc003pjq.2_Intron	NM_198920	NP_944602	Q7Z6J8	UB2CB_HUMAN	ubiquitin-conjugating enzyme E2C binding							cytoplasm	ligase activity			ovary(1)	1		all_cancers(76;0.000374)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0548)		BRCA - Breast invasive adenocarcinoma(397;0.0944)		tgAAAAGGGGTTTTTAATCAC	0.199													4	2	---	---	---	---	
DOPEY1	23033	broad.mit.edu	37	6	83851099	83851099	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83851099delT	uc003pjs.1	+						DOPEY1_uc011dyy.1_Intron|DOPEY1_uc010kbl.1_Intron|DOPEY1_uc003pjt.2_Intron	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1						protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		ccaaatGCTGTGCCATGTCAA	0.244													4	2	---	---	---	---	
GJB7	375519	broad.mit.edu	37	6	88010321	88010322	+	Intron	DEL	AT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88010321_88010322delAT	uc003plo.2	-							NM_198568	NP_940970	Q6PEY0	CXB7_HUMAN	gap junction protein, beta 7, 25kDa						cell communication	connexon complex|integral to membrane					0		all_cancers(76;1.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;7.38e-10)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00323)		BRCA - Breast invasive adenocarcinoma(108;0.0167)		TCAGTTGACAATATATAATGGG	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92455828	92455828	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92455828delT								None (None upstream) : None (None downstream)																							ATTGAAAAAGTTTTTTTTTTC	0.313													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	100626054	100626055	+	IGR	DEL	GT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100626054_100626055delGT								MCHR2 (183940 upstream) : SIM1 (210696 downstream)																							AGAAAATGAAGTGTGTGTGAGA	0.436													4	2	---	---	---	---	
TUBE1	51175	broad.mit.edu	37	6	112396203	112396206	+	Intron	DEL	AGTT	-	-	rs143220594		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112396203_112396206delAGTT	uc003pvq.2	-						TUBE1_uc003pvr.2_Intron	NM_016262	NP_057346	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1						centrosome cycle|microtubule-based movement|protein polymerization	microtubule|pericentriolar material	GTP binding|GTPase activity|structural constituent of cytoskeleton			ovary(1)	1		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		TATTAGTGAAAGTTAGTATCAGAA	0.225													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	114220543	114220543	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114220543delA								MARCKS (35893 upstream) : FLJ34503 (5008 downstream)																							TCTCTGGATTAAAAAAGCATC	0.413													4	2	---	---	---	---	
TRDN	10345	broad.mit.edu	37	6	123937921	123937922	+	Intron	DEL	TT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123937921_123937922delTT	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_Intron|TRDN_uc010keo.1_Intron	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		TATTTCTAACTTTTATTTTTAC	0.317													4	2	---	---	---	---	
PTPRK	5796	broad.mit.edu	37	6	128694717	128694717	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128694717delA	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron|PTPRK_uc003qbm.3_Intron	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		agtgTTTCATAACTGTCTTAC	0.164													4	2	---	---	---	---	
EPB41L2	2037	broad.mit.edu	37	6	131287661	131287664	+	Intron	DEL	ACAT	-	-	rs144071667	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131287661_131287664delACAT	uc003qch.2	-						EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.1_Intron	NM_001431	NP_001422	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		GAATATGCACACATACACACACAC	0.392													4	2	---	---	---	---	
NHSL1	57224	broad.mit.edu	37	6	138808263	138808263	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138808263delA	uc003qhx.2	-						NHSL1_uc011edp.1_Intron|NHSL1_uc003qhy.2_Intron	NM_020464	NP_065197	Q5SYE7	NHSL1_HUMAN	NHS-like 1 isoform 1												0						GGCACAAAGTAAAAAAAATTG	0.428													4	2	---	---	---	---	
PCMT1	5110	broad.mit.edu	37	6	150123751	150123751	+	Intron	DEL	G	-	-	rs59103152		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150123751delG	uc003qne.2	+						PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		GGCTTTTTTTGTTTGTTTGTT	0.323													8	4	---	---	---	---	
PCMT1	5110	broad.mit.edu	37	6	150123759	150123760	+	Intron	INS	-	T	T	rs66659632		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150123759_150123760insT	uc003qne.2	+						PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		TTGTTTGTTTGTTTGTTTTTTT	0.312													6	3	---	---	---	---	
LRP11	84918	broad.mit.edu	37	6	150173960	150173961	+	Intron	DEL	CT	-	-	rs142047967		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150173960_150173961delCT	uc003qng.2	-						LRP11_uc003qnh.1_Intron	NM_032832	NP_116221	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein							integral to membrane	receptor activity				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		TTGCTGCTCACTCTCAGCAGAA	0.421													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	153528481	153528482	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153528481_153528482delCA								RGS17 (76092 upstream) : OPRM1 (803154 downstream)																							tgttattcttcacatAAATTAC	0.203													4	2	---	---	---	---	
ARID1B	57492	broad.mit.edu	37	6	157337648	157337648	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157337648delA	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron|ARID1B_uc003qqq.1_Intron	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		cttggaggagaaaaaaaaata	0.000													4	2	---	---	---	---	
SNX9	51429	broad.mit.edu	37	6	158296430	158296431	+	Intron	INS	-	ATTA	ATTA	rs142174818	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158296430_158296431insATTA	uc003qqv.1	+							NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9						cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		AAAGGCAGGGTATTGAGGGTTG	0.391													7	4	---	---	---	---	
MAP3K4	4216	broad.mit.edu	37	6	161522201	161522201	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161522201delT	uc003qtn.2	+						MAP3K4_uc010kkc.1_Intron|MAP3K4_uc003qto.2_Intron|MAP3K4_uc011efz.1_Intron|MAP3K4_uc011ega.1_Intron|MAP3K4_uc003qtp.2_Intron|MAP3K4_uc003qtq.2_5'UTR	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4						activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		TTAGTTTTAATTTTTACTCTT	0.269													4	2	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162835227	162835227	+	Intron	DEL	A	-	-	rs79220797	byFrequency	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162835227delA	uc003qtx.3	-						PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		caataacaacaaaaaaGATTT	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165664349	165664349	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165664349delA								None (None upstream) : C6orf118 (28806 downstream)																							tccaaaatccaaaaaagatcc	0.124													4	2	---	---	---	---	
SMOC2	64094	broad.mit.edu	37	6	168978426	168978426	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168978426delG	uc003qws.1	+						SMOC2_uc003qwr.1_Intron	NM_022138	NP_071421	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2						signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		GCAGTGCTGAGGGCAACACAT	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169455636	169455636	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169455636delT								SMOC2 (386965 upstream) : THBS2 (160240 downstream)																							gatgagatcatttttttctag	0.000													4	2	---	---	---	---	
COL28A1	340267	broad.mit.edu	37	7	7496540	7496540	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7496540delT	uc003src.1	-						COL28A1_uc011jxe.1_Intron|COL28A1_uc003srd.2_Intron	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	collagen, type XXVIII precursor						cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			skin(3)	3		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		atgattttggttaagatgtcc	0.000													4	2	---	---	---	---	
NXPH1	30010	broad.mit.edu	37	7	8475126	8475126	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8475126delT	uc003srv.2	+						NXPH1_uc011jxh.1_Intron	NM_152745	NP_689958	P58417	NXPH1_HUMAN	neurexophilin 1 precursor							extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		CCTCCCTCCCTTTTTTTTTTG	0.572													5	4	---	---	---	---	
TAX1BP1	8887	broad.mit.edu	37	7	27835649	27835654	+	Intron	DEL	ATACTG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27835649_27835654delATACTG	uc003szl.2	+						TAX1BP1_uc011jzo.1_Intron|TAX1BP1_uc003szk.2_Intron|TAX1BP1_uc011jzp.1_Intron	NM_006024	NP_006015	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I)						anti-apoptosis|apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production	cytosol	identical protein binding|kinase binding|zinc ion binding			breast(1)	1			GBM - Glioblastoma multiforme(3;0.0823)			ATTTTACAGTATACTGACCTTTAAGT	0.301													32	16	---	---	---	---	
CPVL	54504	broad.mit.edu	37	7	29053939	29053943	+	Intron	DEL	TTTTG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29053939_29053943delTTTTG	uc003szv.2	-						CPVL_uc003szw.2_Intron|CPVL_uc003szx.2_Intron	NM_031311	NP_112601	Q9H3G5	CPVL_HUMAN	serine carboxypeptidase vitellogenic-like						proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2						AGCCAAAGCTttttgttttgttttg	0.234													4	2	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	32585682	32585682	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32585682delT	uc003tcv.1	+						AVL9_uc011kai.1_Intron|AVL9_uc010kwj.1_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						acctggagacttttttttttt	0.025													4	2	---	---	---	---	
TXNDC3	51314	broad.mit.edu	37	7	37923588	37923589	+	Intron	INS	-	A	A	rs5883616		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37923588_37923589insA	uc003tfn.2	+							NM_016616	NP_057700	Q8N427	TXND3_HUMAN	thioredoxin domain containing 3						cell differentiation|cell redox homeostasis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatogenesis|UTP biosynthetic process	cytoplasm|microtubule cytoskeleton	ATP binding|nucleoside diphosphate kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3						cacacacacacccacacaatca	0.163									Kartagener_syndrome				5	3	---	---	---	---	
UBE2D4	51619	broad.mit.edu	37	7	43968393	43968393	+	Intron	DEL	G	-	-	rs146319492	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43968393delG	uc003tja.1	+						URGCP_uc003tiz.2_5'Flank|URGCP_uc011kbj.1_5'Flank|UBE2D4_uc003tjb.1_Intron	NM_015983	NP_057067	Q9Y2X8	UB2D4_HUMAN	ubiquitin-conjugating enzyme E2D 4 (putative)						protein K11-linked ubiquitination|protein K27-linked ubiquitination|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination		ATP binding|protein binding|ubiquitin-protein ligase activity				0						tgtctaggatggggaatcaga	0.000													4	2	---	---	---	---	
VWC2	375567	broad.mit.edu	37	7	49886409	49886409	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49886409delC	uc003tot.1	+							NM_198570	NP_940972	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2						negative regulation of BMP signaling pathway|positive regulation of neuron differentiation	basement membrane|extracellular space					0						ATGTAAATTTCCCCAGCCTCA	0.363													4	2	---	---	---	---	
GRB10	2887	broad.mit.edu	37	7	50809249	50809249	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50809249delA	uc003tpk.2	-						GRB10_uc010kzb.2_Intron|GRB10_uc003tpl.2_Intron|GRB10_uc003tpm.2_Intron|GRB10_uc003tpn.2_Intron	NM_001001555	NP_001001555	Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10 isoform						insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)					acatgtgtttaaaaaaaaaaa	0.209									Russell-Silver_syndrome				2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53446186	53446186	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53446186delA								POM121L12 (341569 upstream) : HPVC1 (822731 downstream)																							CACTGCACTGAAAAAAAAAAT	0.368													6	3	---	---	---	---	
FKBP9L	360132	broad.mit.edu	37	7	55774617	55774617	+	5'Flank	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55774617delA	uc010kzl.2	-							NR_003949				SubName: Full=cDNA, FLJ79189, highly similar to FK506-binding protein 9 (EC 5.2.1.8);												0						accctgtctcaaaaaaaaaga	0.010													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57498589	57498589	+	IGR	DEL	T	-	-	rs75462970		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57498589delT								ZNF479 (291018 upstream) : ZNF716 (11294 downstream)																							CCCTGCCTCCTTTTTTTTTTC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57723412	57723413	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57723412_57723413insA								ZNF716 (190147 upstream) : None (None downstream)																							GCTAGCTTTCTAAAAAATCAAT	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62547646	62547646	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62547646delT								None (None upstream) : LOC643955 (204026 downstream)																							ATTTGTAGCAttttttttttg	0.179													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64960749	64960750	+	IGR	DEL	TA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64960749_64960750delTA								ZNF92 (94752 upstream) : INTS4L2 (152027 downstream)																							TACATTCATTTATTTTTTTAGA	0.356													5	3	---	---	---	---	
GUSB	2990	broad.mit.edu	37	7	65429637	65429637	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65429637delA	uc003tun.2	-						GUSB_uc011kdt.1_Intron	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor						glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0						AAGGAGGTTTAAAAAAAAAAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67273395	67273398	+	IGR	DEL	GGGC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67273395_67273398delGGGC								STAG3L4 (486883 upstream) : None (None downstream)																							TTCTTTTTGTGGGCAGAAAGGGGC	0.456													4	2	---	---	---	---	
RFC2	5982	broad.mit.edu	37	7	73181923	73181923	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73181923delC	uc011kfa.1	-							NM_181471		P35250	RFC2_HUMAN	replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2						agttgaaactcccagattcca	0.010													4	2	---	---	---	---	
SRCRB4D	136853	broad.mit.edu	37	7	76028661	76028662	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76028661_76028662insT	uc003ufb.2	-						ZP3_uc003ufc.3_Intron	NM_080744	NP_542782	Q8WTU2	SRB4D_HUMAN	scavenger receptor cysteine rich domain							extracellular region|membrane	scavenger receptor activity			pancreas(1)	1						gttcacctcccttgggaactgt	0.030													4	2	---	---	---	---	
CCDC132	55610	broad.mit.edu	37	7	92987201	92987201	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92987201delT	uc003umo.2	+						CCDC132_uc003umq.2_Intron|CCDC132_uc003ump.2_Intron|CCDC132_uc003umr.2_Intron|CCDC132_uc011khz.1_Intron	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a												0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			TTGTTGGAGATTTTTTTTTTA	0.313													4	2	---	---	---	---	
CALCR	799	broad.mit.edu	37	7	93065669	93065671	+	Intron	DEL	TGT	-	-	rs144127533		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93065669_93065671delTGT	uc003umv.1	-						CALCR_uc011kia.1_Intron|CALCR_uc003ums.1_Intron|CALCR_uc003umt.1_Intron|CALCR_uc003umu.1_Intron|CALCR_uc003umw.2_Intron	NM_001742	NP_001733	P30988	CALCR_HUMAN	calcitonin receptor isoform 2 precursor						activation of adenylate cyclase activity by G-protein signaling pathway|elevation of cytosolic calcium ion concentration|positive regulation of adenylate cyclase activity|response to glucocorticoid stimulus	integral to plasma membrane	calcitonin binding|calcitonin binding|calcitonin receptor activity|calcitonin receptor activity|protein binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Salmon Calcitonin(DB00017)	tttaattttatgttccctccagc	0.113													3	3	---	---	---	---	
PPP1R9A	55607	broad.mit.edu	37	7	94557556	94557557	+	Intron	DEL	GT	-	-	rs113030678		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94557556_94557557delGT	uc003unp.2	+						PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Intron	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)							cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			catgaagggggtgtgtgtgtgt	0.124										HNSCC(28;0.073)			4	2	---	---	---	---	
SMURF1	57154	broad.mit.edu	37	7	98718432	98718432	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98718432delA	uc003upu.1	-						SMURF1_uc003upv.1_Intron|SMURF1_uc003upt.2_Intron	NM_020429	NP_065162	Q9HCE7	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 isoform						BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			GGAAAGGGAGAAAAAAAAAAA	0.358													2	4	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101762573	101762574	+	Intron	INS	-	CT	CT	rs147984542	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101762573_101762574insCT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						ATCCCTCTCCCGTTTTGGAGAG	0.599													3	3	---	---	---	---	
NAMPT	10135	broad.mit.edu	37	7	105893889	105893890	+	Intron	DEL	TT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105893889_105893890delTT	uc003vdq.2	-							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						CATGTGACCCTTAAGGTATCTC	0.371													4	2	---	---	---	---	
IMMP2L	83943	broad.mit.edu	37	7	110540809	110540809	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110540809delG	uc003vfq.1	-						IMMP2L_uc010ljr.1_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)		aactagagctggtagcatcca	0.129													4	2	---	---	---	---	
IFRD1	3475	broad.mit.edu	37	7	112090771	112090771	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112090771delC	uc003vgh.2	+	2	471	c.28delC	c.(28-30)CCCfs	p.P10fs	IFRD1_uc011kmn.1_Intron|IFRD1_uc003vgi.2_Frame_Shift_Del_p.P10fs|IFRD1_uc003vgj.2_Frame_Shift_Del_p.P10fs|IFRD1_uc011kmo.1_RNA|IFRD1_uc011kmp.1_5'Flank	NM_001007245	NP_001007246	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	10					multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2						GCGGAACACTCCCCACCgcgg	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114845617	114845617	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114845617delG								MDFIC (186354 upstream) : TFEC (729585 downstream)																							ACATTTTTTTGGGGGTGTGtg	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	122629954	122629955	+	IGR	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122629954_122629955insC								CADPS2 (103400 upstream) : TAS2R16 (4804 downstream)																							AGATCTACTTTCCCCTGCAAAT	0.287													4	2	---	---	---	---	
SPAM1	6677	broad.mit.edu	37	7	123611066	123611067	+	3'UTR	INS	-	A	A	rs150920351	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123611066_123611067insA	uc003vle.2	+	7						NM_003117	NP_003108	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 1						binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)	TTTAGGAAATGAAAAAACCATG	0.361													3	4	---	---	---	---	
TSGA13	114960	broad.mit.edu	37	7	130357306	130357306	+	Intron	DEL	T	-	-	rs71960059		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130357306delT	uc003vqi.2	-						TSGA13_uc003vqj.2_Intron	NM_052933	NP_443165	Q96PP4	TSG13_HUMAN	testis specific, 13											ovary(2)	2	Melanoma(18;0.0435)					TTGAGGGTACTTTTTTTTTTT	0.378													4	2	---	---	---	---	
KIAA1549	57670	broad.mit.edu	37	7	138599402	138599402	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138599402delG	uc011kql.1	-						KIAA1549_uc003vuk.3_Intron|KIAA1549_uc011kqj.1_Intron	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1							integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						TACTTCCTCTGGGTCAAAGGT	0.448			O	BRAF	pilocytic astrocytoma								4	2	---	---	---	---	
ZC3HAV1	56829	broad.mit.edu	37	7	138770764	138770764	+	Intron	DEL	A	-	-	rs10716830		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138770764delA	uc003vun.2	-						ZC3HAV1_uc003vup.2_Intron	NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1						response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1						ctcaaaaaagaaaaaaaaaaa	0.189													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	140961455	140961455	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140961455delC								MRPS33 (246674 upstream) : AGK (289623 downstream)																							TGAGCTCCGGCCCCGCTCCAG	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141198282	141198283	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141198282_141198283insA								MRPS33 (483501 upstream) : AGK (52795 downstream)																							TATACCATGGGAATCATTCATG	0.119													4	2	---	---	---	---	
