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
NBPF1	55672	broad.mit.edu	37	1	16918543	16918543	+	5'UTR	SNP	A	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918543A>G	uc009vos.1	-	7					NBPF1_uc010oce.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		GAAGAGGTGGAGCCAGGGACT	0.458													19	457	---	---	---	---	PASS
TCEB3	6924	broad.mit.edu	37	1	24082845	24082845	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24082845C>T	uc001bho.2	+	9	2192	c.2132C>T	c.(2131-2133)ACG>ATG	p.T711M		NM_003198	NP_003189	Q14241	ELOA1_HUMAN	elongin A	711					positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|viral reproduction	integral to membrane	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		AAGTTTGGAACGGGAGGAGCA	0.517													7	151	---	---	---	---	PASS
SPOCD1	90853	broad.mit.edu	37	1	32266115	32266115	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32266115A>T	uc001bts.1	-	4	1587	c.1529T>A	c.(1528-1530)GTC>GAC	p.V510D	SPOCD1_uc001btt.2_5'Flank|SPOCD1_uc001btu.2_Missense_Mutation_p.V510D|SPOCD1_uc001btv.2_Missense_Mutation_p.V3D|SPOCD1_uc001btw.1_5'Flank	NM_144569	NP_653170	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	510					transcription, DNA-dependent					ovary(5)|breast(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		GGGTGAGCTGACCTCCATCAA	0.507													13	58	---	---	---	---	PASS
ST3GAL3	6487	broad.mit.edu	37	1	44386570	44386570	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44386570T>A	uc001ckc.2	+	11	1185	c.1008T>A	c.(1006-1008)TAT>TAA	p.Y336*	ST3GAL3_uc001cjz.2_Nonsense_Mutation_p.Y351*|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Nonsense_Mutation_p.Y405*|ST3GAL3_uc001ckd.2_Nonsense_Mutation_p.Y390*|ST3GAL3_uc001cke.2_Nonsense_Mutation_p.Y320*|ST3GAL3_uc001ckf.2_Nonsense_Mutation_p.Y374*|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Nonsense_Mutation_p.Y306*|ST3GAL3_uc001ckj.2_RNA|ST3GAL3_uc009vww.2_RNA|ST3GAL3_uc001ckk.2_Nonsense_Mutation_p.Y305*|ST3GAL3_uc009vwy.2_Nonsense_Mutation_p.Y242*|ST3GAL3_uc009vwx.2_Intron|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Nonsense_Mutation_p.Y110*|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Intron|ST3GAL3_uc009vxa.2_Nonsense_Mutation_p.Y123*|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Intron|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270	Q11203	SIAT6_HUMAN	sialyltransferase 6 isoform j	336	Lumenal (Potential).				protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				TGCACTACTATGAGACCGTTC	0.577													17	92	---	---	---	---	PASS
SCNM1	79005	broad.mit.edu	37	1	151138557	151138557	+	5'UTR	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151138557C>T	uc001ewz.2	+	1					LYSMD1_uc001ewy.2_5'Flank|LYSMD1_uc010pcr.1_5'Flank|SCNM1_uc010pcs.1_5'UTR|SCNM1_uc009wmn.2_RNA	NM_024041	NP_076946	Q9BWG6	SCNM1_HUMAN	sodium channel modifier 1						mRNA processing|RNA splicing	nucleus	metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|skin(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CTGTCCCGCTCTTGCTACGGT	0.547													21	214	---	---	---	---	PASS
CELF3	11189	broad.mit.edu	37	1	151681728	151681728	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151681728G>A	uc001eys.1	-	4	1168	c.374C>T	c.(373-375)ACT>ATT	p.T125I	CELF3_uc010pdh.1_5'Flank|CELF3_uc001eyr.2_Missense_Mutation_p.T124I|CELF3_uc009wmy.2_Missense_Mutation_p.T125I|CELF3_uc009wmx.1_Missense_Mutation_p.T125I|CELF3_uc001eyt.2_Missense_Mutation_p.T48I|CELF3_uc010pdi.1_Missense_Mutation_p.T125I|C1orf230_uc001eyu.2_5'Flank	NM_007185	NP_009116	Q5SZQ8	CELF3_HUMAN	trinucleotide repeat containing 4	125	RRM 2.				nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	mRNA binding|nucleotide binding			ovary(1)|central_nervous_system(1)	2						CCGGAGCACAGTGCACTCGTC	0.612													20	138	---	---	---	---	PASS
METTL13	51603	broad.mit.edu	37	1	171759689	171759689	+	Silent	SNP	G	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171759689G>T	uc001ghz.2	+	5	1754	c.1407G>T	c.(1405-1407)CTG>CTT	p.L469L	METTL13_uc001gia.2_Silent_p.L383L|METTL13_uc001gib.2_Silent_p.L313L|METTL13_uc010pml.1_Silent_p.L468L	NM_015935	NP_057019	Q8N6R0	MTL13_HUMAN	CGI-01 protein isoform 1	469							methyltransferase activity|protein binding			kidney(1)	1						AGAGTTACCTGTGTTGTGAAC	0.567													6	96	---	---	---	---	PASS
PFKFB2	5208	broad.mit.edu	37	1	207236745	207236745	+	Silent	SNP	T	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207236745T>C	uc001hfg.2	+	6	538	c.429T>C	c.(427-429)TTT>TTC	p.F143F	PFKFB2_uc010psc.1_Silent_p.F45F|PFKFB2_uc001hfh.2_Silent_p.F143F|PFKFB2_uc009xcc.2_Silent_p.F101F|PFKFB2_uc010psd.1_5'Flank	NM_006212	NP_006203	O60825	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,	143	6-phosphofructo-2-kinase.				fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity			ovary(1)	1	Prostate(682;0.19)					TTTTGAACTTTGCTGAACAGA	0.468													15	517	---	---	---	---	PASS
IL1A	3552	broad.mit.edu	37	2	113532612	113532612	+	3'UTR	SNP	A	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113532612A>C	uc002tig.2	-	7						NM_000575	NP_000566	P01583	IL1A_HUMAN	interleukin 1, alpha proprotein						anti-apoptosis|apoptosis|cell proliferation|cellular response to heat|cytokine-mediated signaling pathway|fever generation|immune response|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of cell division|positive regulation of cytokine secretion|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation vascular endothelial growth factor production|response to copper ion	cytosol|extracellular space	copper ion binding|cytokine activity|interleukin-1 receptor binding			lung(1)	1						AACTGTCAACACTGCACAAGT	0.443													6	69	---	---	---	---	PASS
CXCR2	3579	broad.mit.edu	37	2	218999551	218999551	+	Silent	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218999551C>T	uc002vgz.1	+	4	252	c.27C>T	c.(25-27)GAC>GAT	p.D9D	CXCR2_uc002vha.1_Silent_p.D9D|CXCR2_uc002vhb.1_Silent_p.D9D	NM_001557	NP_001548	P25025	CXCR2_HUMAN	interleukin 8 receptor beta	9	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cellular defense response|dendritic cell chemotaxis|inflammatory response|neutrophil activation|neutrophil chemotaxis|positive regulation of cell proliferation	cell surface|integral to plasma membrane|mast cell granule	interleukin-8 receptor activity			lung(1)|breast(1)	2						TGGAGAGTGACAGCTTTGAAG	0.388													14	161	---	---	---	---	PASS
C2orf83	56918	broad.mit.edu	37	2	228497787	228497787	+	Silent	SNP	G	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228497787G>A	uc002vph.2	-	1	250	c.15C>T	c.(13-15)GCC>GCT	p.A5A	C2orf83_uc010zlu.1_Silent_p.A5A	NM_020161	NP_064546	Q53S99	CB083_HUMAN	hypothetical protein LOC56918 isoform 1	5						membrane	folic acid binding|reduced folate carrier activity				0						CAAACGTCAGGGCATAGTCTT	0.418													27	140	---	---	---	---	PASS
TRIP12	9320	broad.mit.edu	37	2	230724254	230724254	+	Silent	SNP	T	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230724254T>C	uc002vpw.1	-	3	244	c.135A>G	c.(133-135)CAA>CAG	p.Q45Q	TRIP12_uc002vpx.1_Silent_p.Q87Q|TRIP12_uc002vpy.1_Intron|TRIP12_uc010zlz.1_RNA|TRIP12_uc010fxh.1_Silent_p.Q45Q	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	45					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		GATCCTCTGGTTGTGGAACTA	0.418													12	259	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52442512	52442512	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52442512T>C	uc003ddx.2	-	4	348	c.233A>G	c.(232-234)AAT>AGT	p.N78S	PHF7_uc003ddy.2_5'Flank|PHF7_uc003ddz.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	78					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GAACATGTTATTCACAATATC	0.488			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								11	61	---	---	---	---	PASS
WDR52	55779	broad.mit.edu	37	3	113127995	113127995	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113127995T>G	uc003eae.1	-	7	894	c.848A>C	c.(847-849)GAT>GCT	p.D283A		NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2	283	WD 2.									central_nervous_system(1)	1						CTCTTCCTTATCAGGATTGAA	0.413													49	279	---	---	---	---	PASS
ADCY5	111	broad.mit.edu	37	3	123049743	123049743	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123049743C>T	uc003egh.1	-	5	1639	c.1639G>A	c.(1639-1641)GCC>ACC	p.A547T	ADCY5_uc003egg.1_Missense_Mutation_p.A180T|ADCY5_uc003egi.1_Missense_Mutation_p.A106T	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	547	Guanylate cyclase 1.|Cytoplasmic (Potential).				activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)		TACGAGATGGCCTCGATCATG	0.612													5	56	---	---	---	---	PASS
PCCB	5096	broad.mit.edu	37	3	136016909	136016909	+	Silent	SNP	T	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136016909T>C	uc003eqy.1	+	8	930	c.879T>C	c.(877-879)GAT>GAC	p.D293D	PCCB_uc003eqz.1_Silent_p.D293D|PCCB_uc011bmc.1_Silent_p.D313D|PCCB_uc011bmd.1_Silent_p.D210D	NM_000532	NP_000523	P05166	PCCB_HUMAN	propionyl Coenzyme A carboxylase, beta	293	Carboxyltransferase.				fatty acid beta-oxidation	mitochondrial matrix	ATP binding|propionyl-CoA carboxylase activity				0					Biotin(DB00121)|L-Valine(DB00161)	AGTGCCACGATCCCAGGTGGG	0.557													6	170	---	---	---	---	PASS
ECE2	9718	broad.mit.edu	37	3	183976136	183976136	+	Intron	SNP	T	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183976136T>G	uc003fni.3	+						ECE2_uc003fnh.3_Missense_Mutation_p.F181V	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A						brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGCCCCCCACTTTCGGACCAG	0.557													5	39	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506746	195506746	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506746G>A	uc011bto.1	-	3	11781	c.11321C>T	c.(11320-11322)GCC>GTC	p.A3774V	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)		AAGAGGGGTGGCGTGACGTGT	0.597													4	53	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195508249	195508249	+	Missense_Mutation	SNP	A	G	G	rs145582541	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195508249A>G	uc011bto.1	-	3	10278	c.9818T>C	c.(9817-9819)GTA>GCA	p.V3273A	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)		ACCTGTGGATACTGAGGAAGT	0.577													7	107	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195515304	195515304	+	Silent	SNP	T	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195515304T>A	uc011bto.1	-	2	3607	c.3147A>T	c.(3145-3147)GCA>GCT	p.A1049A	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)		CACCTGTGGATGCTGAGGAAA	0.562													5	91	---	---	---	---	PASS
LOC220729	220729	broad.mit.edu	37	3	197348646	197348646	+	RNA	SNP	T	C	C	rs138265355	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197348646T>C	uc011bug.1	-	4		c.445A>G			LOC220729_uc003fxw.2_RNA|LOC220729_uc003fxy.2_RNA|LOC220729_uc010iao.1_Intron					Homo sapiens cDNA FLJ60865 complete cds, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1).												0						TGGGCCTGCCTGCCCTTTCCA	0.532													10	174	---	---	---	---	PASS
POLN	353497	broad.mit.edu	37	4	2214836	2214836	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2214836T>A	uc003ger.2	-	2	151	c.151A>T	c.(151-153)AAG>TAG	p.K51*	POLN_uc011bvi.1_Nonsense_Mutation_p.K51*	NM_181808	NP_861524	Q7Z5Q5	DPOLN_HUMAN	DNA-directed DNA polymerase nu	51					DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			ACACTGGACTTGTTTATCACT	0.299								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					21	608	---	---	---	---	PASS
PAPSS1	9061	broad.mit.edu	37	4	108641361	108641361	+	5'UTR	SNP	G	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108641361G>A	uc003hyk.2	-	1					PAPSS1_uc011cfh.1_RNA	NM_005443	NP_005434	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		TGAGCAGCCGGGGTTCTCTGC	0.697													16	57	---	---	---	---	PASS
HMGB2	3148	broad.mit.edu	37	4	174253044	174253044	+	3'UTR	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174253044C>T	uc011ckc.1	-	4					HMGB2_uc003ita.3_3'UTR|HMGB2_uc003itb.2_3'UTR|HMGB2_uc003itc.2_3'UTR	NM_001130689	NP_001124161	P26583	HMGB2_HUMAN	high-mobility group box 2						base-excision repair, DNA ligation|cell chemotaxis|cellular response to lipopolysaccharide|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|negative regulation of transcription, DNA-dependent|nucleosome assembly|phosphatidylinositol-mediated signaling|positive regulation of DNA binding|positive regulation of endothelial cell proliferation|positive regulation of erythrocyte differentiation|positive regulation of megakaryocyte differentiation|positive regulation of nuclease activity|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	condensed chromosome|extracellular space|nucleolus|nucleoplasm|perinuclear region of cytoplasm|protein complex	chemoattractant activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding|transcription regulatory region DNA binding				0		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		ATGAGTAGCCCATCAAAAAGC	0.303													4	31	---	---	---	---	PASS
ADAMTS12	81792	broad.mit.edu	37	5	33561238	33561238	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33561238C>T	uc003jia.1	-	20	4182	c.4019G>A	c.(4018-4020)TGC>TAC	p.C1340Y	ADAMTS12_uc010iuq.1_Missense_Mutation_p.C1255Y	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1340	TSP type-1 5.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						CTGGGTGCTGCACTCCACCCT	0.577										HNSCC(64;0.19)			14	171	---	---	---	---	PASS
ITGA1	3672	broad.mit.edu	37	5	52145320	52145320	+	Splice_Site	SNP	G	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52145320G>T	uc003jou.2	+	2	234	c.182_splice	c.e2+1	p.W61_splice	ITGA1_uc003jov.2_Splice_Site	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor						axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				AAGGAAAATGGTAAGCCAGTG	0.318													18	251	---	---	---	---	PASS
ENC1	8507	broad.mit.edu	37	5	73931537	73931537	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73931537C>G	uc003kdc.3	-	2	1905	c.774G>C	c.(772-774)AAG>AAC	p.K258N	ENC1_uc011css.1_Missense_Mutation_p.K185N	NM_003633	NP_003624	O14682	ENC1_HUMAN	ectodermal-neural cortex (with BTB-like domain)	258					nervous system development	cytoplasm|cytoskeleton|nuclear matrix	actin binding			ovary(1)|pancreas(1)|skin(1)	3		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		TCTTTCTCTGCTTGGTGATGA	0.512													28	126	---	---	---	---	PASS
PCDHGA3	56112	broad.mit.edu	37	5	140725547	140725547	+	Silent	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140725547C>T	uc003ljm.1	+	1	1947	c.1947C>T	c.(1945-1947)CAC>CAT	p.H649H	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Silent_p.H409H|PCDHGA3_uc011dap.1_Silent_p.H649H	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	649	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAGGACCACGGCCAGCCCC	0.711													3	17	---	---	---	---	PASS
GALNT10	55568	broad.mit.edu	37	5	153783470	153783470	+	Intron	SNP	C	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153783470C>A	uc003lvh.2	+						GALNT10_uc010jic.2_Intron|GALNT10_uc010jid.2_Intron|uc003lvi.2_Intron|GALNT10_uc003lvj.2_5'UTR	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			caatggtaagcactcagtGCT	0.204													4	18	---	---	---	---	PASS
LCP2	3937	broad.mit.edu	37	5	169680135	169680135	+	Silent	SNP	G	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169680135G>A	uc003man.1	-	18	1440	c.1233C>T	c.(1231-1233)CCC>CCT	p.P411P	LCP2_uc011des.1_Silent_p.P206P|LCP2_uc011det.1_Silent_p.P240P	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2	411					immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		CTTCCTCCGCGGGGGATGGGG	0.458													7	165	---	---	---	---	PASS
CLK4	57396	broad.mit.edu	37	5	178050273	178050273	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178050273A>G	uc003mjf.1	-	2	253	c.145T>C	c.(145-147)TTT>CTT	p.F49L	CLK4_uc003mjg.1_5'UTR|CLK4_uc010jku.1_5'UTR|CLK4_uc003mjh.1_5'UTR|CLK4_uc010jkv.1_RNA|CLK4_uc011dgg.1_Missense_Mutation_p.F49L|CLK4_uc011dgh.1_5'UTR|CLK4_uc011dgi.1_Missense_Mutation_p.F49L|CLK4_uc011dgj.1_Missense_Mutation_p.F49L|CLK4_uc003mji.2_Missense_Mutation_p.F49L|CLK4_uc010jkw.1_Missense_Mutation_p.F49L	NM_020666	NP_065717	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	49						nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(1)	1	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|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)	all cancers(165;0.235)		GATTCTTTAAACTGGTGATGT	0.368													116	298	---	---	---	---	PASS
COL9A1	1297	broad.mit.edu	37	6	70951673	70951673	+	Silent	SNP	A	T	T	rs138810927	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70951673A>T	uc003pfg.3	-	30	2151	c.1992T>A	c.(1990-1992)GGT>GGA	p.G664G	COL9A1_uc003pfe.3_Intron|COL9A1_uc003pff.3_Silent_p.G421G	NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor	664	Triple-helical region (COL2).				axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding			ovary(4)	4						TTACCCTGTCACCTTTCATTC	0.512													9	145	---	---	---	---	PASS
C6orf70	55780	broad.mit.edu	37	6	170179296	170179296	+	Silent	SNP	T	A	A	rs79095717		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170179296T>A	uc003qxg.1	+	17	1791	c.1758T>A	c.(1756-1758)CCT>CCA	p.P586P	C6orf70_uc011ehb.1_Silent_p.P460P|C6orf70_uc003qxh.1_Silent_p.P513P|C6orf70_uc010kky.1_Silent_p.P413P|C6orf70_uc003qxi.1_Silent_p.P234P	NM_018341	NP_060811	Q5T6L9	CF070_HUMAN	hypothetical protein LOC55780	586						integral to membrane				ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.2e-22)|BRCA - Breast invasive adenocarcinoma(81;1.49e-07)|GBM - Glioblastoma multiforme(31;0.00191)		TACTGTCCCCTGTGCTCAGCC	0.393													47	429	---	---	---	---	PASS
STK31	56164	broad.mit.edu	37	7	23750185	23750185	+	Intron	SNP	C	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23750185C>A	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_5'UTR	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						TCCATGAAGACGCGGTCACGC	0.512													3	8	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	64529883	64529883	+	Intron	SNP	C	T	T	rs2691644	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64529883C>T	uc003ttt.1	+						uc010kzt.1_RNA|uc003ttu.1_5'Flank					Homo sapiens cDNA clone IMAGE:4215179, partial cds.																		TGGTTTTCAGCTGGTTGATGG	0.323													5	27	---	---	---	---	PASS
GTF2IRD2P1	401375	broad.mit.edu	37	7	72664015	72664015	+	5'UTR	SNP	C	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72664015C>G	uc003txs.1	-	11					FKBP6_uc003twz.2_Intron	NR_002164				RecName: Full=General transcription factor II-I repeat domain-containing protein 2B; AltName: Full=GTF2I repeat domain-containing protein 2B; AltName: Full=Transcription factor GTF2IRD2-beta;												0						ATACCACCCCCGGGGCATGCC	0.507													4	18	---	---	---	---	PASS
LOC100132832	100132832	broad.mit.edu	37	7	76681226	76681226	+	RNA	SNP	G	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76681226G>C	uc003ufy.2	+	5		c.1203G>C				NR_028058				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						TGTCACACTTGAAGGAGGCAG	0.453													4	35	---	---	---	---	PASS
DOCK4	9732	broad.mit.edu	37	7	111462482	111462482	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111462482G>A	uc003vfx.2	-	27	3135	c.2866C>T	c.(2866-2868)CGA>TGA	p.R956*	DOCK4_uc003vfw.2_Nonsense_Mutation_p.R397*|DOCK4_uc003vfy.2_Nonsense_Mutation_p.R992*	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	956					cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)				ATCAATATTCGGAACACAGTA	0.373													9	278	---	---	---	---	PASS
DPP6	1804	broad.mit.edu	37	7	154595638	154595638	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154595638T>C	uc003wlk.2	+	14	1601	c.1472T>C	c.(1471-1473)CTA>CCA	p.L491P	DPP6_uc003wli.2_Missense_Mutation_p.L427P|DPP6_uc003wlm.2_Missense_Mutation_p.L429P|DPP6_uc011kvq.1_Missense_Mutation_p.L384P	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1	491	Extracellular (Potential).				cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			ACCAAGATCCTAGCCTACGAT	0.517													5	157	---	---	---	---	PASS
VCP	7415	broad.mit.edu	37	9	35068351	35068351	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35068351C>A	uc003zvy.2	-	2	415	c.26G>T	c.(25-27)GGT>GTT	p.G9V	VCP_uc003zvz.2_RNA|VCP_uc010mkh.1_5'UTR|VCP_uc010mki.1_5'UTR	NM_007126	NP_009057	P55072	TERA_HUMAN	valosin-containing protein	9					activation of caspase activity|double-strand break repair|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|retrograde protein transport, ER to cytosol	cytosol|endoplasmic reticulum|microsome|nucleus|proteasome complex	ATP binding|ATPase activity|lipid binding|polyubiquitin binding|protein domain specific binding|protein phosphatase binding			upper_aerodigestive_tract(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TAGGTCATCACCTTTTGAACT	0.448													17	140	---	---	---	---	PASS
KLF9	687	broad.mit.edu	37	9	73027946	73027946	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73027946C>A	uc004aht.2	-	1	1628	c.334G>T	c.(334-336)GAG>TAG	p.E112*		NM_001206	NP_001197	Q13886	KLF9_HUMAN	Kruppel-like factor 9	112	Asp/Glu-rich (acidic).				regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TGTCTCTCCTCCGGGCTGTGG	0.627													22	116	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79469063	79469063	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79469063T>C	uc010mpk.2	-	2	222	c.98A>G	c.(97-99)GAT>GGT	p.D33G	PRUNE2_uc004akn.2_Missense_Mutation_p.D33G	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	33					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						AATGAGAGAATCCAAGTCACA	0.353													43	246	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55700700	55700700	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55700700G>A	uc001jju.1	-	24	3553	c.3158C>T	c.(3157-3159)ACC>ATC	p.T1053I	PCDH15_uc010qhq.1_Missense_Mutation_p.T1058I|PCDH15_uc010qhr.1_Missense_Mutation_p.T1053I|PCDH15_uc010qhs.1_Missense_Mutation_p.T1065I|PCDH15_uc010qht.1_Missense_Mutation_p.T1060I|PCDH15_uc010qhu.1_Missense_Mutation_p.T1053I|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.T1053I|PCDH15_uc010qhw.1_Missense_Mutation_p.T1016I|PCDH15_uc010qhx.1_Missense_Mutation_p.T982I|PCDH15_uc010qhy.1_Missense_Mutation_p.T1058I|PCDH15_uc010qhz.1_Missense_Mutation_p.T1053I|PCDH15_uc010qia.1_Missense_Mutation_p.T1031I|PCDH15_uc010qib.1_Missense_Mutation_p.T1031I	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1053	Cadherin 10.|Extracellular (Potential).				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)				ACCAACCATGGTCCCTTTGGT	0.328										HNSCC(58;0.16)			10	72	---	---	---	---	PASS
