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
KLHL21	9903	broad.mit.edu	37	1	6655388	6655388	+	Intron	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6655388G>A	uc001aoa.2	-						KLHL21_uc001anz.1_3'UTR|KLHL21_uc009vme.2_Intron	NM_014851	NP_055666	Q9UJP4	KLH21_HUMAN	kelch-like 21						anaphase|cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex|cytoplasm|polar microtubule				central_nervous_system(1)	1	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)		gtctcagtgagccttaagtgc	0.229													3	45	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974243	16974243	+	RNA	SNP	G	C	C	rs142213352	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974243G>C	uc009vow.2	+	5		c.1053G>C			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_Intron|MST1P2_uc001azm.3_Intron					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GATCTCAGCTGTCGCTCGGGG	0.652													4	54	---	---	---	---	PASS
ZNF683	257101	broad.mit.edu	37	1	26689575	26689575	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26689575A>G	uc001bmg.1	-	5	1203	c.1085T>C	c.(1084-1086)CTT>CCT	p.L362P	ZNF683_uc001bmh.1_Missense_Mutation_p.L362P|ZNF683_uc009vsj.1_Missense_Mutation_p.L362P	NM_173574	NP_775845	Q8IZ20	ZN683_HUMAN	zinc finger protein 683	362	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		CAGGTGGGCAAGTTGAGTGAA	0.572													5	97	---	---	---	---	PASS
EPB41	2035	broad.mit.edu	37	1	29342253	29342253	+	Silent	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29342253A>G	uc001brm.1	+	5	886	c.879A>G	c.(877-879)CCA>CCG	p.P293P	EPB41_uc001brg.1_Silent_p.P84P|EPB41_uc001brh.1_Silent_p.P84P|EPB41_uc001bri.1_Silent_p.P258P|EPB41_uc001brj.1_Silent_p.P84P|EPB41_uc009vtk.1_Silent_p.P258P|EPB41_uc001brk.2_Silent_p.P293P|EPB41_uc001brl.1_Silent_p.P293P|EPB41_uc009vtl.1_Silent_p.P84P|EPB41_uc009vtm.1_5'UTR	NM_203342	NP_976217	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	293	FERM.				blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		CACCTGACCCAGCACAGTTAA	0.274													7	346	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34189862	34189862	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34189862C>A	uc001bxn.1	-	19	2845	c.2816G>T	c.(2815-2817)GGG>GTG	p.G939V	CSMD2_uc001bxm.1_Missense_Mutation_p.G979V	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	939	Extracellular (Potential).|CUB 6.					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTCAGGGAACCCTGGCGACAA	0.532													34	108	---	---	---	---	PASS
LRRIQ3	127255	broad.mit.edu	37	1	74575181	74575181	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74575181G>T	uc001dfy.3	-	5	956	c.764C>A	c.(763-765)GCA>GAA	p.A255E	LRRIQ3_uc001dfz.3_RNA	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	255										ovary(2)	2						AATCCATTTTGCTTCATATCC	0.328													7	766	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144220807	144220807	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144220807A>C	uc010oxr.1	+	19	2184	c.2180A>C	c.(2179-2181)GAT>GCT	p.D727A	NBPF9_uc010oxn.1_Missense_Mutation_p.D598A|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Missense_Mutation_p.D515A|NBPF9_uc001ekg.1_Missense_Mutation_p.D27A|NBPF9_uc001ekk.1_Missense_Mutation_p.D271A|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Missense_Mutation_p.D27A|uc010oxz.1_Missense_Mutation_p.D515A	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	700	NBPF 5.					cytoplasm					0						GAGCTGCTGGATGAGAAAGAG	0.483													6	11	---	---	---	---	PASS
HIST2H2BF	440689	broad.mit.edu	37	1	149783835	149783835	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149783835G>A	uc001esr.2	-	1	94	c.44C>T	c.(43-45)TCC>TTC	p.S15F	HIST2H2BF_uc010pbj.1_Missense_Mutation_p.S15F|HIST2H2BF_uc010pbk.1_Missense_Mutation_p.S15F	NM_001024599	NP_001019770	Q5QNW6	H2B2F_HUMAN	histone cluster 2, H2bf isoform a	15					nucleosome assembly	nucleosome|nucleus	DNA binding				0	Breast(34;0.0124)|all_hematologic(923;0.127)					AGCCTTTTTGGAGCCCTTCTT	0.502													6	199	---	---	---	---	PASS
THBS3	7059	broad.mit.edu	37	1	155172612	155172612	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155172612G>T	uc001fix.2	-	8	971	c.948C>A	c.(946-948)GAC>GAA	p.D316E	RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Missense_Mutation_p.D307E|THBS3_uc001fiz.2_Missense_Mutation_p.D316E|THBS3_uc001fiy.2_5'UTR|THBS3_uc010pfu.1_Missense_Mutation_p.D196E|THBS3_uc010pfv.1_RNA|THBS3_uc001fja.2_RNA	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor	316	EGF-like 2; calcium-binding (Potential).				cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CCTCATTGATGTCACTGCAGT	0.612													6	26	---	---	---	---	PASS
THBS3	7059	broad.mit.edu	37	1	155172613	155172613	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155172613T>A	uc001fix.2	-	8	970	c.947A>T	c.(946-948)GAC>GTC	p.D316V	RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Missense_Mutation_p.D307V|THBS3_uc001fiz.2_Missense_Mutation_p.D316V|THBS3_uc001fiy.2_5'UTR|THBS3_uc010pfu.1_Missense_Mutation_p.D196V|THBS3_uc010pfv.1_RNA|THBS3_uc001fja.2_RNA	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor	316	EGF-like 2; calcium-binding (Potential).				cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CTCATTGATGTCACTGCAGTG	0.607													6	26	---	---	---	---	PASS
DCAF8	50717	broad.mit.edu	37	1	160194899	160194899	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160194899T>C	uc001fvo.2	-	9	1466	c.1154A>G	c.(1153-1155)GAG>GGG	p.E385G	DCAF8_uc001fvn.2_Missense_Mutation_p.E385G|DCAF8_uc009wth.2_Missense_Mutation_p.E385G|DCAF8_uc010pjb.1_Missense_Mutation_p.E385G|DCAF8_uc010pjc.1_Missense_Mutation_p.E539G	NM_015726	NP_056541	Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8	385	WD 5.					CUL4 RING ubiquitin ligase complex	protein binding			skin(2)	2						TGCTTTGGACTCACTGTTCAC	0.532													7	382	---	---	---	---	PASS
POU2F1	5451	broad.mit.edu	37	1	167381430	167381430	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167381430C>T	uc001gec.2	+	15	1883	c.1721C>T	c.(1720-1722)GCT>GTT	p.A574V	POU2F1_uc001ged.2_Missense_Mutation_p.A572V|POU2F1_uc001gee.2_Missense_Mutation_p.A574V|POU2F1_uc010plh.1_Missense_Mutation_p.A511V|POU2F1_uc001gef.2_Missense_Mutation_p.A586V|POU2F1_uc001geg.2_Missense_Mutation_p.A472V|POU2F1_uc009wvg.1_RNA	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1	574					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5						ACAGCAGCAGCTGCTGCCCTT	0.572													3	43	---	---	---	---	PASS
TPR	7175	broad.mit.edu	37	1	186324540	186324540	+	Splice_Site	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186324540A>G	uc001grv.2	-	17	2468	c.2171_splice	c.e17+1	p.R724_splice		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		AAGAAAACTTACCGTTTAGAA	0.279			T	NTRK1	papillary thyroid								6	801	---	---	---	---	PASS
TNNI1	7135	broad.mit.edu	37	1	201384351	201384351	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201384351A>G	uc010ppq.1	-	4	140	c.47T>C	c.(46-48)CTC>CCC	p.L16P	TNNI1_uc001gwo.1_RNA|TNNI1_uc001gwp.2_5'UTR	NM_003281	NP_003272	P19237	TNNI1_HUMAN	troponin I, skeletal, slow	16	Involved in binding TNC.				muscle filament sliding|regulation of striated muscle contraction	cytosol|troponin complex	actin binding|tropomyosin binding				0						CTTCAGCAAGAGTTTGCGGGA	0.582													17	64	---	---	---	---	PASS
JMJD4	65094	broad.mit.edu	37	1	227921679	227921679	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227921679C>T	uc001hrb.2	-	3	621	c.621G>A	c.(619-621)TGG>TGA	p.W207*	SNAP47_uc001hqz.2_Intron|SNAP47_uc001hra.2_Intron|SNAP47_uc001hrd.2_5'Flank|SNAP47_uc001hre.2_5'Flank|SNAP47_uc001hrf.2_5'Flank|LOC100130093_uc001hqx.3_RNA|LOC100130093_uc001hqy.3_RNA|JMJD4_uc001hrc.2_Nonsense_Mutation_p.W207*	NM_023007	NP_075383	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4 isoform 1	207	JmjC.										0		Prostate(94;0.0885)				ACTCATTCAGCCAGTCGGACG	0.617													40	113	---	---	---	---	PASS
OR2L8	391190	broad.mit.edu	37	1	248112480	248112480	+	Silent	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248112480A>G	uc001idt.1	+	1	321	c.321A>G	c.(319-321)GGA>GGG	p.G107G	OR2L13_uc001ids.2_Intron	NM_001001963	NP_001001963	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L,	107	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			TGGCATTAGGAGGTGCAGAAG	0.443													9	733	---	---	---	---	PASS
LPIN1	23175	broad.mit.edu	37	2	11919652	11919652	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11919652G>A	uc010yjn.1	+	7	1004	c.730G>A	c.(730-732)GGT>AGT	p.G244S	LPIN1_uc010yjm.1_Missense_Mutation_p.G329S|LPIN1_uc002rbt.2_Missense_Mutation_p.G244S|LPIN1_uc002rbs.2_Missense_Mutation_p.G280S	NM_145693	NP_663731	Q14693	LPIN1_HUMAN	lipin 1	244					fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		AAGTCCTTCCGGTTCCCGACC	0.453											OREG0014444	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	91	299	---	---	---	---	PASS
WDR35	57539	broad.mit.edu	37	2	20153619	20153619	+	Missense_Mutation	SNP	C	T	T	rs146380332		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20153619C>T	uc002rdi.2	-	13	1517	c.1409G>A	c.(1408-1410)CGG>CAG	p.R470Q	WDR35_uc002rdj.2_Missense_Mutation_p.R459Q|WDR35_uc010ext.2_RNA|WDR35_uc002rdh.2_Missense_Mutation_p.R35Q|WDR35_uc002rdk.3_Missense_Mutation_p.R35Q	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1	470										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTTCGAGACCGTGTGATCTG	0.378													6	621	---	---	---	---	PASS
ASXL2	55252	broad.mit.edu	37	2	25965672	25965672	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25965672T>C	uc002rgs.2	-	12	3755	c.3534A>G	c.(3532-3534)GAA>GAG	p.E1178E	ASXL2_uc002rgt.1_Silent_p.E661E	NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2	1178					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGTGTCATCTTCTTTGCTGC	0.473													6	309	---	---	---	---	PASS
TRMT61B	55006	broad.mit.edu	37	2	29073074	29073074	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29073074T>C	uc002rmm.2	-	7	1457	c.1425A>G	c.(1423-1425)CAA>CAG	p.Q475Q	SPDYA_uc002rmj.2_3'UTR|SPDYA_uc002rmk.2_3'UTR|TRMT61B_uc002rmn.2_Silent_p.Q466Q|TRMT61B_uc010ezk.2_RNA	NM_017910	NP_060380	Q9BVS5	TR61B_HUMAN	tRNA methyltransferase 61 homolog B	475							tRNA (adenine-N1-)-methyltransferase activity				0						CTCAGTTAAGTTGTGGTTTGA	0.289													171	452	---	---	---	---	PASS
LTBP1	4052	broad.mit.edu	37	2	33622348	33622348	+	Silent	SNP	C	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33622348C>G	uc002ros.2	+	33	4986	c.4986C>G	c.(4984-4986)GTC>GTG	p.V1662V	LTBP1_uc002rot.2_Silent_p.V1336V|LTBP1_uc002rou.2_Silent_p.V1335V|LTBP1_uc002rov.2_Silent_p.V1282V|LTBP1_uc010ymz.1_Silent_p.V1293V|LTBP1_uc010yna.1_Silent_p.V1240V|LTBP1_uc010ynb.1_Silent_p.V559V	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1661				V -> F (in Ref. 1; AAA61160).	negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				TGACCTGTGTCGGTAAGAATG	0.413													121	295	---	---	---	---	PASS
PLEKHH2	130271	broad.mit.edu	37	2	43939364	43939364	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43939364T>C	uc010yny.1	+	15	2385	c.2302T>C	c.(2302-2304)TTG>CTG	p.L768L	PLEKHH2_uc002rte.3_3'UTR|PLEKHH2_uc002rtf.3_Silent_p.L767L	NM_172069	NP_742066	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H	768	PH 1.					cytoplasm|cytoskeleton|integral to membrane	binding			skin(2)|central_nervous_system(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TGCATTCTAGTTGACCACTGA	0.358													12	547	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61450407	61450407	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61450407G>T	uc002sbe.2	-	63	7642	c.7620C>A	c.(7618-7620)GAC>GAA	p.D2540E		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	2540					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)			ATGCTGCCATGTCAGTCTGTG	0.308													191	568	---	---	---	---	PASS
AAK1	22848	broad.mit.edu	37	2	69709848	69709848	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69709848A>G	uc002sfp.2	-	18	2967	c.2462T>C	c.(2461-2463)GTA>GCA	p.V821A	AAK1_uc010fdk.2_Missense_Mutation_p.V821A|AAK1_uc010yqm.1_Missense_Mutation_p.V822A	NM_014911	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	821						coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0						TTTACCAATTACAGCATCAGA	0.423													12	427	---	---	---	---	PASS