ARHGEF5	7984	broad.mit.edu	37	7	144071639	144071640	+	Intron	DEL	GT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144071639_144071640delGT	uc003wel.2	+						ARHGEF5_uc003wek.2_Intron|ARHGEF5_uc003wem.2_Intron	NM_005435	NP_005426	Q12774	ARHG5_HUMAN	rho guanine nucleotide exchange factor 5						intracellular signal transduction|regulation of Rho protein signal transduction	intracellular	GTP binding|protein binding|Rho guanyl-nucleotide exchange factor activity			skin(2)	2	Melanoma(164;0.14)					GACAGTGGTAGTTAGAGGGTTC	0.480													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	144757368	144757368	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144757368delA								TPK1 (224222 upstream) : None (None downstream)																							CACCAAGACCAAAAGGACCAC	0.189													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147577087	147577087	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147577087delT	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)			AAAAATGAAATTGAAAACAGT	0.453										HNSCC(39;0.1)			4	2	---	---	---	---	
GIMAP5	55340	broad.mit.edu	37	7	150437273	150437273	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150437273delA	uc003whr.1	+						GIMAP5_uc010lpu.2_Intron	NM_018384	NP_060854	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5							integral to membrane|mitochondrial outer membrane	GTP binding			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACAATGCTGGAAACCCGGAGC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155006305	155006305	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155006305delA								HTR5A (128846 upstream) : INSIG1 (83181 downstream)																							GGTGAGCAGGACACCTCATCA	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157257032	157257032	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157257032delA								DNAJB6 (46900 upstream) : PTPRN2 (74719 downstream)																							GTTTCTTAAGAAAAAAAAATC	0.448													4	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157788500	157788501	+	Intron	DEL	TT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157788500_157788501delTT	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)		CAAACTCAAGTTTAAGCAAAAG	0.361													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158155401	158155401	+	Intron	DEL	G	-	-	rs55835654		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158155401delG	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)		tcacaaccacgctcatcctgg	0.224													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	423201	423201	+	5'Flank	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:423201delC	uc003wpb.1	+											Homo sapiens cDNA FLJ32061 fis, clone OCBBF1000030.																		AAAGCAGTGTCCCCCCGCGTC	0.532													4	2	---	---	---	---	
ERICH1	157697	broad.mit.edu	37	8	598408	598408	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:598408delT	uc011kwh.1	-						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)		GGGGAGGTGCTGGGGACCTGT	0.478													4	2	---	---	---	---	
DLGAP2	9228	broad.mit.edu	37	8	1569101	1569101	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1569101delC	uc003wpl.2	+						DLGAP2_uc003wpm.2_Intron|uc003wpn.1_Intron	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2						neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GAATGCCTTTCCCCCTTTACC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2304820	2304820	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2304820delA								MYOM2 (211441 upstream) : CSMD1 (488056 downstream)																							tactatggagaaaaaaaaaga	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	7327110	7327110	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7327110delA								SPAG11B (5918 upstream) : DEFB104A (721 downstream)																							cgctgttgacattccttggct	0.015													4	2	---	---	---	---	
SH2D4A	63898	broad.mit.edu	37	8	19170776	19170776	+	5'Flank	DEL	A	-	-	rs111978715		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19170776delA	uc003wzb.2	+						SH2D4A_uc011kym.1_5'Flank|SH2D4A_uc003wzc.2_5'Flank	NM_022071	NP_071354	Q9H788	SH24A_HUMAN	SH2 domain containing 4A							cytoplasm|nucleus	protein binding				0				Colorectal(111;0.0732)		TCAACAAAAGAAAAAAAAAAA	0.483													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20932590	20932590	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20932590delT								LZTS1 (819787 upstream) : GFRA2 (616940 downstream)																							tgcatcatcatttttttttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21263826	21263826	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21263826delC								None (None upstream) : GFRA2 (285704 downstream)																							AGCCACCAGTCCCCATGCACC	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	22073566	22073566	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22073566delC								BMP1 (3729 upstream) : PHYHIP (3651 downstream)																							ACCCTCCCTTCCCCCACCCCT	0.627													4	2	---	---	---	---	
SLC39A14	23516	broad.mit.edu	37	8	22232087	22232088	+	Intron	INS	-	TGA	TGA	rs142079010	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22232087_22232088insTGA	uc003xbq.3	+						SLC39A14_uc011kzg.1_Intron|SLC39A14_uc003xbp.3_Intron|SLC39A14_uc011kzh.1_Intron	NM_001128431	NP_001121903	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter),							endoplasmic reticulum|Golgi apparatus|integral to membrane|lamellipodium|plasma membrane	zinc ion transmembrane transporter activity				0				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		CCCAGAGTGGCTGAGAGGGAGC	0.545													3	6	---	---	---	---	
PBK	55872	broad.mit.edu	37	8	27697882	27697882	+	5'Flank	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27697882delA	uc003xgi.2	-						PBK_uc011lap.1_5'Flank	NM_018492	NP_060962	Q96KB5	TOPK_HUMAN	PDZ binding kinase						mitosis		ATP binding|protein binding|protein serine/threonine kinase activity				0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		CTGCCAATGGAAAAAAAAACa	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	33205927	33205927	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33205927delA								NRG1 (583369 upstream) : FUT10 (22419 downstream)																							AATTTCAACCAAAAAAAAAGT	0.398													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	36843653	36843654	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36843653_36843654delCA								KCNU1 (50012 upstream) : ZNF703 (709647 downstream)																							ctctctctttcACACACACACA	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	38419943	38419943	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38419943delA								C8orf86 (33763 upstream) : RNF5P1 (37752 downstream)																							TCAGTTTGGGAAAAAAATTTA	0.413													4	2	---	---	---	---	
CPA6	57094	broad.mit.edu	37	8	68396310	68396310	+	Intron	DEL	T	-	-	rs71554608		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68396310delT	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)			ttgccttctcttttttttttt	0.055													4	3	---	---	---	---	
CPA6	57094	broad.mit.edu	37	8	68482335	68482335	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-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													6	4	---	---	---	---	
SLCO5A1	81796	broad.mit.edu	37	8	70678777	70678778	+	Intron	DEL	TG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70678777_70678778delTG	uc003xyl.2	-						SLCO5A1_uc010lzb.2_Intron|SLCO5A1_uc011lfa.1_Intron|SLCO5A1_uc003xyk.2_Intron|SLCO5A1_uc010lzc.2_Intron	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,							integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			tgtgtgtgcatgtgtgtgtttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	78350815	78350816	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78350815_78350816insA								PEX2 (438291 upstream) : None (None downstream)																							AAATCTGTTTTAAAAGCGTGTT	0.168													4	2	---	---	---	---	
CNBD1	168975	broad.mit.edu	37	8	88069148	88069148	+	Intron	DEL	T	-	-	rs73693008	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88069148delT	uc003ydy.2	+							NM_173538	NP_775809	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1											ovary(3)	3						aagaaagccctcatgatctgt	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	89747685	89747685	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89747685delT								MMP16 (407968 upstream) : None (None downstream)																							TGACGAATGATTTGCAGAAGA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	93616684	93616684	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93616684delA								RUNX1T1 (508978 upstream) : C8orf83 (279181 downstream)																							TAGTCTTTTTAAAAAATAAGT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	97367449	97367449	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97367449delC								PTDSS1 (20675 upstream) : SDC2 (138433 downstream)																							TGGCTCAGTGCCCATCAGTTA	0.483													4	2	---	---	---	---	
PGCP	10404	broad.mit.edu	37	8	97667203	97667204	+	Intron	DEL	AA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97667203_97667204delAA	uc003yhw.2	+							NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)					cagctgcattaaaaccctgttt	0.000													4	2	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99607998	99607998	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99607998delA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		GGAACAGAAGAAAAAAAAAAC	0.318													4	2	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	102755511	102755511	+	Intron	DEL	A	-	-	rs67529557		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102755511delA	uc003yke.2	-						NCALD_uc003ykf.2_Intron|NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_032041	NP_114430	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			CAGTAGGTCCAAAGCATGATA	0.403													2	4	---	---	---	---	
RRM2B	50484	broad.mit.edu	37	8	103247530	103247530	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103247530delG	uc003ykn.2	-						RRM2B_uc003yko.2_Intron|RRM2B_uc010mbv.1_Intron|RRM2B_uc010mbw.1_Intron|RRM2B_uc010mbx.1_Intron|RRM2B_uc010mby.1_Intron	NM_015713	NP_056528	Q7LG56	RIR2B_HUMAN	ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process|DNA repair|nucleobase, nucleoside and nucleotide interconversion	nucleoplasm	ribonucleoside-diphosphate reductase activity|transition metal ion binding			ovary(2)	2	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000728)			TTTGGGACAAGGGGCAAGAAC	0.388								Direct_reversal_of_damage|Modulation_of_nucleotide_pools					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	111762700	111762701	+	IGR	DEL	AG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111762700_111762701delAG								KCNV1 (774624 upstream) : None (None downstream)																							CAATAGTATTagagagagagag	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	117827867	117827867	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117827867delC								UTP23 (40948 upstream) : RAD21 (30307 downstream)																							AGATGATGTACAAAACCTAAT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120013157	120013157	+	IGR	DEL	A	-	-	rs138296702		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120013157delA								TNFRSF11B (48774 upstream) : COLEC10 (66267 downstream)																							agtcaaccataaatgcagagg	0.000													2	5	---	---	---	---	
ZHX2	22882	broad.mit.edu	37	8	123856960	123856961	+	Intron	INS	-	TA	TA	rs146798797	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123856960_123856961insTA	uc003ypk.1	+							NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2							cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			ctctctctctttctctctctct	0.317													4	2	---	---	---	---	
MTSS1	9788	broad.mit.edu	37	8	125727155	125727155	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125727155delC	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GCTTAATCCTCCCCAGAATAA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127576426	127576426	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127576426delT								FAM84B (5960 upstream) : LOC727677 (725636 downstream)																							GAAATTGATGTTTTAGTCCAG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136339450	136339451	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136339450_136339451delCA								LOC286094 (27491 upstream) : KHDRBS3 (130265 downstream)																							GGGGTGCAGCCACTGCAGCTCA	0.525													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144220174	144220174	+	IGR	DEL	G	-	-	rs78429705		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144220174delG								C8orf31 (84454 upstream) : LY6H (19158 downstream)																							cacactgggtggggggatgct	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	5286960	5286960	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5286960delG								INSL4 (52994 upstream) : RLN2 (12908 downstream)																							tttaagttcaggggtacatgt	0.000													4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	9348833	9348833	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9348833delT	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CTAATTAGGGTGCTCTCTTAA	0.388										TSP Lung(15;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	11119238	11119238	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11119238delA								PTPRD (506515 upstream) : None (None downstream)																							CCTCCCCATCAAAAAAAAGTA	0.348													4	2	---	---	---	---	
FREM1	158326	broad.mit.edu	37	9	14749751	14749751	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14749751delG	uc003zlm.2	-						FREM1_uc010mic.2_Intron|FREM1_uc003zlk.2_Intron|FREM1_uc003zll.2_Intron	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor						cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)		ACACTACAGTGGGGGCTCAGA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16267952	16267954	+	IGR	DEL	TGC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16267952_16267954delTGC								C9orf93 (296057 upstream) : BNC2 (141548 downstream)																							AATCACTGTTTGCTGCTGCTGCT	0.389													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16899404	16899404	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16899404delG								BNC2 (28618 upstream) : CNTLN (235634 downstream)																							GAGCCCTTTTGGGGAAAACAT	0.353													4	2	---	---	---	---	
FAM154A	158297	broad.mit.edu	37	9	18937904	18937904	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18937904delA	uc003zni.1	-						FAM154A_uc010mip.1_Intron	NM_153707	NP_714918	Q8IYX7	F154A_HUMAN	hypothetical protein LOC158297											pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)		AGTAGTATTCAAAAAAAAACC	0.169													4	2	---	---	---	---	
ELAVL2	1993	broad.mit.edu	37	9	23783791	23783791	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23783791delA	uc003zpu.2	-						ELAVL2_uc003zps.2_Intron|ELAVL2_uc003zpt.2_Intron|ELAVL2_uc003zpv.2_Intron|ELAVL2_uc003zpw.2_Intron	NM_004432	NP_004423	Q12926	ELAV2_HUMAN	ELAV (embryonic lethal, abnormal vision,						regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		ATGACAGATGAAAAAAAAAAA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	25955951	25955951	+	IGR	DEL	A	-	-	rs74593513		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25955951delA								TUSC1 (277095 upstream) : C9orf82 (884733 downstream)																							ctagagttagaaaaaaaaagt	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33564910	33564910	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33564910delT								SUGT1P1 (53863 upstream) : ANXA2P2 (59313 downstream)																							attatttttgtttactgtcag	0.000													4	2	---	---	---	---	
UNC13B	10497	broad.mit.edu	37	9	35214821	35214821	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35214821delT	uc003zwq.2	+						UNC13B_uc010mkl.1_Intron|UNC13B_uc003zwr.2_Intron	NM_006377	NP_006368	O14795	UN13B_HUMAN	UNC13 (C. elegans)-like						excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			CTATCTAGAATTTTTTTACTA	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	38484479	38484479	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38484479delA								IGFBPL1 (60035 upstream) : C9orf122 (136606 downstream)																							ggaaaattttaaaaacttgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68490476	68490476	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68490476delA								FAM27B (696287 upstream) : MIR1299 (511763 downstream)																							TGAAAGGTTTAAAAATATAAT	0.209													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69056460	69056461	+	IGR	INS	-	A	A	rs145372655		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69056460_69056461insA								MIR1299 (54139 upstream) : PGM5P2 (23784 downstream)																							ccaaataagacaaaaaaatcac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	76335973	76335973	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76335973delA								ANXA1 (550666 upstream) : RORB (776279 downstream)																							ttacctccagaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	87235145	87235145	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87235145delT								SLC28A3 (251732 upstream) : NTRK2 (48321 downstream)																							GCTCTGTTTCTTTTTCTCCAG	0.468													4	2	---	---	---	---	
NAA35	60560	broad.mit.edu	37	9	88592940	88592940	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88592940delA	uc004aoi.3	+						NAA35_uc004aoj.3_Intron|NAA35_uc004aok.1_Intron	NM_024635	NP_078911	Q5VZE5	NAA35_HUMAN	corneal wound healing-related protein						smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3						TTTTATTGTGAAAAAAAAAAC	0.269													6	3	---	---	---	---	
SEMA4D	10507	broad.mit.edu	37	9	92080377	92080377	+	Intron	DEL	G	-	-	rs34759545		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92080377delG	uc004aqo.1	-						SEMA4D_uc011ltm.1_Intron|SEMA4D_uc011ltn.1_Intron|SEMA4D_uc011lto.1_Intron|SEMA4D_uc004aqp.1_Intron	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1						anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2						GGAGTTggctgggggaatggg	0.035													3	4	---	---	---	---	
LOC100129066	100129066	broad.mit.edu	37	9	92295684	92295684	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92295684delA	uc004aqs.2	+							NR_024280				Homo sapiens cDNA FLJ42342 fis, clone UTERU2000794.												0						AAAGTAAGCTAAAAAAAAAAA	0.463													6	4	---	---	---	---	
NCBP1	4686	broad.mit.edu	37	9	100431489	100431489	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100431489delA	uc004axq.2	+							NM_002486	NP_002477	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa						gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA cleavage|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of mRNA 3'-end processing|positive regulation of viral transcription|regulation of translational initiation|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm|ribonucleoprotein complex	protein binding|RNA cap binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.158)				TCCATGCTTGAAAAAAAATTG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	101963231	101963232	+	IGR	INS	-	T	T	rs139939393	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101963231_101963232insT								TGFBR1 (46760 upstream) : ALG2 (15476 downstream)																							GGCTCTTATCGTGGGGAATCTG	0.401													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102327866	102327867	+	IGR	INS	-	A	A	rs113588181		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102327866_102327867insA								SEC61B (334966 upstream) : NR4A3 (256270 downstream)																							TATTTGTCCTGAAAAAAAAAAT	0.351													4	2	---	---	---	---	