JMJD1C	221037	broad.mit.edu	37	10	64957169	64957169	+	Splice_Site	SNP	A	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64957169A>C	uc001jmn.2	-	13	5944	c.5644_splice	c.e13+1	p.D1882_splice	JMJD1C_uc001jml.2_Splice_Site_p.D1663_splice|JMJD1C_uc001jmm.2_Splice_Site_p.D1594_splice|JMJD1C_uc010qiq.1_Splice_Site_p.D1700_splice|JMJD1C_uc009xpi.2_Splice_Site_p.D1700_splice|JMJD1C_uc009xpj.1_Splice_Site|JMJD1C_uc009xpk.1_Splice_Site_p.D780_splice	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					TTATACACCAACCTCTAGAAC	0.323													8	330	---	---	---	---	PASS
AP3M1	26985	broad.mit.edu	37	10	75893904	75893904	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75893904T>A	uc001jwf.2	-	4	894	c.464A>T	c.(463-465)GAC>GTC	p.D155V	AP3M1_uc001jwg.2_Missense_Mutation_p.D155V|AP3M1_uc001jwh.2_Missense_Mutation_p.D155V|AP3M1_uc010qla.1_Missense_Mutation_p.D101V	NM_207012	NP_996895	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit	155					protein targeting to lysosome|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus|lysosome	protein binding				0	Prostate(51;0.0112)					GGGGAGTGTGTCCCCAACATT	0.418													14	194	---	---	---	---	PASS
GRID1	2894	broad.mit.edu	37	10	87628903	87628903	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87628903T>G	uc001kdl.1	-	6	916	c.815A>C	c.(814-816)CAT>CCT	p.H272P	GRID1_uc009xsu.1_RNA	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	272	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	AAGGGCACTATGGACCAGATC	0.507										Multiple Myeloma(13;0.14)			34	164	---	---	---	---	PASS
RASGRP2	10235	broad.mit.edu	37	11	64503123	64503123	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64503123G>A	uc009ypu.2	-	11	1414	c.1187C>T	c.(1186-1188)ACG>ATG	p.T396M	RASGRP2_uc001oat.2_Missense_Mutation_p.T298M|RASGRP2_uc001oau.2_Missense_Mutation_p.T251M|RASGRP2_uc009ypv.2_Missense_Mutation_p.T396M|RASGRP2_uc009ypw.2_Missense_Mutation_p.T396M	NM_001098671	NP_001092141	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2	396					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						GGTGCAACTCGTGGGGCTGGT	0.662													17	68	---	---	---	---	PASS
C11orf63	79864	broad.mit.edu	37	11	122756652	122756652	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122756652A>C	uc001pym.2	+	2	392	c.95A>C	c.(94-96)AAA>ACA	p.K32T	C11orf63_uc001pyl.1_Missense_Mutation_p.K32T	NM_024806	NP_079082	Q6NUN7	CK063_HUMAN	hypothetical protein LOC79864 isoform 1	32										ovary(3)	3		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		CCTTTGAAGAAAGAAGACTTA	0.408													21	269	---	---	---	---	PASS
LTBR	4055	broad.mit.edu	37	12	6495606	6495606	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6495606G>T	uc001qny.1	+	6	831	c.663G>T	c.(661-663)ATG>ATT	p.M221I	LTBR_uc010sfc.1_Missense_Mutation_p.M202I|LTBR_uc001qnz.1_Missense_Mutation_p.M216I	NM_002342	NP_002333	P36941	TNR3_HUMAN	lymphotoxin beta receptor precursor	221	Extracellular (Potential).				apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	protein binding|receptor activity			lung(2)	2						CCCCAGAGATGTCAGGTGAGG	0.547													15	117	---	---	---	---	PASS
ARHGAP9	64333	broad.mit.edu	37	12	57871324	57871324	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57871324G>T	uc001sod.2	-	7	1080	c.887C>A	c.(886-888)CCC>CAC	p.P296H	ARHGAP9_uc001sny.2_5'Flank|ARHGAP9_uc001snz.2_Missense_Mutation_p.P41H|ARHGAP9_uc001soa.2_5'UTR|ARHGAP9_uc001sob.2_Missense_Mutation_p.P225H|ARHGAP9_uc001soc.2_Missense_Mutation_p.P225H|ARHGAP9_uc001soe.1_Missense_Mutation_p.P304H|ARHGAP9_uc010sro.1_Missense_Mutation_p.P225H	NM_032496	NP_115885	Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9 isoform 1	225	WW.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1			GBM - Glioblastoma multiforme(3;3.37e-34)			TCCAGAGTTGGGGTCCAGGTG	0.642													7	59	---	---	---	---	PASS
DAOA	267012	broad.mit.edu	37	13	106118549	106118549	+	5'UTR	SNP	G	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106118549G>T	uc001vqb.2	+	1					DAOA_uc010tjf.1_Intron|DAOA_uc001vpz.2_Intron|DAOA_uc010agd.2_5'Flank|DAOA_uc010tjg.1_5'Flank|DAOA_uc001vqc.2_5'Flank|DAOA_uc001vqe.2_5'Flank	NM_172370	NP_758958	P59103	DAOA_HUMAN	D-amino acid oxidase activator isoform 1							Golgi apparatus					0	Lung NSC(43;0.01)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					tgtatatgatgattctgttgg	0.055													6	97	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22772309	22772309	+	Intron	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22772309C>T	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc010ajq.1_Silent_p.L68L					SubName: Full=Alpha-chain C region; Flags: Fragment;																		GTTTGTGTTGCTATCAAATGG	0.468													16	142	---	---	---	---	PASS
EIF2AK4	440275	broad.mit.edu	37	15	40257936	40257936	+	Silent	SNP	C	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40257936C>A	uc001zkm.1	+	8	959	c.909C>A	c.(907-909)GCC>GCA	p.A303A	EIF2AK4_uc001zkl.2_Silent_p.A303A|EIF2AK4_uc010bbj.1_Silent_p.A32A	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha	303	Protein kinase 1.				translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		TGGAAACAGCCACTGGTGGCT	0.393													14	540	---	---	---	---	PASS
C15orf52	388115	broad.mit.edu	37	15	40631251	40631251	+	Intron	SNP	A	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40631251A>G	uc001zlh.3	-						C15orf52_uc001zli.1_Missense_Mutation_p.C5R|C15orf52_uc010ucn.1_5'Flank	NM_207380	NP_997263	Q6ZUT6	CO052_HUMAN	hypothetical protein LOC388115											large_intestine(1)	1		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		GGGTGTTCACATGCCAATGGC	0.627													4	25	---	---	---	---	PASS
MTHFS	10588	broad.mit.edu	37	15	80137836	80137836	+	Intron	SNP	T	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80137836T>C	uc002bex.3	-						MTHFS_uc002bey.2_RNA	NM_006441	NP_006432	P49914	MTHFS_HUMAN	5,10-methenyltetrahydrofolate synthetase						folic acid-containing compound biosynthetic process|formate metabolic process|tetrahydrofolate metabolic process	cytosol|Golgi apparatus|plasma membrane	5-formyltetrahydrofolate cyclo-ligase activity|ATP binding|folic acid binding				0				all cancers(203;0.00467)		TGAAAGATCATTTCAGGATGT	0.363													4	70	---	---	---	---	PASS
C16orf88	400506	broad.mit.edu	37	16	19718398	19718398	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19718398A>G	uc002dgq.2	-	5	1226	c.1211T>C	c.(1210-1212)CTC>CCC	p.L404P		NM_001012991	NP_001013009	Q1ED39	CP088_HUMAN	hypothetical protein LOC400506	404	Interaction with ZFP106 (By similarity).					nucleolus					0						CTTCTTGCCGAGGGCCATGTT	0.602													8	46	---	---	---	---	PASS
BEAN	146227	broad.mit.edu	37	16	66511499	66511499	+	Translation_Start_Site	SNP	G	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66511499G>T	uc002eoq.2	+	3	396	c.-1G>T	c.(-3-1)CAGGA>CATGA		BEAN_uc002eop.1_RNA	NM_001136106	NP_001129578	Q3B7T3	BEAN1_HUMAN	brain expressed, associated with Nedd4						cell death	integral to membrane					0						TCAAGCCGCAGGATGCGCTAT	0.632													6	30	---	---	---	---	PASS
RRAD	6236	broad.mit.edu	37	16	66956073	66956073	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66956073G>T	uc002eqn.2	-	5	985	c.833C>A	c.(832-834)GCG>GAG	p.A278E	RRAD_uc002eqo.2_Missense_Mutation_p.A278E	NM_001128850	NP_001122322	P55042	RAD_HUMAN	Ras-related associated with diabetes	278	Calmodulin-binding.				small GTPase mediated signal transduction	plasma membrane	calmodulin binding|GTP binding|GTPase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)		GAAGCGCTTCGCCTTTTTGCC	0.612													7	77	---	---	---	---	PASS
AMAC1L3	643664	broad.mit.edu	37	17	7384817	7384817	+	5'UTR	SNP	G	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7384817G>C	uc010cmj.1	+	1					ZBTB4_uc002ghc.3_5'Flank|ZBTB4_uc002ghd.3_Intron	NM_001102614	NP_001096084	P0C7Q6	AMCL3_HUMAN	acyl-malonyl condensing enzyme 1-like 3							integral to membrane					0		Prostate(122;0.173)				CAGGAGGAGAGGAGAAAGTCC	0.582													24	141	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	20319971	20319971	+	RNA	SNP	G	A	A	rs71263795		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20319971G>A	uc010vzg.1	+	2		c.342G>A			uc002gwx.2_RNA					Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.																		CTCTCATTACGCTTGATTGCC	0.557													8	135	---	---	---	---	PASS
ARHGAP23	57636	broad.mit.edu	37	17	36654047	36654047	+	Silent	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36654047C>T	uc010wdp.1	+	21	3677	c.3015C>T	c.(3013-3015)GAC>GAT	p.D1005D	ARHGAP23_uc002hqc.2_Silent_p.D893D	NM_020876	NP_065927	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	1099					signal transduction	intracellular	GTPase activator activity			lung(1)	1						TCTTCAGTGACGAAGAGGACA	0.587													7	278	---	---	---	---	PASS
HSD17B1	3292	broad.mit.edu	37	17	40705762	40705762	+	Intron	SNP	G	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40705762G>T	uc002hzw.2	+						HSD17B1_uc002hzx.2_Intron|HSD17B1_uc010wgm.1_Intron|uc002hzy.2_5'UTR|HSD17B1_uc010cyi.2_Intron	NM_000413	NP_000404	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1						estrogen biosynthetic process	cytosol	binding|estradiol 17-beta-dehydrogenase activity				0		all_cancers(22;5.59e-08)|all_epithelial(22;7e-07)|Ovarian(249;0.0261)		BRCA - Breast invasive adenocarcinoma(366;0.129)	NADH(DB00157)	GTCTGCCCGGGGATGACCCCC	0.642													6	27	---	---	---	---	PASS
C17orf57	124989	broad.mit.edu	37	17	45452174	45452174	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45452174C>G	uc002iln.2	+	12	1625	c.1214C>G	c.(1213-1215)TCT>TGT	p.S405C	C17orf57_uc002ilm.2_Missense_Mutation_p.S309C|C17orf57_uc002ill.1_Missense_Mutation_p.S161C|C17orf57_uc010daz.1_Missense_Mutation_p.S357C	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989	405							calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3						GACTCAAAGTCTAAACCACAA	0.383													19	153	---	---	---	---	PASS
TEX14	56155	broad.mit.edu	37	17	56651592	56651592	+	Silent	SNP	T	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56651592T>C	uc010dcz.1	-	23	3595	c.3477A>G	c.(3475-3477)GAA>GAG	p.E1159E	TEX14_uc002iwr.1_Silent_p.E1153E|TEX14_uc002iws.1_Silent_p.E1113E|TEX14_uc010dda.1_Silent_p.E893E	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a	1159						cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TTGATGTCTCTTCTTGTTCAT	0.383													55	626	---	---	---	---	PASS
ANKRD24	170961	broad.mit.edu	37	19	4202045	4202045	+	Silent	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4202045C>T	uc010dtt.1	+	6	642	c.366C>T	c.(364-366)GCC>GCT	p.A122A	ANKRD24_uc002lzs.2_Silent_p.A93A|ANKRD24_uc002lzt.2_Silent_p.A94A	NM_133475	NP_597732	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	122	ANK 2.										0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		TCCACCTGGCCGCCAAATACG	0.527													11	154	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9069489	9069489	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9069489G>T	uc002mkp.2	-	3	18161	c.17957C>A	c.(17956-17958)GCA>GAA	p.A5986E		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5988	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GAAGCTACTTGCACTTGGTAA	0.483													12	208	---	---	---	---	PASS
ZNF180	7733	broad.mit.edu	37	19	44980835	44980835	+	Silent	SNP	A	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44980835A>G	uc002ozf.3	-	5	2145	c.1863T>C	c.(1861-1863)ACT>ACC	p.T621T	ZNF180_uc002ozh.3_Silent_p.T278T|ZNF180_uc002ozi.3_Silent_p.T594T|ZNF180_uc002ozg.3_Silent_p.T620T|ZNF180_uc010ejm.2_Silent_p.T596T	NM_013256	NP_037388	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	621	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)				TCTGATGTTGAGTAAGGCATG	0.398													4	55	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	19	54007225	54007225	+	RNA	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54007225C>T	uc002qbv.2	+	2		c.1054C>T								full-length cDNA clone CS0DI081YH01 of Placenta Cot 25-normalized of Homo sapiens (human).																		GGGGCTCATGCTCTGGGGCAG	0.597													3	16	---	---	---	---	PASS
ADAMTS5	11096	broad.mit.edu	37	21	28306977	28306977	+	Silent	SNP	C	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28306977C>T	uc002ymg.2	-	4	2226	c.1497G>A	c.(1495-1497)CTG>CTA	p.L499L		NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1	499	Disintegrin.				proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						GCCCGAATGTCAGGTTGCACT	0.577													11	205	---	---	---	---	PASS
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	C	C	rs142470496	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29091840T>C	uc003adu.1	-	11	1189	c.1117A>G	c.(1117-1119)AAG>GAG	p.K373E	CHEK2_uc003ads.1_Missense_Mutation_p.K152E|CHEK2_uc010gvh.1_Missense_Mutation_p.K282E|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Missense_Mutation_p.K416E|CHEK2_uc003adv.1_Missense_Mutation_p.K344E|CHEK2_uc003adw.1_Missense_Mutation_p.K373E|CHEK2_uc003adx.1_Missense_Mutation_p.K152E|CHEK2_uc003ady.1_Missense_Mutation_p.K373E|CHEK2_uc003adz.1_Missense_Mutation_p.K177E	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a	373	Protein kinase.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.K373E(2)		central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				4	86	---	---	---	---	PASS
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	A	A	rs146546850	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29091841G>A	uc003adu.1	-	11	1188	c.1116C>T	c.(1114-1116)TCC>TCT	p.S372S	CHEK2_uc003ads.1_Silent_p.S151S|CHEK2_uc010gvh.1_Silent_p.S281S|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Silent_p.S415S|CHEK2_uc003adv.1_Silent_p.S343S|CHEK2_uc003adw.1_Silent_p.S372S|CHEK2_uc003adx.1_Silent_p.S151S|CHEK2_uc003ady.1_Silent_p.S372S|CHEK2_uc003adz.1_Silent_p.S176S	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a	372	Protein kinase.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.S372S(1)		central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				4	85	---	---	---	---	PASS
ELK1	2002	broad.mit.edu	37	X	47498682	47498682	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47498682G>A	uc004dik.3	-	4	588	c.266C>T	c.(265-267)CCT>CTT	p.P89L	ELK1_uc010nhv.2_Missense_Mutation_p.P89L|ELK1_uc010nhw.2_5'UTR|ELK1_uc004dil.3_RNA	NM_001114123	NP_001107595	P19419	ELK1_HUMAN	ELK1 protein	89					innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						TGCGACCTCAGGGTAGGACAC	0.587													5	42	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	713786	713787	+	RNA	INS	-	GCT	GCT	rs142583823		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:713786_713787insGCT	uc001abo.2	-	1		c.220_221insAGC								Homo sapiens cDNA clone IMAGE:4129277, partial cds.																		catgttgctaggctgctcttgg	0.208													3	6	---	---	---	---	
LOC100128842	100128842	broad.mit.edu	37	1	1195951	1195952	+	3'UTR	DEL	CA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1195951_1195952delCA	uc010nyh.1	-	1					UBE2J2_uc001adm.2_Intron|UBE2J2_uc001adn.2_Intron|UBE2J2_uc001ado.2_Intron|UBE2J2_uc001adp.2_Intron|UBE2J2_uc001adq.2_Intron|UBE2J2_uc001adr.2_Intron|UBE2J2_uc001ads.2_Intron	NR_027361				Homo sapiens cDNA FLJ36836 fis, clone ASTRO2011149.												0						CACCAAGAGCCACACACACACA	0.589													4	2	---	---	---	---	
SSU72	29101	broad.mit.edu	37	1	1505664	1505664	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1505664delA	uc001agd.2	-						SSU72_uc009vkg.1_Intron|SSU72_uc001age.1_Intron	NM_014188	NP_054907	Q9NP77	SSU72_HUMAN	Ssu72 RNA polymerase II CTD phosphatase homolog						mRNA processing	cytoplasm|nucleus	phosphoprotein phosphatase activity				0	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-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)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		ctctggcttgaaaaaaaaaac	0.174													4	2	---	---	---	---	
SSU72	29101	broad.mit.edu	37	1	1505675	1505675	+	Intron	DEL	A	-	-	rs67493327		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1505675delA	uc001agd.2	-						SSU72_uc009vkg.1_Intron|SSU72_uc001age.1_Intron	NM_014188	NP_054907	Q9NP77	SSU72_HUMAN	Ssu72 RNA polymerase II CTD phosphatase homolog						mRNA processing	cytoplasm|nucleus	phosphoprotein phosphatase activity				0	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-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)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		aaaaaaaaacaaaaaaaaAAG	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5695686	5695686	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5695686delA	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																		AGCTTGCCAGAAAAAAACGCC	0.592													4	2	---	---	---	---	
CLSTN1	22883	broad.mit.edu	37	1	9836035	9836035	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9836035delT	uc001aqh.2	-						CLSTN1_uc001aqi.2_Intron|CLSTN1_uc010oag.1_Intron	NM_001009566	NP_001009566	O94985	CSTN1_HUMAN	calsyntenin 1 isoform 1						homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		GCCTCCTCTCttttttttttt	0.289													6	3	---	---	---	---	
CELA3B	23436	broad.mit.edu	37	1	22315422	22315425	+	Intron	DEL	ATAC	-	-	rs71918322		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22315422_22315425delATAC	uc001bfk.2	+						CELA3B_uc009vqf.2_Intron	NM_007352	NP_031378	P08861	CEL3B_HUMAN	elastase 3B, pancreatic preproprotein						cholesterol metabolic process|proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1						TTTTGTTtatatacatacatacat	0.064													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	24477554	24477554	+	IGR	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24477554delG								IL22RA1 (7943 upstream) : IL28RA (3094 downstream)																							tcacgagggagaaacctcaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	28300771	28300772	+	IGR	DEL	AG	-	-	rs34863997		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28300771_28300772delAG								XKR8 (6167 upstream) : EYA3 (47 downstream)																							GGATAAagacagagagagagag	0.223													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31059981	31059982	+	IGR	INS	-	C	C	rs144729644	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31059981_31059982insC								None (None upstream) : MATN1 (124144 downstream)																							CTCCTCCCACAACCAACACACA	0.574													6	4	---	---	---	---	
PRDX1	5052	broad.mit.edu	37	1	45977385	45977385	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45977385delA	uc001cnz.2	-						PRDX1_uc001coa.2_Intron|PRDX1_uc001cob.2_Intron|PRDX1_uc001coc.2_Intron	NM_181697	NP_859048	Q06830	PRDX1_HUMAN	peroxiredoxin 1						cell proliferation|cell redox homeostasis|hydrogen peroxide catabolic process|skeletal system development	melanosome|mitochondrion|nucleus	protein binding|thioredoxin peroxidase activity				0	Acute lymphoblastic leukemia(166;0.155)					CCTTAAGGGGAAAAAAAAGCT	0.244													4	3	---	---	---	---	
ACOT11	26027	broad.mit.edu	37	1	55072199	55072199	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55072199delG	uc001cxm.1	+						ACOT11_uc001cxj.1_Intron|ACOT11_uc001cxl.1_Intron	NM_015547	NP_056362	Q8WXI4	ACO11_HUMAN	thioesterase, adipose associated isoform BFIT1						fatty acid metabolic process|intracellular signal transduction|response to cold		acyl-CoA thioesterase activity|carboxylesterase activity			central_nervous_system(1)	1						GCCTGGGCCTGGGGATACATc	0.308													4	2	---	---	---	---	
NFIA	4774	broad.mit.edu	37	1	61872001	61872001	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61872001delT	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron|NFIA_uc001czx.2_Intron|NFIA_uc009wae.2_5'Flank	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						AAGAGATAAGTTTAGGATGCA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	101820997	101820998	+	IGR	DEL	CA	-	-	rs149562710		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101820997_101820998delCA								S1PR1 (113921 upstream) : OLFM3 (447129 downstream)																							cacctgactccagtttgtgaga	0.050													4	2	---	---	---	---	
NTNG1	22854	broad.mit.edu	37	1	107752082	107752082	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107752082delC	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697	Q9Y2I2	NTNG1_HUMAN	netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		TGGGAGATGACAGCCTTAACA	0.438													4	2	---	---	---	---	
LRIG2	9860	broad.mit.edu	37	1	113666350	113666351	+	Intron	DEL	TG	-	-	rs66524955		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113666350_113666351delTG	uc001edf.1	+						LRIG2_uc009wgn.1_Intron	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like							cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		TGGTGGTTTTtgtgtgtgtgtg	0.287													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116692846	116692847	+	IGR	INS	-	CCT	CCT	rs139656074	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116692846_116692847insCCT								C1orf161 (14985 upstream) : ATP1A1 (222157 downstream)																							gtccaggtaggcctcataccct	0.000													4	2	---	---	---	---	