POLR1A	25885	broad.mit.edu	37	2	86292646	86292646	+	Intron	SNP	A	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86292646A>T	uc002sqs.2	-						POLR1A_uc010ytb.1_5'UTR	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						GTCAAACTCTAATCCCTAATC	0.448													10	22	---	---	---	---	PASS
RGPD1	400966	broad.mit.edu	37	2	88125182	88125182	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88125182C>G	uc010fhc.1	-	1	134	c.67G>C	c.(67-69)GGA>CGA	p.G23R		NM_001024457	NP_001019628	Q68DN6	RGPD1_HUMAN	RANBP2-like and GRIP domain containing 1	Error:Variant_position_missing_in_Q68DN6_after_alignment					intracellular transport		binding				0						CTCACCTTTCCAGGCGACGGG	0.433													3	4	---	---	---	---	PASS
LYG1	129530	broad.mit.edu	37	2	99901199	99901199	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99901199C>A	uc002szy.2	-	6	668	c.418G>T	c.(418-420)GAA>TAA	p.E140*	MRPL30_uc002szl.1_Intron|LYG1_uc010yvo.1_Nonsense_Mutation_p.E140*	NM_174898	NP_777558	Q8N1E2	LYG1_HUMAN	lysozyme g-like protein 1 precursor	140					cell wall macromolecule catabolic process|peptidoglycan catabolic process	extracellular region	lysozyme activity				0						CTCTGGATTTCTTTGATTCTA	0.498													56	221	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	125555696	125555696	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125555696G>A	uc002tno.2	+	19	3377	c.3013G>A	c.(3013-3015)GGC>AGC	p.G1005S	CNTNAP5_uc010flu.2_Missense_Mutation_p.G1006S	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	1005	Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		TTTTGAGGCTGGCACGTCGGT	0.423													5	386	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152515677	152515677	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152515677A>G	uc010fnx.2	-	47	6168	c.5977T>C	c.(5977-5979)TAC>CAC	p.Y1993H		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	1993	Nebulin 52.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		GCTTGTTTGTAGAGATGCTAG	0.333													6	658	---	---	---	---	PASS
GALNT13	114805	broad.mit.edu	37	2	154801009	154801009	+	5'UTR	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154801009A>G	uc002tyr.3	+	3					GALNT13_uc002tyt.3_5'UTR	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						TCAAGGAAAGACATGAGGAGA	0.408													6	331	---	---	---	---	PASS
WDSUB1	151525	broad.mit.edu	37	2	160092574	160092574	+	Silent	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160092574G>T	uc002uaj.3	-	11	1550	c.1401C>A	c.(1399-1401)ATC>ATA	p.I467I	WDSUB1_uc002uak.3_Silent_p.I467I|WDSUB1_uc002ual.3_Silent_p.I467I|WDSUB1_uc002uam.3_Silent_p.I420I|WDSUB1_uc010foo.2_Silent_p.I375I	NM_152528	NP_689741	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain	467	U-box.					ubiquitin ligase complex	ubiquitin-protein ligase activity				0						GCCATCTATTGATGGCCATTT	0.333													6	465	---	---	---	---	PASS
KIF1A	547	broad.mit.edu	37	2	241727549	241727549	+	Silent	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241727549G>A	uc002vzy.2	-	4	428	c.282C>T	c.(280-282)TTC>TTT	p.F94F	KIF1A_uc010fzk.2_Silent_p.F94F|KIF1A_uc002vzz.1_Silent_p.F94F	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	94	Kinesin-motor.				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		GCCCATAGGCGAAGATGCACA	0.612													4	103	---	---	---	---	PASS
HDLBP	3069	broad.mit.edu	37	2	242168842	242168842	+	3'UTR	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242168842C>A	uc002waz.2	-	28					HDLBP_uc002wba.2_3'UTR|HDLBP_uc002wbb.2_3'UTR	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein						cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		CACGGCCAGGCCTGGAGGAGC	0.622													9	47	---	---	---	---	PASS
SGOL1	151648	broad.mit.edu	37	3	20225415	20225415	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20225415T>C	uc003cbs.2	-	2	292	c.105A>G	c.(103-105)AAA>AAG	p.K35K	SGOL1_uc003cbr.2_Silent_p.K35K|SGOL1_uc010hfa.2_Silent_p.K35K|SGOL1_uc003cbt.2_Silent_p.K35K|SGOL1_uc003cbu.2_Silent_p.K35K|SGOL1_uc003cbv.2_Silent_p.K35K|SGOL1_uc003cbw.2_Silent_p.K35K|SGOL1_uc003cbx.2_Silent_p.K35K|SGOL1_uc003cby.2_Silent_p.K35K|SGOL1_uc003cbz.2_Silent_p.K35K|SGOL1_uc003cca.2_Silent_p.K35K|SGOL1_uc003ccb.2_Silent_p.K35K|SGOL1_uc003ccc.2_Silent_p.K35K	NM_001012410	NP_001012410	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 isoform A2	35	Potential.|Necessary for interaction with PPP2CA and PPP2R1A.				attachment of spindle microtubules to kinetochore|cell division|centriole-centriole cohesion|meiotic chromosome segregation|mitotic prometaphase	centrosome|condensed chromosome kinetochore|cytosol|mitotic cohesin complex|spindle pole	protein binding				0						AAGACCTGCGTTTGCCAATCT	0.328													7	459	---	---	---	---	PASS
CNOT10	25904	broad.mit.edu	37	3	32804524	32804524	+	Intron	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32804524C>A	uc003cfc.1	+						CNOT10_uc011axi.1_3'UTR|CNOT10_uc003cfd.1_Intron|CNOT10_uc003cfe.1_Intron|CNOT10_uc010hfv.1_Intron|CNOT10_uc011axj.1_Intron|CNOT10_uc010hfw.1_Intron	NM_015442	NP_056257	Q9H9A5	CNOTA_HUMAN	CCR4-NOT transcription complex, subunit 10						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2						CTAAGTAGACCTGAGAGTTAA	0.338													3	26	---	---	---	---	PASS
EPHA6	285220	broad.mit.edu	37	3	97198177	97198177	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97198177G>C	uc010how.1	+	9	2086	c.2043G>C	c.(2041-2043)GAG>GAC	p.E681D	EPHA6_uc011bgo.1_RNA|EPHA6_uc011bgp.1_Missense_Mutation_p.E47D|EPHA6_uc003drs.3_Missense_Mutation_p.E73D|EPHA6_uc003drr.3_Missense_Mutation_p.E73D|EPHA6_uc003drt.2_Missense_Mutation_p.E73D|EPHA6_uc010hox.1_RNA	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	586	Cytoplasmic (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						AGTCAGAAGAGAAGAGAAGAA	0.343													126	570	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	3	156527957	156527957	+	Intron	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156527957G>T	uc003fax.1	-						PA2G4P4_uc003fay.1_RNA					Homo sapiens cDNA FLJ31839 fis, clone NT2RP7000086.																		TGCTTCAACTGGTGTGACAGC	0.438													4	134	---	---	---	---	PASS
FNDC3B	64778	broad.mit.edu	37	3	171851295	171851295	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171851295T>C	uc003fhy.2	+	3	318	c.146T>C	c.(145-147)TTC>TCC	p.F49S	FNDC3B_uc003fhz.3_Missense_Mutation_p.F49S|FNDC3B_uc003fia.2_5'UTR|FNDC3B_uc003fhx.2_RNA	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	49						endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		GGTGAGACTTTCACAATAAGA	0.333													7	759	---	---	---	---	PASS
NLGN1	22871	broad.mit.edu	37	3	173322464	173322464	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173322464G>T	uc003fio.1	+	3	499	c.76G>T	c.(76-78)GGT>TGT	p.G26C	NLGN1_uc010hww.1_Missense_Mutation_p.G26C|NLGN1_uc003fip.1_Missense_Mutation_p.G26C	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	26					calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			CCGGGGATTGGGTGCCCCATT	0.502													5	347	---	---	---	---	PASS
PPP1R2	5504	broad.mit.edu	37	3	195243598	195243598	+	3'UTR	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195243598G>T	uc003fup.2	-	6						NM_006241	NP_006232	P41236	IPP2_HUMAN	protein phosphatase 1, regulatory subunit 2						glycogen metabolic process|regulation of phosphoprotein phosphatase activity|regulation of signal transduction		protein binding|protein serine/threonine phosphatase inhibitor activity			urinary_tract(1)	1	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)		Epithelial(36;2.64e-22)|all cancers(36;2.69e-20)|OV - Ovarian serous cystadenocarcinoma(49;3.52e-19)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;9.55e-05)		TATGCATTTTGGTACTTAAGT	0.323													4	240	---	---	---	---	PASS
MUC20	200958	broad.mit.edu	37	3	195447775	195447775	+	5'UTR	SNP	A	G	G	rs7620138	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195447775A>G	uc010hzo.2	+	1						NM_152673	NP_689886	Q8N307	MUC20_HUMAN	mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		ACCTGGTCACACACCTGGGCA	0.617													13	55	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195512921	195512921	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195512921T>C	uc011bto.1	-	2	5990	c.5530A>G	c.(5530-5532)ACC>GCC	p.T1844A	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)		GAAGGGATGGTGACAGGAAGA	0.577													33	83	---	---	---	---	PASS
WHSC2	7469	broad.mit.edu	37	4	1993533	1993533	+	Intron	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1993533G>T	uc003gem.2	-						WHSC2_uc003gel.2_5'UTR|WHSC2_uc003gen.2_Intron	NM_005663	NP_005654	Q9H3P2	NELFA_HUMAN	Wolf-Hirschhorn syndrome candidate 2 protein						multicellular organismal development|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm				skin(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0155)			CTGGGCAGTGGCCGGGCTCTC	0.667													5	25	---	---	---	---	PASS
CENPE	1062	broad.mit.edu	37	4	104066234	104066234	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104066234T>C	uc003hxb.1	-	32	4920	c.4830A>G	c.(4828-4830)AAA>AAG	p.K1610K	CENPE_uc003hxc.1_Silent_p.K1585K	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	1610	Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TAGTGTTTTCTTTCAGTTGGT	0.323													8	763	---	---	---	---	PASS
TLL1	7092	broad.mit.edu	37	4	166915629	166915629	+	Missense_Mutation	SNP	C	A	A	rs115824698	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166915629C>A	uc003irh.1	+	4	1105	c.458C>A	c.(457-459)ACG>AAG	p.T153K	TLL1_uc011cjn.1_Missense_Mutation_p.T153K|TLL1_uc011cjo.1_5'UTR	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	153	Metalloprotease (By similarity).				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		ACATCAAGAACGGAAAGAATA	0.413													4	249	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13913969	13913969	+	Silent	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13913969G>A	uc003jfd.2	-	11	1461	c.1419C>T	c.(1417-1419)TTC>TTT	p.F473F	DNAH5_uc003jfe.1_RNA	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	473	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					GAAAAGTTTCGAATTTTCCAA	0.373									Kartagener_syndrome				17	665	---	---	---	---	PASS
SPEF2	79925	broad.mit.edu	37	5	35691297	35691297	+	Silent	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35691297A>G	uc003jjo.2	+	11	1794	c.1683A>G	c.(1681-1683)AAA>AAG	p.K561K	SPEF2_uc003jjq.3_Silent_p.K561K|SPEF2_uc003jjp.1_Silent_p.K52K	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	561					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TTGCTGTTAAAGGATGCTTAT	0.403													7	428	---	---	---	---	PASS
NNT	23530	broad.mit.edu	37	5	43656875	43656875	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43656875T>C	uc003joe.2	+	16	2669	c.2414T>C	c.(2413-2415)ATC>ACC	p.I805T	NNT_uc003jof.2_Missense_Mutation_p.I805T	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	805	Helical; (Potential).				tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)	ACTACTGGCATCACCTGTCTG	0.468													6	422	---	---	---	---	PASS
ZFYVE16	9765	broad.mit.edu	37	5	79745491	79745491	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79745491T>C	uc003kgr.3	+	9	3487	c.3185T>C	c.(3184-3186)GTC>GCC	p.V1062A	ZFYVE16_uc003kgp.2_Missense_Mutation_p.V1062A|ZFYVE16_uc003kgq.3_Missense_Mutation_p.V1062A|ZFYVE16_uc003kgs.3_Missense_Mutation_p.V1062A|ZFYVE16_uc003kgt.3_Missense_Mutation_p.V150A	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1062					BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		GTTACATTTGTCCTAAATGCT	0.313													7	602	---	---	---	---	PASS
YTHDC2	64848	broad.mit.edu	37	5	112902905	112902905	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112902905G>T	uc003kqn.2	+	22	3142	c.2959G>T	c.(2959-2961)GAC>TAC	p.D987Y		NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	987							ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		AGTCCACGTGGACAGAGAGAA	0.433													119	459	---	---	---	---	PASS