ALDOB	229	broad.mit.edu	37	9	104193311	104193312	+	Intron	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104193311_104193312insA	uc004bbk.2	-							NM_000035	NP_000026	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate						fructose 1,6-bisphosphate metabolic process|fructose catabolic process|gluconeogenesis|glycolysis|NADH oxidation|positive regulation of ATPase activity|vacuolar proton-transporting V-type ATPase complex assembly	centriolar satellite|cytosol	ATPase binding|cytoskeletal protein binding|fructose binding|fructose-bisphosphate aldolase activity|identical protein binding			skin(1)	1		Acute lymphoblastic leukemia(62;0.0559)				CACAGGTGGATAAGCAAATGAG	0.465													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110615425	110615425	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110615425delA								KLF4 (363378 upstream) : None (None downstream)																							cccatctcttaaaaaaaaaca	0.030													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119781091	119781091	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119781091delT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						GAAAATGGGATTTTTTTTTAC	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	128796180	128796180	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128796180delA								PBX3 (66527 upstream) : FAM125B (292948 downstream)																							ATTGCAGTCCAGGGGTCTGCT	0.303													4	2	---	---	---	---	
ENG	2022	broad.mit.edu	37	9	130596315	130596315	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130596315delT	uc004bsj.3	-						ENG_uc011mam.1_Intron|ENG_uc004bsk.3_Intron	NM_001114753	NP_001108225	P17813	EGLN_HUMAN	endoglin isoform 1 precursor						artery morphogenesis|BMP signaling pathway|cell adhesion|cell chemotaxis|central nervous system vasculogenesis|chronological cell aging|detection of hypoxia|extracellular matrix disassembly|heart looping|negative regulation of endothelial cell proliferation|negative regulation of nitric-oxide synthase activity|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of protein autophosphorylation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|patterning of blood vessels|positive regulation of BMP signaling pathway|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of systemic arterial blood pressure|positive regulation of transcription from RNA polymerase II promoter|regulation of cell adhesion|regulation of cell proliferation|regulation of transcription, DNA-dependent|regulation of transforming growth factor beta receptor signaling pathway|smooth muscle tissue development|transforming growth factor beta receptor signaling pathway|venous blood vessel morphogenesis|wound healing	cell surface|external side of plasma membrane|extracellular space|membrane fraction	activin binding|galactose binding|glycosaminoglycan binding|protein homodimerization activity|transforming growth factor beta binding|transforming growth factor beta receptor activity|transforming growth factor beta receptor, cytoplasmic mediator activity|transmembrane receptor activity|type I transforming growth factor beta receptor binding|type II transforming growth factor beta receptor binding				0						gtaaacacaattTTTTTTTTC	0.050									Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	136122653	136122653	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136122653delA								OBP2B (38025 upstream) : ABO (7910 downstream)																							TGAGGATCAGAGGGGCACATC	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	318412	318415	+	IGR	DEL	ACTC	-	-	rs71857079		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:318412_318415delACTC								ZMYND11 (17836 upstream) : DIP2C (1717 downstream)																							TCAGGCACAAACTCACTGTGCCCA	0.544													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2088826	2088827	+	IGR	DEL	GA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2088826_2088827delGA								ADARB2 (309108 upstream) : None (None downstream)																							TCATTGAATGgagagagagaga	0.248													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4863782	4863782	+	IGR	DEL	A	-	-	rs113465730		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4863782delA								LOC100216001 (143520 upstream) : AKR1E2 (4620 downstream)																							GTCCAGCTGCAAAAAAAAAAA	0.448													3	3	---	---	---	---	
TAF3	83860	broad.mit.edu	37	10	7880871	7880871	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7880871delG	uc010qbd.1	+							NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140						maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						GGCATTGCTTGTttttttttt	0.388													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11000339	11000339	+	IGR	DEL	G	-	-	rs62209	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11000339delG								LOC254312 (6213 upstream) : CELF2 (46920 downstream)																							GTCAGGGAGAGGGAAGTGAGA	0.463													4	2	---	---	---	---	
UCMA	221044	broad.mit.edu	37	10	13274145	13274146	+	Intron	INS	-	G	G	rs139170966	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13274145_13274146insG	uc001imd.2	-							NM_145314	NP_660357	Q8WVF2	UCMA_HUMAN	upper zone of growth plate and cartilage matrix							proteinaceous extracellular matrix					0						aggccgaggcaggggggtcacc	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	15937629	15937629	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15937629delA								FAM188A (35110 upstream) : PTER (541338 downstream)																							ACTTACCAGCAAAAAATCACT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	19417975	19417975	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19417975delT								ARL5B (451035 upstream) : PLXDC2 (687397 downstream)																							cagatgcatgttttttttcca	0.164													4	3	---	---	---	---	
MLLT10	8028	broad.mit.edu	37	10	22030455	22030455	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22030455delT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001ira.2_Intron|MLLT10_uc001irb.2_Intron	NM_004641	NP_004632	P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2						TGTAACTCCATTTTTTTTATA	0.388			T	MLL|PICALM|CDK6	AL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37971519	37971520	+	IGR	INS	-	AC	AC	rs146381246	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37971519_37971520insAC								ANKRD30A (450024 upstream) : ZNF248 (118927 downstream)																							ACATGGGAGAGACACACACACA	0.495													4	2	---	---	---	---	
SEPT7L	285961	broad.mit.edu	37	10	38682274	38682277	+	Intron	DEL	AGAC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38682274_38682277delAGAC	uc009xmd.1	-							NR_027269				Homo sapiens similar to cell division cycle 10, mRNA (cDNA clone IMAGE:5296867).												0						GTATAAAGAAAGACAGAGGAACTG	0.314													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42781394	42781394	+	IGR	DEL	T	-	-	rs111295536		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42781394delT								None (None upstream) : LOC441666 (45921 downstream)																							catataatggttactgatcta	0.000													5	3	---	---	---	---	
FRMPD2	143162	broad.mit.edu	37	10	49383345	49383345	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49383345delT	uc001jgi.2	-						FRMPD2_uc001jgh.2_Intron|FRMPD2_uc001jgj.2_Intron|FRMPD2L1_uc001jgf.2_5'Flank|FRMPD2_uc001jgg.2_Intron|FRMPD2_uc001jgk.2_Intron	NM_001018071	NP_001018081	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2 isoform 3						tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)		CCAGCATGTATTTTTTTTATT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	51810704	51810705	+	Intron	INS	-	A	A	rs5784817		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51810704_51810705insA	uc001jiz.1	-											Homo sapiens cDNA FLJ31813 fis, clone NT2RI2009517.																		TACACCATGCTAAAAAAATAAA	0.406													4	3	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53134735	53134738	+	Intron	DEL	GAGA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53134735_53134738delGAGA	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		aagtcagaaggagagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54339095	54339098	+	IGR	DEL	AGAA	-	-	rs10599752		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54339095_54339098delAGAA								DKK1 (261679 upstream) : MBL2 (186043 downstream)																							GACGGTCAGGAGAAAGAAACGTGT	0.392													1	5	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	57022101	57022102	+	Intron	INS	-	G	G	rs140207809	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57022101_57022102insG	uc001jjv.1	-							NM_001142770	NP_001136242	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ccatggatctagtgacgacagg	0.000										HNSCC(58;0.16)			2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	58551295	58551295	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58551295delA								ZWINT (430261 upstream) : None (None downstream)																							CAGTTAAGATAAAAAAAAAAA	0.333													3	3	---	---	---	---	
ANK3	288	broad.mit.edu	37	10	62144056	62144057	+	Intron	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62144056_62144057insA	uc001jky.2	-						ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						CAAAAAATTTTAAAAAAGAATC	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65527084	65527085	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65527084_65527085insA								REEP3 (145113 upstream) : None (None downstream)																							TGATTCAAGAGAAAAAAAAAAT	0.396													4	3	---	---	---	---	
P4HA1	5033	broad.mit.edu	37	10	74804019	74804020	+	Intron	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74804019_74804020insC	uc010qka.1	-						P4HA1_uc001jtg.2_Intron|P4HA1_uc001jth.2_Intron|P4HA1_uc010qkb.1_Intron|P4HA1_uc001jti.2_Intron	NM_001142595	NP_001136067	P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha I subunit isoform 2							endoplasmic reticulum lumen|mitochondrion	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity			ovary(1)	1	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	ACAGAAACTTTCTCAGATCTAG	0.257													4	2	---	---	---	---	
USP54	159195	broad.mit.edu	37	10	75323072	75323073	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75323072_75323073insT	uc001juo.2	-						USP54_uc001jup.2_Intron|USP54_uc010qkl.1_Intron	NM_152586	NP_689799	Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54						ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)					ctcaatttacatttcttagatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85582371	85582371	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85582371delA								NRG3 (835436 upstream) : GHITM (316814 downstream)																							gccaTATTCTAAAGTGTTCCA	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91659587	91659587	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91659587delT								KIF20B (124887 upstream) : HTR7 (840991 downstream)																							GTCTTTTTTCTTTTTTTCCCC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	92303221	92303221	+	IGR	DEL	A	-	-	rs113048209		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92303221delA								KIF20B (768521 upstream) : HTR7 (197357 downstream)																							TGAGAGAGAGAAAAAAAAAAT	0.393													4	2	---	---	---	---	
LOC100188947	100188947	broad.mit.edu	37	10	93302303	93302303	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93302303delA	uc010qnl.1	-							NR_024467				Homo sapiens, clone IMAGE:6063621, mRNA.												0						TGACTTAAACAAAACACTCTG	0.284													4	2	---	---	---	---	
IDE	3416	broad.mit.edu	37	10	94238817	94238817	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94238817delA	uc001kia.2	-						IDE_uc010qnp.1_Intron|IDE_uc001khz.2_Intron	NM_004969	NP_004960	P14735	IDE_HUMAN	insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AAAGACGTTTAAAAAAAAAGA	0.269													4	2	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95125795	95125796	+	Intron	INS	-	TG	TG	rs145681166	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95125795_95125796insTG	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						atctgtgaaactgacgggggac	0.020													3	3	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100290475	100290476	+	Intron	DEL	AC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100290475_100290476delAC	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)		TGTAGTGTATACACAGCATCCA	0.545													4	2	---	---	---	---	
SEC31B	25956	broad.mit.edu	37	10	102276430	102276431	+	Intron	DEL	AG	-	-	rs10527289		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102276430_102276431delAG	uc001krc.1	-						SEC31B_uc010qpo.1_Intron|SEC31B_uc001krd.1_Intron|SEC31B_uc001krf.1_Intron|SEC31B_uc001kre.1_Intron|SEC31B_uc010qpp.1_Intron|SEC31B_uc009xwn.1_Intron|SEC31B_uc009xwo.1_Intron|SEC31B_uc010qpq.1_Intron|SEC31B_uc010qpr.1_Intron	NM_015490	NP_056305	Q9NQW1	SC31B_HUMAN	SEC31 homolog B						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane				ovary(1)	1		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		aaaaaaaaaaaGACGTACCTAA	0.238													4	2	---	---	---	---	
COL17A1	1308	broad.mit.edu	37	10	105797045	105797046	+	Intron	INS	-	TT	TT	rs34553613		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105797045_105797046insTT	uc001kxr.2	-							NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen						cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TGTTGTTGGGATTTTTTTTTTT	0.416													4	2	---	---	---	---	
SORCS1	114815	broad.mit.edu	37	10	108670384	108670384	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108670384delT	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TTGACAGTTGTTTTTCAATAG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	111017514	111017514	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111017514delC								None (None upstream) : XPNPEP1 (607010 downstream)																							AAATATTGCTCCCACTTTTTC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	112301361	112301361	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112301361delG								DUSP5 (30061 upstream) : SMC3 (26088 downstream)																							TTTGACTTAAGGGGAAAGAAA	0.338													4	2	---	---	---	---	
ABLIM1	3983	broad.mit.edu	37	10	116304544	116304544	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116304544delT	uc010qsg.1	-						ABLIM1_uc010qsh.1_Intron|ABLIM1_uc010qsi.1_Intron|ABLIM1_uc010qsk.1_Intron|ABLIM1_uc009xyp.2_Intron|ABLIM1_uc009xyo.2_Intron	NM_002313	NP_002304	O14639	ABLM1_HUMAN	actin-binding LIM protein 1 isoform a						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		TTTATCATTCTTTTTTTTTTC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	120052624	120052624	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120052624delT								CASC2 (82965 upstream) : C10orf84 (15948 downstream)																							TTCTAATGTCTTTTAGCCTGT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	124217902	124217903	+	IGR	INS	-	AGAG	AGAG	rs113547953		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124217902_124217903insAGAG								ARMS2 (1035 upstream) : HTRA1 (3138 downstream)																							AAGAATCTAAAAGAAAGAGCAA	0.426													2	6	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126711842	126711842	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126711842delG	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron|CTBP2_uc001lie.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		TCTTTGGGCTGGGACTGCGTT	0.493													4	2	---	---	---	---	
PTPRE	5791	broad.mit.edu	37	10	129848618	129848619	+	Intron	INS	-	GGAC	GGAC	rs148051817	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129848618_129848619insGGAC	uc001lkb.2	+						PTPRE_uc009yat.2_Intron|PTPRE_uc010qup.1_Intron|PTPRE_uc009yau.2_Intron|PTPRE_uc001lkc.1_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)				gatggatggatggatggatgga	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130252841	130252841	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130252841delT								MKI67 (328373 upstream) : None (None downstream)																							GTCTTTCCTCTTGCATTTCAG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130263297	130263297	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130263297delC								MKI67 (338829 upstream) : None (None downstream)																							AGGATCAGGTCCCAGATTTCT	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130750514	130750514	+	IGR	DEL	C	-	-	rs67738260		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130750514delC								MKI67 (826046 upstream) : MGMT (514940 downstream)																							ACTTTTTTTTCCCCCTTAACA	0.398													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132690061	132690062	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132690061_132690062delCA								GLRX3 (707277 upstream) : TCERG1L (200594 downstream)																							taggtgtgcgcacacacacaca	0.307													4	2	---	---	---	---	
CYP2E1	1571	broad.mit.edu	37	10	135351623	135351623	+	Intron	DEL	T	-	-	rs71474737		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135351623delT	uc001lnj.1	+						CYP2E1_uc001lnk.1_Intron|CYP2E1_uc009ybl.1_Intron|CYP2E1_uc009ybm.1_Intron|CYP2E1_uc001lnl.1_Intron	NM_000773	NP_000764	P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E,						drug metabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding			central_nervous_system(3)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Dacarbazine(DB00851)|Dapsone(DB00250)|Enflurane(DB00228)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethosuximide(DB00593)|Fomepizole(DB01213)|Glutathione(DB00143)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Isoniazid(DB00951)|Menadione(DB00170)|Mephenytoin(DB00532)|Methoxyflurane(DB01028)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitrofurantoin(DB00698)|Orphenadrine(DB01173)|Phenelzine(DB00780)|Quinidine(DB00908)|S-Adenosylmethionine(DB00118)|Sevoflurane(DB01236)|Theophylline(DB00277)|Tolbutamide(DB01124)	TGTAGGTGGATTTTTTTTTTC	0.348									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	142105	142105	+	5'Flank	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:142105delA	uc010qvj.1	-						LOC100133161_uc001lnx.3_5'Flank|uc001lnz.2_Intron					Homo sapiens cDNA FLJ61476 complete cds.																		aaaaagttagaaaaaaaaaga	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	1667074	1667075	+	IGR	DEL	AC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1667074_1667075delAC								KRTAP5-5 (14917 upstream) : FAM99A (19754 downstream)																							CTAAACTCTTACAGCTTGTATT	0.446													4	2	---	---	---	---	
SCUBE2	57758	broad.mit.edu	37	11	9060796	9060798	+	Intron	DEL	GAC	-	-	rs80019039		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9060796_9060798delGAC	uc001mhh.1	-						SCUBE2_uc001mhi.1_Intron|SCUBE2_uc001mhj.1_Intron	NM_020974	NP_066025	Q9NQ36	SCUB2_HUMAN	CEGP1 protein precursor							extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		agctagagatgacggtggcttga	0.000													0	7	---	---	---	---	
IPO7	10527	broad.mit.edu	37	11	9456826	9456827	+	Intron	DEL	AT	-	-	rs142659173		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9456826_9456827delAT	uc001mho.2	+							NM_006391	NP_006382	O95373	IPO7_HUMAN	importin 7						interspecies interaction between organisms|signal transduction	Golgi apparatus|nuclear pore|soluble fraction	protein transporter activity|Ran GTPase binding|small GTPase regulator activity			lung(1)|breast(1)	2				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		TTTAACTAACATAGTCTTATGG	0.351													3	4	---	---	---	---	
GALNTL4	374378	broad.mit.edu	37	11	11531983	11531984	+	Intron	INS	-	TCAC	TCAC	rs146114442	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11531983_11531984insTCAC	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		CTCTattcaggtcacttctgca	0.238													2	4	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16090238	16090238	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16090238delT	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						TATTGCACCATTttttccttt	0.219													4	2	---	---	---	---	
ZDHHC13	54503	broad.mit.edu	37	11	19173525	19173525	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19173525delT	uc001mpi.2	+						ZDHHC13_uc001mpj.2_Intron	NM_019028	NP_061901	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC domain containing 13 isoform						positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|palmitoyltransferase activity|signal transducer activity|zinc ion binding				0						AATAGATGTCTTTTTTTTTAA	0.289													4	2	---	---	---	---	
TRIM44	54765	broad.mit.edu	37	11	35805298	35805298	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35805298delA	uc001mwi.2	+							NM_017583	NP_060053	Q96DX7	TRI44_HUMAN	DIPB protein							intracellular	protein binding|zinc ion binding			skin(1)	1	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				CCCTTCCTGGAAGGGCACTTT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44526217	44526218	+	IGR	DEL	AC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44526217_44526218delAC								ALX4 (194501 upstream) : CD82 (60923 downstream)																							cacacattctacacacacacac	0.153													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44563928	44563930	+	IGR	DEL	CAC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44563928_44563930delCAC								ALX4 (232212 upstream) : CD82 (23211 downstream)																							tcatcactatcaccaccaccacc	0.000													4	2	---	---	---	---	