WARS2	10352	broad.mit.edu	37	1	119576188	119576188	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119576188delA	uc001ehn.2	-						WARS2_uc010oxf.1_Intron|WARS2_uc001ehm.2_Intron|WARS2_uc010oxg.1_Intron|WARS2_uc010oxh.1_Intron|WARS2_uc010oxi.1_3'UTR	NM_015836	NP_056651	Q9UGM6	SYWM_HUMAN	mitochondrial tryptophanyl tRNA synthetase 2						tryptophanyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|tryptophan-tRNA ligase activity				0	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	tcagtatagtattcaataaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143397663	143397664	+	IGR	DEL	AA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143397663_143397664delAA								None (None upstream) : LOC100286793 (249975 downstream)																							TTAGAGAAACAAAGAGAAGTAC	0.248													9	6	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144886552	144886553	+	Intron	INS	-	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144886552_144886553insG	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_uc001elv.3_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)		CCCATGGAGAAGAGGAGAATCC	0.480			T	PDGFRB	MPD								7	4	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148349431	148349432	+	5'Flank	INS	-	G	G	rs67020224		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148349431_148349432insG	uc001eqf.2	-						LOC200030_uc001eqe.2_5'Flank|LOC200030_uc001eqg.2_5'Flank|NBPF14_uc009wkf.1_5'Flank|uc001erd.3_5'Flank|uc001erc.3_5'Flank|uc010paj.1_5'Flank|uc010pav.1_5'Flank|uc010paw.1_5'Flank	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						GGGCTGACACTGGGGGGCCAGA	0.559													7	4	---	---	---	---	
RAG1AP1	55974	broad.mit.edu	37	1	155110965	155110965	+	3'UTR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155110965delT	uc001fhj.3	+	6					RAG1AP1_uc010pey.1_RNA|RAG1AP1_uc001fhk.3_3'UTR|RAG1AP1_uc001fhl.3_3'UTR	NM_018845	NP_061333	Q9BRV3	SWET1_HUMAN	recombination activating gene 1 activating						positive regulation of gene expression, epigenetic	Golgi membrane|integral to membrane|plasma membrane	glucoside transmembrane transporter activity				0	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)			TTTTTAGAGATTTTTTTTTTT	0.239													5	3	---	---	---	---	
RABGAP1L	9910	broad.mit.edu	37	1	174219938	174219938	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174219938delT	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.2_Intron	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						Atttctttccttttttttttg	0.139													12	7	---	---	---	---	
LAMC1	3915	broad.mit.edu	37	1	183105897	183105898	+	Intron	INS	-	ATTG	ATTG	rs140331463	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183105897_183105898insATTG	uc001gpy.3	+							NM_002293	NP_002284	P11047	LAMC1_HUMAN	laminin, gamma 1 precursor						axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TAGGTATCCACATTGAGGAGGG	0.391													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	200476389	200476390	+	IGR	DEL	CT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200476389_200476390delCT								ZNF281 (97223 upstream) : KIF14 (44235 downstream)																							TCAAAACCCACTCTCTCTCTCT	0.287													4	2	---	---	---	---	
CDK18	5129	broad.mit.edu	37	1	205494569	205494569	+	Intron	DEL	T	-	-	rs80154131		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205494569delT	uc001hcr.2	+						CDK18_uc010pri.1_Intron|CDK18_uc001hcp.2_Intron|CDK18_uc001hcq.2_Intron|CDK18_uc010prj.1_Intron|CDK18_uc001hcs.2_Intron|CDK18_uc009xbm.1_Intron	NM_212503	NP_997668	Q07002	CDK18_HUMAN	PCTAIRE protein kinase 3 isoform a								ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity			stomach(2)	2						GAATCCAGTCTTTTTTTTTTC	0.328													5	5	---	---	---	---	
SRGAP2	23380	broad.mit.edu	37	1	206611672	206611673	+	Intron	INS	-	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206611672_206611673insT	uc001hdy.2	+						SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron|SRGAP2_uc010prv.1_Intron	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)					TACTCCTGGCCTTTTTTTTTTT	0.396													4	3	---	---	---	---	
IKBKE	9641	broad.mit.edu	37	1	206654411	206654411	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206654411delG	uc001hdz.1	+						IKBKE_uc009xbv.1_Intron|IKBKE_uc001hea.1_Intron	NM_014002	NP_054721	Q14164	IKKE_HUMAN	IKK-related kinase epsilon						DNA damage response, signal transduction resulting in induction of apoptosis|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane|PML body	ATP binding|IkappaB kinase activity|NF-kappaB-inducing kinase activity|protein binding			ovary(3)|lung(3)|central_nervous_system(1)|skin(1)	8	Breast(84;0.137)					GGGCTAATAAGGGGGGATGGG	0.542													4	2	---	---	---	---	
CAPN2	824	broad.mit.edu	37	1	223932184	223932185	+	Intron	INS	-	A	A	rs6682412	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223932184_223932185insA	uc001hob.3	+						CAPN2_uc010puy.1_Intron	NM_001748	NP_001739	P17655	CAN2_HUMAN	calpain 2 isoform 1						proteolysis	cytoplasm|plasma membrane				lung(3)|breast(1)|skin(1)	5				GBM - Glioblastoma multiforme(131;0.109)		ATTCCCAAGTTTAAAAAAAAAA	0.406													4	2	---	---	---	---	
ENAH	55740	broad.mit.edu	37	1	225758091	225758091	+	Intron	DEL	T	-	-	rs112014685		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225758091delT	uc001hpc.1	-						ENAH_uc001hpd.1_Intron	NM_001008493	NP_001008493	Q8N8S7	ENAH_HUMAN	enabled homolog isoform a						axon guidance|intracellular transport|T cell receptor signaling pathway	cytosol|filopodium|focal adhesion|lamellipodium|synapse	actin binding|SH3 domain binding|WW domain binding			ovary(1)|skin(1)	2	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)		tatacatggatttttttTTTC	0.209													6	4	---	---	---	---	
CDC42BPA	8476	broad.mit.edu	37	1	227268982	227268983	+	Intron	INS	-	T	T	rs141743743	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227268982_227268983insT	uc001hqr.2	-						CDC42BPA_uc001hqq.2_Intron|CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron|CDC42BPA_uc001hqp.2_5'Flank|CDC42BPA_uc001hqu.1_5'Flank	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				TTGGTAATAGCTTTTTTTTTTC	0.262													0	6	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237941741	237941741	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237941741delC	uc001hyl.1	+						RYR2_uc010pya.1_Intron	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)			CCTTGAGAAACTTTTTTTGGA	0.308													4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	245930530	245930530	+	Intron	DEL	A	-	-	rs67473766		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245930530delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron|SMYD3_uc001ibi.2_Intron|SMYD3_uc001ibj.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		GACCGGGATTAAGAGTCCAAA	0.478													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	1611059	1611059	+	IGR	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1611059delC								TPO (64561 upstream) : PXDN (24601 downstream)																							AACATCCCCACCATAGCAACC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2687027	2687027	+	IGR	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2687027delG								MYT1L (351982 upstream) : TSSC1 (505714 downstream)																							GGGGAAGTCAGGGGTTCCTTC	0.577													4	2	---	---	---	---	
ASAP2	8853	broad.mit.edu	37	2	9399650	9399651	+	Intron	DEL	GG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9399650_9399651delGG	uc002qzh.2	+						ASAP2_uc002qzi.2_Intron	NM_003887	NP_003878	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0						CCTGCTCCCTGGTAGGTGGATG	0.574													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	11531567	11531567	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11531567delA								ROCK2 (46856 upstream) : E2F6 (52935 downstream)																							CACTCACCACAAgctaagcac	0.179													4	2	---	---	---	---	
SF3B14	51639	broad.mit.edu	37	2	24291727	24291728	+	Intron	INS	-	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24291727_24291728insT	uc002rev.2	-						SF3B14_uc010eyb.2_Intron	NM_016047	NP_057131	Q9Y3B4	PM14_HUMAN	splicing factor 3B, 14 kDa subunit						nuclear mRNA splicing, via spliceosome	nucleoplasm|U12-type spliceosomal complex	nucleotide binding|protein binding|RNA binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ttttgtttttgtttttttgaga	0.183													4	2	---	---	---	---	
CIB4	130106	broad.mit.edu	37	2	26806959	26806959	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26806959delG	uc002rhm.2	-							NM_001029881	NP_001025052	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAATACCaatggtagtaagta	0.284													4	2	---	---	---	---	
C2orf18	54978	broad.mit.edu	37	2	26998920	26998920	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26998920delA	uc002rhp.1	+						C2orf18_uc002rhq.1_Intron|C2orf18_uc010eyo.1_Intron|C2orf18_uc010ylc.1_Intron	NM_017877	NP_060347	Q8N357	CB018_HUMAN	ANT2-binding protein precursor							integral to membrane|lysosomal membrane					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ttttacaatgaaatgactgTC	0.234													4	2	---	---	---	---	
GALNT14	79623	broad.mit.edu	37	2	31144646	31144646	+	Intron	DEL	A	-	-	rs35178348		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31144646delA	uc002rnr.2	-						GALNT14_uc002rnq.2_Intron|GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					ctcagggggcatttggtcatg	0.174													5	7	---	---	---	---	
CAPN14	440854	broad.mit.edu	37	2	31437843	31437845	+	Intron	DEL	CAT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31437843_31437845delCAT	uc010yms.1	-						CAPN14_uc002rnt.1_Intron	NM_001145122	NP_001138594	A8MX76	CAN14_HUMAN	calpain 14						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity				0						AGCCCTGGGGCATCATCTCTTCT	0.473													4	2	---	---	---	---	
BIRC6	57448	broad.mit.edu	37	2	32832258	32832260	+	Intron	DEL	ATC	-	-	rs68076204	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32832258_32832260delATC	uc010ezu.2	+							NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6						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)					TATTATTATTATCATCTATCTTC	0.212													7	4	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61601373	61601373	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61601373delA	uc002sbe.2	-							NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			ccttatgcctaaacaagtgtt	0.055													4	2	---	---	---	---	
KDM3A	55818	broad.mit.edu	37	2	86681739	86681739	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86681739delA	uc002sri.3	+						KDM3A_uc010ytj.1_Intron|KDM3A_uc010ytk.1_Intron	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A						androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5						tatataaaataaaaaaaaaaC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89278729	89278731	+	Intron	DEL	CTC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89278729_89278731delCTC	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		GAGTGTAGAACTCCTCCCTTGTG	0.473													17	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	95596482	95596482	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95596482delA	uc002stv.1	-											Homo sapiens cDNA FLJ44118 fis, clone TESTI4047069.																		tctaaaaaagaaaaaaaaaga	0.159													3	3	---	---	---	---	
STARD7	56910	broad.mit.edu	37	2	96850807	96850808	+	3'UTR	DEL	TC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96850807_96850808delTC	uc002svm.3	-	8					STARD7_uc002svl.2_3'UTR	NM_020151	NP_064536	Q9NQZ5	STAR7_HUMAN	START domain containing 7 precursor							mitochondrion					0						ACACACATATTCTCTCTCTCTC	0.500													4	2	---	---	---	---	
NCAPH	23397	broad.mit.edu	37	2	97024564	97024564	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97024564delA	uc002svz.1	+						NCAPH_uc010fhu.1_Intron|NCAPH_uc010fhv.1_Intron|NCAPH_uc010yum.1_Intron|NCAPH_uc010fhw.1_Intron|NCAPH_uc010yun.1_Intron|NCAPH_uc002swa.1_Intron	NM_015341	NP_056156	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|microtubule cytoskeleton|nucleus				urinary_tract(1)|skin(1)	2		Ovarian(717;0.0221)				CTAGCATTTTATGGTGCACTT	0.224													4	2	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97817315	97817315	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97817315delT	uc010yva.1	+						ANKRD36_uc010yuz.1_Intron|ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						AAATTACATATGAGTACATTT	0.249													15	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	99397380	99397380	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99397380delA								MGAT4A (49791 upstream) : C2orf55 (12929 downstream)																							tttattttttaaaaaaaGTGt	0.050													4	2	---	---	---	---	
NPAS2	4862	broad.mit.edu	37	2	101606537	101606537	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101606537delG	uc002tap.1	+						NPAS2_uc010yvt.1_Intron|NPAS2_uc010fit.1_Intron	NM_002518	NP_002509	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2						central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4						CTAGGCCCAAGGGATTCAAAT	0.373													4	2	---	---	---	---	
IL1RL1	9173	broad.mit.edu	37	2	102930779	102930779	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102930779delC	uc002tbu.1	+						IL1RL1_uc010ywa.1_Intron|IL18R1_uc002tbw.3_Intron	NM_016232	NP_057316	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1 isoform 1						innate immune response	integral to membrane	interleukin-1 receptor activity|receptor signaling protein activity			skin(2)|ovary(1)|central_nervous_system(1)	4						CTTGTGAGGGCCCCAGGCCCC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103502114	103502114	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103502114delA								TMEM182 (67978 upstream) : None (None downstream)																							aaggtacaagaaaaaaaaaaa	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	110494538	110494538	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110494538delA								ANKRD57 (117975 upstream) : RGPD5 (55797 downstream)																							TTTCAAGCTGAAAAAAAAAAA	0.418													6	4	---	---	---	---	
GLI2	2736	broad.mit.edu	37	2	121615266	121615266	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121615266delT	uc010flp.2	+						GLI2_uc010yyu.1_Intron|GLI2_uc002tmp.1_Intron|GLI2_uc010fln.1_Intron|GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_Intron|GLI2_uc002tmw.1_Intron	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				ATCCAATGCATTTTTCATCAA	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131009759	131009760	+	IGR	INS	-	CCG	CCG	rs138344915	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131009759_131009760insCCG								TUBA3E (53725 upstream) : CCDC115 (86056 downstream)																							GGGATGGCGCACCAGAACTTCA	0.653													4	2	---	---	---	---	
POTEE	445582	broad.mit.edu	37	2	131983277	131983281	+	Intron	DEL	CAGTA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131983277_131983281delCAGTA	uc002tsn.2	+						PLEKHB2_uc002tsh.2_Intron|POTEE_uc002tsk.2_Intron|POTEE_uc002tsl.2_Intron	NM_001083538	NP_001077007	Q6S8J3	POTEE_HUMAN	protein expressed in prostate, ovary, testis,								ATP binding				0						ttttttttttcagtagagatgaggt	0.000													16	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132593208	132593208	+	IGR	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132593208delG								C2orf27B (33974 upstream) : NCRNA00164 (311956 downstream)																							CTGCTCGGGCGCCCTGGAGGC	0.706													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133066592	133066592	+	Intron	DEL	G	-	-	rs78544491		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133066592delG	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		AAAAGGAAAAGAATGTGCAGG	0.433													2	5	---	---	---	---	
ZEB2	9839	broad.mit.edu	37	2	145153750	145153750	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145153750delT	uc002tvu.2	-						ZEB2_uc002tvv.2_Intron|ZEB2_uc010zbm.1_Intron|ZEB2_uc010fnp.2_Intron	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b							cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)		CTAAATTTGGTTTACAGAATA	0.363													4	2	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	159891719	159891719	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159891719delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						CTCTATGAAGTTTTTTTTTGA	0.343													4	2	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	159912831	159912831	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159912831delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						tatttatttattttttttttt	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	192785751	192785751	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192785751delA								SDPR (73770 upstream) : TMEFF2 (28998 downstream)																							GATGAAGCACAAATGGAAGTC	0.403													4	2	---	---	---	---	
HECW2	57520	broad.mit.edu	37	2	197280257	197280258	+	Intron	INS	-	TTCCTG	TTCCTG	rs144634819	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197280257_197280258insTTCCTG	uc002utm.1	-							NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						gtgtttgctgcttcctgtggtg	0.084													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	206981155	206981155	+	RNA	DEL	C	-	-	rs71410864		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206981155delC	uc002vbc.1	-	1		c.1134delG								Homo sapiens cDNA FLJ35491 fis, clone SMINT2008625, moderately similar to GLYCINE CLEAVAGE SYSTEM H PROTEIN PRECURSOR.																		AGGCAGGGCGCGGCAGGTGCC	0.627													4	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	217877985	217877985	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217877985delA								TNP1 (153203 upstream) : DIRC3 (270763 downstream)																							aaaaagaaggaaaaaaggagg	0.050													4	2	---	---	---	---	
NHEJ1	79840	broad.mit.edu	37	2	219942373	219942373	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219942373delT	uc002vjp.3	-						NHEJ1_uc002vjq.3_Intron	NM_024782	NP_079058	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1						B cell differentiation|central nervous system development|DNA recombination|double-strand break repair via nonhomologous end joining|positive regulation of ligase activity|response to ionizing radiation|T cell differentiation	nonhomologous end joining complex|nucleus	DNA binding|identical protein binding			lung(1)	1		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		TGGAGATTAAttttttttttt	0.234								Direct_reversal_of_damage|NHEJ					4	2	---	---	---	---	
CCL20	6364	broad.mit.edu	37	2	228680515	228680515	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228680515delT	uc002vpl.2	+						CCL20_uc002vpm.2_Intron	NM_004591	NP_004582	P78556	CCL20_HUMAN	chemokine (C-C motif) ligand 20 isoform 1						cell-cell signaling|chemotaxis|defense response to bacterium|immune response|inflammatory response|signal transduction	extracellular space	chemokine activity				0		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;7.3e-11)|all cancers(144;4.13e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		TTTTTAAAAATTTTTTTTGGT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	22424176	22424176	+	RNA	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22424176delG	uc003ccf.2	+	1		c.131delG								Homo sapiens HMG1 mRNA, 3' untranslated region.																		GGTACAGTATGGGGGTTGTAA	0.388													5	3	---	---	---	---	
XYLB	9942	broad.mit.edu	37	3	38405774	38405775	+	Intron	INS	-	T	T	rs149812294	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38405774_38405775insT	uc003cic.2	+						XYLB_uc011ayp.1_Intron|XYLB_uc003cid.1_Intron	NM_005108	NP_005099	O75191	XYLB_HUMAN	xylulokinase						D-xylose metabolic process|generation of precursor metabolites and energy|xylulose catabolic process		ATP binding|xylulokinase activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		TGACTCTTGACTCTACCATCTC	0.386													11	7	---	---	---	---	
KIF15	56992	broad.mit.edu	37	3	44846308	44846309	+	Intron	INS	-	GA	GA			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44846308_44846309insGA	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc003cny.1_Intron	NM_020242	NP_064627	Q9NS87	KIF15_HUMAN	kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		TGTCAAACACTGAAGTTGTAAA	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	48171923	48171924	+	IGR	INS	-	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48171923_48171924insA								MAP4 (41154 upstream) : CDC25A (26744 downstream)																							ATCGTGGTGGGAAAAGCAGGCG	0.500													4	2	---	---	---	---	
IQCF6	440956	broad.mit.edu	37	3	51813295	51813295	+	5'Flank	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51813295delC	uc011bdv.1	-							NM_001143833	NP_001137305			IQ motif containing F6												0						TTGTCTTTAGCCCCACCCTCA	0.517													4	2	---	---	---	---	
DNAH1	25981	broad.mit.edu	37	3	52381242	52381243	+	Intron	DEL	GG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52381242_52381243delGG	uc011bef.1	+						DNAH1_uc003ddt.1_Intron	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1						ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		gatgtgaggtggaggcaggtac	0.000													4	2	---	---	---	---	
FHIT	2272	broad.mit.edu	37	3	60485502	60485502	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60485502delC	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003	P49789	FHIT_HUMAN	fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		gacttggctgcccattgtccc	0.000			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	70129844	70129844	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70129844delT								MITF (112358 upstream) : FOXP1 (874893 downstream)																							CCTGACTCCGTTTTTTTTTTT	0.308													7	5	---	---	---	---	
FOXP1	27086	broad.mit.edu	37	3	71380000	71380000	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71380000delT	uc003dop.2	-						FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003dos.2_Intron	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|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 activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		AGTCCCCACATAAAAACATAC	0.383			T	PAX5	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	72373448	72373448	+	IGR	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72373448delG								PROK2 (539091 upstream) : RYBP (50303 downstream)																							AAAACACCCAGAACATCCTCA	0.587													4	2	---	---	---	---	
HSPBAP1	79663	broad.mit.edu	37	3	122508712	122508713	+	Intron	DEL	TT	-	-	rs67699437		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122508712_122508713delTT	uc003efu.1	-						HSPBAP1_uc003efv.1_Intron	NM_024610	NP_078886	Q96EW2	HBAP1_HUMAN	Hspb associated protein 1							cytoplasm				ovary(1)|lung(1)	2				GBM - Glioblastoma multiforme(114;0.0531)		CCAAAGCttctttttttttttt	0.248													3	3	---	---	---	---	