RAPGEF6	51735	broad.mit.edu	37	5	130825242	130825242	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130825242A>C	uc003kvn.1	-	15	2043	c.1837T>G	c.(1837-1839)TTT>GTT	p.F613V	RAPGEF6_uc003kvp.1_Missense_Mutation_p.F663V|RAPGEF6_uc003kvo.1_Missense_Mutation_p.F613V|RAPGEF6_uc010jdi.1_Missense_Mutation_p.F613V|RAPGEF6_uc010jdj.1_Missense_Mutation_p.F613V|RAPGEF6_uc003kvq.2_Missense_Mutation_p.F330V|RAPGEF6_uc003kvr.2_Missense_Mutation_p.F613V|RAPGEF6_uc011cxe.1_RNA|RAPGEF6_uc010jdk.2_Missense_Mutation_p.F613V	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide	613	PDZ.				Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		AACTCACCAAAAATGTTGGTC	0.299													141	552	---	---	---	---	PASS
PCDHA2	56146	broad.mit.edu	37	5	140184764	140184764	+	Intron	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140184764C>A	uc003lhd.2	+						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_5'Flank|PCDHA4_uc003lhh.1_5'Flank|PCDHA2_uc011czy.1_3'UTR|PCDHA4_uc011daa.1_5'Flank	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGATGCTATGCCAAATAAATA	0.323													6	251	---	---	---	---	PASS
PCDHGA6	56109	broad.mit.edu	37	5	140754609	140754609	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140754609A>G	uc003ljy.1	+	1	959	c.959A>G	c.(958-960)GAA>GGA	p.E320G	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc011dau.1_Missense_Mutation_p.E320G	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	320	Cadherin 3.|Extracellular (Potential).				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)			CTGGGTGTTGAAGCCCGGGAT	0.408													5	254	---	---	---	---	PASS
PCDH1	5097	broad.mit.edu	37	5	141242928	141242928	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141242928T>A	uc003llq.2	-	3	3085	c.2968A>T	c.(2968-2970)AAG>TAG	p.K990*	PCDH1_uc003llp.2_Nonsense_Mutation_p.K990*|PCDH1_uc011dbf.1_Nonsense_Mutation_p.K968*	NM_002587	NP_002578	Q08174	PCDH1_HUMAN	protocadherin 1 isoform 1 precursor	990	Cytoplasmic (Potential).				cell-cell signaling|homophilic cell adhesion|nervous system development	cell-cell junction|integral to plasma membrane	calcium ion binding			ovary(5)	5		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		ACCTGGTGCTTCTTGGAGGCT	0.627													22	119	---	---	---	---	PASS
NHP2	55651	broad.mit.edu	37	5	177576774	177576774	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177576774C>G	uc003mir.2	-	4	545	c.402G>C	c.(400-402)GAG>GAC	p.E134D	NHP2_uc003mis.2_3'UTR	NM_017838	NP_060308	Q9NX24	NHP2_HUMAN	nucleolar protein family A, member 2 isoform a	134					rRNA pseudouridine synthesis	Cajal body|nucleolus|small nucleolar ribonucleoprotein complex	protein binding|snoRNA binding				0						CCTCCTGGTACTCCTCATGGG	0.602													14	58	---	---	---	---	PASS
SLC22A23	63027	broad.mit.edu	37	6	3284081	3284081	+	Intron	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3284081C>T	uc003mvm.3	-						uc003mvi.1_Intron|SLC22A23_uc003mvn.3_Intron|SLC22A23_uc003mvo.3_Intron|SLC22A23_uc003mvp.1_Intron|SLC22A23_uc010jnn.2_Missense_Mutation_p.V570I	NM_015482	NP_056297	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23 isoform a						ion transport	integral to membrane	transmembrane transporter activity			ovary(1)	1	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				TCTCCCATGACGCACCTTATC	0.597													16	57	---	---	---	---	PASS
ERVFRDE1	405754	broad.mit.edu	37	6	11105212	11105212	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11105212C>A	uc003mzt.2	-	2	702	c.332G>T	c.(331-333)GGA>GTA	p.G111V	LOC221710_uc003mzr.2_Intron|LOC221710_uc011dio.1_Intron	NM_207582	NP_997465	P60508	EFRD1_HUMAN	syncytin 2	111	Extracellular (Potential).					integral to membrane|plasma membrane|virion					0						AAAGATGGGTCCGAAAATGGG	0.423													58	153	---	---	---	---	PASS
MYLIP	29116	broad.mit.edu	37	6	16146960	16146960	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16146960T>C	uc003nbq.2	+	7	1553	c.1316T>C	c.(1315-1317)CTT>CCT	p.L439P	MYLIP_uc003nbr.2_Missense_Mutation_p.L258P	NM_013262	NP_037394	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting	439					cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			CACACCAGTCTTCTCAATCTG	0.443													94	291	---	---	---	---	PASS
MRS2	57380	broad.mit.edu	37	6	24423464	24423464	+	Intron	SNP	A	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24423464A>C	uc003neb.2	+						MRS2_uc003nea.2_3'UTR|MRS2_uc011djl.1_Intron|MRS2_uc011djm.1_Intron|MRS2_uc011djn.1_Intron|MRS2_uc003nec.2_Intron	NM_020662	NP_065713	Q9HD23	MRS2_HUMAN	MRS2-like, magnesium homeostasis factor						ion transport	integral to membrane|mitochondrial inner membrane					0						tatgggaagaattaaacaata	0.070													13	23	---	---	---	---	PASS
GPLD1	2822	broad.mit.edu	37	6	24429111	24429111	+	3'UTR	SNP	T	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24429111T>G	uc003ned.1	-	25						NM_001503	NP_001494	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific							extracellular region	glycosylphosphatidylinositol phospholipase D activity			ovary(2)|kidney(1)	3						GGTGTGGCTGTTAGTGTGTCT	0.458													8	33	---	---	---	---	PASS
KIAA0319	9856	broad.mit.edu	37	6	24596226	24596226	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24596226C>T	uc011djo.1	-	3	913	c.676G>A	c.(676-678)GCC>ACC	p.A226T	KIAA0319_uc011djp.1_Missense_Mutation_p.A181T|KIAA0319_uc003neh.1_Missense_Mutation_p.A226T|KIAA0319_uc011djq.1_Missense_Mutation_p.A217T|KIAA0319_uc011djr.1_Missense_Mutation_p.A226T	NM_014809	NP_055624	Q5VV43	K0319_HUMAN	KIAA0319 precursor	226	Extracellular (Potential).				negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2						AGTTTTGGGGCAGGGGTTGAA	0.562													18	79	---	---	---	---	PASS
SLC26A8	116369	broad.mit.edu	37	6	35959572	35959572	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35959572T>C	uc003olm.2	-	7	917	c.806A>G	c.(805-807)TAC>TGC	p.Y269C	SLC26A8_uc003oln.2_Missense_Mutation_p.Y269C|SLC26A8_uc003oll.2_Intron	NM_052961	NP_443193	Q96RN1	S26A8_HUMAN	solute carrier family 26, member 8 isoform a	269	Extracellular (Potential).				cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2						AGCTACACAGTAATTAATTAT	0.343													5	304	---	---	---	---	PASS
GCLC	2729	broad.mit.edu	37	6	53373486	53373486	+	Silent	SNP	G	C	C	rs17879847	byFrequency	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53373486G>C	uc003pbw.1	-	8	1240	c.852C>G	c.(850-852)CCC>CCG	p.P284P	GCLC_uc003pbv.1_Silent_p.P8P	NM_001498	NP_001489	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	284					anti-apoptosis|cell redox homeostasis|cysteine metabolic process|glutamate metabolic process|glutathione biosynthetic process|negative regulation of transcription, DNA-dependent|regulation of blood vessel size|response to heat|response to hormone stimulus|response to oxidative stress|xenobiotic metabolic process	cytosol	ADP binding|ATP binding|coenzyme binding|glutamate binding|glutamate-cysteine ligase activity|magnesium ion binding			ovary(1)|central_nervous_system(1)	2	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)	CTCGGTAAAAGGGAGATGCAG	0.443													8	282	---	---	---	---	PASS
RNGTT	8732	broad.mit.edu	37	6	89322311	89322311	+	3'UTR	SNP	A	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89322311A>T	uc003pmr.2	-	16					RNGTT_uc003pms.2_3'UTR|RNGTT_uc011dzu.1_3'UTR	NM_003800	NP_003791	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		TTCTTTTTTTAAAAAAAATTC	0.348													10	81	---	---	---	---	PASS
FIG4	9896	broad.mit.edu	37	6	110064360	110064360	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110064360T>C	uc003ptt.2	+	9	1139	c.924T>C	c.(922-924)GCT>GCC	p.A308A	FIG4_uc011eau.1_Intron	NM_014845	NP_055660	Q92562	FIG4_HUMAN	Sac domain-containing inositol phosphatase 3	308	SAC.				cell death	endosome membrane	protein binding			ovary(1)	1		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		TCTGCGATGCTTCTGTGATGT	0.363													8	761	---	---	---	---	PASS
HIVEP2	3097	broad.mit.edu	37	6	143081503	143081503	+	Silent	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143081503A>G	uc003qjd.2	-	9	6665	c.5922T>C	c.(5920-5922)ACT>ACC	p.T1974T		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	1974					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TACTTGGCAAAGTAACCAAAT	0.473													156	395	---	---	---	---	PASS
PEX3	8504	broad.mit.edu	37	6	143793617	143793617	+	Intron	SNP	A	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143793617A>C	uc003qjl.2	+						PEX3_uc011edx.1_3'UTR	NM_003630	NP_003621	P56589	PEX3_HUMAN	peroxisomal biogenesis factor 3						protein import into peroxisome membrane|transmembrane transport	integral to peroxisomal membrane	protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(155;5.73e-06)|GBM - Glioblastoma multiforme(68;0.0117)		ATTTAGAAAAACAGCCATTAT	0.279													7	14	---	---	---	---	PASS
CCR6	1235	broad.mit.edu	37	6	167417367	167417367	+	5'UTR	SNP	A	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167417367A>C	uc003qvl.2	+	3					FGFR1OP_uc011egp.1_Intron|FGFR1OP_uc003qvj.2_Intron|FGFR1OP_uc003qvk.2_Intron	NM_031409	NP_113597	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6						cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|humoral immune response	integral to plasma membrane	C-C chemokine receptor activity			ovary(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		ATTAAGCTGAAAGTTAATAGA	0.274													153	411	---	---	---	---	PASS
NPVF	64111	broad.mit.edu	37	7	25268017	25268017	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25268017T>C	uc003sxo.2	-	1	89	c.42A>G	c.(40-42)TTA>TTG	p.L14L		NM_022150	NP_071433	Q9HCQ7	RFRP_HUMAN	neuropeptide VF precursor	14					neuropeptide signaling pathway	extracellular region|membrane	G-protein coupled receptor activity			ovary(1)	1						TTGAAGTGGCTAAAGTCAATA	0.299													7	448	---	---	---	---	PASS
SEC61G	23480	broad.mit.edu	37	7	54820109	54820109	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54820109C>T	uc003tqf.2	-	4	293	c.202G>A	c.(202-204)GGC>AGC	p.G68S	SEC61G_uc003tqg.2_Missense_Mutation_p.G68S	NM_001012456	NP_001012474	P60059	SC61G_HUMAN	Sec61 gamma subunit	68	Extracellular (Potential).				protein targeting to ER	endoplasmic reticulum membrane|integral to membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			lung(1)	1	Esophageal squamous(2;7.55e-08)|Breast(14;0.0654)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)			TGTATTCAGCCACCACTGTAA	0.308													9	467	---	---	---	---	PASS
ABCB1	5243	broad.mit.edu	37	7	87225082	87225082	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87225082C>A	uc003uiz.1	-	4	535	c.117G>T	c.(115-117)ATG>ATT	p.M39I	ABCB1_uc011khc.1_Missense_Mutation_p.M39I	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	39	Cytoplasmic (Potential).				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	CAAAACTCACCATTGAAAATA	0.279													5	519	---	---	---	---	PASS
CTTNBP2	83992	broad.mit.edu	37	7	117351583	117351583	+	3'UTR	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117351583A>G	uc003vjf.2	-	23						NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2											ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		AGAATATTGTAGGCAGGCCTA	0.299													6	862	---	---	---	---	PASS
MGAM	8972	broad.mit.edu	37	7	141752123	141752123	+	Silent	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141752123C>A	uc003vwy.2	+	25	2889	c.2835C>A	c.(2833-2835)CTC>CTA	p.L945L		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	945	Lumenal (Potential).				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTGATCTTCTCCTGGGAGAAG	0.403													90	208	---	---	---	---	PASS
IKBKB	3551	broad.mit.edu	37	8	42183534	42183534	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42183534C>T	uc003xow.1	+	20	2210	c.2033C>T	c.(2032-2034)GCC>GTC	p.A678V	IKBKB_uc010lxj.1_Missense_Mutation_p.A455V|IKBKB_uc003xox.1_Missense_Mutation_p.A399V|IKBKB_uc011lcp.1_RNA|IKBKB_uc011lcq.1_Missense_Mutation_p.A676V|IKBKB_uc010lxi.1_RNA|IKBKB_uc011lcr.1_Missense_Mutation_p.A619V	NM_001556	NP_001547	O14920	IKKB_HUMAN	inhibitor of nuclear factor kappa B kinase beta	678					anti-apoptosis|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 I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|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	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)	AGCATGAATGCCTCTCGACTT	0.527													4	155	---	---	---	---	PASS