MAPK8IP1	9479	broad.mit.edu	37	11	45905357	45905357	+	5'Flank	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45905357delT	uc001nbr.2	+							NM_005456	NP_005447	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting						vesicle-mediated transport	nucleus|perinuclear region of cytoplasm	kinesin binding|MAP-kinase scaffold activity|protein kinase inhibitor activity			ovary(2)|breast(1)|skin(1)	4				GBM - Glioblastoma multiforme(35;0.231)		GACTGAAAGCTTTATTAGCTC	0.562													4	2	---	---	---	---	
SLC39A13	91252	broad.mit.edu	37	11	47377527	47377527	+	Intron	DEL	C	-	-	rs148379555		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47377527delC	uc001nfd.2	+						SPI1_uc001nfb.1_Intron|SPI1_uc001nfc.1_Intron			Q96H72	S39AD_HUMAN	RecName: Full=Zinc transporter ZIP13; AltName: Full=Zrt- and Irt-like protein 13;          Short=ZIP-13; AltName: Full=Solute carrier family 39 member 13; AltName: Full=LIV-1 subfamily of ZIP zinc transporter 9; AltName: Full=LZT-Hs9;						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				Lung(87;0.0936)		ctcatgctcacacccacacac	0.025													3	4	---	---	---	---	
FOLH1	2346	broad.mit.edu	37	11	49184399	49184399	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49184399delG	uc001ngy.2	-						FOLH1_uc001ngz.2_Intron|FOLH1_uc009yly.2_Intron|FOLH1_uc009ylz.2_Intron|FOLH1_uc009yma.2_Intron	NM_004476	NP_004467	Q04609	FOLH1_HUMAN	folate hydrolase 1 isoform 1						proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity			large_intestine(1)|ovary(1)|skin(1)	3					Capromab(DB00089)|L-Glutamic Acid(DB00142)	gtgttgtgctggggggtcgac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59211793	59211793	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59211793delA								OR5A1 (204 upstream) : OR4D6 (12641 downstream)																							ATTTCTTCAGaaaaaaaaaaa	0.303													4	2	---	---	---	---	
MAP6	4135	broad.mit.edu	37	11	75303317	75303317	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75303317delC	uc001owu.2	-							NM_033063	NP_149052	Q96JE9	MAP6_HUMAN	microtubule-associated protein 6 isoform 1							Golgi apparatus|microtubule|perinuclear region of cytoplasm	calmodulin binding				0	Ovarian(111;0.11)					tctcacatatccccactgcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	75447098	75447098	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75447098delT								MOGAT2 (4768 upstream) : DGAT2 (32680 downstream)																							CCCTTTTAGCttttttttttg	0.214													4	2	---	---	---	---	
CAPN5	726	broad.mit.edu	37	11	76804630	76804644	+	Intron	DEL	GTCTGTGTCTGTCAC	-	-	rs3832735		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76804630_76804644delGTCTGTGTCTGTCAC	uc001oxx.2	+						CAPN5_uc009yup.2_Intron|CAPN5_uc009yuq.2_Intron|CAPN5_uc001oxy.2_Intron	NM_004055	NP_004046	O15484	CAN5_HUMAN	calpain 5						proteolysis|signal transduction	intracellular	calcium-dependent cysteine-type endopeptidase activity				0						CACACAGCAAGTCTGTGTCTGTCACGTCTGTGTCT	0.642													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	81346811	81346812	+	IGR	DEL	TC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81346811_81346812delTC								None (None upstream) : None (None downstream)																							gtgtagggcttctctctctctg	0.000													4	2	---	---	---	---	
ME3	10873	broad.mit.edu	37	11	86170865	86170866	+	Intron	INS	-	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86170865_86170866insG	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron|ME3_uc010rtr.1_Intron	NM_001014811	NP_001014811	Q16798	MAON_HUMAN	mitochondrial malic enzyme 3 precursor						aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)	GGAGCCTTTATGGGCGTCTGGC	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93553505	93553505	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93553505delG								MED17 (7010 upstream) : C11orf90 (230 downstream)																							CGAAGCTCCTGGTTCAAAGCC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	96834454	96834455	+	IGR	INS	-	TCT	TCT	rs58161547		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96834454_96834455insTCT								JRKL (707727 upstream) : None (None downstream)																							tatggtaattgggagagtagct	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	96834455	96834456	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96834455_96834456insA								JRKL (707728 upstream) : None (None downstream)																							atggtaattgggagagtagctt	0.005													4	2	---	---	---	---	
YAP1	10413	broad.mit.edu	37	11	102047876	102047876	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102047876delG	uc001pgt.2	+						YAP1_uc001pgs.2_Intron|YAP1_uc001pgu.2_Intron|YAP1_uc001pgv.2_Intron|YAP1_uc010ruo.1_Intron|YAP1_uc001pgw.2_Intron	NM_001130145	NP_001123617	P46937	YAP1_HUMAN	Yes-associated protein 1, 65kDa isoform 1						cell proliferation|cellular response to gamma radiation|contact inhibition|hippo signaling cascade|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		agatgtttgaggaactgagag	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	111772924	111772924	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111772924delT								C11orf1 (18129 upstream) : CRYAB (6426 downstream)																							cttttgctcctttttttgcta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	113107217	113107217	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113107217delT								NCAM1 (-41940 upstream) : NCAM1 (-275222 downstream)																							TGTAGGTTACTCCAAGAGGCT	0.423													67	30	---	---	---	---	
DRD2	1813	broad.mit.edu	37	11	113303835	113303835	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113303835delA	uc001poa.3	-						DRD2_uc001pob.3_Intron|DRD2_uc009yyr.1_Intron	NM_000795	NP_000786	P14416	DRD2_HUMAN	dopamine receptor D2 isoform long						activation of phospholipase C activity by dopamine receptor signaling pathway|adenohypophysis development|adult walking behavior|arachidonic acid secretion|axonogenesis|behavioral response to cocaine|behavioral response to ethanol|branching morphogenesis of a nerve|cerebral cortex GABAergic interneuron migration|circadian regulation of gene expression|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|intracellular protein kinase cascade|negative regulation of blood pressure|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of dopamine receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|negative regulation of synaptic transmission, glutamatergic|neurological system process involved in regulation of systemic arterial blood pressure|peristalsis|phosphatidylinositol metabolic process|positive regulation of dopamine uptake|positive regulation of growth hormone secretion|positive regulation of neuroblast proliferation|prepulse inhibition|protein localization|regulation of heart rate|regulation of long-term neuronal synaptic plasticity|regulation of potassium ion transport|regulation of sodium ion transport|regulation of synaptic transmission, GABAergic|release of sequestered calcium ion into cytosol|response to amphetamine|response to drug|response to histamine|response to morphine|sensory perception of smell|synapse assembly|temperature homeostasis|visual learning	integral to plasma membrane	dopamine D2 receptor activity|dopamine receptor activity, coupled via Gi/Go|drug binding|potassium channel regulator activity|protein binding			pancreas(1)|skin(1)	2		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Carphenazine(DB01038)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Domperidone(DB01184)|Droperidol(DB00450)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Mesoridazine(DB00933)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Sulpiride(DB00391)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Ziprasidone(DB00246)|Zuclopenthixol(DB01624)	TGTGGCGAGGAAAAAAAGGAG	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116532380	116532380	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116532380delG								None (None upstream) : BUD13 (86508 downstream)																							gagataatgagggggtttatg	0.184													4	2	---	---	---	---	
SORL1	6653	broad.mit.edu	37	11	121464061	121464061	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121464061delC	uc001pxx.2	+						SORL1_uc010rzp.1_Intron|SORL1_uc010rzq.1_Intron	NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class						cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		ttgttttgtaccatttgccaa	0.085													4	7	---	---	---	---	
PKNOX2	63876	broad.mit.edu	37	11	125163637	125163638	+	Intron	INS	-	CA	CA			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125163637_125163638insCA	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron	NM_022062	NP_071345	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		acacacacactcacacacactc	0.183													4	2	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126776517	126776517	+	Intron	DEL	T	-	-	rs34346465		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126776517delT	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		CCTTTCACTGTTTTTTTTAGC	0.398													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128078077	128078078	+	IGR	INS	-	AC	AC	rs146658373	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128078077_128078078insAC								None (None upstream) : ETS1 (250578 downstream)																							cacacatacatacacacacaca	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	131191067	131191067	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131191067delC								SNX19 (404685 upstream) : NTM (49304 downstream)																							AGCACCTTCTCTTCCCGTCTC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	131191070	131191070	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131191070delC								SNX19 (404688 upstream) : NTM (49301 downstream)																							ACCTTCTCTTCCCGTCTCTGT	0.438													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132323342	132323342	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132323342delC	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		CCAGGGGCATCCCCAGGGCCG	0.478													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133099783	133099784	+	Intron	DEL	TG	-	-	rs35892298		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133099783_133099784delTG	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		TCAGTTTTATTGTGTGTGTGTG	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134905420	134905421	+	IGR	INS	-	ATGG	ATGG	rs71964714		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134905420_134905421insATGG								B3GAT1 (623608 upstream) : None (None downstream)																							tggatagatttatggatggatg	0.000													3	3	---	---	---	---	
B4GALNT3	283358	broad.mit.edu	37	12	612921	612925	+	Intron	DEL	GAACA	-	-	rs139403411		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:612921_612925delGAACA	uc001qii.1	+							NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			actgatctctgaacagctgcctccc	0.161													4	2	---	---	---	---	
WNT5B	81029	broad.mit.edu	37	12	1713797	1713798	+	Intron	DEL	AA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1713797_1713798delAA	uc009zdq.2	+							NM_032642	NP_116031	Q9H1J7	WNT5B_HUMAN	wingless-type MMTV integration site family,						angiogenesis|anterior/posterior pattern formation|cell migration involved in gastrulation|cellular response to retinoic acid|chondrocyte differentiation|convergent extension involved in axis elongation|convergent extension involved in gastrulation|dorsal/ventral axis specification|endocrine pancreas development|fat cell differentiation|lens fiber cell development|negative regulation of canonical Wnt receptor signaling pathway|neuron differentiation|positive regulation of cell migration|positive regulation of fat cell differentiation|respiratory system development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)			TGGCTTGGGGAAAAAAAAGAGT	0.431													4	2	---	---	---	---	
WNT5B	81029	broad.mit.edu	37	12	1729711	1729711	+	Intron	DEL	T	-	-	rs111366537		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1729711delT	uc009zdq.2	+						WNT5B_uc001qjj.2_Intron	NM_032642	NP_116031	Q9H1J7	WNT5B_HUMAN	wingless-type MMTV integration site family,						angiogenesis|anterior/posterior pattern formation|cell migration involved in gastrulation|cellular response to retinoic acid|chondrocyte differentiation|convergent extension involved in axis elongation|convergent extension involved in gastrulation|dorsal/ventral axis specification|endocrine pancreas development|fat cell differentiation|lens fiber cell development|negative regulation of canonical Wnt receptor signaling pathway|neuron differentiation|positive regulation of cell migration|positive regulation of fat cell differentiation|respiratory system development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)			tttgttgttgttttttttttt	0.000													4	3	---	---	---	---	
TULP3	7289	broad.mit.edu	37	12	3035045	3035045	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3035045delA	uc010seh.1	+						TULP3_uc010sef.1_Intron|TULP3_uc009zec.1_Intron|TULP3_uc010seg.1_Intron|TULP3_uc001qlj.2_Intron|TULP3_uc010sei.1_Intron	NM_003324	NP_003315	O75386	TULP3_HUMAN	tubby like protein 3 isoform 1						G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			GCACTGCTCTATGAAATGGCT	0.249													4	2	---	---	---	---	
PRMT8	56341	broad.mit.edu	37	12	3649524	3649524	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3649524delA	uc001qmf.2	+						PRMT8_uc009zed.2_Intron|PRMT8_uc009zee.1_Intron	NM_019854	NP_062828	Q9NR22	ANM8_HUMAN	HMT1 hnRNP methyltransferase-like 4						regulation of protein binding	cytoplasm|plasma membrane	histone-arginine N-methyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity			ovary(3)|central_nervous_system(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			tcacctagctaataagagctg	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8403560	8403561	+	5'Flank	DEL	AT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8403560_8403561delAT	uc001quj.1	+											full-length cDNA clone CS0DB004YI02 of Neuroblastoma Cot 10-normalized of Homo sapiens (human).																		tattctgggcatatatatatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	9969684	9969684	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9969684delA								CD69 (56187 upstream) : KLRF1 (10393 downstream)																							GAGCTGAAGTAAGACCCAAGG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16907112	16907112	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16907112delC								LMO3 (144354 upstream) : None (None downstream)																							GTgcttacctccgtacctggc	0.184													4	2	---	---	---	---	
PIK3C2G	5288	broad.mit.edu	37	12	18666311	18666311	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18666311delT	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				attggtattctttttttttta	0.000													4	2	---	---	---	---	
PLEKHA5	54477	broad.mit.edu	37	12	19413636	19413636	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19413636delA	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					ctaaaaatacaaaaaaaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	22530969	22530970	+	Intron	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22530969_22530970insA	uc001rfp.1	-											full-length cDNA clone CS0DI081YP04 of Placenta Cot 25-normalized of Homo sapiens (human).																		ATTAATAAAAGAAAAAAAAATC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	33900279	33900280	+	IGR	DEL	GT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33900279_33900280delGT								SYT10 (307525 upstream) : ALG10 (274936 downstream)																							atctgagtcagtgtgtgtgtgt	0.054													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34303707	34303707	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34303707delT								ALG10 (122473 upstream) : None (None downstream)																							gctctctgggtttttttgttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	37942654	37942655	+	IGR	DEL	TG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37942654_37942655delTG								None (None upstream) : ALG10B (767902 downstream)																							AGTTTGGGCTTGTGAAGGTCTG	0.515													4	2	---	---	---	---	
HDAC7	51564	broad.mit.edu	37	12	48215918	48215918	+	5'Flank	DEL	T	-	-	rs79457758		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48215918delT	uc010slo.1	-						HDAC7_uc001rqj.3_5'Flank|HDAC7_uc001rqk.3_5'Flank	NM_015401	NP_056216	Q8WUI4	HDAC7_HUMAN	histone deacetylase 7 isoform a						negative regulation of interleukin-2 production|negative regulation of osteoblast differentiation|positive regulation of cell migration involved in sprouting angiogenesis|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.137)		AGGTATGTCATCCCCAGCCCT	0.507													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48566114	48566123	+	IGR	DEL	AAAACAAAAC	-	-	rs112856407		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48566114_48566123delAAAACAAAAC								ASB8 (14737 upstream) : C12orf68 (11243 downstream)																							ctccatctcaaaaacaaaacaaaacaaaac	0.119													6	4	---	---	---	---	
ADCY6	112	broad.mit.edu	37	12	49167327	49167327	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49167327delT	uc001rsh.3	-	15	3206	c.2546delA	c.(2545-2547)TATfs	p.Y849fs	ADCY6_uc001rsj.3_Frame_Shift_Del_p.Y849fs|ADCY6_uc001rsi.3_Frame_Shift_Del_p.Y796fs|ADCY6_uc010slw.1_Frame_Shift_Del_p.Y80fs	NM_015270	NP_056085	O43306	ADCY6_HUMAN	adenylate cyclase 6 isoform a	849	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane	ATP binding|metal ion binding				0						CAGCACCAAATAGATGAGCCC	0.512													109	49	---	---	---	---	
ARF3	377	broad.mit.edu	37	12	49346978	49346979	+	Intron	DEL	TC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49346978_49346979delTC	uc001rsr.2	-						ARF3_uc010smc.1_Intron	NM_001659	NP_001650	P61204	ARF3_HUMAN	ADP-ribosylation factor 3						protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	Golgi apparatus|perinuclear region of cytoplasm	GTP binding|GTPase activity				0						AAGACTGTATTCTATAGGTGGT	0.401													4	2	---	---	---	---	
SPATS2	65244	broad.mit.edu	37	12	49779658	49779658	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49779658delT	uc001rud.2	+						SPATS2_uc001ruc.2_Intron|SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron	NM_023071	NP_075559	Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1						ttgttttttgttttttttttt	0.000													5	3	---	---	---	---	
DIP2B	57609	broad.mit.edu	37	12	51112215	51112215	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51112215delC	uc001rwv.2	+						DIP2B_uc009zlt.2_Intron	NM_173602	NP_775873	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6						cttccctccaccccaatccct	0.065													4	2	---	---	---	---	
BIN2	51411	broad.mit.edu	37	12	51697506	51697506	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51697506delT	uc001ryg.2	-						BIN2_uc009zlz.2_Intron|BIN2_uc001ryh.2_Intron|BIN2_uc010sng.1_Intron	NM_016293	NP_057377	Q9UBW5	BIN2_HUMAN	bridging integrator 2							cytoplasm	protein binding			ovary(1)	1						TGAAATCTCATTTTTTTAGGC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	52479464	52479465	+	Intron	INS	-	ACAGTACT	ACAGTACT	rs142641413	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52479464_52479465insACAGTACT	uc009zme.1	+											Homo sapiens olfactory receptor, family 7, subfamily E, member 47 pseudogene, mRNA (cDNA clone IMAGE:5590288).																		ctaaccctgaaacagtactacg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	52512454	52512454	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52512454delG								C12orf44 (41176 upstream) : KRT80 (50327 downstream)																							tgctttcactgggatgtccta	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	59008058	59008059	+	Intron	INS	-	AGTC	AGTC	rs141220558	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59008058_59008059insAGTC	uc001sqq.1	-											Homo sapiens cDNA FLJ35805 fis, clone TESTI2005982.																		ATGGAAGAGAAAGCCTATTATG	0.426													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	63708270	63708271	+	IGR	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63708270_63708271insT								AVPR1A (161680 upstream) : DPY19L2 (244422 downstream)																							TGGTGGTAAACTTTTTTTTTTA	0.347													4	2	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	67107401	67107401	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67107401delC	uc010sta.1	-							NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		ccatcacccaccagacgcatc	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68193906	68193907	+	IGR	DEL	TG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68193906_68193907delTG								DYRK2 (137463 upstream) : IFNG (354643 downstream)																							TCtgtgtgtttgtgtgtgtgtg	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	73183781	73183782	+	IGR	DEL	AT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73183781_73183782delAT								TRHDE (124360 upstream) : None (None downstream)																							tccaaaatccatatagaactta	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	73453180	73453180	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73453180delA								TRHDE (393759 upstream) : None (None downstream)																							tcaacatgagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	74087115	74087115	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74087115delG								None (None upstream) : ATXN7L3B (844436 downstream)																							AAGTGGGCCAGGTGTCAATAA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	78889215	78889215	+	IGR	DEL	T	-	-	rs63433262		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78889215delT								NAV3 (282427 upstream) : SYT1 (368558 downstream)																							ATACGttttgttttttttttt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	79944910	79944911	+	IGR	DEL	AG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79944910_79944911delAG								SYT1 (99123 upstream) : PAWR (40836 downstream)																							ccatgataaaagagagagagag	0.005													4	2	---	---	---	---	