ADCY5	111	broad.mit.edu	37	3	123159848	123159848	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123159848delT	uc003egh.1	-							NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)		ATTGTGCTTCTTTTAAACAGG	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	128256841	128256841	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128256841delT								LOC90246 (27414 upstream) : C3orf27 (34003 downstream)																							tcttGACTCCTTTTTTTTTTT	0.249													5	3	---	---	---	---	
KIAA1257	57501	broad.mit.edu	37	3	128707386	128707386	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128707386delA	uc003elj.3	-						KIAA1257_uc003elg.1_Intron|KIAA1257_uc003eli.3_Intron	NM_020741	NP_065792	Q9ULG3	K1257_HUMAN	hypothetical protein LOC57501												0						ctgactcaacaaaaaaaaaaa	0.055													8	4	---	---	---	---	
IFT122	55764	broad.mit.edu	37	3	129197276	129197277	+	Intron	INS	-	TTTTA	TTTTA	rs146257299	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129197276_129197277insTTTTA	uc003emm.2	+						IFT122_uc003eml.2_Intron|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Intron|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc003emr.2_Intron|IFT122_uc011bla.1_Intron|IFT122_uc011bkx.1_Intron|IFT122_uc011bkz.1_Intron	NM_052989	NP_443715	Q9HBG6	IF122_HUMAN	WD repeat domain 10 isoform 2						camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2						ATGtttttttgttttattttat	0.193													4	2	---	---	---	---	
RNF13	11342	broad.mit.edu	37	3	149570113	149570114	+	Intron	INS	-	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149570113_149570114insA	uc003exn.3	+						RNF13_uc003exp.3_Intron	NM_007282	NP_009213	O43567	RNF13_HUMAN	ring finger protein 13						protein autoubiquitination	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane|nuclear inner membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TAAGCAGTTGTATATGTTGTAA	0.277													4	2	---	---	---	---	
USP13	8975	broad.mit.edu	37	3	179506683	179506683	+	3'UTR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179506683delT	uc003fkh.2	+	21						NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			AGAAAGCAGATTTTTTTTTTC	0.388													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187148030	187148030	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187148030delT								RTP4 (58663 upstream) : SST (238666 downstream)																							ccctgagtagtttttttgttt	0.000													4	2	---	---	---	---	
IL1RAP	3556	broad.mit.edu	37	3	190337871	190337871	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190337871delA	uc003fsm.1	+						IL1RAP_uc003fsk.2_Intron|IL1RAP_uc003fsl.2_Intron|IL1RAP_uc010hzf.2_Intron|IL1RAP_uc010hzg.1_Intron|IL1RAP_uc003fsn.1_Intron|IL1RAP_uc003fso.1_Intron|IL1RAP_uc003fsp.1_Intron|IL1RAP_uc003fsq.2_Intron	NM_002182	NP_002173	Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein isoform						inflammatory response|innate immune response|protein complex assembly	extracellular region|integral to plasma membrane				ovary(1)	1	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		TCATGATCAGAAAAGATAATG	0.323													4	2	---	---	---	---	
MFI2	4241	broad.mit.edu	37	3	196743879	196743879	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196743879delG	uc003fxk.3	-							NM_005929	NP_005920	P08582	TRFM_HUMAN	melanoma-associated antigen p97 isoform 1						cellular iron ion homeostasis|iron ion transport	anchored to membrane|extracellular region|integral to plasma membrane	ferric iron binding|protein binding				0	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		GACAGTCTCTGGGTCCTGCCC	0.677													4	2	---	---	---	---	
BDH1	622	broad.mit.edu	37	3	197255175	197255176	+	Intron	DEL	GT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197255175_197255176delGT	uc003fxr.2	-						BDH1_uc003fxs.2_Intron|BDH1_uc003fxt.2_Intron|BDH1_uc003fxu.2_Intron	NM_203314	NP_976059	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1						cellular lipid metabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	3-hydroxybutyrate dehydrogenase activity			ovary(1)	1	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)	NADH(DB00157)	gagtgagtgagtgtgtgtgtgt	0.243													4	2	---	---	---	---	
PCGF3	10336	broad.mit.edu	37	4	738600	738601	+	Intron	INS	-	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:738600_738601insC	uc011bva.1	+						PCGF3_uc003gbd.1_Intron|PCGF3_uc003gbe.2_Intron|PCGF3_uc010ibh.2_Intron|PCGF3_uc003gbg.1_Intron|PCGF3_uc003gbh.2_Intron	NM_006315	NP_006306	Q3KNV8	PCGF3_HUMAN	ring finger protein 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PcG protein complex	zinc ion binding				0						GGTGGGCGGGGCCCGGGGGTCG	0.708													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3622445	3622446	+	IGR	INS	-	G	G	rs147769479	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3622445_3622446insG								LRPAP1 (88221 upstream) : ADRA2C (145629 downstream)																							gcagaaaaggaggggggtttgc	0.000													1	6	---	---	---	---	
ATP8A1	10396	broad.mit.edu	37	4	42448913	42448913	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42448913delA	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)	CCACAAGATTAAAAAAAAAAA	0.358													6	4	---	---	---	---	
KIT	3815	broad.mit.edu	37	4	55556608	55556608	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55556608delG	uc010igr.2	+						KIT_uc010igs.2_Intron	NM_000222	NP_000213	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral						male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	ccaagtagctgggataagtat	0.184		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				4	2	---	---	---	---	
EXOC1	55763	broad.mit.edu	37	4	56726892	56726895	+	Intron	DEL	TGAC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56726892_56726895delTGAC	uc003hbe.1	+						EXOC1_uc003hbf.1_Intron|EXOC1_uc003hbg.1_Intron	NM_018261	NP_060731	Q9NV70	EXOC1_HUMAN	exocyst complex component 1 isoform 1						exocytosis|protein transport	exocyst	protein binding			ovary(2)|skin(2)|lung(1)|central_nervous_system(1)	6	Glioma(25;0.08)|all_neural(26;0.101)					AAAATTACTTTGACTGTATACATT	0.211													2	4	---	---	---	---	
IGFBP7	3490	broad.mit.edu	37	4	57972446	57972446	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57972446delG	uc003hcn.2	-						IGFBP7_uc011cag.1_Intron	NM_001553	NP_001544	Q16270	IBP7_HUMAN	insulin-like growth factor binding protein 7						cell adhesion|negative regulation of cell proliferation|regulation of cell growth	extracellular space	insulin-like growth factor binding			lung(2)|central_nervous_system(1)	3	Glioma(25;0.08)|all_neural(26;0.181)				Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	taaaaggtttgggggcgacat	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69863502	69863503	+	IGR	INS	-	CGGA	CGGA	rs78806655	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69863502_69863503insCGGA								UGT2A3 (45993 upstream) : UGT2B7 (98690 downstream)																							aatggatgatttggatgttagc	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69863503	69863504	+	IGR	INS	-	GATTC	GATTC	rs141141985	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69863503_69863504insGATTC								UGT2A3 (45994 upstream) : UGT2B7 (98689 downstream)																							atggatgatttggatgttagct	0.045													4	2	---	---	---	---	
RASSF6	166824	broad.mit.edu	37	4	74486356	74486356	+	5'Flank	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74486356delG	uc003hhd.1	-						RASSF6_uc003hhc.1_5'Flank|RASSF6_uc010iik.1_5'Flank|RASSF6_uc010iil.1_5'Flank	NM_201431	NP_958834	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family 6						apoptosis|signal transduction		protein binding			pancreas(2)	2	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			AGTGCATGTTGGGAGTGTTTA	0.473													4	2	---	---	---	---	
CNOT6L	246175	broad.mit.edu	37	4	78739602	78739602	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78739602delA	uc011ccd.1	-						CNOT6L_uc003hks.2_Intron|CNOT6L_uc011cce.1_Intron	NM_144571	NP_653172	Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	exonuclease activity|protein binding			large_intestine(1)	1						TTGTCTAATTAAAAAAAAAAA	0.378											OREG0016242	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
PTPN13	5783	broad.mit.edu	37	4	87723300	87723301	+	Intron	DEL	GT	-	-	rs34599425		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87723300_87723301delGT	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron|PTPN13_uc003hqc.1_Intron	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CAAGATTTTAgtgtgtgtgtgt	0.243													5	4	---	---	---	---	
FAM13A	10144	broad.mit.edu	37	4	89654456	89654456	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89654456delC	uc003hse.1	-						FAM13A_uc011cdp.1_Intron|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	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						AAAGGACTATCATATAACTGA	0.328													2	4	---	---	---	---	
GRID2	2895	broad.mit.edu	37	4	94133926	94133927	+	Intron	INS	-	G	G	rs33994570		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94133926_94133927insG	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron|GRID2_uc010ikz.1_Intron	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	ttttttgttgttttttttttct	0.134													4	2	---	---	---	---	
BMPR1B	658	broad.mit.edu	37	4	95806014	95806014	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95806014delT	uc003htm.3	+							NM_001203	NP_001194	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB						BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity			lung(4)|skin(2)|stomach(1)|breast(1)	8		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		tgtgatttgctttagccaata	0.000													4	2	---	---	---	---	
BDH2	56898	broad.mit.edu	37	4	104007882	104007882	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104007882delG	uc003hwz.2	-						BDH2_uc003hxa.2_Intron	NM_020139	NP_064524	Q9BUT1	BDH2_HUMAN	3-hydroxybutyrate dehydrogenase, type 2						fatty acid beta-oxidation|heme metabolic process|iron ion homeostasis|siderophore biosynthetic process	cytoplasm	3-hydroxybutyrate dehydrogenase activity|NAD binding|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.02e-08)		AACTATTGCTGGGAAATGATG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	134203517	134203518	+	IGR	DEL	AG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134203517_134203518delAG								PCDH10 (90786 upstream) : PABPC4L (913973 downstream)																							ccaagaccttagtaaggccata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	187682241	187682241	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187682241delA								FAT1 (34391 upstream) : None (None downstream)																							CCTACATTATACATCTGGTTT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189553261	189553262	+	IGR	INS	-	CT	CT	rs149220638	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189553261_189553262insCT								TRIML1 (484612 upstream) : None (None downstream)																							aaggactgcccctatattggag	0.015													1	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5375692	5375693	+	IGR	INS	-	TG	TG	rs10636948		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5375692_5375693insTG								ADAMTS16 (55281 upstream) : KIAA0947 (47114 downstream)																							GAGGAAGTCTAtgtgtgtgtgt	0.322													7	4	---	---	---	---	
FBXL7	23194	broad.mit.edu	37	5	15552451	15552451	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15552451delC	uc003jfn.1	+							NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3						cagtcactgaccactggacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	73546695	73546696	+	IGR	DEL	CA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73546695_73546696delCA								RGNEF (309282 upstream) : ENC1 (376539 downstream)																							catgagcactcacacacacaca	0.252													4	2	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112407517	112407518	+	Intron	DEL	CC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112407517_112407518delCC	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron|MCC_uc011cwb.1_Intron|MCC_uc010jcd.1_Intron	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ACAGAGAGAACCAAAGGAAGAA	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134371927	134371927	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134371927delT	uc003laj.1	+						PITX1_uc010jea.2_5'Flank|PITX1_uc011cxy.1_5'Flank					Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																		AGATCCCTCCTTTCAAGGAGA	0.502													4	2	---	---	---	---	
SPOCK1	6695	broad.mit.edu	37	5	136516066	136516066	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136516066delG	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GGGGTGGGTAGGTGACAAAGA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139134786	139134786	+	IGR	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139134786delG								CXXC5 (72106 upstream) : PSD2 (40620 downstream)																							TGGATCCTCTGGGGTCTGTGT	0.502													4	2	---	---	---	---	
HARS	3035	broad.mit.edu	37	5	140054993	140054994	+	Intron	INS	-	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140054993_140054994insT	uc003lgv.2	-						DND1_uc003lgt.2_5'Flank|HARS_uc003lgu.2_Intron|HARS_uc011czm.1_Intron|HARS_uc003lgw.2_Intron|HARS_uc011czn.1_Intron|HARS_uc010jfu.2_Intron|HARS_uc011czo.1_Intron|HARS_uc011czp.1_Intron	NM_002109	NP_002100	P12081	SYHC_HUMAN	histidyl-tRNA synthetase						histidyl-tRNA aminoacylation	cytosol	ATP binding|histidine-tRNA ligase activity			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		L-Histidine(DB00117)	CATGTAGTACCttttttttttt	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157908823	157908824	+	IGR	INS	-	T	T	rs144799962	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157908823_157908824insT								CLINT1 (622655 upstream) : EBF1 (214100 downstream)																							agccagaatgattttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	167703213	167703213	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167703213delA								ODZ2 (12052 upstream) : WWC1 (15852 downstream)																							tgctgtctctaaaaaacatcc	0.104													4	2	---	---	---	---	
GABRP	2568	broad.mit.edu	37	5	170220192	170220193	+	Intron	DEL	GA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170220192_170220193delGA	uc003mau.2	+						GABRP_uc011dev.1_Intron	NM_014211	NP_055026	O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi							cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			breast(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			cccttcccatgaccctgtgatg	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	177410482	177410482	+	IGR	DEL	A	-	-	rs11313053		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177410482delA								LOC728554 (99215 upstream) : PROP1 (8754 downstream)																							ACATCCACATAACCTGGGCAA	0.547													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	1377115	1377115	+	IGR	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1377115delC								FOXQ1 (62123 upstream) : FOXF2 (12954 downstream)																							GGCACGGCTACCCACAGGTTC	0.547													4	2	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5448301	5448302	+	Intron	INS	-	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5448301_5448302insT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	gatccagaatgtttatttgagg	0.000													4	2	---	---	---	---	
HIVEP1	3096	broad.mit.edu	37	6	12016144	12016144	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12016144delG	uc003nac.2	+							NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				ACCATTAGATGGGGTATTAAA	0.249													4	2	---	---	---	---	
TRIM10	10107	broad.mit.edu	37	6	30128778	30128779	+	5'Flank	DEL	CA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30128778_30128779delCA	uc003npo.3	-						TRIM10_uc003npn.2_5'Flank|TRIM15_uc010jrx.2_5'Flank	NM_006778	NP_006769	Q9UDY6	TRI10_HUMAN	tripartite motif-containing 10 isoform 1							cytoplasm	zinc ion binding				0						CCCATATCGTCACACACTTGCA	0.545													4	2	---	---	---	---	
FRS3	10817	broad.mit.edu	37	6	41744363	41744363	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41744363delA	uc003orc.1	-							NM_006653	NP_006644	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3						fibroblast growth factor receptor signaling pathway	plasma membrane	fibroblast growth factor receptor binding|insulin receptor binding			ovary(2)	2	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGTTTTCTCTAAAAAAAAAAG	0.080													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	42700747	42700747	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42700747delT								PRPH2 (10389 upstream) : TBCC (11488 downstream)																							CTCAGTAGACTCCACCCTTTG	0.373													4	2	---	---	---	---	
COL19A1	1310	broad.mit.edu	37	6	70733844	70733845	+	Intron	INS	-	ATAC	ATAC			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70733844_70733845insATAC	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						TTTTTTTTCTGTCTTTTTTCAT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112647042	112647042	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112647042delT								LAMA4 (71214 upstream) : RFPL4B (21490 downstream)																							GCTTTGCAGCTTTTTTTTTTC	0.453													4	5	---	---	---	---	
RFX6	222546	broad.mit.edu	37	6	117236657	117236658	+	Intron	DEL	GT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117236657_117236658delGT	uc003pxm.2	+							NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6						glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	protein binding|transcription regulatory region DNA binding			ovary(1)|pancreas(1)|skin(1)	3						aagtagtgcagtgaaggtgggc	0.054													4	2	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	124216209	124216209	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124216209delT	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010kep.1_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		CCTACACCCCTTTTTTTTTTG	0.328													4	2	---	---	---	---	
PDE7B	27115	broad.mit.edu	37	6	136468301	136468302	+	Intron	INS	-	A	A	rs149299885	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136468301_136468302insA	uc003qgp.2	+						uc003qgq.1_Intron|PDE7B_uc003qgr.2_Intron	NM_018945	NP_061818	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B						signal transduction|synaptic transmission	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(1)	1	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Dyphylline(DB00651)|Ketotifen(DB00920)	aagtaaaaattaaaaaaaaaaC	0.114													3	5	---	---	---	---	
MTHFD1L	25902	broad.mit.edu	37	6	151259608	151259608	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151259608delT	uc003qob.2	+						MTHFD1L_uc011een.1_Intron|MTHFD1L_uc011eeo.1_Intron|MTHFD1L_uc003qoc.2_Intron	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+						folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		TATTTTTACCTTTTTTTTTTA	0.294													11	6	---	---	---	---	
PRKAR1B	5575	broad.mit.edu	37	7	604492	604492	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:604492delC	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CAGGCGGATGCCCCCCAACCT	0.592													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3861457	3861457	+	Intron	DEL	A	-	-	rs149976390		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3861457delA	uc003smx.2	+							NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TTTGGGAATTAAAAAAAAAAG	0.328													3	3	---	---	---	---	
WIPI2	26100	broad.mit.edu	37	7	5255936	5255936	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5255936delA	uc003snv.2	+						WIPI2_uc003snw.2_Intron|WIPI2_uc003snx.2_Intron|WIPI2_uc003sny.2_Intron|WIPI2_uc010ksv.2_Intron|WIPI2_uc003snz.2_Intron|WIPI2_uc003soa.2_Intron	NM_015610	NP_056425	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2						autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)		ggtggcagtcacctgtaattc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	6921712	6921713	+	IGR	INS	-	GG	GG	rs139821239	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6921712_6921713insGG								C7orf28B (55851 upstream) : C1GALT1 (300533 downstream)																							CTCGAAGTCCCGGGTACTATAC	0.347													18	14	---	---	---	---	
LOC441204	441204	broad.mit.edu	37	7	26507019	26507019	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26507019delG	uc003sxy.1	+						LOC441204_uc003sxz.2_Intron					Homo sapiens cDNA FLJ31922 fis, clone NT2RP7005219.												0						ggccagcagcggagagcagaa	0.000													4	2	---	---	---	---	
ADCYAP1R1	117	broad.mit.edu	37	7	31117314	31117314	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31117314delT	uc003tca.1	+						ADCYAP1R1_uc003tcb.1_Intron|ADCYAP1R1_uc003tcc.1_Intron|ADCYAP1R1_uc003tcd.1_Intron|ADCYAP1R1_uc003tce.1_Intron	NM_001118	NP_001109	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1						gtgtgtggtgtgtgtgatgtg	0.000													4	2	---	---	---	---	
ADCYAP1R1	117	broad.mit.edu	37	7	31117320	31117320	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31117320delA	uc003tca.1	+						ADCYAP1R1_uc003tcb.1_Intron|ADCYAP1R1_uc003tcc.1_Intron|ADCYAP1R1_uc003tcd.1_Intron|ADCYAP1R1_uc003tce.1_Intron	NM_001118	NP_001109	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1						ggtgtgtgtgatgtgtgtgta	0.000													4	2	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	32537266	32537266	+	Intron	DEL	T	-	-	rs59504023		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32537266delT	uc003tcv.1	+						AVL9_uc011kai.1_Intron|LSM5_uc011kag.1_5'Flank|LSM5_uc011kah.1_5'Flank	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						CCATTAGttcttttttttttt	0.204													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	34118337	34118338	+	Intron	INS	-	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34118337_34118338insT	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						AAAACGACCACTTTTTTTTTTA	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35643720	35643720	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35643720delT								TBX20 (350478 upstream) : HERPUD2 (28552 downstream)																							tgaccccttcttaccacctcc	0.000													5	3	---	---	---	---	