TRAM1	23471	broad.mit.edu	37	8	71495415	71495415	+	Silent	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71495415A>G	uc003xyo.1	-	10	1205	c.1035T>C	c.(1033-1035)TCT>TCC	p.S345S	TRAM1_uc011lfc.1_Silent_p.S314S	NM_014294	NP_055109	Q15629	TRAM1_HUMAN	translocation associated membrane protein 1	345	Cytoplasmic (Potential).				cotranslational protein targeting to membrane|transmembrane transport	endoplasmic reticulum membrane|integral to membrane	protein binding|receptor activity			ovary(1)	1			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)			CTTTTTTAGAAGATCTGCCTT	0.338													7	750	---	---	---	---	PASS
TMEM67	91147	broad.mit.edu	37	8	94827622	94827622	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94827622T>C	uc011lgk.1	+	27	2925	c.2854T>C	c.(2854-2856)TTG>CTG	p.L952L	TMEM67_uc003yga.3_Silent_p.L871L|TMEM67_uc011lgl.1_Silent_p.L351L	NM_153704	NP_714915	Q5HYA8	MKS3_HUMAN	meckelin isoform 1	952	Helical; (Potential).				cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			TGTTGTGGATTTGGCTTGCCA	0.308													7	739	---	---	---	---	PASS
FZD6	8323	broad.mit.edu	37	8	104337163	104337163	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104337163T>C	uc003ylh.2	+	4	1113	c.829T>C	c.(829-831)TCT>CCT	p.S277P	FZD6_uc003yli.2_Missense_Mutation_p.S277P|FZD6_uc003ylj.2_Missense_Mutation_p.S277P|FZD6_uc011lhn.1_Missense_Mutation_p.S243P|FZD6_uc011lho.1_Intron|FZD6_uc011lhp.1_Missense_Mutation_p.S222P	NM_003506	NP_003497	O60353	FZD6_HUMAN	frizzled 6 isoform a precursor	277	Extracellular (Potential).				angiogenesis|axonogenesis|cell proliferation in midbrain|establishment of planar polarity|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|neural tube closure|non-canonical Wnt receptor signaling pathway	apical part of cell|apicolateral plasma membrane|cytoplasm|integral to plasma membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			TGTCCTAGGCTCTCAAAATAA	0.423													8	599	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110492353	110492353	+	Silent	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110492353C>A	uc003yne.2	+	55	9416	c.9312C>A	c.(9310-9312)ACC>ACA	p.T3104T		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	3104	Extracellular (Potential).|G8 2.				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TGAATGCTACCTACATATCAC	0.333										HNSCC(38;0.096)			5	387	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68414523	68414523	+	RNA	SNP	A	G	G	rs4352957		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68414523A>G	uc004aex.2	+	1		c.1078A>G								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		tgctctagaaatggaacatca	0.000													4	30	---	---	---	---	PASS
SYK	6850	broad.mit.edu	37	9	93657907	93657907	+	3'UTR	SNP	G	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93657907G>C	uc004aqz.2	+	14					SYK_uc004ara.2_3'UTR|SYK_uc004arb.2_3'UTR|SYK_uc004arc.2_3'UTR|SYK_uc011ltr.1_RNA|SYK_uc011lts.1_RNA|SYK_uc011ltt.1_RNA	NM_003177	NP_003168	P43405	KSYK_HUMAN	spleen tyrosine kinase isoform 1						cell proliferation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|neutrophil chemotaxis|organ morphogenesis|platelet activation|protein complex assembly	cytosol|T cell receptor complex	ATP binding|integrin binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5						GTCGGTGGCTGCCTTTGATCA	0.547			T	ETV6|ITK	MDS|peripheral T-cell lymphoma						OREG0019297	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	25	68	---	---	---	---	PASS
CTNNAL1	8727	broad.mit.edu	37	9	111714630	111714630	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111714630A>G	uc004bdo.1	-	14	1736	c.1694T>C	c.(1693-1695)ATA>ACA	p.I565T	CTNNAL1_uc010mts.1_Missense_Mutation_p.I217T|CTNNAL1_uc010mtt.1_Missense_Mutation_p.I565T|CTNNAL1_uc004bdp.1_Missense_Mutation_p.I565T|CTNNAL1_uc004bdq.1_Missense_Mutation_p.I51T	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	catenin, alpha-like 1	565					cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)		AAGCTTTGCTATCTTGGCTTG	0.418													6	782	---	---	---	---	PASS
ZFP37	7539	broad.mit.edu	37	9	115805562	115805562	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115805562A>G	uc004bgm.1	-	4	1364	c.1336T>C	c.(1336-1338)TCA>CCA	p.S446P	ZFP37_uc011lwz.1_Missense_Mutation_p.S461P|ZFP37_uc011lxa.1_Missense_Mutation_p.S447P	NM_003408	NP_003399	Q9Y6Q3	ZFP37_HUMAN	zinc finger protein 37 homolog	446	C2H2-type 6.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2						GTAAGGGATGAGCTATACTTA	0.368													6	280	---	---	---	---	PASS
NMT2	9397	broad.mit.edu	37	10	15175143	15175143	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15175143G>A	uc001inz.1	-	5	595	c.511C>T	c.(511-513)CTC>TTC	p.L171F	NMT2_uc001ioa.1_Missense_Mutation_p.L158F|NMT2_uc009xjo.1_Missense_Mutation_p.L171F|NMT2_uc010qbz.1_5'UTR	NM_004808	NP_004799	O60551	NMT2_HUMAN	N-myristoyltransferase 2	171					N-terminal protein myristoylation|protein lipoylation	Golgi apparatus|plasma membrane	glycylpeptide N-tetradecanoyltransferase activity			ovary(1)	1						AACTCCTTGAGCTATAAGATA	0.378													15	352	---	---	---	---	PASS
RTKN2	219790	broad.mit.edu	37	10	63958010	63958010	+	Missense_Mutation	SNP	T	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63958010T>G	uc001jlw.2	-	12	1584	c.1487A>C	c.(1486-1488)GAT>GCT	p.D496A	RTKN2_uc009xpf.1_Intron|RTKN2_uc001jlv.2_Missense_Mutation_p.D150A	NM_145307	NP_660350	Q8IZC4	RTKN2_HUMAN	rhotekin 2	496					signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)					CCCTTTTTCATCATGTAATGG	0.418													108	314	---	---	---	---	PASS
JMJD1C	221037	broad.mit.edu	37	10	64968907	64968907	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64968907G>C	uc001jmn.2	-	9	3083	c.2783C>G	c.(2782-2784)TCC>TGC	p.S928C	JMJD1C_uc001jml.2_Missense_Mutation_p.S709C|JMJD1C_uc001jmm.2_Missense_Mutation_p.S640C|JMJD1C_uc010qiq.1_Missense_Mutation_p.S746C|JMJD1C_uc009xpi.2_Missense_Mutation_p.S746C|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc009xpk.1_5'Flank	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	928					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)					CTCTGCACTGGAAGGTCTGAC	0.448													114	383	---	---	---	---	PASS
UNC5B	219699	broad.mit.edu	37	10	73050863	73050863	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73050863C>T	uc001jro.2	+	9	1736	c.1291C>T	c.(1291-1293)CCC>TCC	p.P431S	UNC5B_uc001jrp.2_Missense_Mutation_p.P420S	NM_170744	NP_734465	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B precursor	431	Cytoplasmic (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3						GACGGCAAGGCCCAGTAAGAA	0.602													20	78	---	---	---	---	PASS
FAS	355	broad.mit.edu	37	10	90762874	90762874	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90762874C>T	uc001kfr.2	+	2	465	c.119C>T	c.(118-120)ACT>ATT	p.T40I	FAS_uc010qna.1_RNA|FAS_uc001kfs.2_Missense_Mutation_p.T40I|FAS_uc001kft.2_Missense_Mutation_p.T40I|FAS_uc010qnb.1_RNA|FAS_uc010qnc.1_RNA|FAS_uc001kfw.2_Missense_Mutation_p.T40I|FAS_uc010qnd.1_RNA|FAS_uc010qne.1_RNA|FAS_uc009xtp.2_RNA	NM_000043	NP_000034	P25445	TNR6_HUMAN	tumor necrosis factor receptor superfamily,	40	Extracellular (Potential).				activation of caspase activity|activation of pro-apoptotic gene products|anti-apoptosis|cellular response to mechanical stimulus|positive regulation of necrotic cell death	cytosol|extracellular region|integral to membrane|soluble fraction	identical protein binding|kinase binding			upper_aerodigestive_tract(1)|breast(1)	2		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)		TTGAGGAAGACTGTTACTACA	0.428									Autoimmune_Lymphoproliferative_syndrome_type_I				87	271	---	---	---	---	PASS
CEP55	55165	broad.mit.edu	37	10	95276776	95276776	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95276776T>C	uc009xug.2	+	6	946	c.764T>C	c.(763-765)ATA>ACA	p.I255T	CEP55_uc001kiq.3_Missense_Mutation_p.I255T	NM_001127182	NP_001120654	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	255	Potential.				cell division|mitosis	centriole|cleavage furrow|midbody					0		Colorectal(252;0.207)				CGACAAACCATAACTCAGCTG	0.348													7	301	---	---	---	---	PASS
PPRC1	23082	broad.mit.edu	37	10	103907139	103907139	+	Silent	SNP	A	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103907139A>C	uc001kum.2	+	9	4429	c.4390A>C	c.(4390-4392)AGG>CGG	p.R1464R	PPRC1_uc001kun.2_Silent_p.R1344R|PPRC1_uc010qqj.1_Intron|PPRC1_uc009xxa.2_Intron	NM_015062	NP_055877	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor	1464	Arg-rich.|Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		CCCACACAAGAGGTGGCGAAG	0.527													18	36	---	---	---	---	PASS
CYP17A1	1586	broad.mit.edu	37	10	104596868	104596868	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104596868T>A	uc001kwg.2	-	1	423	c.251A>T	c.(250-252)GAG>GTG	p.E84V		NM_000102	NP_000093	P05093	CP17A_HUMAN	cytochrome P450, family 17	84					androgen biosynthetic process|glucocorticoid biosynthetic process|sex differentiation|xenobiotic metabolic process	endoplasmic reticulum membrane	electron carrier activity|heme binding|oxygen binding|steroid 17-alpha-monooxygenase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	NADH(DB00157)|Progesterone(DB00396)	AATAAGCACCTCCTTGGCCAG	0.532													33	139	---	---	---	---	PASS
JAKMIP3	282973	broad.mit.edu	37	10	133978203	133978203	+	Silent	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133978203A>G	uc001lkx.3	+	20	2448	c.2448A>G	c.(2446-2448)GAA>GAG	p.E816E	JAKMIP3_uc009yba.1_Silent_p.E253E	NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		AAAGAATAGAAGCTCAGAAGA	0.398													8	740	---	---	---	---	PASS
NUP98	4928	broad.mit.edu	37	11	3797234	3797234	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3797234T>C	uc001lyh.2	-	5	664	c.373A>G	c.(373-375)AGC>GGC	p.S125G	NUP98_uc001lyi.2_Missense_Mutation_p.S125G|NUP98_uc001lyj.1_Missense_Mutation_p.S125G|NUP98_uc001lyk.1_Missense_Mutation_p.S125G|NUP98_uc010qxv.1_Missense_Mutation_p.S88G	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1	125	Gly/Thr-rich.				carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		CCTCCACTGCTAGTACTGGTT	0.403			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								5	377	---	---	---	---	PASS
ZNF214	7761	broad.mit.edu	37	11	7021244	7021244	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7021244G>C	uc001mfa.2	-	3	1973	c.1670C>G	c.(1669-1671)GCT>GGT	p.A557G	ZNF214_uc010ray.1_Missense_Mutation_p.A557G|ZNF214_uc009yfh.1_Missense_Mutation_p.A557G	NM_013249	NP_037381	Q9UL59	ZN214_HUMAN	zinc finger protein 214	557	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		ACCACACTTAGCACATTGATA	0.403													6	325	---	---	---	---	PASS
ALKBH3	221120	broad.mit.edu	37	11	43919196	43919196	+	Intron	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43919196A>G	uc001mxs.2	+						ALKBH3_uc009ykp.2_Intron|ALKBH3_uc001mxt.2_Intron|ALKBH3_uc009ykq.2_Intron|LOC729799_uc010rfk.1_RNA	NM_139178	NP_631917	Q96Q83	ALKB3_HUMAN	AlkB homolog 3						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation	mitochondrion|nucleoplasm	damaged DNA binding|DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0					Vitamin C(DB00126)	CTGGATGTAGATGCACCAAGA	0.448								Direct_reversal_of_damage					5	177	---	---	---	---	PASS
CD82	3732	broad.mit.edu	37	11	44639740	44639740	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44639740A>G	uc001myc.2	+	8	715	c.467A>G	c.(466-468)TAC>TGC	p.Y156C	CD82_uc001myd.2_Missense_Mutation_p.Y131C	NM_002231	NP_002222	P27701	CD82_HUMAN	CD82 antigen isoform 1	156	Extracellular (Potential).					integral to plasma membrane	protein binding			ovary(1)	1						GTCAGCTTCTACAACTGGACA	0.602													3	18	---	---	---	---	PASS
OR5L1	219437	broad.mit.edu	37	11	55579578	55579578	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55579578G>T	uc001nhw.1	+	1	636	c.636G>T	c.(634-636)ATG>ATT	p.M212I		NM_001004738	NP_001004738	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L,	212	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(2)	5		all_epithelial(135;0.208)				TTACCATCATGATCATCCTCA	0.502													79	250	---	---	---	---	PASS