TMTC2	160335	broad.mit.edu	37	12	83489009	83489009	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83489009delG	uc001szt.2	+						TMTC2_uc010suk.1_Intron	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2						ttttttttttgtttttttttt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	84683496	84683496	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84683496delT								None (None upstream) : SLC6A15 (569773 downstream)																							AATTAATCAATTTTTTTTGGT	0.199													4	2	---	---	---	---	
RASSF9	9182	broad.mit.edu	37	12	86216440	86216440	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86216440delT	uc001taf.1	-							NM_005447	NP_005438	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family						endosome transport|protein targeting|signal transduction	cytosol|endosome|trans-Golgi network transport vesicle membrane	protein binding|transporter activity			ovary(1)	1						TTTTAAACTCTTTAATATGCT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	91044585	91044585	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91044585delA								LOC338758 (938857 upstream) : C12orf12 (301408 downstream)																							aaggctctataaacatacatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93569462	93569462	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93569462delT								EEA1 (246355 upstream) : NUDT4 (202239 downstream)																							TACTTCTCCCTTGAATTCTAC	0.353													4	2	---	---	---	---	
CRADD	8738	broad.mit.edu	37	12	94191968	94191969	+	Intron	INS	-	G	G	rs147568939	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94191968_94191969insG	uc001tda.2	+						CRADD_uc010sur.1_Intron|CRADD_uc010sus.1_Intron	NM_003805	NP_003796	P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1						ACTTTTTCTTTTTTCCCAGGAA	0.401													3	3	---	---	---	---	
RMST	196475	broad.mit.edu	37	12	97871249	97871249	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97871249delA	uc001tey.1	+							NR_024037				Homo sapiens C23up NCRMS mRNA, partial sequence; alternatively spliced.												0						TGTGAAAACCAAAAAGGGGGA	0.323													4	2	---	---	---	---	
SLC17A8	246213	broad.mit.edu	37	12	100802393	100802393	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100802393delT	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						TCTTAAATGCTTTTTTTTCCA	0.323													4	2	---	---	---	---	
NUP37	79023	broad.mit.edu	37	12	102468600	102468600	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102468600delA	uc001tjc.2	-							NM_024057	NP_076962	Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa						carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			ovary(1)	1						TGTAAACATCAAAAAAAAACC	0.269													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	103197798	103197798	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103197798delC								IGF1 (323420 upstream) : PAH (34306 downstream)																							tccaaataaaccccctgcact	0.065													4	2	---	---	---	---	
WSCD2	9671	broad.mit.edu	37	12	108594266	108594267	+	Intron	INS	-	TTCA	TTCA	rs140389107	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108594266_108594267insTTCA	uc001tms.2	+						WSCD2_uc001tmt.2_Intron	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2							integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3						tcatttattctttcattcattc	0.050													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	111264590	111264591	+	IGR	INS	-	TGTT	TGTT	rs145215590	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111264590_111264591insTGTT								PPP1CC (83833 upstream) : CCDC63 (20220 downstream)																							GAGGGAGGCAGTGTTGTCAGCA	0.366											OREG0022117	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	5	---	---	---	---	
C12orf43	64897	broad.mit.edu	37	12	121453755	121453755	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121453755delG	uc001tzh.1	-						C12orf43_uc009zxa.1_Intron|C12orf43_uc010szo.1_Intron|C12orf43_uc010szp.1_Intron|C12orf43_uc001tzi.1_Intron	NM_022895	NP_075046	Q96C57	CL043_HUMAN	hypothetical protein LOC64897												0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTGATGTGCTGGGCACTGCTC	0.308													4	2	---	---	---	---	
SETD8	387893	broad.mit.edu	37	12	123889740	123889740	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123889740delT	uc001uew.2	+						SETD8_uc001uex.2_Intron	NM_020382	NP_065115	Q9NQR1	SETD8_HUMAN	SET domain-containing 8						cell division|mitosis|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine monomethylation|regulation of DNA damage response, signal transduction by p53 class mediator|transcription, DNA-dependent	chromosome|nucleus	histone-lysine N-methyltransferase activity|p53 binding|transcription corepressor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		TGTTGTTGACttttttttttt	0.254													6	3	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124953385	124953386	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124953385_124953386insT	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)		cctcatcaccccatcatcctca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125752257	125752257	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125752257delG								AACS (124385 upstream) : TMEM132B (58905 downstream)																							gcatgggttaggggggcagtg	0.119													4	2	---	---	---	---	
RIMBP2	23504	broad.mit.edu	37	12	130966480	130966482	+	Intron	DEL	CCA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130966480_130966482delCCA	uc001uil.2	-						RIMBP2_uc001uim.2_Intron	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CCCCAAGCCGCCACCACCACCAC	0.621													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22748817	22748817	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22748817delG	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																		CACAGTGGCAGGGATTCCTGT	0.488													4	2	---	---	---	---	
ATP12A	479	broad.mit.edu	37	13	25269000	25269005	+	Intron	DEL	CACACA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25269000_25269005delCACACA	uc001upp.2	+						ATP12A_uc010aaa.2_Intron	NM_001676	NP_001667	P54707	AT12A_HUMAN	hydrogen/potassium-exchanging ATPase 12A						ATP biosynthetic process	hydrogen:potassium-exchanging ATPase complex	ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1)	6		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)	Esomeprazole(DB00736)|Pantoprazole(DB00213)	CTCTCTCTCTcacacacacacacaca	0.456													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30251484	30251484	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30251484delA								SLC7A1 (81659 upstream) : UBL3 (87062 downstream)																							ATCACTGGCCAAAAAAAAAAG	0.368													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31605608	31605608	+	IGR	DEL	C	-	-	rs111507924		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31605608delC								C13orf26 (56457 upstream) : HSPH1 (105157 downstream)																							TTTTCTTCTACCCCTCATCCT	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	35395341	35395342	+	IGR	INS	-	G	G	rs142326050	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35395341_35395342insG								RFC3 (854647 upstream) : NBEA (121114 downstream)																							GTTATCTTAATGCCAACAATGC	0.277													2	5	---	---	---	---	
ENOX1	55068	broad.mit.edu	37	13	43930489	43930489	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43930489delG	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron|ENOX1_uc001uyz.3_5'Flank|ENOX1_uc010tfm.1_Intron	NM_001127615	NP_001121087	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		TTACAGGTTTGGGGATAAACA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	49514638	49514638	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49514638delT								CYSLTR2 (231140 upstream) : FNDC3A (35410 downstream)																							GCCCCCTGGCTTTCTCAGGCT	0.313													4	2	---	---	---	---	
DLEU1	10301	broad.mit.edu	37	13	50767083	50767084	+	Intron	INS	-	A	A	rs138454444	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50767083_50767084insA	uc010adl.1	+						DLEU1_uc001vee.1_Intron|DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron|uc001vek.1_Intron|uc001vel.1_Intron|uc001vem.1_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0						AATTCAGATATAAAAAAAAATA	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	58046293	58046293	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58046293delC								PRR20B (301941 upstream) : PCDH17 (159496 downstream)																							TAAAGAGGCTCCATGCACTCG	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63630797	63630798	+	IGR	INS	-	ATG	ATG	rs142732820		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63630797_63630798insATG								None (None upstream) : OR7E156P (680770 downstream)																							ACATCTTAGTAATGATTTTTTT	0.213													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	66124050	66124051	+	IGR	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66124050_66124051insT								None (None upstream) : PCDH9 (752916 downstream)																							attgttgaggatttttgcatct	0.000													4	2	---	---	---	---	
KLHL1	57626	broad.mit.edu	37	13	70621413	70621413	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70621413delA	uc001vip.2	-						KLHL1_uc010thm.1_Intron	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TGGTTAACTGAAAAAAAAAAA	0.279													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	74831052	74831052	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74831052delT	uc001vji.1	+											Homo sapiens cDNA FLJ32127 fis, clone PEBLM2000126.																		AATCTTCTACTTTTTTTTGTT	0.308													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94802243	94802244	+	Intron	INS	-	AG	AG	rs144628989	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94802243_94802244insAG	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				CTCAGGAAAAAAGGTATAGGCC	0.396													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	97835751	97835751	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97835751delC								OXGR1 (189147 upstream) : MBNL2 (38823 downstream)																							CTTCTCTGAGCCCTCTCCAAA	0.473													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102428818	102428818	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102428818delG	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)					CCTCAGTTCTGGGACAATAGA	0.453													4	2	---	---	---	---	
KDELC1	79070	broad.mit.edu	37	13	103446586	103446586	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103446586delA	uc001vpq.3	-						KDELC1_uc001vpr.3_Intron	NM_024089	NP_076994	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1 precursor							endoplasmic reticulum lumen				ovary(1)	1	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					cgtttcaaagaaaaaaaaaGT	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	103780708	103780709	+	IGR	DEL	GT	-	-	rs146484079	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103780708_103780709delGT								SLC10A2 (61512 upstream) : None (None downstream)																							CAGTGGGGACGTGATGAGATTA	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107539676	107539676	+	IGR	DEL	A	-	-	rs11365329		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107539676delA								ARGLU1 (319162 upstream) : FAM155A (281204 downstream)																							CAGAGATGGCAAAGGATACCA	0.448													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	114060955	114060955	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114060955delT								GRTP1 (42492 upstream) : ADPRHL1 (15305 downstream)																							TGTGTGGGCATTTTCAACCAC	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19795889	19795890	+	IGR	DEL	TC	-	-	rs150326417		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19795889_19795890delTC								POTEG (210947 upstream) : P704P (188064 downstream)																							attgcaattttctctctctcaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20168815	20168815	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20168815delA								P704P (148543 upstream) : OR4Q3 (46772 downstream)																							AATCCTGGGGAAAAAAAAGAG	0.398													3	3	---	---	---	---	
OR4Q3	441669	broad.mit.edu	37	14	20214571	20214572	+	5'Flank	DEL	TC	-	-	rs112684937		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20214571_20214572delTC	uc010tkt.1	+							NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TAGCAAATCTTCTTTATTTTCT	0.366													4	2	---	---	---	---	
STXBP6	29091	broad.mit.edu	37	14	25448624	25448624	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25448624delG	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpx.1_Intron	NM_014178	NP_054897	Q8NFX7	STXB6_HUMAN	amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)		ATGTCACCCTGGAAGACTCTG	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26791511	26791511	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26791511delA								None (None upstream) : NOVA1 (123579 downstream)																							TAGCCATTGCAAAAAAATAAG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	32641777	32641778	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32641777_32641778insA								ARHGAP5 (12845 upstream) : AKAP6 (156701 downstream)																							gactccatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
C14orf19	280655	broad.mit.edu	37	14	35409694	35409694	+	RNA	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35409694delA	uc010tpo.1	+	1		c.567delA				NR_002937				Homo sapiens chromosome 14 open reading frame 19 protein (C14orf19) mRNA, 3' UTR.												0						TCCAGTGATTAAAAAAAATTT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	45390559	45390559	+	IGR	DEL	T	-	-	rs112809875		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45390559delT								C14orf28 (14100 upstream) : KLHL28 (2969 downstream)																							GAGGGTTTTGTTTTTTTTTGT	0.363													4	2	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50148686	50148686	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50148686delT	uc010anj.1	-						POLE2_uc001wwu.2_Intron|POLE2_uc001wwv.2_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		AATGACCATCTTTTATAGAAT	0.244													4	2	---	---	---	---	
CDKN3	1033	broad.mit.edu	37	14	54866900	54866901	+	Intron	DEL	TT	-	-	rs72386503		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54866900_54866901delTT	uc001xap.2	+						CDKN3_uc001xar.2_Intron|CDKN3_uc001xaq.2_Intron|CDKN3_uc010aoi.1_Intron|CDKN3_uc001xas.1_Intron|CDKN3_uc010aoj.1_Intron	NM_005192	NP_005183	Q16667	CDKN3_HUMAN	cyclin-dependent kinase inhibitor 3 isoform 1						cell cycle arrest|G1/S transition of mitotic cell cycle|negative regulation of cell proliferation|regulation of cyclin-dependent protein kinase activity	perinuclear region of cytoplasm	protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0						AATAAGACCCTTTTTTTTTTTT	0.292													4	3	---	---	---	---	
SPTB	6710	broad.mit.edu	37	14	65335109	65335109	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65335109delA	uc001xhs.2	-						SPTB_uc001xhu.2_Intron	NM_001024858	NP_001020029	P11277	SPTB1_HUMAN	spectrin beta isoform a						actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		ACCTAGCTATAAAAAAAAACA	0.433													4	3	---	---	---	---	
GPHN	10243	broad.mit.edu	37	14	67607697	67607697	+	Intron	DEL	T	-	-	rs5809331		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67607697delT	uc001xiy.2	+						GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		TATGTCAGGGTTTTTTTTTTT	0.308			T	MLL	AL								4	2	---	---	---	---	
ZFYVE26	23503	broad.mit.edu	37	14	68282128	68282130	+	Intron	DEL	ACA	-	-	rs141206591	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68282128_68282130delACA	uc001xka.2	-						ZFYVE26_uc010tsz.1_Intron|ZFYVE26_uc001xkc.3_Intron|ZFYVE26_uc010tta.1_Intron	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26						cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		AAGTAAAGCGACAACAATATTTT	0.197													2	4	---	---	---	---	
ENTPD5	957	broad.mit.edu	37	14	74441984	74441984	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74441984delC	uc010tuo.1	-						ENTPD5_uc001xpi.2_Intron	NM_001249	NP_001240	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5						'de novo' posttranslational protein folding|ATP metabolic process|cell growth|cell proliferation|glycolysis|protein N-linked glycosylation|regulation of phosphatidylinositol 3-kinase cascade	endoplasmic reticulum lumen	guanosine-diphosphatase activity|uridine-diphosphatase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00394)		TAGCTCCTAGCCCCAACTGGG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	75217260	75217260	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75217260delG								FCF1 (13763 upstream) : YLPM1 (12809 downstream)																							CGCTCACTCTGGAAATTAAAA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	75659345	75659345	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75659345delA								TMED10 (15996 upstream) : FOS (86136 downstream)																							aatctgtcttaaaaaaaaaaa	0.000													2	4	---	---	---	---	
TTLL5	23093	broad.mit.edu	37	14	76212205	76212205	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76212205delA	uc001xrx.2	+						TTLL5_uc010ask.1_Intron|TTLL5_uc001xrz.2_Intron|TTLL5_uc001xry.1_Intron	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)		ccttgatttgaaaaaaaaaat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	77169228	77169228	+	IGR	DEL	C	-	-	rs59616280		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77169228delC								ESRRB (201050 upstream) : VASH1 (59007 downstream)																							acaaaaattacgctgaataaa	0.000													1	6	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	78999084	78999084	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78999084delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TTTCTTCTTCTTTTTTTTTTC	0.353													6	5	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79133024	79133024	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79133024delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TGTCCTCTGCTTCCTGGTCCT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	92719772	92719773	+	IGR	INS	-	AC	AC	rs140262686		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92719772_92719773insAC								CPSF2 (89229 upstream) : SLC24A4 (69152 downstream)																							tgccctgagggacacacacaca	0.000													8	4	---	---	---	---	