VPS41	27072	broad.mit.edu	37	7	38785485	38785486	+	Intron	INS	-	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38785485_38785486insA	uc003tgy.2	-						VPS41_uc003tgz.2_Intron|VPS41_uc010kxn.2_Intron|VPS41_uc003tgx.2_5'Flank	NM_014396	NP_055211	P49754	VPS41_HUMAN	vacuolar protein sorting 41 isoform 1						Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4						CAAATGAAAAGAAAGGGCCTTT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	39874545	39874545	+	IGR	DEL	A	-	-	rs75446802		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39874545delA								LOC349114 (40324 upstream) : CDK13 (115414 downstream)																							CAAAACTCTCAAAAAAAAAAA	0.333													5	4	---	---	---	---	
NUDCD3	23386	broad.mit.edu	37	7	44426100	44426100	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44426100delC	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3												0						GAGGGAGTGTCCCAGCCCACC	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54250938	54250938	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54250938delA								None (None upstream) : HPVC1 (17979 downstream)																							aaaaaggcagaaaaaaaattg	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	55781186	55781186	+	IGR	DEL	G	-	-	rs71547947		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55781186delG								FKBP9L (8926 upstream) : SEPT14 (80051 downstream)																							ACTCTCTCCAGAAAAACAAAA	0.313													6	3	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71488430	71488430	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71488430delA	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				TCCCTAATGCAAAAAAAAATT	0.363													6	4	---	---	---	---	
AKAP9	10142	broad.mit.edu	37	7	91621992	91621993	+	Intron	INS	-	C	C	rs10270342		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91621992_91621993insC	uc003ulg.2	+						AKAP9_uc003uld.3_Intron|AKAP9_uc003ule.2_Intron|AKAP9_uc003ulf.2_Intron	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			aaaaaaaaaaaaaaaaaaCTCA	0.173			T	BRAF	papillary thyroid								4	3	---	---	---	---	
TRRAP	8295	broad.mit.edu	37	7	98496812	98496812	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98496812delA	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_5'Flank	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			actccatctcaaaaaaaaaga	0.129													5	4	---	---	---	---	
NRCAM	4897	broad.mit.edu	37	7	107821070	107821070	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107821070delC	uc003vfb.2	-						NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron	NM_001037132	NP_001032209	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule isoform A						angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5						TAAATTACAGCCACATGACAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114378641	114378641	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114378641delA								FOXP2 (47549 upstream) : MDFIC (183568 downstream)																							AAAAAAAATCAAAGGCAACAA	0.353													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141944717	141944717	+	IGR	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141944717delC								LOC100124692 (23629 upstream) : TRYX3 (7247 downstream)																							GTTGACCACACCCCCTGCTCT	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142587385	142587385	+	IGR	DEL	A	-	-	rs4987576		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142587385delA								TRPV6 (3908 upstream) : TRPV5 (18263 downstream)																							TGTTTCGCTCAAGTTTTTCCT	0.308													3	5	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151412920	151412921	+	Intron	INS	-	AGGGC	AGGGC	rs144264137	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151412920_151412921insAGGGC	uc003wkk.2	-						PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.2_Intron|PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		AGGCAGGAGAGAGGGCGGGGCG	0.589													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	156234076	156234077	+	Splice_Site	INS	-	AATA	AATA	rs142930868	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156234076_156234077insAATA	uc003wml.1	-	2		c.1341_splice	c.e2-1							Homo sapiens cDNA FLJ33533 fis, clone BRAMY2007308.																		TGAATACACCTaataaataaat	0.426													6	3	---	---	---	---	
LMBR1	64327	broad.mit.edu	37	7	156520417	156520417	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156520417delA	uc003wmw.3	-						LMBR1_uc003wmv.3_Intron|LMBR1_uc003wmx.3_Intron|LMBR1_uc010lqn.2_Intron|LMBR1_uc011kvx.1_Intron	NM_022458	NP_071903	Q8WVP7	LMBR1_HUMAN	limb region 1 protein							integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		CCAACACTTGAAAAAAGGCCC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	10305811	10305812	+	IGR	INS	-	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10305811_10305812insA								MSRA (19412 upstream) : PRSS55 (77269 downstream)																							ttcagaacttcaaaaaaaactg	0.000													4	2	---	---	---	---	
XKR6	286046	broad.mit.edu	37	8	10936345	10936345	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10936345delG	uc003wtk.1	-							NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		GGAGAAGAGTGGACATACCCT	0.572													4	2	---	---	---	---	
EFHA2	286097	broad.mit.edu	37	8	16956079	16956080	+	Intron	DEL	AC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16956079_16956080delAC	uc003wxd.2	+							NM_181723	NP_859074	Q86XE3	EFHA2_HUMAN	EF-hand domain family, member A2							integral to membrane	calcium ion binding			skin(1)	1				Colorectal(111;0.0686)|COAD - Colon adenocarcinoma(73;0.239)		TTAAACCTCAACAAGGTCCTTG	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23448192	23448193	+	IGR	INS	-	AAAC	AAAC	rs149751652	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23448192_23448193insAAAC								SLC25A37 (18131 upstream) : NKX3-1 (88014 downstream)																							acaaaaattaaaaacaaacaaa	0.178													3	5	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32167293	32167294	+	Intron	INS	-	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32167293_32167294insT	uc003xip.2	+							NM_013962	NP_039256	Q02297	NRG1_HUMAN	neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TTGTGTCCTTGTTCCCATGGTG	0.406													4	2	---	---	---	---	
DDHD2	23259	broad.mit.edu	37	8	38099572	38099572	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38099572delA	uc003xlb.2	+						DDHD2_uc003xlc.2_Intron|DDHD2_uc011lbl.1_Intron	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1						lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			actccatctcaaaaaaaaaaa	0.139													5	5	---	---	---	---	
SLC20A2	6575	broad.mit.edu	37	8	42317139	42317139	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42317139delT	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron|SLC20A2_uc011lcu.1_Intron	NM_006749	NP_006740	Q08357	S20A2_HUMAN	solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			ggggatttaatttttttttct	0.080													4	2	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48632333	48632333	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48632333delC	uc003xqd.2	+						KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron|KIAA0146_uc011ldg.1_Intron|KIAA0146_uc003xqg.1_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				CTGAAGGAAACCAGGGAAGCC	0.607													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58094098	58094099	+	IGR	INS	-	G	G	rs141203085	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58094098_58094099insG								IMPAD1 (187671 upstream) : C8orf71 (98003 downstream)																							CTGGAGCCTGTGTATGGGACCC	0.381													5	3	---	---	---	---	
DNAJC5B	85479	broad.mit.edu	37	8	66941076	66941076	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66941076delC	uc003xvs.1	+						DNAJC5B_uc003xvt.1_Intron	NM_033105	NP_149096	Q9UF47	DNJ5B_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5						protein folding	membrane	heat shock protein binding|unfolded protein binding				0		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)			AACCGGCACTCCCCAGTTTCA	0.473													4	2	---	---	---	---	
MRPS28	28957	broad.mit.edu	37	8	80924365	80924366	+	Intron	INS	-	A	A	rs34366408		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80924365_80924366insA	uc003ybp.2	-						MRPS28_uc003ybo.2_Intron|TPD52_uc010lzr.2_Intron	NM_014018	NP_054737	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S28							mitochondrial small ribosomal subunit					0	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)			TCTCCTCCATTTTTTGCCTCTA	0.297													4	2	---	---	---	---	
MRPS28	28957	broad.mit.edu	37	8	80924366	80924367	+	Intron	INS	-	TC	TC	rs112994734		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80924366_80924367insTC	uc003ybp.2	-						MRPS28_uc003ybo.2_Intron|TPD52_uc010lzr.2_Intron	NM_014018	NP_054737	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S28							mitochondrial small ribosomal subunit					0	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)			CTCCTCCATTTTTTGCCTCTAT	0.292													4	2	---	---	---	---	
TM7SF4	81501	broad.mit.edu	37	8	105354145	105354145	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105354145delC	uc003ylx.1	+							NM_030788	NP_110415	Q9H295	TM7S4_HUMAN	dendritic cell-specific transmembrane protein						osteoclast differentiation	cell surface|integral to membrane|plasma membrane				pancreas(2)|large_intestine(1)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			AAGCCAGAAACAGGTATTGTA	0.433													4	2	---	---	---	---	
ANGPT1	284	broad.mit.edu	37	8	108348120	108348122	+	Intron	DEL	ACT	-	-	rs75506409		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108348120_108348122delACT	uc003ymn.2	-						ANGPT1_uc011lhv.1_Intron|ANGPT1_uc003ymo.2_Intron	NM_001146	NP_001137	Q15389	ANGP1_HUMAN	angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			TGAGATTTGAACTACTACCATTA	0.261													2	5	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	113529797	113529797	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113529797delA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						ctcgaaactcaaaaaaaaagg	0.000										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120436854	120436855	+	IGR	INS	-	T	T	rs143072343	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120436854_120436855insT								NOV (176 upstream) : ENPP2 (132464 downstream)																							AAGCCCTGATCTTTTTTTTTCT	0.421													4	2	---	---	---	---	
ASAP1	50807	broad.mit.edu	37	8	131073564	131073564	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131073564delA	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|ASAP1_uc011liw.1_Intron	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4						ATCCAGAATTAAAAAAAATAA	0.294													4	2	---	---	---	---	
DMRT1	1761	broad.mit.edu	37	9	910519	910519	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:910519delT	uc003zgv.2	+							NM_021951	NP_068770	Q9Y5R6	DMRT1_HUMAN	doublesex and mab-3 related transcription factor						cell differentiation|male gonad development|sex determination	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232)		Lung(218;0.037)		GTATTTGGGATTTTTTTTTTT	0.318													3	3	---	---	---	---	
KDM4C	23081	broad.mit.edu	37	9	6793347	6793347	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6793347delA	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc010mhw.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc010mhv.2_Intron	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						TCTAAGGCTTAAAAAAAAAAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	34813436	34813436	+	IGR	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34813436delC								C9orf144B (83901 upstream) : C9orf144 (16829 downstream)																							ggtcaggagtccagcttgatc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67917596	67917598	+	IGR	DEL	GAG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67917596_67917598delGAG								FAM27B (123407 upstream) : None (None downstream)																							CATGGAAGATGAGGAGTCCGTTG	0.468													4	2	---	---	---	---	
SMC5	23137	broad.mit.edu	37	9	72900877	72900878	+	Intron	INS	-	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72900877_72900878insA	uc004ahr.2	+							NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3						aataaGACAGGAAGATAAATGT	0.158													4	3	---	---	---	---	
PCSK5	5125	broad.mit.edu	37	9	78549104	78549105	+	Intron	INS	-	GT	GT	rs151217800	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78549104_78549105insGT	uc004ajz.2	+						PCSK5_uc004ajy.2_Intron|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						CCAGCCCAAGGGTACATGCTGC	0.515													6	7	---	---	---	---	
BICD2	23299	broad.mit.edu	37	9	95486552	95486552	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95486552delG	uc004aso.1	-						BICD2_uc004asp.1_Intron	NM_015250	NP_056065	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 isoform 2						microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule	cytoplasmic vesicle|cytoskeleton|Golgi apparatus|plasma membrane	Rab GTPase binding			skin(1)	1						TCATCTGAATGGAACATACTT	0.453													4	2	---	---	---	---	
WNK2	65268	broad.mit.edu	37	9	96009732	96009733	+	Intron	INS	-	CC	CC			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96009732_96009733insCC	uc004ati.1	+						WNK2_uc011lud.1_Intron|WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_Intron|WNK2_uc010mrc.1_Intron|WNK2_uc010mrd.1_Intron	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2						intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1)	12						GTCCTGCGTGGATGAGCCAGTG	0.559													5	3	---	---	---	---	
TMEFF1	8577	broad.mit.edu	37	9	103323993	103323993	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103323993delT	uc004baz.1	+						TMEFF1_uc004bay.1_Intron	NM_003692	NP_003683	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two						multicellular organismal development	integral to membrane|plasma membrane					0		Acute lymphoblastic leukemia(62;0.0452)				AACAAAAATCTTTTTTTTTTT	0.249													6	5	---	---	---	---	
PALM2-AKAP2	445815	broad.mit.edu	37	9	112924036	112924036	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112924036delC	uc004bej.3	+						PALM2-AKAP2_uc004bek.3_Intron|AKAP2_uc011lwi.1_Intron|AKAP2_uc004bem.2_Intron|AKAP2_uc011lwj.1_Intron|PALM2-AKAP2_uc004ben.2_Intron	NM_007203	NP_009134	Q9Y2D5	AKAP2_HUMAN	PALM2-AKAP2 protein isoform 1								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						TCCAAAATGGCCCCCAACGAC	0.438													4	2	---	---	---	---	
CEP110	11064	broad.mit.edu	37	9	123921612	123921613	+	Intron	INS	-	C	C			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123921612_123921613insC	uc004bkx.1	+						CEP110_uc010mvo.1_Intron|CEP110_uc004blb.1_Intron|CEP110_uc010mvp.1_Intron	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						tcatgccacctcctcttagaaa	0.000													4	3	---	---	---	---	
HSPA5	3309	broad.mit.edu	37	9	128002167	128002167	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128002167delA	uc004bpn.2	-							NM_005347	NP_005338	P11021	GRP78_HUMAN	heat shock 70kDa protein 5						anti-apoptosis|cellular response to glucose starvation|ER-associated protein catabolic process|platelet activation|platelet degranulation|regulation of protein folding in endoplasmic reticulum	cell surface|endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|integral to endoplasmic reticulum membrane|melanosome|midbody|nucleus|perinuclear region of cytoplasm	ATP binding|ATPase activity|calcium ion binding|caspase inhibitor activity|chaperone binding|misfolded protein binding|protein binding, bridging|protein domain specific binding|ubiquitin protein ligase binding|unfolded protein binding			ovary(3)|skin(1)	4					Antihemophilic Factor(DB00025)	actccatctcaaaaaaaaaaa	0.124										Prostate(1;0.17)			4	2	---	---	---	---	
FPGS	2356	broad.mit.edu	37	9	130566373	130566373	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130566373delT	uc004bsg.1	+						FPGS_uc004bsf.1_Intron|FPGS_uc004bsh.1_Intron|FPGS_uc011mal.1_Intron|FPGS_uc004bsi.1_Intron	NM_004957	NP_004948	Q05932	FOLC_HUMAN	folylpolyglutamate synthase isoform a precursor						folic acid metabolic process|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|one-carbon metabolic process	cytosol|mitochondrial matrix	ATP binding|tetrahydrofolylpolyglutamate synthase activity				0					L-Glutamic Acid(DB00142)	CAGACTCCCATTTTTGCCAGA	0.577													4	2	---	---	---	---	
SET	6418	broad.mit.edu	37	9	131455513	131455513	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131455513delA	uc004bvt.3	+						SET_uc004bvu.3_Intron|SET_uc010myg.2_Intron|SET_uc011mbj.1_Intron	NM_001122821	NP_001116293	Q01105	SET_HUMAN	SET translocation (myeloid leukemia-associated)						DNA replication|mRNA metabolic process|negative regulation of histone acetylation|negative regulation of neuron apoptosis|negative regulation of transcription, DNA-dependent|nucleocytoplasmic transport|nucleosome assembly|nucleosome disassembly	cytosol|endoplasmic reticulum|nucleoplasm|perinuclear region of cytoplasm|protein complex	histone binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity				0		Myeloproliferative disorder(178;0.204)		GBM - Glioblastoma multiforme(294;3.1e-09)		tccaaaaaacaaaaaaaaaGA	0.224			T	NUP214	AML								3	4	---	---	---	---	
BAT2L1	84726	broad.mit.edu	37	9	134270344	134270344	+	Intron	DEL	G	-	-	rs113188231		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134270344delG	uc004cam.1	+									Q5JSZ5	PRC2B_HUMAN	SubName: Full=BAT2L protein;								protein binding				0						CCTGCCAGATGGGGTTTTTTT	0.473													4	3	---	---	---	---	
CARD9	64170	broad.mit.edu	37	9	139259410	139259411	+	Intron	INS	-	AGG	AGG	rs146336925	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139259410_139259411insAGG	uc004chg.3	-						DNLZ_uc004chf.1_5'Flank|DNLZ_uc011mdv.1_5'Flank|CARD9_uc011mdw.1_Intron	NM_052813	NP_434700	Q9H257	CARD9_HUMAN	caspase recruitment domain protein 9 isoform 1						positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of JNK cascade|positive regulation of stress-activated MAPK cascade|regulation of apoptosis	cytoplasm	CARD domain binding|protein homodimerization activity			pancreas(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		GTGCCCAAGAAAGGGGGATCCA	0.624													2	4	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140681665	140681665	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140681665delA	uc011mfc.1	+						EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		ATCTCTCATTAAAAAAAAATG	0.478													4	2	---	---	---	---	
AKR1C3	8644	broad.mit.edu	37	10	5106044	5106044	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5106044delG	uc001ihr.2	+							NM_003739	NP_003730	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3						prostaglandin metabolic process	cytoplasm	aldo-keto reductase (NADP) activity|androsterone dehydrogenase (A-specific) activity|indanol dehydrogenase activity|prostaglandin-F synthase activity|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			skin(1)	1					Dimethyl sulfoxide(DB01093)|NADH(DB00157)	tgtaatgcctgggctatcttc	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	6320811	6320812	+	IGR	INS	-	T	T	rs142565800	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6320811_6320812insT								PFKFB3 (43306 upstream) : PRKCQ (148293 downstream)																							gtggtgggtggtaaaatcatag	0.045													3	8	---	---	---	---	
MLLT10	8028	broad.mit.edu	37	10	22004096	22004097	+	Intron	DEL	AT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22004096_22004097delAT	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						TGTTGTTAGGATATATATACGC	0.342			T	MLL|PICALM|CDK6	AL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	27620447	27620448	+	IGR	INS	-	TT	TT	rs142562667	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27620447_27620448insTT								LOC387646 (79212 upstream) : PTCHD3 (66669 downstream)																							ACTCAGGCTTCTTTCCGCCAAG	0.465													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29283016	29283017	+	IGR	DEL	AT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29283016_29283017delAT								BAMBI (311148 upstream) : LYZL1 (294973 downstream)																							tgttattgtgatatgttatgat	0.030													3	4	---	---	---	---	
IPMK	253430	broad.mit.edu	37	10	59975732	59975732	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59975732delA	uc001jkb.2	-							NM_152230	NP_689416	Q8NFU5	IPMK_HUMAN	inositol polyphosphate multikinase							nucleus	ATP binding|inositol trisphosphate 6-kinase activity			ovary(1)	1						atcagtgaacaaaaaaaaaaa	0.090													10	5	---	---	---	---	
MYPN	84665	broad.mit.edu	37	10	69925215	69925216	+	Intron	INS	-	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69925215_69925216insA	uc001jnm.3	+						MYPN_uc001jnl.1_Intron|MYPN_uc001jnn.3_Intron|MYPN_uc001jno.3_Intron|MYPN_uc009xps.2_Intron|MYPN_uc009xpt.2_Intron|MYPN_uc010qit.1_Intron|MYPN_uc010qiu.1_Intron	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin							nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5						cctaaaaaaacaaaaaaaTCCC	0.178													4	2	---	---	---	---	
LRRC20	55222	broad.mit.edu	37	10	72127340	72127340	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72127340delA	uc001jqx.1	-						LRRC20_uc001jqy.1_Intron|LRRC20_uc001jqz.1_Intron	NM_207119	NP_997002	Q8TCA0	LRC20_HUMAN	leucine rich repeat containing 20 isoform 1												0						tgctaaagtgaaagaagccag	0.000													4	2	---	---	---	---	
NODAL	4838	broad.mit.edu	37	10	72192384	72192384	+	3'UTR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72192384delA	uc001jrc.2	-	3						NM_018055	NP_060525	Q96S42	NODAL_HUMAN	nodal precursor						growth	extracellular space	cytokine activity|growth factor activity			large_intestine(1)|kidney(1)	2						acagGTTTTTAAAAAATCCAG	0.239													4	2	---	---	---	---	
ADAMTS14	140766	broad.mit.edu	37	10	72477154	72477154	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72477154delG	uc001jrh.2	+						ADAMTS14_uc001jrg.2_Intron	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6						GCAAGGTTGTGGGGGTAGGGT	0.622													4	2	---	---	---	---	