OR8H2	390151	broad.mit.edu	37	11	55872884	55872884	+	Silent	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55872884C>T	uc010riy.1	+	1	366	c.366C>T	c.(364-366)CGC>CGT	p.R122R		NM_001005200	NP_001005200	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H,	122	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	Esophageal squamous(21;0.00693)					CCCATGATCGCTATGCAGCGA	0.463										HNSCC(53;0.14)			8	466	---	---	---	---	PASS
OR5AR1	219493	broad.mit.edu	37	11	56432011	56432011	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56432011A>T	uc010rjm.1	+	1	850	c.850A>T	c.(850-852)ATG>TTG	p.M284L		NM_001004730	NP_001004730	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR,	284	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TATCATCCCCATGTTAAATCC	0.408													40	92	---	---	---	---	PASS
MS4A8B	83661	broad.mit.edu	37	11	60476202	60476202	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60476202G>A	uc001npv.2	+	5	685	c.482G>A	c.(481-483)AGT>AAT	p.S161N	MS4A8B_uc009yne.1_Missense_Mutation_p.S161N	NM_031457	NP_113645	Q9BY19	M4A8B_HUMAN	membrane-spanning 4-domains, subfamily A, member	161	Extracellular (Potential).					integral to membrane	receptor activity				0						ACAGATCTAAGTATTCCCCAC	0.483													6	422	---	---	---	---	PASS
SAPS3	55291	broad.mit.edu	37	11	68315579	68315579	+	Silent	SNP	T	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68315579T>A	uc001onw.2	+	5	726	c.459T>A	c.(457-459)ATT>ATA	p.I153I	SAPS3_uc010rqb.1_Silent_p.I62I|SAPS3_uc001onv.2_Silent_p.I153I|SAPS3_uc001ony.3_Silent_p.I153I|SAPS3_uc001onx.2_Silent_p.I153I|SAPS3_uc009ysh.2_Silent_p.I153I|SAPS3_uc001onu.2_Silent_p.I153I|SAPS3_uc010rqc.1_Silent_p.I62I	NM_001164161	NP_001157633	Q5H9R7	PP6R3_HUMAN	SAPS domain family, member 3 isoform 6	153					regulation of phosphoprotein phosphatase activity	cytoplasm|nucleus	protein phosphatase binding				0			LUAD - Lung adenocarcinoma(13;0.102)			TAGACCTTATTATAAAGCACA	0.388													166	530	---	---	---	---	PASS
C2CD3	26005	broad.mit.edu	37	11	73814453	73814453	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73814453C>T	uc001ouu.2	-	14	2530	c.2303G>A	c.(2302-2304)CGA>CAA	p.R768Q		NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	768						centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)					TGGTGACTTTCGGTTGGGGAG	0.433													6	784	---	---	---	---	PASS
KIAA1731	85459	broad.mit.edu	37	11	93436013	93436013	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93436013G>A	uc009ywb.1	+	17	5675	c.5524G>A	c.(5524-5526)GAC>AAC	p.D1842N	KIAA1731_uc001pdu.1_Intron	NM_033395	NP_203753	Q9C0D2	K1731_HUMAN	hypothetical protein LOC85459	1842						centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ATGTGGTTTGGACTTAAACCA	0.388													47	212	---	---	---	---	PASS
SLC2A3	6515	broad.mit.edu	37	12	8073897	8073897	+	3'UTR	SNP	G	A	A	rs113911085	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8073897G>A	uc001qtr.2	-	10						NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		GATGAGAAAGGAATTAAGTAG	0.498													5	104	---	---	---	---	PASS
SLC2A3	6515	broad.mit.edu	37	12	8073901	8073901	+	3'UTR	SNP	T	C	C	rs111815763	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8073901T>C	uc001qtr.2	-	10						NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		AGAAAGGAATTAAGTAGCAGC	0.507													6	119	---	---	---	---	PASS
SLCO1A2	6579	broad.mit.edu	37	12	21446888	21446888	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21446888T>C	uc001rer.2	-	10	1679	c.1428A>G	c.(1426-1428)GGA>GGG	p.G476G	SLCO1A2_uc001res.2_Silent_p.G476G|SLCO1A2_uc010siq.1_Silent_p.G344G|SLCO1A2_uc010sio.1_Silent_p.G344G|SLCO1A2_uc010sip.1_Silent_p.G344G|SLCO1A2_uc001ret.2_Silent_p.G474G	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A	476	Extracellular (Potential).|Kazal-like.				bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						CCATGTTTATTCCCGTTCCAA	0.383													6	332	---	---	---	---	PASS
CNPY2	10330	broad.mit.edu	37	12	56704304	56704304	+	3'UTR	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56704304T>C	uc001sku.1	-	6						NM_014255	NP_055070	Q9Y2B0	CNPY2_HUMAN	canopy 2 homolog precursor							endoplasmic reticulum|integral to plasma membrane	protein binding				0						CTGGGGGTGATCCATCAAGCC	0.408													5	187	---	---	---	---	PASS
MON2	23041	broad.mit.edu	37	12	62902396	62902396	+	Intron	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62902396G>T	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srf.2_Intron|MON2_uc001srd.1_3'UTR	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		GTGTAGTCTAGGTACTCTAAA	0.368													3	13	---	---	---	---	PASS
DENR	8562	broad.mit.edu	37	12	123238330	123238330	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123238330C>G	uc001uda.2	+	2	218	c.82C>G	c.(82-84)CCA>GCA	p.P28A	DENR_uc010tag.1_Missense_Mutation_p.P28A|DENR_uc001udb.2_5'UTR	NM_003677	NP_003668	O43583	DENR_HUMAN	density-regulated protein	28							protein binding|translation initiation factor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.28e-05)|Epithelial(86;6.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.199)		TGCCGATTACCCACTTCGAGT	0.433													148	423	---	---	---	---	PASS
TPTE2	93492	broad.mit.edu	37	13	20056679	20056679	+	Missense_Mutation	SNP	T	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20056679T>G	uc001umd.2	-	5	339	c.128A>C	c.(127-129)GAA>GCA	p.E43A	TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Missense_Mutation_p.E43A|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_RNA	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	43						endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		GGAAAGTCGTTCTAACATACT	0.313													5	322	---	---	---	---	PASS
FAM194B	220081	broad.mit.edu	37	13	46124085	46124085	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46124085C>T	uc001val.2	-	13	1754	c.1589G>A	c.(1588-1590)CGG>CAG	p.R530Q		NM_182542	NP_872348	Q5W0A0	F194B_HUMAN	hypothetical protein LOC220081	530										central_nervous_system(1)	1						GATAAGGGCCCGGATCCTCCC	0.443													6	361	---	---	---	---	PASS
LOC647288	647288	broad.mit.edu	37	13	75812784	75812784	+	3'UTR	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75812784A>G	uc010ths.1	-	1						NR_027466				Homo sapiens mRNA; cDNA DKFZp434F0327 (from clone DKFZp434F0327).												0						TGGTAATCTGATGGTCCAGAG	0.522													7	534	---	---	---	---	PASS
SLITRK6	84189	broad.mit.edu	37	13	86369560	86369560	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86369560G>T	uc001vll.1	-	2	1543	c.1084C>A	c.(1084-1086)CCG>ACG	p.P362T	SLITRK6_uc010afe.1_Missense_Mutation_p.P127T	NM_032229	NP_115605	Q9H5Y7	SLIK6_HUMAN	slit and trk like 6 precursor	362	Extracellular (Potential).					integral to membrane				large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		GGATTTTGCGGAGGAGGTCTC	0.413													80	209	---	---	---	---	PASS
RNASE12	493901	broad.mit.edu	37	14	21058759	21058759	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21058759G>T	uc001vxt.2	-	1	224	c.124C>A	c.(124-126)CCT>ACT	p.P42T	RNASE11_uc010ahv.2_5'Flank|RNASE11_uc010ahx.2_5'Flank|RNASE11_uc010ahw.2_5'Flank|RNASE11_uc001vxs.2_5'Flank|uc001vxu.1_RNA	NM_001024822	NP_001019993	Q5GAN4	RNS12_HUMAN	ribonuclease, RNase A family, 12 (non-active)	42						extracellular region	nucleic acid binding|pancreatic ribonuclease activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(95;0.00238)		Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.013)		TACCTTGCAGGAACGGGAACG	0.453													12	332	---	---	---	---	PASS
DHRS4	10901	broad.mit.edu	37	14	24424420	24424420	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24424420C>T	uc001wla.2	+	2	338	c.305C>T	c.(304-306)ACG>ATG	p.T102M	C14orf167_uc001wkz.2_5'Flank|C14orf167_uc001wky.2_5'Flank|C14orf167_uc001wkx.2_5'Flank|C14orf167_uc010akx.1_5'Flank|DHRS4_uc010aky.2_Missense_Mutation_p.T102M|DHRS4_uc001wlb.2_Missense_Mutation_p.T102M|DHRS4_uc010akz.2_Missense_Mutation_p.T102M|DHRS4_uc001wlc.3_Missense_Mutation_p.T102M|DHRS4L2_uc001wld.3_Missense_Mutation_p.T102M|DHRS4L2_uc001wle.3_Missense_Mutation_p.T102M	NM_021004	NP_066284	Q9BTZ2	DHRS4_HUMAN	peroxisomal short-chain alcohol dehydrogenase	102				T -> M (in Ref. 1; AAD02292).		mitochondrion|nuclear membrane|peroxisome	binding|carbonyl reductase (NADPH) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CTGGTGGCCACGGTGAGCTGC	0.652													6	14	---	---	---	---	PASS
LRFN5	145581	broad.mit.edu	37	14	42356893	42356893	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42356893T>A	uc001wvm.2	+	3	2263	c.1065T>A	c.(1063-1065)TTT>TTA	p.F355L	LRFN5_uc010ana.2_Missense_Mutation_p.F355L	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	355	Extracellular (Potential).|Ig-like.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		CAGGTGCTTTTACCTGCATTG	0.393										HNSCC(30;0.082)			17	191	---	---	---	---	PASS
TRIM9	114088	broad.mit.edu	37	14	51475810	51475810	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51475810C>T	uc001wyx.3	-	5	2059	c.1294G>A	c.(1294-1296)GTG>ATG	p.V432M	TRIM9_uc001wyy.2_Missense_Mutation_p.V432M|TRIM9_uc001wyz.3_Missense_Mutation_p.V432M	NM_015163	NP_055978	Q9C026	TRIM9_HUMAN	tripartite motif protein 9 isoform 1	432	COS.				proteasomal ubiquitin-dependent protein catabolic process	cell junction|cytoskeleton|dendrite|synaptic vesicle	protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			skin(2)|lung(1)	3	all_epithelial(31;0.00418)|Breast(41;0.148)					TTCACTTGCACGAAATCCAGC	0.517													4	187	---	---	---	---	PASS
RTN1	6252	broad.mit.edu	37	14	60212905	60212905	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60212905T>C	uc001xen.1	-	2	745	c.536A>G	c.(535-537)AAC>AGC	p.N179S		NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	179					neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TAAGATCTTGTTCACTTCCGT	0.493													6	405	---	---	---	---	PASS
FLRT2	23768	broad.mit.edu	37	14	86089421	86089421	+	Silent	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86089421C>T	uc001xvr.2	+	2	2330	c.1563C>T	c.(1561-1563)AAC>AAT	p.N521N	FLRT2_uc010atd.2_Silent_p.N521N	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	521	Extracellular (Potential).				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)		ATCTGAACAACGGCAGCAACA	0.567													9	39	---	---	---	---	PASS
PPP4R4	57718	broad.mit.edu	37	14	94722860	94722860	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94722860T>C	uc001ycs.1	+	17	2083	c.1929T>C	c.(1927-1929)CAT>CAC	p.H643H		NM_058237	NP_478144	Q6NUP7	PP4R4_HUMAN	HEAT-like repeat-containing protein isoform 1	643						cytoplasm|protein serine/threonine phosphatase complex	protein binding			skin(3)|upper_aerodigestive_tract(1)	4						CTGATAAGCATCTACTTCAGC	0.353													7	657	---	---	---	---	PASS
DICER1	23405	broad.mit.edu	37	14	95599728	95599728	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95599728G>T	uc001ydw.2	-	3	250	c.68C>A	c.(67-69)CCA>CAA	p.P23Q	DICER1_uc001ydv.2_Missense_Mutation_p.P13Q|DICER1_uc001ydx.2_Missense_Mutation_p.P23Q|DICER1_uc001ydz.1_RNA|DICER1_uc001yea.1_RNA|DICER1_uc001yeb.1_RNA|DICER1_uc001yec.1_RNA	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	23					negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		AGGACCCATTGGTGAGGAAGC	0.443			Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				5	420	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106134536	106134536	+	Intron	SNP	T	C	C	rs3211548		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106134536T>C	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001ysb.1_RNA					Parts of antibodies, mostly variable regions.												0						AGCATCCTCGTGCGACCGCGA	0.642													5	84	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107062402	107062402	+	RNA	SNP	G	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107062402G>C	uc010tyt.1	-	131		c.6193C>G								Parts of antibodies, mostly variable regions.												0						TCCTGGGCCCGACTCCTGCAG	0.597													4	84	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	20193216	20193216	+	RNA	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20193216G>T	uc010tyv.1	-	2		c.54C>A								Homo sapiens immunoglobulin heavy chain leader and variable region mRNA, partial cds.																		ACCTCACACTGGACACCTGCA	0.537													43	121	---	---	---	---	PASS