ITPK1	3705	broad.mit.edu	37	14	93512252	93512253	+	Intron	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93512252_93512253insC	uc001ybg.2	-						ITPK1_uc001ybe.2_Intron|ITPK1_uc001ybf.2_Intron|ITPK1_uc001ybh.2_Intron	NM_014216	NP_055031	Q13572	ITPK1_HUMAN	inositol 1,3,4-triphosphate 5/6 kinase isoform						blood coagulation|inositol trisphosphate metabolic process|signal transduction	cytosol	ATP binding|hydrolase activity|inositol tetrakisphosphate 1-kinase activity|inositol-1,3,4-trisphosphate 5/6-kinase activity|isomerase activity|ligase activity|magnesium ion binding				0		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		GCTCCCCAGTGCCCCCAAATGA	0.584													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95233282	95233282	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95233282delT								SERPINA13 (119952 upstream) : GSC (1279 downstream)																							ACTGCCTCTCTTTTGTCTAGG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95367725	95367726	+	IGR	DEL	TC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95367725_95367726delTC								GSC (131226 upstream) : DICER1 (184839 downstream)																							tttcttgccttctctctctcac	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	96069418	96069418	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96069418delG								GLRX5 (58363 upstream) : TCL6 (47417 downstream)																							gggagctacagggacatgatg	0.000													4	2	---	---	---	---	
EML1	2009	broad.mit.edu	37	14	100375144	100375144	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100375144delG	uc001ygs.2	+						EML1_uc010avt.1_Intron|EML1_uc010tww.1_Intron|EML1_uc001ygq.2_Intron|EML1_uc001ygr.2_Intron	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				GGAACTCCCTGGGGAAACGGG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	104750082	104750082	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104750082delG								KIF26A (102848 upstream) : C14orf180 (295974 downstream)																							CAGAGCTGGTGGGGGTGGAAG	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23140656	23140660	+	IGR	DEL	AAAGG	-	-	rs144644532		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23140656_23140660delAAAGG								NIPA1 (53813 upstream) : WHAMML1 (47071 downstream)																							GTAAAAAAAAAAAGGAAGAATACAT	0.263													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23606318	23606319	+	5'Flank	INS	-	TTC	TTC			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23606318_23606319insTTC	uc001ywe.2	-											DQ578839																		tttcttttcttttttttttttt	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	34882951	34882951	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34882951delG								GOLGA8B (54729 upstream) : GJD2 (161728 downstream)																							ccttctctccgccatctttaa	0.000													4	2	---	---	---	---	
TTBK2	146057	broad.mit.edu	37	15	43114796	43114796	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43114796delA	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		ACCATGAGAGAAAAAAAAACA	0.323													4	2	---	---	---	---	
ELL3	80237	broad.mit.edu	37	15	44067304	44067304	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44067304delA	uc001zsw.1	-						ELL3_uc001zsv.1_Intron|ELL3_uc001zsx.1_Intron|uc001zsy.2_5'Flank	NM_025165	NP_079441	Q9HB65	ELL3_HUMAN	elongation factor RNA polymerase II-like 3						positive regulation of transcription elongation, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				ovary(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		tgagaataagaaaaaaaaaaa	0.060													4	2	---	---	---	---	
FRMD5	84978	broad.mit.edu	37	15	44188991	44188992	+	Intron	DEL	AA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44188991_44188992delAA	uc001ztl.2	-						FRMD5_uc001ztj.1_Intron|FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		GACTCAAACTAATTCAATTTTG	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	56347349	56347349	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56347349delG								NEDD4 (61514 upstream) : RFX7 (32130 downstream)																							cagatcatcaggcattactta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	56552955	56552955	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56552955delA								RFX7 (17472 upstream) : TEX9 (104689 downstream)																							ttctagcctcaaaaaaatgaa	0.000													4	2	---	---	---	---	
CA12	771	broad.mit.edu	37	15	63619700	63619700	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63619700delT	uc002amc.2	-						CA12_uc002amd.2_Intron|CA12_uc002ame.2_Intron	NM_001218	NP_001209	O43570	CAH12_HUMAN	carbonic anhydrase XII isoform 1 precursor						one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)	aaatgtagggttttttttttt	0.104													5	3	---	---	---	---	
DENND4A	10260	broad.mit.edu	37	15	66006216	66006216	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66006216delA	uc002aph.2	-						DENND4A_uc002api.2_Intron|DENND4A_uc002apj.3_Intron	NM_005848	NP_005839	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						caaaatctatacattaggtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	71370712	71370712	+	IGR	DEL	A	-	-	rs1660969	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71370712delA								LRRC49 (28278 upstream) : CT62 (31871 downstream)																							AAATGATATTAAAAAAAAAGA	0.199													4	2	---	---	---	---	
CCDC33	80125	broad.mit.edu	37	15	74532944	74532945	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74532944_74532945insT	uc002axo.2	+							NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5						aaacctaggtcttttttttgtt	0.000													4	2	---	---	---	---	
ETFA	2108	broad.mit.edu	37	15	76579868	76579869	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76579868_76579869insT	uc002bbt.2	-						ETFA_uc010bkq.1_Intron|ETFA_uc002bbu.1_Intron	NM_000126	NP_000117	P13804	ETFA_HUMAN	electron transfer flavoprotein, alpha						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity				0						TGAGAATACTATTTTTTTTTAA	0.223													4	2	---	---	---	---	
IREB2	3658	broad.mit.edu	37	15	78747715	78747715	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78747715delA	uc002bdr.2	+						IREB2_uc010unb.1_Intron|IREB2_uc002bdq.2_Intron	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2								4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		GAAAGGAAATAAATGGGCCTT	0.363													4	2	---	---	---	---	
IREB2	3658	broad.mit.edu	37	15	78765228	78765228	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78765228delT	uc002bdr.2	+						IREB2_uc010unb.1_Intron|IREB2_uc002bdq.2_Intron	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2								4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		ttttttgtgctttttcattag	0.000													4	2	---	---	---	---	
FAM174B	400451	broad.mit.edu	37	15	93246088	93246088	+	Intron	DEL	C	-	-	rs873919	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93246088delC	uc002bsl.3	-									Q3ZCQ3	F174B_HUMAN	Homo sapiens cDNA PSEC0264 fis, clone NT2RP3002337.							integral to membrane					0						ttactcaaaacaacatttttg	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98189018	98189018	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98189018delT								SPATA8 (860174 upstream) : LOC91948 (96828 downstream)																							tacatatccattataacagtc	0.000													4	2	---	---	---	---	
LRRC28	123355	broad.mit.edu	37	15	99852729	99852729	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99852729delT	uc002bva.1	+						LRRC28_uc010urs.1_Intron|LRRC28_uc002bvb.1_Intron|LRRC28_uc010urt.1_Intron|LRRC28_uc002bvc.1_Intron|LRRC28_uc010uru.1_Intron|LRRC28_uc002bvd.1_Intron	NM_144598	NP_653199	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28												0	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			ttacaattaattttttttata	0.000													4	2	---	---	---	---	
LRRK1	79705	broad.mit.edu	37	15	101506985	101506985	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101506985delA	uc002bwr.2	+						LRRK1_uc010usb.1_Intron|LRRK1_uc010usc.1_Intron|LRRK1_uc002bwq.1_Intron	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1						small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TTTATAATGTAAAGAAAACTG	0.403													4	2	---	---	---	---	
LRRK1	79705	broad.mit.edu	37	15	101565364	101565364	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101565364delA	uc002bwr.2	+						LRRK1_uc010usb.1_Intron|LRRK1_uc010usc.1_Intron	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1						small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CTGGTGATGTAATTTCCCCGC	0.522													4	2	---	---	---	---	
PCSK6	5046	broad.mit.edu	37	15	101851320	101851320	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101851320delT	uc002bwy.2	-						PCSK6_uc010bpd.2_Intron|PCSK6_uc010bpe.2_Intron	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4						glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			aactcctgacttttttttttc	0.000													4	2	---	---	---	---	
ZNF500	26048	broad.mit.edu	37	16	4818854	4818854	+	5'Flank	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4818854delG	uc002cxp.1	-						ZNF500_uc002cxo.1_5'Flank|ZNF500_uc010uxt.1_5'Flank	NM_021646	NP_067678	O60304	ZN500_HUMAN	zinc finger protein 500						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3						TGGGGACGCCGGATTCAGGAA	0.662													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	6019808	6019808	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6019808delT								FAM86A (872019 upstream) : A2BP1 (49324 downstream)																							CTTTGTTTCATTTTTTTTTCT	0.413													5	3	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6455776	6455777	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6455776_6455777insT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		cacatgggctatttttacattt	0.173													4	2	---	---	---	---	
TEKT5	146279	broad.mit.edu	37	16	10778253	10778253	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10778253delT	uc002czz.1	-							NM_144674	NP_653275	Q96M29	TEKT5_HUMAN	tektin 5						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2						cccctccatcttttttttttt	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11496197	11496197	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11496197delT								C16orf75 (50580 upstream) : LITAF (145385 downstream)																							TTTGTCACCATTACCACTCGA	0.373													4	2	---	---	---	---	
SHISA9	729993	broad.mit.edu	37	16	13045909	13045909	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13045909delT	uc010uyy.1	+							NM_001145204	NP_001138676	B4DS77	SHSA9_HUMAN	shisa homolog 9 isoform 1						regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0						ACTTAAATGATTTTTTTTTGT	0.403													4	2	---	---	---	---	
IQCK	124152	broad.mit.edu	37	16	19733562	19733563	+	Intron	DEL	GC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19733562_19733563delGC	uc002dgr.2	+						IQCK_uc002dgs.2_Intron|IQCK_uc010vat.1_Intron|IQCK_uc010bwc.2_Intron|IQCK_uc010vau.1_Intron	NM_153208	NP_694940	Q8N0W5	IQCK_HUMAN	IQ motif containing K											skin(1)	1						GAAGAGTCAGGCAGTCAGGAGT	0.510													4	2	---	---	---	---	
SLC7A5P2	387254	broad.mit.edu	37	16	21531066	21531066	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21531066delG	uc002djd.2	-	1	700	c.621delC	c.(619-621)CCCfs	p.P207fs	uc002diq.3_Intron|LOC100271836_uc002dja.2_Intron|LOC100271836_uc002djb.2_Intron	NR_002594				RecName: Full=Putative L-type amino acid transporter 1-like protein MLAS; AltName: Full=hLAT1 3-transmembrane protein MLAS;          Short=hLAT1 3TM MLAS;												0						GTAGAGATGTGGGAGCCAGGG	0.572													4	2	---	---	---	---	
GGA2	23062	broad.mit.edu	37	16	23520113	23520113	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23520113delT	uc002dlq.2	-						GGA2_uc010bxo.1_Intron	NM_015044	NP_055859	Q9UJY4	GGA2_HUMAN	ADP-ribosylation factor binding protein 2						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|clathrin-coated vesicle|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.0386)		agggcatctcttttttgacta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29208641	29208642	+	Intron	INS	-	GATG	GATG	rs142863488	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29208641_29208642insGATG	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		gtggatgggtagatggatggat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	31987420	31987423	+	IGR	DEL	CCTG	-	-	rs28670649	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31987420_31987423delCCTG								ZNF267 (58794 upstream) : HERC2P4 (175187 downstream)																							AGAGTCACCTCCTGCCCCTGCCTA	0.652													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32817485	32817486	+	IGR	INS	-	TCA	TCA			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32817485_32817486insTCA								TP53TG3B (128607 upstream) : SLC6A10P (71311 downstream)																							ttgatttcatgtcatttcatca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33054406	33054407	+	IGR	INS	-	A	A	rs149505951		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33054406_33054407insA								SLC6A10P (157943 upstream) : MIR1826 (911101 downstream)																							cgactagtgccccgtggaaaac	0.030													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33583341	33583341	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33583341delA								SLC6A10P (686878 upstream) : MIR1826 (382167 downstream)																							AGTCATTTTTATTTGCCATTT	0.328													5	4	---	---	---	---	
GPT2	84706	broad.mit.edu	37	16	46951598	46951599	+	Intron	DEL	AC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46951598_46951599delAC	uc002eel.2	+						GPT2_uc002eem.2_Intron	NM_133443	NP_597700	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase 2 isoform 1						2-oxoglutarate metabolic process|cellular amino acid biosynthetic process|L-alanine metabolic process	mitochondrial matrix	L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	ataaatgcagacacacacacac	0.233													4	2	---	---	---	---	
ZNF423	23090	broad.mit.edu	37	16	49528209	49528209	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49528209delA	uc002efs.2	-						ZNF423_uc010vgn.1_Intron	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)				ACAGAAGGATAAAACTTCCTT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59699776	59699776	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59699776delA								GOT2 (931530 upstream) : None (None downstream)																							GCAATTCCTGAAAAAAAAAAT	0.383													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	62216635	62216635	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62216635delA								CDH8 (146599 upstream) : None (None downstream)																							taaggcttacaaaaaaaagtc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	62381721	62381721	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62381721delT								CDH8 (311685 upstream) : None (None downstream)																							AAATTCTTTATTTTTTTTTTA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66517208	66517208	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66517208delT								BEAN (464 upstream) : TK2 (26144 downstream)																							CAGGAGTTGCTTTTTTTTTTT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	76785593	76785593	+	IGR	DEL	C	-	-	rs144338442	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76785593delC								CNTNAP4 (192458 upstream) : MON1B (439243 downstream)																							ACTTATCCATCCAGGCTACTG	0.478													4	2	---	---	---	---	
RNMTL1	55178	broad.mit.edu	37	17	694415	694415	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:694415delG	uc002frw.2	+							NM_018146	NP_060616	Q9HC36	RMTL1_HUMAN	RNA methyltransferase like 1						RNA processing		protein binding|RNA binding|RNA methyltransferase activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0219)		ATGACTGTGTGGGTGCTTCTT	0.284													4	2	---	---	---	---	
WDR81	124997	broad.mit.edu	37	17	1636960	1636960	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1636960delC	uc002fti.2	+	7	1209	c.948delC	c.(946-948)GACfs	p.D316fs	WDR81_uc002fth.2_Frame_Shift_Del_p.D492fs|WDR81_uc010vqp.1_Frame_Shift_Del_p.D340fs|WDR81_uc002ftj.2_Frame_Shift_Del_p.D1543fs|WDR81_uc010vqq.1_Frame_Shift_Del_p.D174fs	NM_001163811	NP_001157283	Q562E7	WDR81_HUMAN	WD repeat domain 81 isoform 4	316										skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCGAGTGGGACCCCCATGGTG	0.677													4	2	---	---	---	---	
ITGAE	3682	broad.mit.edu	37	17	3654762	3654763	+	Intron	INS	-	G	G			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3654762_3654763insG	uc002fwo.3	-							NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor						cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		CTGAAGGGGCTGAGGTGAGGCC	0.619													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6652184	6652184	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6652184delG								SLC13A5 (35444 upstream) : XAF1 (6610 downstream)																							cagatactatggaggccaaat	0.000													4	2	---	---	---	---	
ALOX12	239	broad.mit.edu	37	17	6907057	6907059	+	Intron	DEL	ATT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6907057_6907059delATT	uc002gdx.3	+						uc002gdy.1_Intron	NM_000697	NP_000688	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase						anti-apoptosis|cellular component movement|fatty acid oxidation|leukotriene biosynthetic process|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of cell proliferation|superoxide anion generation	cytosol|sarcolemma	arachidonate 12-lipoxygenase activity|hepoxilin-epoxide hydrolase activity|iron ion binding|lipoxygenase activity|protein binding			central_nervous_system(1)	1						AGTTCTTGCAATTATTATTATTA	0.064													4	2	---	---	---	---	
TOM1L2	146691	broad.mit.edu	37	17	17759277	17759277	+	Intron	DEL	A	-	-	rs112291065		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17759277delA	uc002grz.3	-						TOM1L2_uc002gry.3_Intron|TOM1L2_uc010vwy.1_Intron|TOM1L2_uc010cpr.2_Intron|TOM1L2_uc010vwz.1_Intron|TOM1L2_uc010vxa.1_Intron|TOM1L2_uc002grv.3_Intron	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3						intracellular protein transport	intracellular					0	all_neural(463;0.228)					TGTTGTAAAGAAAAAAAAAAA	0.378													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25281690	25281691	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25281690_25281691insA								None (None upstream) : WSB1 (339415 downstream)																							TTAATGGAGAGAAAAAATATTA	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25286286	25286287	+	IGR	INS	-	A	A	rs142103642	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25286286_25286287insA								None (None upstream) : WSB1 (334819 downstream)																							taatatttGTGAAAGAATGTAT	0.238													5	3	---	---	---	---	
MYO18A	399687	broad.mit.edu	37	17	27495742	27495742	+	Intron	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27495742delC	uc002hdt.1	-						MYO18A_uc010csa.1_Intron|MYO18A_uc002hdu.1_Intron	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a						anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CTAATTGCTTCCCCCTGCCCA	0.453													4	2	---	---	---	---	
CCL23	6368	broad.mit.edu	37	17	34340465	34340465	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34340465delT	uc002hkt.1	-						CCL23_uc002hks.1_Intron	NM_145898	NP_665905	P55773	CCL23_HUMAN	small inducible cytokine A23 isoform CKbeta8						cell-cell signaling|cellular calcium ion homeostasis|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response|negative regulation of cell proliferation	extracellular space	chemokine activity|heparin binding				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	Treprostinil(DB00374)	TTTTTTTTTCTTTTTTTTTTC	0.507													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35103332	35103332	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35103332delT								MRM1 (137926 upstream) : LHX1 (191167 downstream)																							actacggagatttttttttaa	0.025													4	2	---	---	---	---	
ERBB2	2064	broad.mit.edu	37	17	37863460	37863460	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37863460delG	uc002hso.2	+						ERBB2_uc002hsm.2_Intron|ERBB2_uc010cwa.2_Intron|ERBB2_uc002hsp.2_Intron|ERBB2_uc010cwb.2_Intron|ERBB2_uc010wek.1_Intron|ERBB2_uc002hsl.2_Intron|ERBB2_uc002hsn.1_Intron	NM_004448	NP_004439	P04626	ERBB2_HUMAN	erbB-2 isoform a						cell proliferation|heart development|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell adhesion|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|protein autophosphorylation|regulation of angiogenesis|regulation of microtubule-based process|regulation of transcription, DNA-dependent|transcription, DNA-dependent|wound healing	integral to membrane|nucleus|perinuclear region of cytoplasm|receptor complex	ATP binding|DNA binding|epidermal growth factor receptor activity|ErbB-3 class receptor binding|identical protein binding|protein C-terminus binding|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(73)|central_nervous_system(16)|ovary(16)|stomach(14)|breast(9)|upper_aerodigestive_tract(5)|large_intestine(3)|liver(3)|endometrium(2)|skin(1)|pancreas(1)	143	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	Lapatinib(DB01259)|Letrozole(DB01006)|Trastuzumab(DB00072)	GTTTACAGGTGGGTGGCAGAA	0.572		1	A|Mis|O		breast|ovarian|other tumour types|NSCLC|gastric					TCGA GBM(5;<1E-08)			4	2	---	---	---	---	