SFTPA2	729238	broad.mit.edu	37	10	81316166	81316166	+	3'UTR	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81316166delG	uc001kal.3	-	6					SFTPA2_uc001kan.3_3'UTR	NM_006926	NP_008857	Q8IWL1	SFPA2_HUMAN	RecName: Full=Pulmonary surfactant-associated protein A2;          Short=SP-A2;          Short=SP-A;          Short=PSP-A;          Short=PSPA; AltName: Full=Alveolar proteinosis protein; AltName: Full=35 kDa pulmonary surfactant-associated protein; Flags: Precursor;						cell junction assembly|respiratory gaseous exchange	collagen|extracellular space	sugar binding				0	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			CCGGTGGCATGGGGGGTGGTG	0.507									Pulmonary_Fibrosis_Idiopathic				4	2	---	---	---	---	
TNKS2	80351	broad.mit.edu	37	10	93600113	93600113	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93600113delA	uc001khp.2	+							NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related						positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)				ataataagacaaaaaaaaaGG	0.174													3	4	---	---	---	---	
PLCE1	51196	broad.mit.edu	37	10	95972939	95972939	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95972939delA	uc001kjk.2	+						PLCE1_uc010qnx.1_Intron|PLCE1_uc001kjm.2_Intron	NM_016341	NP_057425	Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1 isoform 1						activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)				GGTGGGACACATCCAGCATTT	0.428													4	2	---	---	---	---	
SORBS1	10580	broad.mit.edu	37	10	97290030	97290030	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97290030delT	uc001kkw.2	-						SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron|SORBS1_uc001kkx.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		caggtgttccttcctacctct	0.000													4	2	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100754024	100754025	+	Intron	DEL	CC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100754024_100754025delCC	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)		ctgtaatctgcccaggtctcag	0.000													4	2	---	---	---	---	
FGF8	2253	broad.mit.edu	37	10	103529922	103529922	+	3'UTR	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103529922delC	uc001ktp.1	-	6					FGF8_uc001ktq.1_3'UTR|FGF8_uc001ktr.1_3'UTR|FGF8_uc001kts.1_3'UTR|FGF8_uc009xwr.1_3'UTR	NM_033164	NP_149354	P55075	FGF8_HUMAN	fibroblast growth factor 8 isoform E precursor						bone development|dopaminergic neuron differentiation|fibroblast growth factor receptor signaling pathway|gastrulation|gonad development|insulin receptor signaling pathway|mesonephros development|metanephros development|negative regulation of cardiac muscle tissue development|neuroepithelial cell differentiation|odontogenesis|positive regulation of cell division|positive regulation of cell proliferation	extracellular region|extracellular space	growth factor activity|growth factor activity|type 1 fibroblast growth factor receptor binding|type 2 fibroblast growth factor receptor binding				0		Colorectal(252;0.122)		Epithelial(162;3.94e-09)|all cancers(201;2.13e-07)		aaaaaaaaaaCAGCAAAAACC	0.433													4	3	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	106448223	106448224	+	Intron	INS	-	C	C	rs140883818	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106448223_106448224insC	uc001kyi.1	+							NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CTGCCAGCCAGCGTGGGCAGAG	0.599													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	123099345	123099345	+	IGR	DEL	C	-	-	rs142623233	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123099345delC								WDR11 (430310 upstream) : FGFR2 (138500 downstream)																							CAAGTAGGATCCCCCCATCCC	0.398													4	2	---	---	---	---	
BTBD16	118663	broad.mit.edu	37	10	124054641	124054641	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124054641delG	uc001lgc.1	+						BTBD16_uc001lgd.1_Intron	NM_144587	NP_653188	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16											skin(1)	1		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				GGATTTGTATGGGGAGCGCTG	0.542													4	2	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126829930	126829930	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126829930delG	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		GGTTGAAAGTGGAGCCCAGGA	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132343325	132343326	+	IGR	INS	-	T	T	rs146946464	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132343325_132343326insT								GLRX3 (360541 upstream) : TCERG1L (547330 downstream)																							GCCCGTGGTGGTGGAGGGAGTG	0.604													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133913388	133913389	+	IGR	INS	-	T	T	rs150100407	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133913388_133913389insT								BNIP3 (117953 upstream) : JAKMIP3 (4924 downstream)																							GCTCACCCTGGTGATGGTGGTC	0.634													5	6	---	---	---	---	
DPYSL4	10570	broad.mit.edu	37	10	134012500	134012501	+	Intron	DEL	TG	-	-	rs148943316	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134012500_134012501delTG	uc009ybb.2	+							NM_006426	NP_006417	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4						axon guidance|pyrimidine base catabolic process	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			central_nervous_system(2)	2		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		CCGCCTCTGATGCCGAGGGGCC	0.688													6	3	---	---	---	---	
DPYSL4	10570	broad.mit.edu	37	10	134012503	134012508	+	Intron	DEL	CGAGGG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134012503_134012508delCGAGGG	uc009ybb.2	+							NM_006426	NP_006417	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4						axon guidance|pyrimidine base catabolic process	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			central_nervous_system(2)	2		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		CCTCTGATGCCGAGGGGCCATGGTCT	0.689													6	3	---	---	---	---	
DCHS1	8642	broad.mit.edu	37	11	6674444	6674445	+	Intron	INS	-	CA	CA			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6674444_6674445insCA	uc001mem.1	-							NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor						calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		gctttatccctcacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44650510	44650510	+	IGR	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44650510delG								CD82 (9197 upstream) : TSPAN18 (231369 downstream)																							GCTGACCCCTGGGGTCTCCTA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	47902673	47902673	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47902673delA								NUP160 (32616 upstream) : PTPRJ (99437 downstream)																							agaaggaaagaaaaaaaaaag	0.323													12	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49867863	49867863	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49867863delT								LOC440040 (35896 upstream) : OR4C13 (106112 downstream)																							AGGAATAAACTTTTTTTTTTT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56279563	56279563	+	IGR	DEL	T	-	-	rs11301459		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56279563delT								OR5M8 (20717 upstream) : OR5M11 (30254 downstream)																							TAAATACTCATTTTTTCTTGT	0.284													2	4	---	---	---	---	
P2RY6	5031	broad.mit.edu	37	11	72991563	72991563	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72991563delA	uc001otm.2	+						P2RY6_uc001otn.2_Intron|P2RY6_uc001oto.2_Intron|P2RY6_uc001otp.2_Intron|P2RY6_uc001otq.2_Intron|P2RY6_uc001otr.2_Intron|P2RY6_uc001ots.2_Intron	NM_176796	NP_789766	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y6						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1						CCTCCTCACCAAGCCTTCTCT	0.527													4	2	---	---	---	---	
DGAT2	84649	broad.mit.edu	37	11	75482211	75482211	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75482211delA	uc001oxa.2	+						DGAT2_uc001oxb.2_Intron|uc001owz.2_5'Flank	NM_032564	NP_115953	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2						glycerol metabolic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	diacylglycerol O-acyltransferase activity				0	Ovarian(111;0.103)					TTTCTTGGCCAAAAAAAAAGG	0.318													6	3	---	---	---	---	
CUL5	8065	broad.mit.edu	37	11	107917405	107917406	+	Intron	INS	-	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107917405_107917406insT	uc001pjv.2	+						CUL5_uc001pju.2_Intron	NM_003478	NP_003469	Q93034	CUL5_HUMAN	Vasopressin-activated calcium-mobilizing						cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		CCACACAGATCTTTTTTTTTCT	0.317													6	3	---	---	---	---	
ATM	472	broad.mit.edu	37	11	108191805	108191805	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108191805delG	uc001pkb.1	+						ATM_uc009yxr.1_Intron|C11orf65_uc010rvx.1_Intron|ATM_uc001pke.1_Intron|ATM_uc001pkg.1_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		gtggcaaggtgggagaaactc	0.030			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116574615	116574616	+	IGR	DEL	TG	-	-	rs145701444		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116574615_116574616delTG								None (None upstream) : BUD13 (44272 downstream)																							GCTTCACATCTGTGGACCCATT	0.312													3	3	---	---	---	---	
TRIM29	23650	broad.mit.edu	37	11	120002035	120002035	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120002035delG	uc001pwz.2	-						TRIM29_uc010rzi.1_5'Flank|TRIM29_uc010rzj.1_5'Flank|TRIM29_uc001pxa.2_Intron	NM_012101	NP_036233	Q14134	TRI29_HUMAN	tripartite motif protein TRIM29						transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)|kidney(1)|skin(1)	4		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		GCCAAGGGCAGGGAGAGGCCA	0.532													4	2	---	---	---	---	
SORL1	6653	broad.mit.edu	37	11	121348583	121348583	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121348583delA	uc001pxx.2	+							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)		ctaaaaatacaaaaaaaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	123721565	123721566	+	IGR	DEL	GG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123721565_123721566delGG								OR6M1 (44508 upstream) : TMEM225 (32069 downstream)																							ctttatttttggaaggttttag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133527813	133527814	+	IGR	DEL	TG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133527813_133527814delTG								OPCML (125410 upstream) : SPATA19 (182703 downstream)																							CACGACACACTGTGAATAAGGA	0.411													5	3	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2609935	2609935	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2609935delA	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	GGAGTAGGTCAGTACCATGGG	0.582													4	2	---	---	---	---	
HTR7P1	93164	broad.mit.edu	37	12	13157843	13157843	+	Intron	DEL	A	-	-	rs35516160		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13157843delA	uc001rbh.2	+											Homo sapiens cDNA FLJ43688 fis, clone TBAES2003492.												0						cagcgtccataatgctttgta	0.169													9	4	---	---	---	---	
DDX11	1663	broad.mit.edu	37	12	31245503	31245503	+	Intron	DEL	T	-	-	rs35144288		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31245503delT	uc001rjt.1	+						DDX11_uc010sjx.1_Intron|DDX11_uc001rjr.1_Intron|DDX11_uc001rjs.1_Intron|DDX11_uc001rju.1_Intron|DDX11_uc001rjv.1_Intron|DDX11_uc001rjw.1_Intron|DDX11_uc001rjx.1_Intron|DDX11_uc009zjn.1_Intron	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CGGTGGAAACTTAGCAGGGAG	0.493										Multiple Myeloma(12;0.14)			5	3	---	---	---	---	
FGD4	121512	broad.mit.edu	37	12	32667978	32667978	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32667978delC	uc001rkz.2	+						FGD4_uc001rlc.2_Intron|FGD4_uc001rky.2_Intron|FGD4_uc001rla.2_Intron|FGD4_uc001rkx.3_Intron	NM_139241	NP_640334	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					CACCTTATATCCCCAGCTTTT	0.229													6	3	---	---	---	---	
KRT5	3852	broad.mit.edu	37	12	52913296	52913297	+	Intron	DEL	TT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52913296_52913297delTT	uc001san.2	-						KRT5_uc009zmh.2_Intron	NM_000424	NP_000415	P13647	K2C5_HUMAN	keratin 5						epidermis development|hemidesmosome assembly	cytosol|keratin filament	protein binding|structural constituent of cytoskeleton				0				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCAACAGTTGTTAAGAGGCCCT	0.475													4	2	---	---	---	---	
SOAT2	8435	broad.mit.edu	37	12	53496882	53496883	+	5'Flank	DEL	AT	-	-	rs9658624		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53496882_53496883delAT	uc001sbv.2	+						SOAT2_uc009zms.2_5'Flank	NM_003578	NP_003569	O75908	SOAT2_HUMAN	acyl-CoA:cholesterol acyltransferase 2						cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|macrophage derived foam cell differentiation|very-low-density lipoprotein particle assembly	brush border|endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			ovary(1)	1						ATATTACCACATGTGTCAATCA	0.361													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	58721165	58721166	+	IGR	DEL	AC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58721165_58721166delAC								XRCC6BP1 (370114 upstream) : LRIG3 (544772 downstream)																							ccactttgttaccttctagtca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	70383058	70383059	+	IGR	DEL	GT	-	-	rs12425508	byFrequency	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70383058_70383059delGT								RAB3IP (166076 upstream) : CNOT2 (253718 downstream)																							CTGTCTCCTCgtgtgtgtgtgt	0.371													3	3	---	---	---	---	
C12orf50	160419	broad.mit.edu	37	12	88388162	88388163	+	Intron	DEL	CA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88388162_88388163delCA	uc001tam.1	-						C12orf50_uc001tan.2_Intron	NM_152589	NP_689802	Q8NA57	CL050_HUMAN	hypothetical protein LOC160419											skin(2)|ovary(1)	3						cacatacatgcacacacacaca	0.267													6	3	---	---	---	---	
UBE2N	7334	broad.mit.edu	37	12	93825655	93825655	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93825655delA	uc001tcp.2	-							NM_003348	NP_003339	P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N						DNA double-strand break processing|double-strand break repair via homologous recombination|histone ubiquitination|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of DNA repair|positive regulation of histone modification|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity|postreplication repair|protein K63-linked ubiquitination|proteolysis|regulation of histone ubiquitination|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus|UBC13-MMS2 complex|UBC13-UEV1A complex|ubiquitin ligase complex	ATP binding|ubiquitin binding|ubiquitin-protein ligase activity				0						CCCATGTGCCAAAAACTCACT	0.368								Direct_reversal_of_damage|Rad6_pathway					4	2	---	---	---	---	
SART3	9733	broad.mit.edu	37	12	108917794	108917795	+	Intron	INS	-	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108917794_108917795insA	uc001tmz.1	-						SART3_uc001tmy.1_Intron|SART3_uc009zux.1_Intron|SART3_uc010swx.1_Intron	NM_014706	NP_055521	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T						RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1						TGAGATTTCTTTGTAAACACAC	0.436									Porokeratosis				4	2	---	---	---	---	
ARPC3	10094	broad.mit.edu	37	12	110887810	110887811	+	Intron	INS	-	GA	GA	rs144703567	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110887810_110887811insGA	uc001tqq.2	-							NM_005719	NP_005710	O15145	ARPC3_HUMAN	actin related protein 2/3 complex subunit 3						cellular component movement|regulation of actin filament polymerization	Arp2/3 protein complex|cytoplasm	actin binding|structural constituent of cytoskeleton			ovary(1)	1						AGGAGTAGACGGAGAGAGAAAA	0.609											OREG0022114	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114674278	114674278	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114674278delT								RBM19 (270102 upstream) : TBX5 (117458 downstream)																							CAGAGTCACCTAGGAGGCAGG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116021603	116021604	+	IGR	DEL	TT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116021603_116021604delTT								TBX3 (899634 upstream) : MED13L (374779 downstream)																							CTGCATCCTGTTTAAGCCCAGC	0.559													4	2	---	---	---	---	
DNAH10	196385	broad.mit.edu	37	12	124311679	124311679	+	Intron	DEL	G	-	-	rs67584543		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124311679delG	uc001uft.3	+							NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GGTGCAAAGTGGGCGTTTGCA	0.289													6	4	---	---	---	---	
TMEM132B	114795	broad.mit.edu	37	12	126000516	126000519	+	Intron	DEL	ACAC	-	-	rs150732736		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126000516_126000519delACAC	uc001uhe.1	+							NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		TCTTGTGCCGacacacacacatgc	0.113													5	3	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129997967	129997967	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129997967delT	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		tggggaccaattttTTTTTAA	0.090													4	2	---	---	---	---	
CRYL1	51084	broad.mit.edu	37	13	21050283	21050284	+	Intron	DEL	CA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21050283_21050284delCA	uc001une.2	-						CRYL1_uc001unf.2_Intron|CRYL1_uc001ung.2_Intron	NM_015974	NP_057058	Q9Y2S2	CRYL1_HUMAN	lambda-crystallin						fatty acid metabolic process	cytosol	3-hydroxyacyl-CoA dehydrogenase activity|L-gulonate 3-dehydrogenase activity|NAD+ binding|protein homodimerization activity				0		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)		GGTGTCTTCCCACACACAAATG	0.406													4	2	---	---	---	---	
FOXO1	2308	broad.mit.edu	37	13	41168369	41168370	+	Intron	DEL	GA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41168369_41168370delGA	uc001uxl.3	-						FOXO1_uc010acc.1_Intron	NM_002015	NP_002006	Q12778	FOXO1_HUMAN	forkhead box O1						anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|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		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|lung(1)|central_nervous_system(1)	948		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		AGACCCACCTGATCACTTCTAT	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	45333261	45333261	+	IGR	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45333261delC								TSC22D1 (182560 upstream) : NUFIP1 (180123 downstream)																							TATTCACTGGCCAACTGTGAC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	50482015	50482015	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50482015delT								LOC220429 (14499 upstream) : C13orf1 (4827 downstream)																							ttttttttggttttttttttt	0.000													7	4	---	---	---	---	
DIAPH3	81624	broad.mit.edu	37	13	60734890	60734891	+	Intron	DEL	TT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60734890_60734891delTT	uc001vht.2	-						DIAPH3_uc001vhw.1_Intron|DIAPH3_uc010aed.1_Intron|DIAPH3_uc010aee.1_Intron	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		TGCTCACGGCTTAAGATATTTT	0.426													4	2	---	---	---	---	
DNAJC3	5611	broad.mit.edu	37	13	96423721	96423721	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96423721delG	uc001vmq.2	+						DNAJC3_uc001vmr.2_Intron	NM_006260	NP_006251	Q13217	DNJC3_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 3						protein folding|response to unfolded protein|response to virus		heat shock protein binding|protein kinase inhibitor activity|unfolded protein binding				0	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.126)			gagcagagttgggggtcagtg	0.000													4	2	---	---	---	---	
CLYBL	171425	broad.mit.edu	37	13	100273093	100273096	+	Intron	DEL	AAAG	-	-	rs67220471		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100273093_100273096delAAAG	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron	NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					aaagaaagaaaaagaaagaaagaa	0.167													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19437610	19437610	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19437610delT								OR11H12 (59038 upstream) : POTEG (115755 downstream)																							TGTCATTTCAttttttttttt	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	32732856	32732857	+	IGR	DEL	TG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32732856_32732857delTG								ARHGAP5 (103924 upstream) : AKAP6 (65622 downstream)																							cctcaggtgatggagctgcaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	40184997	40184998	+	IGR	DEL	CC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40184997_40184998delCC								FBXO33 (283293 upstream) : None (None downstream)																							acccccacctccatccctctta	0.119													4	2	---	---	---	---	
MNAT1	4331	broad.mit.edu	37	14	61246525	61246525	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61246525delA	uc001xfd.2	+						MNAT1_uc010apq.1_Intron|MNAT1_uc001xfe.2_Intron	NM_002431	NP_002422	P51948	MAT1_HUMAN	menage a trois 1 (CAK assembly factor)						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|protein complex assembly|protein phosphorylation|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	cytoplasm|holo TFIIH complex	protein N-terminus binding|zinc ion binding			ovary(1)|lung(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.0174)		agaaaaaaagaaaaaaaaaag	0.204								Direct_reversal_of_damage|NER					4	2	---	---	---	---	
SIPA1L1	26037	broad.mit.edu	37	14	72200108	72200108	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72200108delA	uc001xms.2	+						SIPA1L1_uc001xmt.2_Intron|SIPA1L1_uc001xmu.2_Intron|SIPA1L1_uc001xmv.2_Intron|SIPA1L1_uc010ttm.1_Intron|SIPA1L1_uc001xmw.2_Intron	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like						actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CAGCTCTCACAAAAGCAGACT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	74674088	74674088	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74674088delA								LIN52 (6971 upstream) : VSX2 (32087 downstream)																							TGGTGAATGGAAGGCAATAGG	0.303													4	2	---	---	---	---	