GABRG3	2567	broad.mit.edu	37	15	27572012	27572012	+	Silent	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27572012C>T	uc001zbg.1	+	4	493	c.327C>T	c.(325-327)TTC>TTT	p.F109F	GABRG3_uc001zbf.2_Silent_p.F109F	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma	109	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		GCCTTCGATTCAACAGCACAA	0.423													5	341	---	---	---	---	PASS
TRPM1	4308	broad.mit.edu	37	15	31294653	31294653	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31294653A>G	uc001zfm.2	-	27	4312	c.4184T>C	c.(4183-4185)GTT>GCT	p.V1395A	TRPM1_uc010azy.2_Missense_Mutation_p.V1302A|TRPM1_uc001zfl.2_RNA	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	1395	Cytoplasmic (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		AGTGTTTTGAACATCTGATTT	0.373													7	595	---	---	---	---	PASS
AQR	9716	broad.mit.edu	37	15	35236588	35236588	+	Missense_Mutation	SNP	T	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35236588T>G	uc001ziv.2	-	6	553	c.372A>C	c.(370-372)AAA>AAC	p.K124N		NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius	124						catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TCAAGATGTGTTTAAAAAAGA	0.338													90	321	---	---	---	---	PASS
BUB1B	701	broad.mit.edu	37	15	40504838	40504838	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40504838T>C	uc001zkx.3	+	19	2736	c.2524T>C	c.(2524-2526)TTC>CTC	p.F842L		NM_001211	NP_001202	O60566	BUB1B_HUMAN	budding uninhibited by benzimidazoles 1 beta	842	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		TATAAACTGCTTCACCCTTCA	0.333			Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				9	623	---	---	---	---	PASS
FRMD5	84978	broad.mit.edu	37	15	44168408	44168408	+	Intron	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44168408G>A	uc001ztl.2	-						FRMD5_uc001ztj.1_Intron|FRMD5_uc001ztk.1_Intron|FRMD5_uc010uef.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron|LOC728758_uc010bdt.1_RNA	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		CCCTTTCCCCGCTTTTCCAGA	0.502													59	173	---	---	---	---	PASS
CEP152	22995	broad.mit.edu	37	15	49089548	49089548	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49089548G>T	uc001zwy.2	-	5	524	c.490C>A	c.(490-492)CAA>AAA	p.Q164K	CEP152_uc001zwz.2_Missense_Mutation_p.Q164K|CEP152_uc001zxa.1_Intron	NM_014985	NP_055800	O94986	CE152_HUMAN	centrosomal protein 152kDa	164					centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding			lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TTGGTTGCTTGGTTATTAAAT	0.353													115	438	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54916113	54916113	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54916113G>A	uc002ack.2	+	30	6320	c.6320G>A	c.(6319-6321)AGC>AAC	p.S2107N	UNC13C_uc002acm.2_Missense_Mutation_p.S28N	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	2107	C2 2.				exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AAAACAAAAAGCAACACATGG	0.418													7	534	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	21902088	21902088	+	RNA	SNP	C	T	T	rs55647608	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21902088C>T	uc002djs.3	-	2		c.157G>A			uc010vbo.1_RNA|uc002dju.1_5'Flank					Homo sapiens cDNA FLJ45371 fis, clone BRHIP3017855, highly  similar to Homo sapiens nuclear pore complex interacting protein (NPIP).																		GTCTTACTGTCAGCTAAAAGG	0.373													4	64	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	21902089	21902089	+	RNA	SNP	A	G	G	rs56214519	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21902089A>G	uc002djs.3	-	2		c.156T>C			uc010vbo.1_RNA|uc002dju.1_5'Flank					Homo sapiens cDNA FLJ45371 fis, clone BRHIP3017855, highly  similar to Homo sapiens nuclear pore complex interacting protein (NPIP).																		TCTTACTGTCAGCTAAAAGGC	0.373													4	64	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	21902166	21902166	+	RNA	SNP	C	A	A	rs55667229		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21902166C>A	uc002djs.3	-	2		c.79G>T			uc010vbo.1_RNA|uc002dju.1_5'Flank					Homo sapiens cDNA FLJ45371 fis, clone BRHIP3017855, highly  similar to Homo sapiens nuclear pore complex interacting protein (NPIP).																		TTCTTCATTACAACAGCTACT	0.318													4	78	---	---	---	---	PASS
SLC5A11	115584	broad.mit.edu	37	16	24920266	24920266	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24920266T>A	uc002dmu.2	+	14	1731	c.1499T>A	c.(1498-1500)ATT>AAT	p.I500N	SLC5A11_uc002dms.2_Missense_Mutation_p.I436N|SLC5A11_uc010vcd.1_Missense_Mutation_p.I465N|SLC5A11_uc002dmt.2_Missense_Mutation_p.I344N|SLC5A11_uc010vce.1_Missense_Mutation_p.I430N|SLC5A11_uc010bxt.2_Missense_Mutation_p.I436N|SLC5A11_uc002dmv.2_Missense_Mutation_p.I123N	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	500	Helical; (Potential).				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)		CTGGACTTTATTTACGTGCAG	0.567													37	152	---	---	---	---	PASS
SLC5A11	115584	broad.mit.edu	37	16	24920271	24920271	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24920271G>C	uc002dmu.2	+	14	1736	c.1504G>C	c.(1504-1506)GTG>CTG	p.V502L	SLC5A11_uc002dms.2_Missense_Mutation_p.V438L|SLC5A11_uc010vcd.1_Missense_Mutation_p.V467L|SLC5A11_uc002dmt.2_Missense_Mutation_p.V346L|SLC5A11_uc010vce.1_Missense_Mutation_p.V432L|SLC5A11_uc010bxt.2_Missense_Mutation_p.V438L|SLC5A11_uc002dmv.2_Missense_Mutation_p.V125L	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	502	Extracellular (Potential).				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)		CTTTATTTACGTGCAGCCTCG	0.557													37	143	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	32266379	32266379	+	RNA	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32266379A>G	uc002ecy.2	+	4		c.1018A>G			uc010cav.1_RNA					Homo sapiens mRNA for TP53TG3b, complete cds.																		GTTCTAAGGTAAAGAATGGAA	0.274													4	206	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	32266466	32266466	+	RNA	SNP	A	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32266466A>C	uc002ecy.2	+	4		c.1105A>C			uc010cav.1_RNA					Homo sapiens mRNA for TP53TG3b, complete cds.																		TCTCCAAGACAAAAACTCTAA	0.328													4	63	---	---	---	---	PASS
PSMB10	5699	broad.mit.edu	37	16	67968459	67968459	+	3'UTR	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67968459C>T	uc002eux.1	-	8					CTRL_uc002euw.2_5'Flank	NM_002801	NP_002792	P40306	PSB10_HUMAN	proteasome beta 10 subunit proprotein						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|humoral immune response|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)		CTCTAAGCCTCAGCTTACTCC	0.522													58	239	---	---	---	---	PASS
ESRP2	80004	broad.mit.edu	37	16	68265514	68265514	+	Silent	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68265514C>A	uc010cfa.1	-	11	1601	c.1413G>T	c.(1411-1413)GGG>GGT	p.G471G	ESRP2_uc002evp.1_RNA|ESRP2_uc002evq.1_Silent_p.G461G	NM_024939	NP_079215	Q9H6T0	ESRP2_HUMAN	RNA binding motif protein 35B	471					mRNA processing|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding|nucleotide binding			ovary(1)	1						CCCTCCCAGTCCCAGGTGCCA	0.622													8	168	---	---	---	---	PASS
HYDIN	54768	broad.mit.edu	37	16	71218851	71218851	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71218851C>T	uc002ezr.2	-	3	306	c.178G>A	c.(178-180)GAG>AAG	p.E60K	HYDIN_uc010cfz.1_5'UTR|HYDIN_uc002ezv.2_Missense_Mutation_p.E60K|HYDIN_uc010vmc.1_Missense_Mutation_p.E77K|HYDIN_uc010vmd.1_Missense_Mutation_p.E87K|HYDIN_uc002ezw.3_Missense_Mutation_p.E77K	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	60										ovary(1)|skin(1)	2		Ovarian(137;0.0654)				AGTCTCTGCTCGGTGGTCAGG	0.438													9	436	---	---	---	---	PASS
TERF2IP	54386	broad.mit.edu	37	16	75690596	75690596	+	3'UTR	SNP	C	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75690596C>G	uc002fet.1	+	3						NM_018975	NP_061848	Q9NYB0	TE2IP_HUMAN	telomeric repeat binding factor 2, interacting						negative regulation of DNA recombination at telomere|negative regulation of telomere maintenance|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|regulation of double-strand break repair via homologous recombination|telomere maintenance via telomerase|transcription, DNA-dependent	cytoplasm|nuclear telomere cap complex|nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1						AGAGTTCTTGCATTGGAACTG	0.378													7	27	---	---	---	---	PASS
PLCG2	5336	broad.mit.edu	37	16	81954855	81954855	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81954855G>A	uc002fgt.2	+	21	2440	c.2288G>A	c.(2287-2289)AGT>AAT	p.S763N	PLCG2_uc010chg.1_Missense_Mutation_p.S763N	NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2	763					intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8						GTGGATCCCAGTGAAATCAAT	0.433													68	304	---	---	---	---	PASS
NCOR1	9611	broad.mit.edu	37	17	15976760	15976760	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15976760A>G	uc002gpo.2	-	28	4034	c.3794T>C	c.(3793-3795)GTA>GCA	p.V1265A	NCOR1_uc002gpn.2_Missense_Mutation_p.V1281A|NCOR1_uc002gpp.1_Missense_Mutation_p.V1172A|NCOR1_uc010vwb.1_Intron|NCOR1_uc010coy.2_Missense_Mutation_p.V173A|NCOR1_uc010vwc.1_Missense_Mutation_p.V76A	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1	1265	Interaction with ETO.				cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CGGTGCTGATACAGGAGACTC	0.343													7	474	---	---	---	---	PASS
SLC47A2	146802	broad.mit.edu	37	17	19611861	19611861	+	Intron	SNP	A	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19611861A>C	uc002gwe.3	-						SLC47A2_uc002gwg.3_Intron|SLC47A2_uc002gwf.3_Intron|SLC47A2_uc002gwh.3_RNA|SLC47A2_uc002gwi.2_Intron|SLC47A2_uc010cqs.1_Intron|SLC47A2_uc010cqt.1_Intron	NM_152908	NP_690872	Q86VL8	S47A2_HUMAN	solute carrier family 47, member 2 isoform 1							integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)					ACAGCCTCTCACCTGCCTCTG	0.597													5	21	---	---	---	---	PASS
SUZ12P	440423	broad.mit.edu	37	17	29061807	29061807	+	Intron	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29061807A>G	uc002hfn.1	+						SUZ12P_uc002hfo.2_Intron|SUZ12P_uc002hfp.2_Intron|SUZ12P_uc002hfq.2_RNA					Homo sapiens cDNA clone IMAGE:5299523, containing frame-shift errors.												0						TTAGTGCGTGATTTCCATAGC	0.299													6	159	---	---	---	---	PASS
SOCS7	30837	broad.mit.edu	37	17	36523827	36523827	+	Silent	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36523827A>G	uc002hqa.2	+	6	1377	c.1254A>G	c.(1252-1254)CCA>CCG	p.P418P	SOCS7_uc010cvl.2_Silent_p.P384P|SOCS7_uc002hqb.2_RNA	NM_014598	NP_055413	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	418	Mediates interaction with SORBS3.|SH2.				intracellular signal transduction|negative regulation of signal transduction|regulation of growth	cytoplasm|nucleus|plasma membrane	protein binding|SH3 domain binding			skin(1)	1	Breast(7;3.47e-17)					AAGGGAAACCAGATGGTTCTT	0.478													159	473	---	---	---	---	PASS
IGFBP4	3487	broad.mit.edu	37	17	38610249	38610249	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38610249C>T	uc002hus.2	+	3	889	c.577C>T	c.(577-579)CAC>TAC	p.H193Y		NM_001552	NP_001543	P22692	IBP4_HUMAN	insulin-like growth factor binding protein 4	193	Thyroglobulin type-1.				DNA metabolic process|signal transduction|skeletal system development						0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			GAGCCGCACCCACGAGGACCT	0.657													36	110	---	---	---	---	PASS
MPP2	4355	broad.mit.edu	37	17	41960604	41960604	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41960604C>G	uc010wip.1	-	4	462	c.405G>C	c.(403-405)GAG>GAC	p.E135D	MPP2_uc002ien.1_Missense_Mutation_p.E107D|MPP2_uc010wim.1_Missense_Mutation_p.E79D|MPP2_uc002ieo.1_Missense_Mutation_p.E90D|MPP2_uc010win.1_5'UTR|MPP2_uc010wio.1_Missense_Mutation_p.E79D|MPP2_uc010czm.1_Missense_Mutation_p.E73D	NM_005374	NP_005365	Q14168	MPP2_HUMAN	palmitoylated membrane protein 2	114	L27 2.				signal transduction	cell surface|integral to plasma membrane|membrane fraction	guanylate kinase activity				0		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		TGTGGGCCAGCTCGGCGGCTG	0.657													9	22	---	---	---	---	PASS