KRT28	162605	broad.mit.edu	37	17	38949668	38949668	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38949668delT	uc002hvh.1	-							NM_181535	NP_853513	Q7Z3Y7	K1C28_HUMAN	keratin 25D							cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)				TTCCATTTGATTTTTTTTTTT	0.284													4	3	---	---	---	---	
JUP	3728	broad.mit.edu	37	17	39805937	39805938	+	Intron	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39805937_39805938delCA	uc010wfs.1	-							NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		acacgcagctcacacacacaca	0.282													4	2	---	---	---	---	
MAPT	4137	broad.mit.edu	37	17	44057956	44057957	+	Intron	DEL	AC	-	-	rs72082909		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44057956_44057957delAC	uc002ijr.3	+						MAPT_uc010dau.2_Intron|MAPT_uc002ijs.3_Intron|MAPT_uc002ijx.3_Intron|MAPT_uc002ijt.3_Intron|MAPT_uc002iju.3_Intron|MAPT_uc002ijv.3_Intron	NM_016835	NP_058519	P10636	TAU_HUMAN	microtubule-associated protein tau isoform 1						cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)				CCTCATTGATACACACACACAC	0.307													4	2	---	---	---	---	
HSF5	124535	broad.mit.edu	37	17	56554230	56554230	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56554230delT	uc002iwi.1	-							NM_001080439	NP_001073908	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTTCTTGCTGTTTTTTTTTTC	0.428													9	4	---	---	---	---	
TCAM1P	146771	broad.mit.edu	37	17	61937222	61937222	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61937222delT	uc002jcf.2	+							NR_002947				Homo sapiens TCAM-1 pseudogene mRNA for testicular cell adhesion molecule 1.												0						CTTGTCCTCATTTTTTTGGCA	0.502													7	4	---	---	---	---	
ERN1	2081	broad.mit.edu	37	17	62206465	62206465	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62206465delA	uc002jdz.2	-							NM_001433	NP_001424	O75460	ERN1_HUMAN	endoplasmic reticulum to nucleus signalling 1						activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to endoplasmic reticulum membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1)	9						CAACCAGAAGAAAAAAAAAAG	0.403													6	3	---	---	---	---	
POLG2	11232	broad.mit.edu	37	17	62488057	62488057	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62488057delA	uc002jei.2	-						POLG2_uc010deg.1_Intron	NM_007215	NP_009146	Q9UHN1	DPOG2_HUMAN	DNA polymerase subunit gamma-2, mitochondrial						DNA repair|DNA-dependent DNA replication|glycyl-tRNA aminoacylation	mitochondrial chromosome	ATP binding|DNA-directed DNA polymerase activity|glycine-tRNA ligase activity|identical protein binding|single-stranded DNA binding			central_nervous_system(1)	1	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			aaaaaaaaacaaaaaaaaaac	0.234													3	3	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	64036348	64036348	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64036348delT	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			tgtgattttgtttttttaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68135660	68135661	+	IGR	INS	-	A	A	rs146728881	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68135660_68135661insA								KCNJ16 (3916 upstream) : KCNJ2 (29153 downstream)																							AAAACAAAGGTAAAAAAAAAGA	0.213													4	2	---	---	---	---	
NUP85	79902	broad.mit.edu	37	17	73229481	73229486	+	Intron	DEL	TCTTTC	-	-	rs10567128		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73229481_73229486delTCTTTC	uc002jng.1	+						NUP85_uc010dgd.1_Intron|NUP85_uc010wrv.1_Intron|NUP85_uc002jnh.1_Intron	NM_024844	NP_079120	Q9BW27	NUP85_HUMAN	nucleoporin 85						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|nuclear membrane|Nup107-160 complex|spindle	protein binding			ovary(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			tttctctctttctttctctttctctt	0.146													2	4	---	---	---	---	
RNF157	114804	broad.mit.edu	37	17	74166893	74166893	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74166893delA	uc002jqz.2	-						RNF157_uc002jra.2_Intron	NM_052916	NP_443148	Q96PX1	RN157_HUMAN	ring finger protein 157								zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(166;0.187)			tccagcttctaaaatgttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75584826	75584826	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75584826delA								SEPT9 (88150 upstream) : FLJ45079 (290283 downstream)																							actgagttgtaggagttcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75783515	75783516	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75783515_75783516delCA								SEPT9 (286839 upstream) : FLJ45079 (91593 downstream)																							TCCCCGCGTCCACACACACACG	0.490													4	2	---	---	---	---	
TBCD	6904	broad.mit.edu	37	17	80870491	80870491	+	Intron	DEL	A	-	-	rs145496769		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80870491delA	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|TBCD_uc002kgb.1_Intron	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			GGAAGCTTGGAAAAATCGCGG	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	2329636	2329636	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2329636delA								C18orf2 (922455 upstream) : METTL4 (207889 downstream)																							TGGTTTTATGAAAAAAAAAAA	0.313													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	8457740	8457740	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8457740delA								PTPRM (50882 upstream) : RAB12 (151695 downstream)																							GTATCAAGTGAAAAAAAAAGT	0.075													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	12033402	12033403	+	IGR	INS	-	CCACA	CCACA	rs139760767	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12033402_12033403insCCACA								IMPA2 (2526 upstream) : CIDEA (220915 downstream)																							GGATTGATGTTCAGGTAGCTGT	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	13660946	13660947	+	IGR	INS	-	A	A	rs11372083		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13660946_13660947insA								C18orf1 (8193 upstream) : C18orf19 (2403 downstream)																							ATGTGTTCATTAAAAAAAAAAA	0.337													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	25153916	25153917	+	Intron	DEL	TT	-	-	rs113299929		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25153916_25153917delTT	uc002kwf.1	-											Homo sapiens cDNA FLJ45994 fis, clone SKMUS2009557.																		tgtcttctcctttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	27613208	27613210	+	IGR	DEL	TTG	-	-	rs71987150		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27613208_27613210delTTG								None (None upstream) : MIR302F (265666 downstream)																							AGAAACATCATTGTTGTTTTCAA	0.296													4	2	---	---	---	---	
FAM59A	64762	broad.mit.edu	37	18	29890608	29890608	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29890608delT	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A											ovary(1)|skin(1)	2						TAAATGGTTGTTTTTAACAGT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	31149962	31149962	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31149962delA								C18orf34 (129277 upstream) : ASXL3 (8579 downstream)																							aaaatattagaaaaaaaatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	32725162	32725162	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32725162delA								MAPRE2 (2785 upstream) : ZNF397 (95836 downstream)																							AATTCACTGGAAAAAAAAAAT	0.333													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39489379	39489380	+	IGR	DEL	AT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39489379_39489380delAT								KC6 (388818 upstream) : PIK3C3 (45819 downstream)																							ctcaccctggATAAAAACAGGT	0.158													4	2	---	---	---	---	
DYM	54808	broad.mit.edu	37	18	46885221	46885226	+	Intron	DEL	ACAGAT	-	-	rs149531265		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46885221_46885226delACAGAT	uc002ldi.1	-						DYM_uc010xdf.1_Intron	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin							Golgi apparatus					0						AGCAACAAAAACAGATACAAAGACAA	0.417													2	4	---	---	---	---	
DYM	54808	broad.mit.edu	37	18	46956334	46956335	+	Intron	INS	-	TT	TT			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46956334_46956335insTT	uc002ldi.1	-						DYM_uc010xdf.1_Intron	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin							Golgi apparatus					0						tatTTAAACAATTTTGTGAAAC	0.173													4	2	---	---	---	---	
MAPK4	5596	broad.mit.edu	37	18	48195679	48195679	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48195679delA	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)		CTCAAAAGAGAAAAAAAATGT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	48948160	48948160	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48948160delT	uc010xdq.1	+											Homo sapiens cDNA FLJ37617 fis, clone BRCOC2012229.																		GGCTGTGTCCTTTGCCAAGGC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	52795758	52795759	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52795758_52795759delCA								CCDC68 (169019 upstream) : TCF4 (93803 downstream)																							CATGAGCGAGCACACACACACA	0.465													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	59245072	59245073	+	IGR	DEL	AG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59245072_59245073delAG								CDH20 (22707 upstream) : RNF152 (237231 downstream)																							CAAAGAGGTCAGAGAGAGAGGT	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68618787	68618788	+	IGR	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68618787_68618788insT								SOCS6 (621353 upstream) : None (None downstream)																							atcttcccctgttttttttttc	0.000													4	2	---	---	---	---	
CNDP1	84735	broad.mit.edu	37	18	72227930	72227930	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72227930delA	uc002llq.2	+						uc002llr.2_5'Flank	NM_032649	NP_116038	Q96KN2	CNDP1_HUMAN	carnosinase 1 precursor						proteolysis	extracellular region	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity|tripeptidase activity				0		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		aaaagaaaagaaaaaagaaAA	0.109													4	2	---	---	---	---	
TCF3	6929	broad.mit.edu	37	19	1609801	1609802	+	3'UTR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1609801_1609802insA	uc002ltr.2	-	19					TCF3_uc002ltn.2_3'UTR|TCF3_uc002lto.2_3'UTR|TCF3_uc002ltt.3_3'UTR|TCF3_uc002ltq.2_3'UTR|TCF3_uc002lts.1_3'UTR	NM_003200	NP_003191	P15923	TFE2_HUMAN	transcription factor 3 isoform E12						B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of muscle cell differentiation|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus|protein complex|transcription factor complex	bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|mitogen-activated protein kinase kinase kinase binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|vitamin D response element binding			lung(2)|breast(2)|ovary(1)|large_intestine(1)|skin(1)	7		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		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)		CCCAGGCTCCCAAGCCAGTCTG	0.673			T	PBX1|HLF|TFPT	pre B-ALL								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3473831	3473832	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3473831_3473832insA								NFIC (10229 upstream) : C19orf77 (573 downstream)																							tttgtctaaagaaaaaaaaaga	0.069													4	2	---	---	---	---	
MYO1F	4542	broad.mit.edu	37	19	8623560	8623560	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8623560delT	uc002mkg.2	-						MYO1F_uc002mkh.2_Intron|MYO1F_uc010xkf.1_Intron	NM_012335	NP_036467	O00160	MYO1F_HUMAN	myosin IF							unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3						TGATGGCAACTTGGAGCTACC	0.373													0	6	---	---	---	---	
EMR2	30817	broad.mit.edu	37	19	14887349	14887356	+	Intron	DEL	GGGGTGTG	-	-	rs3217026		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14887349_14887356delGGGGTGTG	uc002mzp.1	-						EMR2_uc010xnw.1_Intron|EMR2_uc002mzo.1_Intron|EMR2_uc002mzq.1_Intron|EMR2_uc002mzr.1_Intron|EMR2_uc002mzs.1_Intron|EMR2_uc002mzt.1_Intron|EMR2_uc002mzu.1_Intron|EMR2_uc010xny.1_Intron	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone						cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			lung(2)|ovary(1)|skin(1)	4						AGTTCCTGCCGGGGTGTGGGGGTGCCCA	0.649													4	3	---	---	---	---	
CPAMD8	27151	broad.mit.edu	37	19	17119514	17119514	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17119514delA	uc002nfb.2	-							NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						ACCCCGGGGCAAAAAAAAAGC	0.488													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24058757	24058757	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24058757delT								RPSAP58 (47840 upstream) : ZNF254 (157490 downstream)																							TGCAATTCCCTTTCCCCCACC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29660073	29660073	+	IGR	DEL	G	-	-	rs35525856		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29660073delG								LOC148145 (200018 upstream) : UQCRFS1 (38094 downstream)																							TCTTATTAATGACATGCCCTT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	33051147	33051147	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33051147delT								DPY19L3 (75911 upstream) : PDCD5 (20957 downstream)																							TAATCATGACttttttttttc	0.030													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36060164	36060164	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36060164delT								ATP4A (5604 upstream) : HAUS5 (43482 downstream)																							CTGCCTGTGCTTCCCCCATCC	0.229													4	2	---	---	---	---	
CAPNS1	826	broad.mit.edu	37	19	36632494	36632494	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36632494delT	uc002odj.2	+						CAPNS1_uc002odi.1_Intron|CAPNS1_uc002odk.2_Intron|CAPNS1_uc002odl.2_Intron	NM_001749	NP_001740	P04632	CPNS1_HUMAN	calpain, small subunit 1						positive regulation of cell proliferation	cytoplasm|plasma membrane	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity				0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CTGAGTGACATTTTACGGAAG	0.527													4	2	---	---	---	---	
POU2F2	5452	broad.mit.edu	37	19	42638469	42638469	+	5'Flank	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42638469delC	uc002osn.2	-						POU2F2_uc002oso.2_5'Flank|POU2F2_uc002osp.2_5'Flank|POU2F2_uc002osq.2_5'Flank|POU2F2_uc002osr.1_5'Flank|uc002oss.2_Intron|hsa-mir-4323|MI0015853_5'Flank	NM_002698	NP_002689	P09086	PO2F2_HUMAN	POU domain, class 2, transcription factor 2						humoral immune response|transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2		Prostate(69;0.059)				CCCATTCCAGCCCCCTAGAGC	0.468													4	2	---	---	---	---	
SPHK2	56848	broad.mit.edu	37	19	49127159	49127159	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49127159delA	uc002pjr.2	+						SPHK2_uc010xzt.1_Intron|SPHK2_uc002pjs.2_Intron|SPHK2_uc002pjt.2_Intron|SPHK2_uc002pju.2_5'Flank|SPHK2_uc002pjv.2_5'Flank|SPHK2_uc002pjw.2_5'Flank|SPHK2_uc010xzu.1_5'Flank	NM_020126	NP_064511	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|cell proliferation|sphinganine-1-phosphate biosynthetic process	cytosol|lysosomal membrane|membrane fraction	ATP binding|D-erythro-sphingosine kinase activity|diacylglycerol kinase activity|Ras GTPase binding|sphinganine kinase activity			lung(1)	1		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		TAACTGTCCGAAAAAAAAGTA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	50223451	50223451	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50223451delT								CPT1C (6463 upstream) : TSKS (19561 downstream)																							ttcttttttcttttttttttt	0.149													4	2	---	---	---	---	
ZNF175	7728	broad.mit.edu	37	19	52077636	52077636	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52077636delA	uc002pxb.2	+							NM_007147	NP_009078	Q9Y473	ZN175_HUMAN	zinc finger protein 175						response to virus	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		TTCTTAAAAGAAAAATTGAAA	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53328944	53328944	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53328944delA								ZNF28 (4059 upstream) : ZNF468 (12842 downstream)																							aaacaacaacaaaaaaATCAT	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57254848	57254849	+	Intron	INS	-	CTT	CTT	rs111379728		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57254848_57254849insCTT	uc010ygp.1	+											Homo sapiens cDNA clone IMAGE:4793694.																		acgtgttgctcctgccatcact	0.188													3	5	---	---	---	---	
KIF16B	55614	broad.mit.edu	37	20	16438542	16438542	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16438542delA	uc002wpg.1	-						KIF16B_uc010gch.1_Intron|KIF16B_uc010gci.1_Intron|KIF16B_uc010gcj.1_Intron	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23						cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						TTTTGAGAAGAAAAAAAAAAA	0.378													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	18979986	18979987	+	IGR	DEL	CT	-	-	rs141232438		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18979986_18979987delCT								C20orf79 (184953 upstream) : SLC24A3 (213303 downstream)																							ACAGAGCCGCCTCTCTCTCTTG	0.505													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22082520	22082523	+	IGR	DEL	TGTG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22082520_22082523delTGTG								PAX1 (385900 upstream) : LOC284788 (298448 downstream)																							aaagtgtgcatgtgtgtgtgtgtg	0.034													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23049171	23049172	+	IGR	DEL	CT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23049171_23049172delCT								THBD (18870 upstream) : CD93 (10822 downstream)																							gacagctcagctctctctctct	0.054													4	2	---	---	---	---	
NINL	22981	broad.mit.edu	37	20	25533940	25533940	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25533940delA	uc002wux.1	-						NINL_uc010gdn.1_Intron|NINL_uc010gdo.1_Intron	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like						G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						ATACTGTTACAAAAAAAACCG	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25959469	25959470	+	IGR	DEL	GC	-	-	rs143068372	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25959469_25959470delGC								FAM182B (110683 upstream) : LOC100134868 (30965 downstream)																							gtgggcagtggcgagtcagcct	0.000													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29616441	29616442	+	Intron	INS	-	T	T	rs138561282		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29616441_29616442insT	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0						tttcttggcagtttttatcata	0.000													4	4	---	---	---	---	
PHF20	51230	broad.mit.edu	37	20	34414910	34414910	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34414910delT	uc002xek.1	+						PHF20_uc002xei.1_Intron|PHF20_uc010gfo.1_Intron|PHF20_uc002xej.1_Intron	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)					CAGCCTTTTGTTTTTTACTAA	0.328													4	2	---	---	---	---	