VIPAR	63894	broad.mit.edu	37	14	77907716	77907716	+	Intron	DEL	T	-	-	rs34716621		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77907716delT	uc001xtt.1	-						VIPAR_uc001xtu.1_Intron|VIPAR_uc010tvj.1_Intron|VIPAR_uc001xtv.1_Intron	NM_022067	NP_071350	Q9H9C1	VIPAR_HUMAN	hypothetical protein LOC63894						endosome to lysosome transport|intracellular protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	early endosome|late endosome|recycling endosome	protein binding			central_nervous_system(1)	1						TTGGTTGTTGTTTTTTTTTTT	0.358													3	3	---	---	---	---	
SERPINA5	5104	broad.mit.edu	37	14	95058714	95058716	+	3'UTR	DEL	ATG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95058714_95058716delATG	uc001ydm.2	+	6					SERPINA3_uc001ydo.3_Intron	NM_000624	NP_000615	P05154	IPSP_HUMAN	serine (or cysteine) proteinase inhibitor, clade						fusion of sperm to egg plasma membrane|regulation of proteolysis|spermatogenesis	extracellular region|membrane|protein complex	acrosin binding|heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(2)	2				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	ATATTACTCTATGATGATTGCTT	0.335													4	2	---	---	---	---	
AK7	122481	broad.mit.edu	37	14	96908702	96908702	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96908702delT	uc001yfn.2	+							NM_152327	NP_689540	Q96M32	KAD7_HUMAN	adenylate kinase 7						cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		TGTGAAAACATTTCTTCTCTA	0.368													4	2	---	---	---	---	
GOLGA9P	283796	broad.mit.edu	37	15	23258265	23258268	+	Intron	DEL	TCTC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23258265_23258268delTCTC	uc001yvh.1	+						uc001yvi.2_5'Flank	NR_024074				RecName: Full=Putative golgin subfamily A member 6-like protein 11;												0						TAATGATTGTTCTCTCTACCTCTC	0.603													12	16	---	---	---	---	
CHRFAM7A	89832	broad.mit.edu	37	15	30663737	30663737	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30663737delG	uc001zdt.1	-						DKFZP434L187_uc001zds.2_Intron|CHRFAM7A_uc001zdu.1_Intron|CHRFAM7A_uc010azn.2_Intron	NM_139320	NP_647536	Q494W8	CRFM7_HUMAN	CHRNA7-FAM7A fusion isoform 1							integral to membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity			skin(1)	1		all_lung(180;3.42e-11)|Breast(32;0.000153)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		tatgcagtcaggagacctgat	0.065													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	34665583	34665583	+	IGR	DEL	A	-	-	rs28460021		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34665583delA								LPCAT4 (6188 upstream) : GOLGA8A (5689 downstream)																							AAAAAAAACCAAAAAAAAAAG	0.363													5	3	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40943489	40943490	+	Intron	DEL	TA	-	-	rs149133455		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40943489_40943490delTA	uc010bbs.1	+						CASC5_uc010bbt.1_Intron	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GATTAATGCttatataaaaaaa	0.327													4	3	---	---	---	---	
PLA2G4D	283748	broad.mit.edu	37	15	42388587	42388587	+	5'Flank	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42388587delA	uc001zox.2	-							NM_178034	NP_828848	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD						phospholipid catabolic process	cytoplasmic vesicle membrane|cytosol	metal ion binding|phospholipase A2 activity			large_intestine(1)|skin(1)	2		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		gtttccagagaaggggtctaG	0.209													4	2	---	---	---	---	
GANC	2595	broad.mit.edu	37	15	42630351	42630351	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42630351delA	uc001zpi.2	+							NM_198141	NP_937784	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C						carbohydrate metabolic process		carbohydrate binding|maltose alpha-glucosidase activity			central_nervous_system(2)	2		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)		AATTATACTTAAAAAAAAGTG	0.219													4	2	---	---	---	---	
FAM63B	54629	broad.mit.edu	37	15	59123743	59123745	+	Intron	DEL	TTA	-	-	rs111318557		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59123743_59123745delTTA	uc002afj.2	+						FAM63B_uc002afi.2_Intron|FAM63B_uc002afk.2_Intron|FAM63B_uc002afl.2_Intron	NM_001040450	NP_001035540	Q8NBR6	FA63B_HUMAN	hypothetical protein LOC54629 isoform a											central_nervous_system(1)	1						atGCATTTGTTTATAAAAAAGAA	0.167													3	5	---	---	---	---	
ADAMTS7	11173	broad.mit.edu	37	15	79106108	79106108	+	5'Flank	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79106108delC	uc002bej.3	-						ADAMTS7_uc010und.1_5'Flank|ADAMTS7_uc002bek.1_5'Flank	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0						GAGATACCCTCCCTGTTCACA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84059112	84059113	+	IGR	INS	-	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84059112_84059113insA								BNC1 (105644 upstream) : SH3GL3 (56978 downstream)																							TCTTCTTGAAGAAAAAAAAAAA	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98698207	98698209	+	IGR	DEL	AAT	-	-	rs142815805		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98698207_98698209delAAT								ARRDC4 (181140 upstream) : FAM169B (282182 downstream)																							gctgtagcacaatgaggagggag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	3239097	3239097	+	IGR	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3239097delG								ZNF213 (46293 upstream) : OR1F1 (15150 downstream)																							CTCGCTTTCTGGGTTTTGGCT	0.627													4	2	---	---	---	---	
ADCY9	115	broad.mit.edu	37	16	4039359	4039360	+	Intron	INS	-	AT	AT	rs139672390	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4039359_4039360insAT	uc002cvx.2	-							NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9						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 plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6						TAGCACACATCATCAGAACCTT	0.223													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	6038699	6038699	+	IGR	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6038699delC								FAM86A (890910 upstream) : A2BP1 (30433 downstream)																							GGGGTTGCATCCCAGGAAGTG	0.483													4	2	---	---	---	---	
SYT17	51760	broad.mit.edu	37	16	19217998	19217998	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19217998delG	uc002dfw.2	+						SYT17_uc002dfx.2_Intron|SYT17_uc002dfy.2_Intron|SYT17_uc002dfv.1_Intron	NM_016524	NP_057608	Q9BSW7	SYT17_HUMAN	B/K protein							membrane|synaptic vesicle	transporter activity			ovary(1)	1						cagcaatcctggtactccttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21534215	21534215	+	Intron	DEL	A	-	-	rs113430297		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21534215delA	uc002diq.3	+						LOC100271836_uc002dja.2_5'Flank|LOC100271836_uc002djb.2_5'Flank|SLC7A5P2_uc002djd.2_5'Flank					Homo sapiens cDNA FLJ59829 complete cds.																		ACTGGTCTTGAAAAAAAAAAA	0.169													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21554218	21554218	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21554218delG	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																		GGGCCACACTGGGGCTGGGCC	0.637													4	2	---	---	---	---	
VWA3A	146177	broad.mit.edu	37	16	22163632	22163632	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22163632delC	uc010vbq.1	+						VWA3A_uc010bxd.2_Intron|VWA3A_uc002dkg.3_Intron|VWA3A_uc010bxe.1_Intron	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		TTCCCTCAAGCAGCAGCAGTT	0.532													6	4	---	---	---	---	
HS3ST4	9951	broad.mit.edu	37	16	25722908	25722908	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25722908delT	uc002dof.2	+							NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)		ATGGTGAAGATTTTTTTTTAG	0.443													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28519632	28519633	+	Intron	DEL	GA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28519632_28519633delGA	uc010vct.1	-						IL27_uc002dqc.2_5'Flank					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		TCACCCCCTTGACCACATGGGG	0.614													4	2	---	---	---	---	
PHKB	5257	broad.mit.edu	37	16	47545360	47545361	+	Intron	INS	-	T	T			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47545360_47545361insT	uc002eev.3	+						PHKB_uc010vgi.1_Intron|PHKB_uc002eeu.3_Intron	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				AGTTGCTGTGCATGTGAAATAT	0.317													6	3	---	---	---	---	
NKD1	85407	broad.mit.edu	37	16	50668529	50668530	+	3'UTR	DEL	CA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50668529_50668530delCA	uc002egg.1	+	10						NM_033119	NP_149110	Q969G9	NKD1_HUMAN	naked cuticle homolog 1						Wnt receptor signaling pathway	cytoplasm|plasma membrane	calcium ion binding|protein binding				0		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		GAGGATGTGGCACATATATACG	0.411													4	2	---	---	---	---	
NLRC5	84166	broad.mit.edu	37	16	57075141	57075142	+	Intron	DEL	CT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57075141_57075142delCT	uc002ekk.1	+						NLRC5_uc010ccq.1_Intron|NLRC5_uc002ekn.2_Intron|NLRC5_uc002ekl.2_Intron|NLRC5_uc002ekm.2_Intron|NLRC5_uc010ccr.1_Intron|NLRC5_uc010ccs.1_Intron|NLRC5_uc002eko.1_Intron|NLRC5_uc002ekp.1_5'Flank|NLRC5_uc002ekq.1_5'Flank	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27						defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)				CTCTGATCTGCTCTCTCTCTCT	0.376													5	4	---	---	---	---	
GPR56	9289	broad.mit.edu	37	16	57661644	57661646	+	Intron	DEL	GGA	-	-	rs35408856		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57661644_57661646delGGA	uc002emb.2	+						GPR56_uc002elz.1_Intron|GPR56_uc002ema.1_Intron|GPR56_uc002emc.2_Intron|GPR56_uc002emf.2_5'Flank|GPR56_uc010vhs.1_5'Flank|GPR56_uc002emd.2_5'Flank|GPR56_uc002eme.2_5'Flank|GPR56_uc010vht.1_5'Flank	NM_005682	NP_005673	Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56 isoform a						brain development|cell adhesion|cell-cell signaling|neuropeptide signaling pathway	integral to plasma membrane	G-protein coupled receptor activity				0						CTCATTGCTCGGAGGAGGAGGGC	0.542													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58926717	58926719	+	IGR	DEL	CCA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58926717_58926719delCCA								GOT2 (158471 upstream) : None (None downstream)																							CACACAGCTGccaccaccaccac	0.153													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	72677123	72677123	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72677123delT								PMFBP1 (470774 upstream) : ZFHX3 (139665 downstream)																							ctgctacatcttttttttccc	0.085													4	2	---	---	---	---	
SERPINF1	5176	broad.mit.edu	37	17	1674116	1674116	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1674116delC	uc002ftl.2	+						SERPINF1_uc010cjw.2_Intron	NM_002615	NP_002606	P36955	PEDF_HUMAN	serine (or cysteine) proteinase inhibitor, clade						cell proliferation|negative regulation of angiogenesis|positive regulation of neurogenesis|regulation of proteolysis	extracellular space|melanosome	serine-type endopeptidase inhibitor activity			ovary(1)	1						CTCCCTCACTCCCACCTTCCA	0.378													4	2	---	---	---	---	
MIR1253	100302208	broad.mit.edu	37	17	2652374	2652374	+	5'Flank	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2652374delG	hsa-mir-1253|MI0006387	-																							0						GGCAGGGGTTGGGGGGGGGAT	0.612													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	7203505	7203505	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7203505delT								YBX2 (5629 upstream) : EIF5A (6813 downstream)																							CTGtcttctctttttttttgt	0.239													4	2	---	---	---	---	
CHD3	1107	broad.mit.edu	37	17	7805739	7805739	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7805739delA	uc002gje.2	+						CHD3_uc002gjd.2_Intron|CHD3_uc002gjf.2_Intron|CHD3_uc002gjh.2_5'Flank	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)				actccatctcaaaaaaaaata	0.154													4	2	---	---	---	---	
TOM1L2	146691	broad.mit.edu	37	17	17831470	17831471	+	Intron	INS	-	A	A	rs148502512	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17831470_17831471insA	uc002grz.3	-						TOM1L2_uc002gry.3_Intron|TOM1L2_uc010vwy.1_Intron|TOM1L2_uc010cpr.2_Intron|TOM1L2_uc010vwz.1_Intron|TOM1L2_uc010vxa.1_Intron|TOM1L2_uc010vxb.1_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)					ttttctgtaacaacaaaaaaaa	0.203													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	17979571	17979571	+	IGR	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17979571delG								C17orf39 (7853 upstream) : DRG2 (11712 downstream)																							GCATGCTCCTGGACCCCATGC	0.303													4	2	---	---	---	---	
PRPSAP2	5636	broad.mit.edu	37	17	18812312	18812312	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18812312delA	uc002gup.1	+						PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_Intron	NM_002767	NP_002758	O60256	KPRB_HUMAN	phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1						TTCAACATTCaaaaaaaaaga	0.144													4	2	---	---	---	---	
ALDH3A1	218	broad.mit.edu	37	17	19643966	19643966	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19643966delT	uc010cqu.2	-						ALDH3A1_uc010vzd.1_Intron|ALDH3A1_uc002gwj.2_Intron|ALDH3A1_uc010cqv.2_Intron|ALDH3A1_uc002gwk.2_Intron|ALDH3A1_uc002gwl.1_Intron	NM_001135168	NP_001128640	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3A1						cellular aldehyde metabolic process	cytosol|endoplasmic reticulum	alcohol dehydrogenase (NADP+) activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(1)|pancreas(1)	2	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)	NADH(DB00157)	gtgcattatcttttttttttc	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21329284	21329284	+	IGR	DEL	C	-	-	rs67728666		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21329284delC								KCNJ12 (6105 upstream) : C17orf51 (102288 downstream)																							GGAGAGGGCACGGGGGTGGAA	0.358													6	3	---	---	---	---	
KIAA0100	9703	broad.mit.edu	37	17	26946300	26946300	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26946300delA	uc002hbu.2	-						KIAA0100_uc002hbt.2_Intron	NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor							extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)					CAGGTTCATTAAAAAAAAAAA	0.249													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31621437	31621438	+	Intron	DEL	TG	-	-	rs12949900		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31621437_31621438delTG	uc002hhu.2	-						ACCN1_uc002hht.2_5'Flank	NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	CCAGATCTGTTGAATGAGCTGT	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	34970564	34970564	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34970564delA								MRM1 (5158 upstream) : LHX1 (323935 downstream)																							TTTTGAAGCTAAAAAAAAATG	0.353													4	2	---	---	---	---	
KRT40	125115	broad.mit.edu	37	17	39141113	39141114	+	Intron	DEL	GT	-	-	rs5820385		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39141113_39141114delGT	uc010cxh.1	-						KRT40_uc002hvq.1_Intron	NM_182497	NP_872303	Q6A162	K1C40_HUMAN	type I hair keratin KA36							intermediate filament	structural molecule activity				0		Breast(137;0.00043)				TGGGTTTAAAGTGTGTGTGTGT	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39464104	39464104	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39464104delA								KRTAP9-9 (51489 upstream) : KRTAP17-1 (7067 downstream)																							AGTTGGCTGGAAGTGGATTTT	0.557													4	2	---	---	---	---	
ACLY	47	broad.mit.edu	37	17	40048933	40048933	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40048933delT	uc002hyg.2	-						ACLY_uc002hyh.2_Intron|ACLY_uc002hyi.2_Intron|ACLY_uc010wfx.1_Intron|ACLY_uc010wfy.1_Intron	NM_001096	NP_001087	P53396	ACLY_HUMAN	ATP citrate lyase isoform 1						ATP catabolic process|cellular carbohydrate metabolic process|citrate metabolic process|coenzyme A metabolic process|energy reserve metabolic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	citrate lyase complex|cytosol|nucleus	ATP binding|ATP citrate synthase activity|citrate (pro-3S)-lyase activity|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			ovary(2)|central_nervous_system(1)	3		Breast(137;0.000143)				AAGCCTTGCCttttttttttc	0.264													8	5	---	---	---	---	
EZH1	2145	broad.mit.edu	37	17	40866695	40866696	+	Intron	INS	-	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40866695_40866696insA	uc002iaz.2	-						EZH1_uc002iba.2_Intron|EZH1_uc010wgt.1_Intron|EZH1_uc010wgu.1_Intron|EZH1_uc010wgv.1_Intron|EZH1_uc010wgw.1_Intron|EZH1_uc010cyp.2_Intron|EZH1_uc010cyq.2_Intron|EZH1_uc010cys.2_Intron|EZH1_uc010cyo.1_Intron|EZH1_uc010cyr.1_Intron	NM_001991	NP_001982	Q92800	EZH1_HUMAN	enhancer of zeste homolog 1						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	chromatin binding|DNA binding			ovary(3)	3		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		taataaaaatgaaaaaaaaata	0.144													4	2	---	---	---	---	
HDAC5	10014	broad.mit.edu	37	17	42165217	42165217	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42165217delT	uc002ifd.1	-						HDAC5_uc002ife.1_Intron|HDAC5_uc002iff.1_Intron|HDAC5_uc010czp.1_Intron|HDAC5_uc002ifg.1_5'Flank|HDAC5_uc002ifh.2_Intron	NM_005474	NP_005465	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 1						B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	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			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		CTGAGAGGACttttttttttt	0.239													9	4	---	---	---	---	
C17orf57	124989	broad.mit.edu	37	17	45419565	45419565	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45419565delA	uc002iln.2	+						ITGB3_uc010wkr.1_Intron|C17orf57_uc002ilm.2_Intron|C17orf57_uc002ill.1_Intron|C17orf57_uc010daz.1_Intron	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989								calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3						TCTTCTCCTTAAAAAAAAAAT	0.269													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48017360	48017360	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48017360delA								TAC4 (91981 upstream) : DLX4 (29202 downstream)																							CCCTGGAGACAAAAAAAAAAA	0.463													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48483504	48483505	+	IGR	DEL	TG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48483504_48483505delTG								LRRC59 (8672 upstream) : ACSF2 (20014 downstream)																							TATGTAGTGCTGTGTGTGTGTG	0.302													4	2	---	---	---	---	
VEZF1	7716	broad.mit.edu	37	17	56058969	56058969	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56058969delT	uc002ivf.1	-						VEZF1_uc010dcn.1_Intron	NM_007146	NP_009077	Q14119	VEZF1_HUMAN	zinc finger protein 161						cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2						AGACTGTAACTTTTTTTTCCT	0.284													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	56130484	56130484	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56130484delA								SFRS1 (45777 upstream) : DYNLL2 (30296 downstream)																							tcccccactgaaaaaaaaaat	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	60255738	60255738	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60255738delA								MED13 (113095 upstream) : TBC1D3P2 (86331 downstream)																							agtacaacttaactccatgta	0.030													4	2	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71570526	71570526	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71570526delC	uc010dfm.2	-							NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						AACATCAGATCCAACCCTGAT	0.393													4	2	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77191686	77191686	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77191686delG	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			ATCTGAGACTGGGGCCTCCTT	0.542													4	2	---	---	---	---	
CCDC137	339230	broad.mit.edu	37	17	79639371	79639371	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79639371delA	uc002kbc.3	+						CCDC137_uc002kbd.2_Intron	NM_199287	NP_954981	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137											central_nervous_system(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			ctgtgtcaagaaaaaaaaaaa	0.269													6	3	---	---	---	---	
FOXK2	3607	broad.mit.edu	37	17	80544130	80544130	+	Intron	DEL	C	-	-	rs57940566	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80544130delC	uc002kfn.2	+						FOXK2_uc002kfm.1_Intron|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter 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 activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			gaaaggtgggccgggggggga	0.149													6	5	---	---	---	---	
LAMA1	284217	broad.mit.edu	37	18	7107647	7107647	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7107647delA	uc002knm.2	-						LAMA1_uc010wzj.1_Intron	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CAAGTGCATGAAAAAAAATTT	0.318													4	2	---	---	---	---	
C18orf45	85019	broad.mit.edu	37	18	20976829	20976829	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20976829delA	uc002kuf.2	-						C18orf45_uc010xaq.1_Intron|C18orf45_uc010xar.1_Intron|C18orf45_uc002kug.2_Intron|C18orf45_uc002kuh.2_Intron	NM_032933	NP_116322	Q24JQ0	CR045_HUMAN	hypothetical protein LOC85019							integral to membrane					0	all_cancers(21;0.000238)|all_epithelial(16;5.29e-06)|Lung NSC(20;0.00925)|Colorectal(14;0.0202)|all_lung(20;0.0255)|Ovarian(20;0.127)					aatgtcttgcaaaaaaaaaaa	0.020													6	5	---	---	---	---	
C18orf32	497661	broad.mit.edu	37	18	47017425	47017425	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47017425delA	uc002ldm.1	-						RPL17_uc002ldn.2_5'Flank|RPL17_uc002ldo.2_Intron|RPL17_uc002ldp.2_Intron|RPL17_uc002ldq.2_Intron|RPL17_uc010xdg.1_Intron|SNORD58C_uc002ldr.2_5'Flank	NM_001035006	NP_001030178	Q8TCD1	CR032_HUMAN	ribosomal protein L17						positive regulation of I-kappaB kinase/NF-kappaB cascade		signal transducer activity				0						CAAGGCAATTAAAAAAACTTG	0.299													4	2	---	---	---	---	