STH	246744	broad.mit.edu	37	17	44076968	44076968	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44076968A>C	uc002ijy.2	+	1	353	c.323A>C	c.(322-324)CAC>CCC	p.H108P	MAPT_uc010dau.2_Intron|MAPT_uc002ijr.3_Intron|MAPT_uc002ijs.3_Intron|MAPT_uc002ijx.3_Intron|MAPT_uc002ijt.3_Intron|MAPT_uc002iju.3_Intron|MAPT_uc002ijv.3_Intron	NM_001007532	NP_001007533	Q8IWL8	STH_HUMAN	saitohin	108						cytoplasm|nucleus					0						TGTCCCTCCCACCCTGCAGCT	0.587													8	35	---	---	---	---	PASS
C17orf47	284083	broad.mit.edu	37	17	56620394	56620394	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56620394A>T	uc002iwq.1	-	1	1290	c.1154T>A	c.(1153-1155)ATG>AAG	p.M385K	SEPT4_uc010wnx.1_5'Flank|SEPT4_uc010wny.1_5'Flank	NM_001038704	NP_001033793	Q8NEP4	CQ047_HUMAN	hypothetical protein LOC284083	385										breast(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCCTTGGGACATGTAAGTAAT	0.507													187	596	---	---	---	---	PASS
WIPI1	55062	broad.mit.edu	37	17	66429705	66429705	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66429705A>G	uc010dey.2	-	8	795	c.704T>C	c.(703-705)ATC>ACC	p.I235T	WIPI1_uc002jhd.3_RNA|WIPI1_uc010wqo.1_Missense_Mutation_p.I153T|WIPI1_uc002jhe.3_RNA	NM_017983	NP_060453	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting	235	WD 2.				macroautophagy|vesicle targeting, trans-Golgi to endosome	autophagic vacuole membrane|clathrin-coated vesicle|cytosol|endosome membrane|PAS complex|pre-autophagosomal structure membrane|trans-Golgi network	androgen receptor binding|estrogen receptor binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding				0						TAGAGAGCTGATTGTCACATA	0.453													5	234	---	---	---	---	PASS
PTPN2	5771	broad.mit.edu	37	18	12802033	12802033	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12802033T>C	uc002krp.2	-	8	1170	c.976A>G	c.(976-978)ACA>GCA	p.T326A	PTPN2_uc002krl.2_Missense_Mutation_p.T326A|PTPN2_uc002krn.2_Missense_Mutation_p.T349A|PTPN2_uc002kro.2_Missense_Mutation_p.T326A|PTPN2_uc002krm.2_Missense_Mutation_p.T326A	NM_002828	NP_002819	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type	326					interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway	endoplasmic reticulum|nucleoplasm	protein binding			skin(2)	2		Lung NSC(161;8.94e-06)				CGGTCACCTGTCAGTTTTTCT	0.388													8	740	---	---	---	---	PASS
CDH2	1000	broad.mit.edu	37	18	25532271	25532271	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25532271A>T	uc002kwg.2	-	16	3026	c.2567T>A	c.(2566-2568)TTA>TAA	p.L856*	CDH2_uc010xbn.1_Nonsense_Mutation_p.L825*	NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein	856	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4						GTCAAACACTAACAGGGAGTC	0.478											OREG0003876	type=REGULATORY REGION|Gene=CDH2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	76	231	---	---	---	---	PASS
GNG7	2788	broad.mit.edu	37	19	2514986	2514986	+	3'UTR	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2514986G>A	uc002lwd.2	-	5					GNG7_uc010dte.1_Intron	NM_052847	NP_443079	O60262	GBG7_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gagagagaaagagagagagag	0.308													4	76	---	---	---	---	PASS
ZNF555	148254	broad.mit.edu	37	19	2853267	2853267	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2853267G>A	uc002lwo.2	+	4	1293	c.1204G>A	c.(1204-1206)GGG>AGG	p.G402R	ZNF555_uc002lwn.3_Missense_Mutation_p.G401R	NM_152791	NP_690004	Q8NEP9	ZN555_HUMAN	zinc finger protein 555	402	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAACCAGTGCGGGAAAGCATT	0.483													20	68	---	---	---	---	PASS
ZNF709	163051	broad.mit.edu	37	19	12574850	12574850	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12574850C>T	uc002mtv.3	-	4	2047	c.1886G>A	c.(1885-1887)CGT>CAT	p.R629H	ZNF709_uc002mtw.3_Missense_Mutation_p.R597H|ZNF709_uc002mtx.3_Missense_Mutation_p.R629H	NM_152601	NP_689814	Q8N972	ZN709_HUMAN	zinc finger protein 709 isoform a	629	C2H2-type 19.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TCGAAAGGAACGGGAACACTT	0.383													57	164	---	---	---	---	PASS
SLC7A9	11136	broad.mit.edu	37	19	33333132	33333132	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33333132G>A	uc002ntv.3	-	11	1283	c.1166C>T	c.(1165-1167)ACG>ATG	p.T389M	SLC7A9_uc002ntt.3_RNA|SLC7A9_uc002ntu.3_Missense_Mutation_p.T389M|SLC7A9_uc002ntw.3_Missense_Mutation_p.T180M	NM_001126335	NP_001119807	P82251	BAT1_HUMAN	solute carrier family 7, member 9	389	Helical; (Potential).				blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	integral to plasma membrane	L-cystine transmembrane transporter activity|neutral amino acid transmembrane transporter activity|peptide antigen binding			skin(1)	1	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	TCCTAGAATCGTCAGGCCATA	0.428													7	181	---	---	---	---	PASS
DEFB127	140850	broad.mit.edu	37	20	139589	139589	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:139589C>T	uc002wcy.1	+	2	224	c.224C>T	c.(223-225)GCA>GTA	p.A75V		NM_139074	NP_620713	Q9H1M4	DB127_HUMAN	defensin, beta 127 preproprotein	75				PATL -> QHLH (in Ref. 5; AAM93920).	defense response to bacterium|innate immune response	extracellular region					0		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			CCAAAGCCAGCAACACTTGCA	0.388													5	320	---	---	---	---	PASS
XRN2	22803	broad.mit.edu	37	20	21335430	21335430	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21335430T>C	uc002wsf.1	+	21	2035	c.1940T>C	c.(1939-1941)GTT>GCT	p.V647A	XRN2_uc002wsg.1_Missense_Mutation_p.V571A|XRN2_uc010zsk.1_Missense_Mutation_p.V593A	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	647					cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1						TTTTCAGGTGTTGCTCTCTTG	0.448													7	534	---	---	---	---	PASS
FAM182A	284800	broad.mit.edu	37	20	26061815	26061815	+	RNA	SNP	C	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26061815C>G	uc010gdq.2	+	4		c.876C>G				NR_026713				Homo sapiens cDNA FLJ38374 fis, clone FEBRA2002552.												0						TTTGATTTCTCCTGCTTAGAA	0.413													5	94	---	---	---	---	PASS
PFDN4	5203	broad.mit.edu	37	20	52835632	52835632	+	Silent	SNP	A	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52835632A>G	uc002xwx.2	+	4	486	c.348A>G	c.(346-348)AAA>AAG	p.K116K		NM_002623	NP_002614	Q9NQP4	PFD4_HUMAN	prefoldin subunit 4	116					'de novo' posttranslational protein folding	prefoldin complex	chaperone binding|unfolded protein binding				0	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		Colorectal(105;0.124)|STAD - Stomach adenocarcinoma(23;0.206)			CAGATTTGAAAGTTCAGTTGT	0.279													9	643	---	---	---	---	PASS
C21orf56	84221	broad.mit.edu	37	21	47588274	47588274	+	Silent	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47588274C>T	uc011afu.1	-	3	1554	c.492G>A	c.(490-492)TCG>TCA	p.S164S	C21orf56_uc002zii.2_Silent_p.S10S	NM_001142854	NP_001136326	Q9H0A9	CU056_HUMAN	hypothetical protein LOC84221 isoform 1	164							protein binding			skin(1)	1	Breast(49;0.214)			Colorectal(79;0.241)		GGCTGCTCTCCGAGAAACACA	0.662													10	24	---	---	---	---	PASS
PATZ1	23598	broad.mit.edu	37	22	31731735	31731735	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31731735C>T	uc003akq.2	-	3	2111	c.1450G>A	c.(1450-1452)GAC>AAC	p.D484N	PATZ1_uc003akp.2_Missense_Mutation_p.D484N|PATZ1_uc003akr.2_Missense_Mutation_p.D484N	NM_014323	NP_055138	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	484					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/PATZ1(2)	soft_tissue(2)	2						TTCAGGTGGTCTGCCATGTAT	0.577													4	148	---	---	---	---	PASS
CYB5R3	1727	broad.mit.edu	37	22	43036196	43036196	+	Intron	SNP	C	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43036196C>T	uc003bcz.2	-						CYB5R3_uc011aps.1_Intron|CYB5R3_uc003bcy.2_Intron|CYB5R3_uc003bcx.2_Intron|ATP5L2_uc003bda.1_RNA	NM_000398	NP_000389	P00387	NB5R3_HUMAN	cytochrome b5 reductase 3 isoform m						blood circulation|cholesterol biosynthetic process|water-soluble vitamin metabolic process	endoplasmic reticulum membrane|hemoglobin complex|mitochondrial outer membrane	cytochrome-b5 reductase activity			skin(1)	1					NADH(DB00157)	TACCAAAATGCGGCCAATCGA	0.507													5	312	---	---	---	---	PASS
MAP3K15	389840	broad.mit.edu	37	X	19398325	19398325	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19398325G>C	uc004czk.1	-	20	2564	c.927C>G	c.(925-927)ATC>ATG	p.I309M	MAP3K15_uc004czj.1_Missense_Mutation_p.I269M	NM_001001671	NP_001001671	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase	834	Protein kinase.						ATP binding|MAP kinase kinase kinase activity|metal ion binding			ovary(3)|lung(2)|stomach(1)|skin(1)	7	Hepatocellular(33;0.183)					CCAGGGACCAGATATCGGCTG	0.542													32	42	---	---	---	---	PASS
USP9X	8239	broad.mit.edu	37	X	41077688	41077688	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41077688C>A	uc004dfb.2	+	37	6906	c.6273C>A	c.(6271-6273)AAC>AAA	p.N2091K	USP9X_uc004dfc.2_Missense_Mutation_p.N2091K	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	2091					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						TTGCTCATAACGTCCTTTTTA	0.378													19	431	---	---	---	---	PASS
CAPN6	827	broad.mit.edu	37	X	110494226	110494226	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110494226G>T	uc004epc.1	-	8	1245	c.1077C>A	c.(1075-1077)TGC>TGA	p.C359*	CAPN6_uc011msu.1_Nonsense_Mutation_p.C104*	NM_014289	NP_055104	Q9Y6Q1	CAN6_HUMAN	calpain 6	359	Domain III.				microtubule bundle formation|proteolysis|regulation of cytoskeleton organization	perinuclear region of cytoplasm|spindle microtubule	calcium-dependent cysteine-type endopeptidase activity|microtubule binding			ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|skin(1)	6						CCACAGTCCAGCATCCCAACA	0.488													77	81	---	---	---	---	PASS
STAG2	10735	broad.mit.edu	37	X	123205068	123205068	+	Silent	SNP	T	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123205068T>C	uc004etz.3	+	24	2767	c.2428T>C	c.(2428-2430)TTA>CTA	p.L810L	STAG2_uc004eua.2_Silent_p.L810L|STAG2_uc004eub.2_Silent_p.L810L|STAG2_uc004euc.2_Silent_p.L810L|STAG2_uc004eud.2_Silent_p.L810L|STAG2_uc004eue.2_Silent_p.L810L	NM_006603	NP_006594	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform b	810					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5						GCGTGACATGTTAGAGCCATT	0.363													6	403	---	---	---	---	PASS
MAGEA3	4102	broad.mit.edu	37	X	151935587	151935587	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151935587G>A	uc004fgp.2	-	3	789	c.580C>T	c.(580-582)CAG>TAG	p.Q194*		NM_005362	NP_005353	P43357	MAGA3_HUMAN	melanoma antigen family A, 3	194	MAGE.										0	Acute lymphoblastic leukemia(192;6.56e-05)					GGCATGATCTGATTGTCACCC	0.572													4	95	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	2881644	2881645	+	IGR	INS	-	ACTA	ACTA	rs146732536	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2881644_2881645insACTA								MMEL1 (317163 upstream) : ACTRT2 (56401 downstream)																							ccatccatcttactactattca	0.000													4	2	---	---	---	---	
KIAA0562	9731	broad.mit.edu	37	1	3745416	3745417	+	Intron	INS	-	AA	AA	rs147402042	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3745416_3745417insAA	uc001aky.2	-						KIAA0562_uc010nzm.1_Intron	NM_014704	NP_055519	O60308	CE104_HUMAN	glycine-, glutamate-,							centriole	binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)		CCCACAGGCTTAGAGTAAGGGC	0.406													2	4	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7346422	7346422	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7346422delG	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		gggtggtcctggaagatcgtc	0.214													4	2	---	---	---	---	
PER3	8863	broad.mit.edu	37	1	7846538	7846541	+	Intron	DEL	TTAG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7846538_7846541delTTAG	uc001aoo.2	+						PER3_uc009vmg.1_Intron|PER3_uc009vmh.1_Intron|PER3_uc001aop.2_Intron|PER3_uc010nzw.1_Intron|PER3_uc001aon.2_Intron	NM_016831	NP_058515	P56645	PER3_HUMAN	period 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			ovary(1)|pancreas(1)|skin(1)	3	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		TCTGAAATTTTTAGTTAGTACCTT	0.343													6	7	---	---	---	---	