HNF4A	3172	broad.mit.edu	37	20	43001418	43001418	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43001418delG	uc002xlv.2	+						HNF4A_uc010zwo.1_Intron|HNF4A_uc002xlt.2_Intron|HNF4A_uc002xlu.2_Intron	NM_175914	NP_787110	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4 alpha isoform d						blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process	cytoplasm	activating transcription factor binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CTTTGTTTTTGGAGAAGATGG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	44079260	44079260	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44079260delG								PIGT (24376 upstream) : WFDC2 (19134 downstream)																							gatggcatttgggagggaatc	0.109													4	2	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51887859	51887861	+	Intron	DEL	AGC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51887859_51887861delAGC	uc002xwo.2	+							NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			tcttctatcaagcagcagcagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9841160	9841160	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9841160delA								None (None upstream) : None (None downstream)																							TTCTGAGATGAAGCTCAAGTA	0.323													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9854127	9854128	+	IGR	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9854127_9854128insC								None (None upstream) : None (None downstream)																							ttcaacctcctcacactgaatt	0.025													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11043037	11043039	+	Intron	DEL	TGC	-	-	rs149525628		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11043037_11043039delTGC	uc002yit.1	-							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)		ttgctgttgttgctgttgttgtt	0.000													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11048067	11048070	+	Intron	DEL	CTCT	-	-	rs140519785		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11048067_11048070delCTCT	uc002yit.1	-							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)		tagactaaagctctctgagtttca	0.020													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11060025	11060027	+	Intron	DEL	AGA	-	-	rs146956675		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11060025_11060027delAGA	uc002yit.1	-						BAGE_uc002yiw.1_5'Flank|BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TTAGAAACACAGAAAAAATATTT	0.261													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11080752	11080753	+	Intron	INS	-	CA	CA			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11080752_11080753insCA	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)		aggctgtaatgggaggatcact	0.084													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11084007	11084008	+	Intron	DEL	TG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11084007_11084008delTG	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)		tttgtgtgtttgtgtgtgtgta	0.188													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11099478	11099479	+	5'Flank	INS	-	A	A	rs3048558		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11099478_11099479insA	uc002yit.1	-						BAGE_uc002yix.2_5'Flank	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)		aagatgttgggaaaaaaaattg	0.000													5	4	---	---	---	---	
CYYR1	116159	broad.mit.edu	37	21	27867966	27867966	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27867966delG	uc002ymd.2	-						CYYR1_uc011ack.1_Intron|CYYR1_uc002yme.2_Intron	NM_052954	NP_443186	Q96J86	CYYR1_HUMAN	cysteine and tyrosine-rich 1 protein precursor							integral to membrane					0						caatatggaaggaggcggagt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	28786738	28786741	+	Intron	DEL	TCTC	-	-	rs139793537		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28786738_28786741delTCTC	uc002ymh.2	-											Homo sapiens, clone IMAGE:5227164, mRNA.																		ctttgattcttctctctttatctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	35372508	35372509	+	IGR	INS	-	C	C	rs141835426	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35372508_35372509insC								ATP5O (84350 upstream) : MRPS6 (73314 downstream)																							GATTTGAGGAATCATAAAAAGT	0.480													2	4	---	---	---	---	
MORC3	23515	broad.mit.edu	37	21	37743744	37743745	+	Intron	INS	-	T	T	rs143895738	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37743744_37743745insT	uc002yvi.2	+							NM_015358	NP_056173	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3						cell aging|maintenance of protein location in nucleus|negative regulation of fibroblast proliferation|peptidyl-serine phosphorylation|protein stabilization	aggresome|intermediate filament cytoskeleton|PML body	ATP binding|zinc ion binding			ovary(2)	2						cctaacctgccttaaagtgctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	42390400	42390401	+	IGR	DEL	AC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42390400_42390401delAC								DSCAM (171361 upstream) : C21orf130 (123026 downstream)																							gaaggaggctacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	43612768	43612768	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43612768delC								UMODL1 (49663 upstream) : ABCG1 (7031 downstream)																							GAAGAAAAATCCCCCACATCT	0.517													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22451593	22451594	+	Intron	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22451593_22451594insT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						ATCTTTTTTCCTTTttttttgt	0.183													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22625260	22625260	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22625260delT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						gaaagacttgttttTTTTTTC	0.144													10	6	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	23050775	23050775	+	Intron	DEL	G	-	-	rs5844514		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23050775delG	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						CAGCAGGACTGTTTCCATGCA	0.512													2	6	---	---	---	---	
RAB36	9609	broad.mit.edu	37	22	23488012	23488012	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23488012delA	uc002zwv.1	+						RAB36_uc010gtw.1_Intron	NM_004914	NP_004905	O95755	RAB36_HUMAN	RAB36, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)		GTCCGGACAGAAAAAGGAGAC	0.607													4	2	---	---	---	---	
KIAA1671	85379	broad.mit.edu	37	22	25491384	25491385	+	Intron	DEL	TG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25491384_25491385delTG	uc003abn.2	+						KIAA1671_uc003abl.2_Intron	NM_001145206	NP_001138678	Q9BY89	K1671_HUMAN	hypothetical protein LOC85379											lung(1)	1						tttgggaggctgaagagggtgg	0.069													4	2	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26179469	26179470	+	Intron	DEL	AC	-	-	rs143307061		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26179469_26179470delAC	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						CATCTCTCAGACACACACATCA	0.564													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	29818797	29818798	+	IGR	INS	-	AC	AC	rs143839296	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29818797_29818798insAC								AP1B1 (34228 upstream) : RFPL1S (14208 downstream)																							Aacacacacatacacacacaca	0.272													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	32578543	32578543	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32578543delA								C22orf42 (23300 upstream) : RFPL2 (7879 downstream)																							GCTTTTTCCTAATGAAATCAG	0.393													4	2	---	---	---	---	
SYN3	8224	broad.mit.edu	37	22	33358546	33358546	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33358546delA	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						CTCAGGAATGAGGCGGCGAGT	0.423													4	2	---	---	---	---	
MCM5	4174	broad.mit.edu	37	22	35806526	35806527	+	Intron	INS	-	CAAT	CAAT	rs147091320	by1000genomes	TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35806526_35806527insCAAT	uc003anu.3	+						MCM5_uc010gwr.2_Intron|MCM5_uc003anv.3_Intron|MCM5_uc010gws.1_Intron|MCM5_uc003anw.1_5'UTR	NM_006739	NP_006730	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5						cell cycle checkpoint|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	MCM complex	ATP binding|DNA binding|helicase activity|protein binding			ovary(1)	1						TGTGGGCAACACCATCCTCCAA	0.594													4	2	---	---	---	---	
TCF20	6942	broad.mit.edu	37	22	42582040	42582041	+	Intron	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42582040_42582041insA	uc003bcj.1	-						TCF20_uc003bck.1_Intron|TCF20_uc003bnt.2_Intron	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5						GCTGCTCCGGCAAAAGTGCCAG	0.416													14	11	---	---	---	---	
FAM118A	55007	broad.mit.edu	37	22	45720027	45720027	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45720027delA	uc003bfz.3	+						FAM118A_uc003bga.3_Intron	NM_001104595	NP_001098065	Q9NWS6	F118A_HUMAN	hypothetical protein LOC55007							integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		agagagcacgaaaaaaagtga	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	50777692	50777695	+	IGR	DEL	TGTG	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50777692_50777695delTGTG								FAM116B (12203 upstream) : SAPS2 (4065 downstream)																							gttgtgtgattgtgtggtgtgtgt	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	668469	668470	+	IGR	INS	-	C	C			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:668469_668470insC								SHOX (48324 upstream) : CRLF2 (646417 downstream)																							GCGTGCGGGTGCCCCCGGGTGC	0.490													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	958822	958823	+	IGR	DEL	GC	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:958822_958823delGC								SHOX (338677 upstream) : CRLF2 (356064 downstream)																							TTTCCAAGCAGCGACTCTGAGA	0.332													4	5	---	---	---	---	
IL3RA	3563	broad.mit.edu	37	X	1467648	1467649	+	Intron	DEL	CT	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1467648_1467649delCT	uc004cps.2	+						IL3RA_uc011mhd.1_Intron	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	tccttctttcctctctttcttt	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	5046283	5046284	+	IGR	INS	-	GT	GT	rs62591030		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5046283_5046284insGT								None (None upstream) : NLGN4X (761800 downstream)																							TTGgtgtatgcgtgtgtgtgtg	0.361													4	2	---	---	---	---	
FIGF	2277	broad.mit.edu	37	X	15402300	15402301	+	Translation_Start_Site	INS	-	CTCATG	CTCATG	rs71871438		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15402300_15402301insCTCATG	uc004cwt.1	-	1	277_278	c.-232_-231insCATGAG	c.(-234--229)GAGAAC>GAGCATGAGAAC			NM_004469	NP_004460	O43915	VEGFD_HUMAN	vascular endothelial growth factor D						angiogenesis|cell differentiation|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of mast cell chemotaxis|vascular endothelial growth factor receptor signaling pathway	extracellular space|membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity|platelet-derived growth factor receptor binding			ovary(1)|breast(1)|central_nervous_system(1)	3	Hepatocellular(33;0.183)					ATCAAAATGTTCTCCAAAAATA	0.327													7	4	---	---	---	---	
POLA1	5422	broad.mit.edu	37	X	24857408	24857408	+	Intron	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24857408delG	uc004dbl.2	+							NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase 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|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)	TCCTTCCCCTGGGGAAAAAAA	0.353													4	2	---	---	---	---	
POLA1	5422	broad.mit.edu	37	X	24857412	24857412	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24857412delA	uc004dbl.2	+							NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase 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|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)	TCCCCTGGGGAAAAAAAAAAT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	25021268	25021269	+	IGR	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25021268_25021269delCA								POLA1 (6168 upstream) : ARX (546 downstream)																							ctctctctctcacacacacacg	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	27924787	27924787	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27924787delA								MAGEB10 (84025 upstream) : DCAF8L1 (71323 downstream)																							GAAAAAAAAGAAAAAAAAAAG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	38790133	38790134	+	IGR	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38790133_38790134insT								MID1IP1 (124352 upstream) : None (None downstream)																							TTGAAATTGCCTTTTTTTTTCC	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	40387203	40387203	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40387203delT								BCOR (350621 upstream) : ATP6AP2 (53013 downstream)																							gcattctctctttttttttgt	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	50984291	50984291	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50984291delA								BMP15 (324685 upstream) : NUDT10 (90792 downstream)																							atattaaatgaaaaaaaaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	52084777	52084777	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52084777delC								MAGED4B (272409 upstream) : XAGE2 (27301 downstream)																							GTTGCAGTCACCCCATCCTCC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	52587462	52587462	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52587462delA								XAGE1D (343511 upstream) : SSX8 (64523 downstream)																							GGGTATTTACAAAAATATTTC	0.333													4	2	---	---	---	---	
PAGE3	139793	broad.mit.edu	37	X	55285267	55285267	+	Intron	DEL	A	-	-	rs34719048		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55285267delA	uc004dul.2	-						PAGE3_uc011mon.1_Intron	NM_001017931	NP_001017931			P antigen family, member 3 (prostate												0						GTAATTTTAGAAAAAAAAAAT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	57607492	57607492	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57607492delA								FAAH2 (91865 upstream) : ZXDB (10777 downstream)																							TTAATACGGTAAAAGGGCAAC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	67979359	67979359	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67979359delT								STARD8 (33682 upstream) : EFNB1 (69481 downstream)																							CTTTGGTGGCTTTTTCTACCC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	72682384	72682384	+	IGR	DEL	C	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72682384delC								CDX4 (7964 upstream) : CHIC1 (100600 downstream)																							cgttttatgtccccctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	78081891	78081892	+	IGR	INS	-	T	T			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78081891_78081892insT								LPAR4 (69315 upstream) : P2RY10 (118937 downstream)																							ATGTTACTTTCTTGTAGAAAGA	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	81104611	81104612	+	IGR	INS	-	A	A	rs112400065		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:81104611_81104612insA								SH3BGRL (550569 upstream) : None (None downstream)																							cttcacccagcaaaaaaaagtc	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	92861443	92861443	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:92861443delT								PCDH11X (983217 upstream) : NAP1L3 (64486 downstream)																							acatgttggcttttggggggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	95427522	95427523	+	IGR	INS	-	TC	TC			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95427522_95427523insTC								None (None upstream) : LOC643486 (164563 downstream)																							CACACTGGCAATCGATTGCCAA	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	99404530	99404530	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99404530delA								LOC442459 (209689 upstream) : PCDH19 (142120 downstream)																							TCCTGTTCATAAAAAAAAAAT	0.348													4	2	---	---	---	---	
PCDH19	57526	broad.mit.edu	37	X	99567994	99567995	+	Intron	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99567994_99567995delCA	uc010nmz.2	-						PCDH19_uc004efw.3_Intron|PCDH19_uc004efx.3_Intron	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7						GCCACAAAATCACACACACACA	0.406													4	2	---	---	---	---	
NOX1	27035	broad.mit.edu	37	X	100120158	100120158	+	Intron	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100120158delT	uc004egj.2	-						uc010nnf.2_Intron|NOX1_uc004egl.3_Intron|NOX1_uc010nne.2_Intron	NM_007052	NP_008983	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1 isoform long						angiogenesis|cell migration|electron transport chain|FADH2 metabolic process|hydrogen peroxide metabolic process|inflammatory response|intracellular pH elevation|positive regulation of integrin biosynthetic process|positive regulation of smooth muscle cell proliferation|positive regulation vascular endothelial growth factor production|respiratory burst|response to pH|signal transduction|superoxide anion generation	cell junction|early endosome|invadopodium membrane|NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|Rac GTPase binding|superoxide-generating NADPH oxidase activity|voltage-gated proton channel activity			ovary(1)	1						ACTCACACCCTGACTGTTTTT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	106755250	106755250	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106755250delT								CXorf41 (267778 upstream) : PRPS1 (116404 downstream)																							TCCTACTTTCTTTTTTTTTTG	0.358													4	2	---	---	---	---	
ATG4A	115201	broad.mit.edu	37	X	107369095	107369095	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107369095delA	uc004enr.2	+						ATG4A_uc004ent.2_Intron|ATG4A_uc004ens.2_Intron|ATG4A_uc011msl.1_Intron|ATG4A_uc010npi.2_Intron|ATG4A_uc004enu.2_5'Flank	NM_052936	NP_443168	Q8WYN0	ATG4A_HUMAN	autophagy-related cysteine endopeptidase 2						autophagy|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity			pancreas(1)	1						GGACCTTGAGAAAGGGAAGGT	0.383													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	124204669	124204669	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124204669delT								ODZ1 (107003 upstream) : None (None downstream)																							aaatggttgcttttgaagttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	125360321	125360321	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125360321delT								DCAF12L2 (60387 upstream) : DCAF12L1 (323047 downstream)																							CTAGCTTCCATTTTTTTTTGT	0.308													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	129549791	129549791	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129549791delT								RBMX2 (2475 upstream) : FAM45B (79124 downstream)																							aacttagatcttgggtccagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	136889220	136889220	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136889220delT								ZIC3 (234963 upstream) : LOC158696 (807672 downstream)																							tttttttttctttttttttga	0.000													2	4	---	---	---	---	
FGF13	2258	broad.mit.edu	37	X	137718766	137718766	+	Intron	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137718766delA	uc004fam.2	-						FGF13_uc004fan.2_Intron|FGF13_uc011mwi.1_Intron|FGF13_uc004faq.2_Intron|FGF13_uc004far.2_Intron|FGF13_uc011mwj.1_Intron|FGF13_uc011mwk.1_Intron	NM_004114	NP_004105	Q92913	FGF13_HUMAN	fibroblast growth factor 13 isoform 1						cell-cell signaling|MAPKKK cascade|nervous system development	cytoplasm|nucleus	growth factor activity|protein kinase activator activity			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)					ATGTATAAGTAATCCATAGAG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	139632953	139632953	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139632953delT								SOX3 (45728 upstream) : RP1-177G6.2 (158979 downstream)																							CCCTCAGGTCTTTTTTTTTTT	0.453													6	3	---	---	---	---	
MAGEC2	51438	broad.mit.edu	37	X	141294665	141294666	+	5'Flank	DEL	CA	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141294665_141294666delCA	uc004fbu.1	-							NM_016249	NP_057333	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2							cytoplasm|nucleus				breast(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)					CTGATTGCTGCAcacacacaca	0.193										HNSCC(46;0.14)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	141709197	141709198	+	IGR	INS	-	A	A	rs146607633		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141709197_141709198insA								MAGEC2 (416121 upstream) : SPANXN4 (404506 downstream)																							GGAGATAAACTGTTAAGGAGGG	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	142567709	142567710	+	IGR	INS	-	CA	CA	rs80354505		TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142567709_142567710insCA								SPANXN4 (445644 upstream) : SPANXN3 (28855 downstream)																							cctttcatagccacacacacct	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	142623160	142623160	+	IGR	DEL	T	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142623160delT								SPANXN3 (17853 upstream) : SLITRK4 (92785 downstream)																							caccacaaactttttttttca	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	144433863	144433864	+	IGR	INS	-	A	A			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144433863_144433864insA								SPANXN1 (96135 upstream) : SLITRK2 (465483 downstream)																							agaatacctggaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	150971527	150971527	+	IGR	DEL	A	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150971527delA								CNGA2 (57491 upstream) : MAGEA4 (109469 downstream)																							attgtctcataaatgtcattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	152663194	152663194	+	IGR	DEL	G	-	-			TCGA-B0-5705-01A-11D-1534-10	TCGA-B0-5705-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152663194delG								ZNF275 (44811 upstream) : ZFP92 (20587 downstream)																							ACGACTTCCAGGGCCGGGCCG	0.622													4	2	---	---	---	---	