MYO5B	4645	broad.mit.edu	37	18	47651222	47651222	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47651222delC	uc002leb.2	-							NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		TCTTAATAAACTGCAGATAAC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	55497894	55497896	+	IGR	DEL	CTT	-	-	rs150875605		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55497894_55497896delCTT								ATP8B1 (98855 upstream) : NEDD4L (213723 downstream)																							caggtgtaaacttcttcctcagg	0.005													3	3	---	---	---	---	
MED16	10025	broad.mit.edu	37	19	873769	873770	+	Intron	INS	-	C	C	rs151113242	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:873769_873770insC	uc002lqd.1	-						MED16_uc010drw.1_Intron|MED16_uc002lqe.2_Intron|MED16_uc002lqf.2_Intron|MED16_uc010xfv.1_Intron|MED16_uc010xfw.1_Intron|MED16_uc010xfx.1_Intron|MED16_uc010xfy.1_Intron|MED16_uc010xfz.1_RNA	NM_005481	NP_005472	Q9Y2X0	MED16_HUMAN	mediator complex subunit 16						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCACTGCCTGCCCCCCCCCGG	0.698													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	2948070	2948071	+	IGR	DEL	TC	-	-	rs112140883		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2948070_2948071delTC								ZNF77 (3101 upstream) : TLE6 (29465 downstream)																							gcgcgcattttctgttttccta	0.000													1	5	---	---	---	---	
ARHGEF18	23370	broad.mit.edu	37	19	7518111	7518111	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7518111delT	uc002mgi.2	+						ARHGEF18_uc010xjm.1_Intron|ARHGEF18_uc002mgh.2_Intron|ARHGEF18_uc002mgj.1_Intron	NM_001130955	NP_001124427	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)				AAAAAAAACCTAAACTCTGAC	0.303													4	2	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17740702	17740731	+	Intron	DEL	CAACTCCAATCTCAATTTAAACCCTAACCC	-	-	rs62119956	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17740702_17740731delCAACTCCAATCTCAATTTAAACCCTAACCC	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						accccaatctcaactccaatctcaatttaaaccctaaccccaactccaac	0.000													5	3	---	---	---	---	
ZNF493	284443	broad.mit.edu	37	19	21589149	21589149	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21589149delT	uc002npx.2	+						ZNF493_uc002npu.2_Intron|ZNF493_uc002npw.2_Intron|ZNF493_uc002npy.2_Intron	NM_175910	NP_787106	Q6ZR52	ZN493_HUMAN	zinc finger protein 493 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						CATTTTTTTGTTTTTTTTTTG	0.343													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30582237	30582237	+	IGR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30582237delA								C19orf2 (75626 upstream) : ZNF536 (281091 downstream)																							AAGGCTCCCCAGTGGGAAGGA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36795972	36795973	+	IGR	DEL	TC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36795972_36795973delTC								ZNF146 (66299 upstream) : ZFP14 (31189 downstream)																							ctctctcacgtctctctctctc	0.109													3	3	---	---	---	---	
ACTN4	81	broad.mit.edu	37	19	39221071	39221071	+	3'UTR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39221071delT	uc002oja.1	+	21					ACTN4_uc002ojb.1_3'UTR|CAPN12_uc010egd.1_3'UTR|CAPN12_uc002ojc.1_3'UTR|CAPN12_uc002ojd.1_3'UTR	NM_004924	NP_004915	O43707	ACTN4_HUMAN	actinin, alpha 4						platelet activation|platelet degranulation|positive regulation of cellular component movement|positive regulation of sodium:hydrogen antiporter activity|protein transport|regulation of apoptosis	extracellular region|nucleolus|perinuclear region of cytoplasm|platelet alpha granule lumen|protein complex|pseudopodium|ribonucleoprotein complex	actin filament binding|calcium ion binding|integrin binding|nucleoside binding|protein homodimerization activity				0	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCCCCCTACCTTTTTTTTTTG	0.478													4	4	---	---	---	---	
APOC2	344	broad.mit.edu	37	19	45452269	45452270	+	Intron	INS	-	CCT	CCT	rs10622462		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45452269_45452270insCCT	uc002pah.2	+							NM_000483	NP_000474	P02655	APOC2_HUMAN	apolipoprotein C-II precursor						cholesterol efflux|chylomicron remnant clearance|high-density lipoprotein particle clearance|lipid catabolic process|lipoprotein metabolic process|negative regulation of cholesterol transport|negative regulation of lipid metabolic process|negative regulation of receptor-mediated endocytosis|negative regulation of very-low-density lipoprotein particle clearance|phospholipid efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of phospholipase activity|positive regulation of phospholipid catabolic process|positive regulation of triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	chylomicron|intermediate-density lipoprotein particle|low-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	lipase inhibitor activity|lipid binding|lipoprotein lipase activator activity|phospholipase activator activity|phospholipase binding|protein homodimerization activity			kidney(1)	1	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)		ggcccccagcccgtcctccctc	0.015													7	4	---	---	---	---	
GRLF1	2909	broad.mit.edu	37	19	47425708	47425708	+	Intron	DEL	A	-	-	rs16980767		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47425708delA	uc010ekv.2	+							NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1						axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		CTATTCTGGTAAAAAAAAAAC	0.388													11	5	---	---	---	---	
GLTSCR1	29998	broad.mit.edu	37	19	48141882	48141883	+	Intron	INS	-	CG	CG			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48141882_48141883insCG	uc002phh.3	+							NM_015711	NP_056526	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1								protein binding			pancreas(3)	3		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		acacacacacacacacacacac	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	50698921	50698922	+	IGR	DEL	AG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50698921_50698922delAG								C19orf41 (32383 upstream) : MYH14 (7963 downstream)																							CAGGGCAAGCAGAGAGAGGAAC	0.322													4	2	---	---	---	---	
ZNF83	55769	broad.mit.edu	37	19	53159176	53159177	+	Intron	DEL	AT	-	-	rs150719246		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53159176_53159177delAT	uc010epz.2	-						ZNF83_uc010eqb.1_Intron	NM_001105554	NP_001099024	P51522	ZNF83_HUMAN	zinc finger protein 83 isoform b							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		AATACAAAAAATATATGTctgg	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57487026	57487027	+	IGR	DEL	AA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57487026_57487027delAA								MIMT1 (127104 upstream) : USP29 (144482 downstream)																							cctcatttgtaaaaaaaaaaaa	0.163													4	2	---	---	---	---	
TRIM28	10155	broad.mit.edu	37	19	59061999	59062000	+	3'UTR	INS	-	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59061999_59062000insG	uc002qtg.1	+	17					TRIM28_uc010eut.1_3'UTR|TRIM28_uc002qth.1_3'UTR	NM_005762	NP_005753	Q13263	TIF1B_HUMAN	tripartite motif-containing 28 protein						epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		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;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		TGGTGGCCTGACTCCCACTCCC	0.594													7	4	---	---	---	---	
TRIM28	10155	broad.mit.edu	37	19	59062005	59062006	+	3'UTR	INS	-	GGAG	GGAG			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59062005_59062006insGGAG	uc002qtg.1	+	17					TRIM28_uc010eut.1_3'UTR|TRIM28_uc002qth.1_3'UTR	NM_005762	NP_005753	Q13263	TIF1B_HUMAN	tripartite motif-containing 28 protein						epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		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;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CCTGACTCCCACTCCCTGGTGG	0.594													7	4	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	16030706	16030706	+	3'UTR	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16030706delA	uc002wou.2	+	18					MACROD2_uc002wot.2_3'UTR|MACROD2_uc002woz.2_3'UTR|MACROD2_uc002wpb.2_3'UTR	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				gaaaaaaaagaaaaaaaaaGT	0.388													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19118230	19118231	+	IGR	INS	-	A	A			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19118230_19118231insA								C20orf79 (323197 upstream) : SLC24A3 (75059 downstream)																							AAAAATACATTAAAAAATTGTA	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	39435399	39435400	+	IGR	INS	-	T	T	rs150730467	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39435399_39435400insT								MAFB (117523 upstream) : TOP1 (222062 downstream)																							AAATGATTGGCTTTGGGGAGAA	0.431													8	4	---	---	---	---	
FAM65C	140876	broad.mit.edu	37	20	49203006	49203009	+	3'UTR	DEL	TTGA	-	-	rs16437		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49203006_49203009delTTGA	uc002xvm.2	-	22					FAM65C_uc010zyt.1_3'UTR	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876											ovary(2)	2						CGAAGCTGGGTTGATTGATTGCAT	0.505													2	4	---	---	---	---	
C20orf11	54994	broad.mit.edu	37	20	61575189	61575189	+	Intron	DEL	T	-	-	rs67614670		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61575189delT	uc002ydy.2	+							NM_017896	NP_060366	Q9NWU2	CT011_HUMAN	chromosome 20 open reading frame 11							nucleus	protein binding				0	Breast(26;5.68e-08)					CCTTCATGGCttttttttttt	0.284													3	3	---	---	---	---	
C21orf99	149992	broad.mit.edu	37	21	14425970	14425972	+	Intron	DEL	CTC	-	-	rs113465228		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14425970_14425972delCTC	uc002yja.3	+							NR_026916				Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						cacgctgttactcctccttacaa	0.000													11	7	---	---	---	---	
HUNK	30811	broad.mit.edu	37	21	33357768	33357768	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33357768delC	uc002yph.2	+							NM_014586	NP_055401	P57058	HUNK_HUMAN	hormonally upregulated Neu-associated kinase						multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity			stomach(1)|skin(1)	2						ACAGGGAGTGCCCAGCTGCAG	0.607													4	2	---	---	---	---	
PDE9A	5152	broad.mit.edu	37	21	44100372	44100372	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44100372delC	uc002zbm.2	+						PDE9A_uc002zbn.2_Intron|PDE9A_uc002zbo.2_Intron|PDE9A_uc002zbp.2_Intron|PDE9A_uc002zbq.2_Intron|PDE9A_uc002zbs.2_Intron|PDE9A_uc002zbr.2_Intron|PDE9A_uc002zbt.2_Intron|PDE9A_uc002zbu.2_Intron|PDE9A_uc002zbv.2_Intron|PDE9A_uc002zbw.2_Intron|PDE9A_uc002zbx.2_Intron|PDE9A_uc002zby.2_Intron|PDE9A_uc002zbz.2_Intron|PDE9A_uc002zca.2_Intron|PDE9A_uc002zcb.2_Intron|PDE9A_uc002zcc.2_Intron|PDE9A_uc002zcd.2_Intron|PDE9A_uc002zce.2_Intron|PDE9A_uc002zcf.2_Intron|PDE9A_uc002zcg.2_Intron	NM_002606	NP_002597	O76083	PDE9A_HUMAN	phosphodiesterase 9A isoform a						platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2						AGTAAAAGTTCCCCCAAAAGA	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16909977	16909981	+	IGR	DEL	CAAAA	-	-	rs111736616		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16909977_16909981delCAAAA								OR11H1 (460173 upstream) : CCT8L2 (161667 downstream)																							ATGGCTCTGTCAAAATAAACAAAAT	0.322													6	6	---	---	---	---	
TXNRD2	10587	broad.mit.edu	37	22	19903671	19903671	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19903671delG	uc011ahc.1	-						TXNRD2_uc002zql.1_Intron|TXNRD2_uc002zqm.1_Intron|TXNRD2_uc002zqn.1_Intron|TXNRD2_uc002zqo.1_Intron|TXNRD2_uc002zqp.1_Intron|TXNRD2_uc002zqr.1_Intron|TXNRD2_uc010grv.1_Intron|TXNRD2_uc002zqj.1_Intron|TXNRD2_uc002zqs.2_Intron	NM_006440	NP_006431	Q9NNW7	TRXR2_HUMAN	thioredoxin reductase 2 precursor						cell redox homeostasis|response to oxygen radical	mitochondrion	flavin adenine dinucleotide binding|NADP binding|thioredoxin-disulfide reductase activity			ovary(2)	2	Colorectal(54;0.0993)					AGAGGTGGCTGGACCTCTCTT	0.582													4	2	---	---	---	---	
IGLL1	3543	broad.mit.edu	37	22	23916001	23916001	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23916001delC	uc002zxd.2	-						IGLL1_uc002zxe.2_Intron	NM_020070	NP_064455	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1 isoform						immune response	extracellular region|membrane					0						GGTGTCCTGGCCCAGCCCTTT	0.612													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27282808	27282808	+	IGR	DEL	T	-	-	rs77242810		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27282808delT								MIAT (167859 upstream) : MN1 (861458 downstream)																							AGTCCCGTTCTTTTTTTTTTG	0.408													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27858647	27858647	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27858647delT								MIAT (743698 upstream) : MN1 (285619 downstream)																							ctttcttttcttttttttttA	0.383													5	3	---	---	---	---	
OSBP2	23762	broad.mit.edu	37	22	31249762	31249762	+	Intron	DEL	T	-	-	rs35208155		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31249762delT	uc003aiy.1	+						OSBP2_uc011ala.1_Intron|OSBP2_uc010gwc.1_Intron|OSBP2_uc003aix.1_Intron|OSBP2_uc011alb.1_Intron|OSBP2_uc003aiz.1_Intron|OSBP2_uc003aja.1_Intron|OSBP2_uc011alc.1_Intron	NM_030758	NP_110385	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2						tctttctttcttttttttttt	0.000													5	3	---	---	---	---	
MYH9	4627	broad.mit.edu	37	22	36708400	36708401	+	Intron	INS	-	A	A	rs143290016	by1000genomes	TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36708400_36708401insA	uc003apg.2	-						MYH9_uc003aph.1_Intron	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle						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						CCAGGAGAAGCAAAGCACTGTT	0.574			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				7	5	---	---	---	---	
MYH9	4627	broad.mit.edu	37	22	36712840	36712841	+	Intron	DEL	AA	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36712840_36712841delAA	uc003apg.2	-						MYH9_uc003aph.1_Intron	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle						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						tatgtgggggaaaaaaaaaaat	0.020			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				3	3	---	---	---	---	
FAM83F	113828	broad.mit.edu	37	22	40418561	40418561	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40418561delG	uc003ayk.1	+							NM_138435	NP_612444	Q8NEG4	FA83F_HUMAN	hypothetical protein LOC113828											breast(1)	1						ACGTCCCTCTGCTGAGTGCTG	0.602													4	2	---	---	---	---	
FAM83F	113828	broad.mit.edu	37	22	40418562	40418563	+	Intron	INS	-	TCT	TCT			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40418562_40418563insTCT	uc003ayk.1	+							NM_138435	NP_612444	Q8NEG4	FA83F_HUMAN	hypothetical protein LOC113828											breast(1)	1						CGTCCCTCTGCTGAGTGCTGTC	0.594													4	2	---	---	---	---	
RANGAP1	5905	broad.mit.edu	37	22	41666944	41666944	+	Intron	DEL	G	-	-	rs34333301		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41666944delG	uc003azs.2	-						RANGAP1_uc003azt.2_Intron|RANGAP1_uc003azu.2_Intron|RANGAP1_uc011aoz.1_Intron	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1						mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0						CTAATGAgctgaacagtcagc	0.279													6	12	---	---	---	---	
SERHL2	253190	broad.mit.edu	37	22	42950183	42950183	+	Intron	DEL	C	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42950183delC	uc003bcr.2	+						SERHL_uc011apm.1_Intron|SERHL2_uc011apn.1_Intron|SERHL2_uc010gyz.2_Intron|SERHL2_uc010gyy.2_Intron|SERHL2_uc011apo.1_Intron	NM_014509	NP_055324	Q9H4I8	SEHL2_HUMAN	serine hydrolase-like 2							perinuclear region of cytoplasm|peroxisome	hydrolase activity				0						CCTCGGCAGTCCCGGGGCATG	0.706													4	3	---	---	---	---	
PACSIN2	11252	broad.mit.edu	37	22	43314438	43314439	+	Intron	DEL	CT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43314438_43314439delCT	uc010gzg.2	-						PACSIN2_uc003bdg.3_Intron|PACSIN2_uc003bde.3_Intron|PACSIN2_uc003bdf.3_Intron	NM_007229	NP_009160	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in						actin cytoskeleton organization|endocytosis	cytoplasmic membrane-bounded vesicle	transporter activity				0		Glioma(61;0.222)				tactcagtacctctcagcacca	0.193													4	2	---	---	---	---	
SCUBE1	80274	broad.mit.edu	37	22	43732964	43732965	+	Intron	DEL	TG	-	-	rs34868094		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43732964_43732965delTG	uc003bdt.1	-						SCUBE1_uc003bdu.1_Intron	NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1						adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)				tgtgtatgtctgtgtgtgtgtg	0.173													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	46041998	46041999	+	IGR	DEL	GC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46041998_46041999delGC								FBLN1 (43301 upstream) : ATXN10 (25688 downstream)																							GGTAAAGAAAGCAAGGAGGTGT	0.535											OREG0026646	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
TBC1D22A	25771	broad.mit.edu	37	22	47427495	47427495	+	Intron	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47427495delG	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		ATGCAAGGGTGGGTCCATGCT	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	678388	678391	+	IGR	DEL	AAAC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:678388_678391delAAAC								SHOX (58243 upstream) : CRLF2 (636496 downstream)																							tttgtctcaaaaacaaacaaacaa	0.010													2	4	---	---	---	---	
XG	7499	broad.mit.edu	37	X	2715628	2715629	+	Intron	DEL	CA	-	-	rs56018214		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2715628_2715629delCA	uc011mhg.1	+						XG_uc004cqp.2_Intron	NM_175569	NP_780778	P55808	XG_HUMAN	XG glycoprotein isoform 1 precursor							integral to membrane|plasma membrane				ovary(1)	1		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				tacacacatgcacacacacaca	0.361													4	2	---	---	---	---	
FAM9A	171482	broad.mit.edu	37	X	8759999	8759999	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8759999delA	uc004csg.2	-							NM_174951	NP_777611	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A							nucleolus					0		Hepatocellular(5;0.219)				ATGCACAAATAAAAAAAATTA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	39231922	39231922	+	IGR	DEL	G	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39231922delG								MID1IP1 (566141 upstream) : BCOR (678579 downstream)																							gctgagtcctgcccagagtgg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	48161487	48161491	+	Intron	DEL	TTGGT	-	-	rs71901189		TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48161487_48161491delTTGGT	uc010nib.1	-							NM_174962	NP_777622			synovial sarcoma, X breakpoint 9																		ATTAAATTGATTGGTTAAGAATCTG	0.205													11	7	---	---	---	---	
DLG3	1741	broad.mit.edu	37	X	69722885	69722886	+	3'UTR	INS	-	G	G			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69722885_69722886insG	uc004dyi.1	+	19					DLG3_uc004dyj.1_3'UTR|DLG3_uc011mpn.1_3'UTR	NM_021120	NP_066943	Q92796	DLG3_HUMAN	synapse-associated protein 102 isoform a						axon guidance|negative regulation of cell proliferation|synaptic transmission	plasma membrane	guanylate kinase activity			large_intestine(1)|pancreas(1)	2	Renal(35;0.156)					GAGAGCTAGGAGGGGTCAGCCT	0.564													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	89712782	89712783	+	IGR	DEL	AG	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89712782_89712783delAG								TGIF2LX (534902 upstream) : PABPC5 (976814 downstream)																							aggcagcataagagagagagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	102602674	102602674	+	IGR	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102602674delT								TCEAL7 (15423 upstream) : WBP5 (8706 downstream)																							TTCTGTTTCCTTTTTCATTTT	0.463													4	2	---	---	---	---	
IGSF1	3547	broad.mit.edu	37	X	130657771	130657772	+	Intron	DEL	TC	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130657771_130657772delTC	uc004ewf.2	-							NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1						regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5						TGAGTCCCTTTCTAGGTGTACC	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	132128803	132128804	+	IGR	DEL	TT	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132128803_132128804delTT								HS6ST2 (33380 upstream) : USP26 (30250 downstream)																							TCCTAAGTTCTTCAGAGATGTT	0.381													4	2	---	---	---	---	
HPRT1	3251	broad.mit.edu	37	X	133620849	133620849	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133620849delA	uc004exl.3	+						HPRT1_uc010nrs.2_Intron	NM_000194	NP_000185	P00492	HPRT_HUMAN	hypoxanthine phosphoribosyltransferase 1						adenine salvage|central nervous system neuron development|cerebral cortex neuron differentiation|cytolysis|dendrite morphogenesis|GMP catabolic process|GMP salvage|grooming behavior|guanine salvage|hypoxanthine salvage|IMP salvage|lymphocyte proliferation|positive regulation of dopamine metabolic process|protein homotetramerization|purine ribonucleoside salvage|response to amphetamine|striatum development	cytosol	guanine phosphoribosyltransferase activity|hypoxanthine phosphoribosyltransferase activity|magnesium ion binding|nucleotide binding|protein homodimerization activity				0	Acute lymphoblastic leukemia(192;0.000127)				Mercaptopurine(DB01033)|Thioguanine(DB00352)	GATAGCCTTTAAAAAAAAAAA	0.308													4	2	---	---	---	---	
GABRA3	2556	broad.mit.edu	37	X	151514298	151514298	+	Intron	DEL	A	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151514298delA	uc010ntk.1	-							NM_000808	NP_000799	P34903	GBRA3_HUMAN	gamma-aminobutyric acid A receptor, alpha 3						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)				Alprazolam(DB00404)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	CCTATATCTTATCCAAAATAG	0.318													4	2	---	---	---	---	
MECP2	4204	broad.mit.edu	37	X	153357461	153357461	+	Intron	DEL	T	-	-			TCGA-CJ-4637-01A-02D-1386-10	TCGA-CJ-4637-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153357461delT	uc004fjv.2	-						MECP2_uc004fjw.2_Intron	NM_004992	NP_004983	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGGAAGTGACTTTTTTTTATT	0.418													6	3	---	---	---	---	