H6PD	9563	broad.mit.edu	37	1	9326518	9326518	+	3'UTR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9326518delA	uc001apt.2	+	5						NM_004285	NP_004276	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase precursor							endoplasmic reticulum lumen	6-phosphogluconolactonase activity|glucose 1-dehydrogenase|glucose-6-phosphate dehydrogenase activity|NADP binding				0	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)	NADH(DB00157)	CATTCTTTTTAAAAACACCAC	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	9700646	9700646	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9700646delA								TMEM201 (25711 upstream) : PIK3CD (11144 downstream)																							tcaaaaaaagaaaaaaaaaaa	0.000													4	4	---	---	---	---	
CASZ1	54897	broad.mit.edu	37	1	10817356	10817356	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10817356delC	uc001aro.2	-						CASZ1_uc001arp.1_Intron	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		catcctggggccctctctttt	0.189													4	2	---	---	---	---	
MTHFR	4524	broad.mit.edu	37	1	11862764	11862765	+	Intron	INS	-	T	T	rs139582202	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11862764_11862765insT	uc001atc.1	-						MTHFR_uc001atb.1_Intron	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase						blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)	TGTGGAGGGACTTTTACAGGCA	0.490													2	5	---	---	---	---	
TNFRSF8	943	broad.mit.edu	37	1	12198204	12198204	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12198204delA	uc001atq.2	+						TNFRSF8_uc010obc.1_Intron|TNFRSF8_uc001atr.2_Intron|TNFRSF8_uc001ats.2_Intron	NM_001243	NP_001234	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily,						cellular response to mechanical stimulus|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of TRAIL biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	cytoplasm|integral to membrane|plasma membrane				skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	5	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)		TGTAGAGATGAAAAAAAAAAG	0.552													6	3	---	---	---	---	
CROCCL2	114819	broad.mit.edu	37	1	16805042	16805042	+	5'Flank	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16805042delG	uc001ayr.3	-						CROCCL2_uc001ayt.2_Intron|CROCCL2_uc001ays.2_Intron					Homo sapiens mRNA for KIAA1922 protein, partial cds.												0						CCTGCCTCCAGGAAGCCTTCC	0.572													4	2	---	---	---	---	
CROCCL1	84809	broad.mit.edu	37	1	16962833	16962836	+	Intron	DEL	CAAA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16962833_16962836delCAAA	uc001azg.1	-						CROCCL1_uc001azf.2_5'Flank|CROCCL1_uc001azi.1_Intron|uc001azj.1_Intron					Homo sapiens mRNA for FLJ00313 protein.												0						gactccatctcaaacaaacaaaca	0.000													4	2	---	---	---	---	
PADI4	23569	broad.mit.edu	37	1	17688118	17688118	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17688118delT	uc001baj.2	+							NM_012387	NP_036519	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV						chromatin modification|peptidyl-citrulline biosynthetic process from peptidyl-arginine|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	ctaattgtcattgcaacggag	0.129													4	2	---	---	---	---	
HSPG2	3339	broad.mit.edu	37	1	22250286	22250287	+	Intron	INS	-	T	T	rs151297504	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22250286_22250287insT	uc001bfj.2	-						HSPG2_uc009vqd.2_Intron	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor						angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	taagcccacggtggtgtttaga	0.168													4	4	---	---	---	---	
SRRM1	10250	broad.mit.edu	37	1	24971091	24971091	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24971091delC	uc001bjm.2	+						SRRM1_uc010oel.1_Intron|SRRM1_uc009vrh.1_Intron	NM_005839	NP_005830	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nuclear matrix|nuclear speck	DNA binding|protein binding|RNA binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		AGAATGTTATCCCCCAAGTAT	0.333													4	2	---	---	---	---	
TMEM57	55219	broad.mit.edu	37	1	25812781	25812781	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25812781delA	uc001bkk.2	+						TMEM57_uc009vru.2_Intron|TMEM57_uc009vrv.2_Intron	NM_018202	NP_060672	Q8N5G2	MACOI_HUMAN	transmembrane protein 57							axon|integral to membrane|neuron projection terminus|nuclear membrane|synapse part					0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)		AATGAAATGGAAAAAAAAAGT	0.358													4	2	---	---	---	---	
PHACTR4	65979	broad.mit.edu	37	1	28793810	28793810	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28793810delT	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron	NM_001048183	NP_001041648	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		TAGATTTAAGTTTTGGGGGTT	0.189													4	2	---	---	---	---	
TAF12	6883	broad.mit.edu	37	1	28962542	28962542	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28962542delC	uc009vti.2	-						TAF12_uc001bqx.2_Intron|TAF12_uc001bqy.2_Intron	NM_005644	NP_005635	Q16514	TAF12_HUMAN	TAF12 RNA polymerase II, TATA box binding						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	PCAF complex|STAGA complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Renal(390;0.00121)|Breast(348;0.00502)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)		Colorectal(126;3.21e-08)|COAD - Colon adenocarcinoma(152;1.74e-06)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(1967;0.0109)|BRCA - Breast invasive adenocarcinoma(304;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		CTGTTTCTTTCCTCTCTGGCT	0.398													4	2	---	---	---	---	
TINAGL1	64129	broad.mit.edu	37	1	32044427	32044428	+	Intron	INS	-	TT	TT	rs74193742		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32044427_32044428insTT	uc001bta.2	+						TINAGL1_uc001bsz.2_Intron|TINAGL1_uc010ogi.1_Intron|TINAGL1_uc010ogj.1_Intron|TINAGL1_uc010ogk.1_Intron	NM_022164	NP_071447	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1						endosome transport|immune response|proteolysis	extracellular region	cysteine-type endopeptidase activity|extracellular matrix structural constituent|polysaccharide binding|scavenger receptor activity				0		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		AGTGAGAGCTGGTGTGTGTGTG	0.342													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	34948195	34948196	+	IGR	INS	-	TGTG	TGTG	rs146013587	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34948195_34948196insTGTG								C1orf94 (263466 upstream) : MIR552 (187004 downstream)																							TTAAGAAATTAtgtgtgtgtgt	0.149													3	3	---	---	---	---	
ZMYM6	9204	broad.mit.edu	37	1	35457393	35457393	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35457393delA	uc001byh.2	-						ZMYM6_uc001byf.1_Intron|ZMYM6_uc010oht.1_Intron|ZMYM6_uc009vup.2_Intron	NM_007167	NP_009098	O95789	ZMYM6_HUMAN	zinc finger protein 258						multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				acaaacaaacaaaaaaaaaCC	0.154													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	36873274	36873274	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36873274delA								LSM10 (9781 upstream) : OSCP1 (10234 downstream)																							ATCAGGATCTAAATGAAGATG	0.438													4	2	---	---	---	---	
GRIK3	2899	broad.mit.edu	37	1	37377812	37377812	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37377812delC	uc001caz.2	-						GRIK3_uc001cba.1_Intron	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3						negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)	CTGATCCCAACCCCAGAGGCC	0.557													4	2	---	---	---	---	
RSPO1	284654	broad.mit.edu	37	1	38093846	38093847	+	Intron	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38093846_38093847delTC	uc001cbl.1	-						RSPO1_uc001cbm.1_Intron|RSPO1_uc009vvf.1_Intron|RSPO1_uc009vvg.1_Intron	NM_001038633	NP_001033722	Q2MKA7	RSPO1_HUMAN	R-spondin1 precursor						positive regulation of canonical Wnt receptor signaling pathway|regulation of receptor internalization		heparin binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TTCCTCCCATtctctctctctc	0.411													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38731060	38731061	+	IGR	INS	-	TCG	TCG			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38731060_38731061insTCG								POU3F1 (218610 upstream) : RRAGC (573954 downstream)																							tctttactgattcatcttctct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	39091081	39091081	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39091081delG								POU3F1 (578631 upstream) : RRAGC (213934 downstream)																							TAAAACAATAGGGCCTTTTGT	0.343													5	4	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42492862	42492863	+	Intron	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42492862_42492863delCA	uc001chb.1	-									Q5T1R4	ZEP3_HUMAN	Homo sapiens kappa B and V(D)J recombination signal sequences binding protein (KRC) mRNA, complete cds.						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				ctctctctctcacacacataac	0.030													4	2	---	---	---	---	
CYP4Z2P	163720	broad.mit.edu	37	1	47353700	47353701	+	Intron	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47353700_47353701delTC	uc001cqo.1	-						CYP4Z2P_uc009vyn.1_Intron	NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0						CCTAGTGTATtctctctctctc	0.376													3	3	---	---	---	---	
TAL1	6886	broad.mit.edu	37	1	47690076	47690077	+	Intron	DEL	AC	-	-	rs143567561		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47690076_47690077delAC	uc001cqx.2	-						TAL1_uc009vyq.2_5'Flank|TAL1_uc001cqy.2_Intron|TAL1_uc001cra.1_Intron|TAL1_uc001cqz.1_Intron	NM_003189	NP_003180	P17542	TAL1_HUMAN	T-cell acute lymphocytic leukemia 1						basophil differentiation|cell fate commitment|cell proliferation|embryonic hemopoiesis|erythrocyte differentiation|megakaryocyte differentiation|positive regulation of cell division|positive regulation of chromatin assembly or disassembly|positive regulation of erythrocyte differentiation|positive regulation of mitotic cell cycle|positive regulation of protein complex assembly|positive regulation of transcription from RNA polymerase II promoter	nuclear chromatin	E-box binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity			lung(1)	1						ACAAAAATGAacacacacacac	0.391			T	TRD@|SIL	lymphoblastic leukemia/biphasic								5	4	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49949140	49949140	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49949140delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		acagaaacataaaaaaattcc	0.000													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	50267274	50267274	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50267274delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		tctcaaatataaaaaaaaagt	0.020													4	2	---	---	---	---	
ELAVL4	1996	broad.mit.edu	37	1	50665979	50665980	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50665979_50665980insA	uc001csb.2	+						ELAVL4_uc001cry.3_Intron|ELAVL4_uc001crz.3_Intron|ELAVL4_uc001csa.3_Intron|ELAVL4_uc001csc.3_Intron|ELAVL4_uc010omz.1_Intron	NM_021952	NP_068771	P26378	ELAV4_HUMAN	ELAV-like 4 isoform 1						mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding			ovary(1)|pancreas(1)	2						AATCTGCCTTTAAAAAAAAAAA	0.317													4	2	---	---	---	---	
FAF1	11124	broad.mit.edu	37	1	51165987	51165988	+	Intron	DEL	CT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51165987_51165988delCT	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity	p.0?(1)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		CTTTTCCCCCCTCTCTCTCTCT	0.470											OREG0002742	type=REGULATORY REGION|Gene=FAF1(intragenic)|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	51992999	51993000	+	IGR	INS	-	TGG	TGG			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51992999_51993000insTGG								EPS15 (8004 upstream) : OSBPL9 (49851 downstream)																							TCCAatgatgatggtgatgatg	0.050													4	3	---	---	---	---	
ZYG11B	79699	broad.mit.edu	37	1	53268366	53268367	+	Intron	DEL	AG	-	-	rs150358279		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53268366_53268367delAG	uc001cuj.2	+						ZYG11B_uc009vzg.2_Intron|ZYG11B_uc010onj.1_Intron|ZYG11B_uc009vzh.2_Intron	NM_024646	NP_078922	Q9C0D3	ZY11B_HUMAN	zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						aaaaaaagaaagagagagagag	0.168													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	55822904	55822907	+	IGR	DEL	TCTT	-	-	rs10542938		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55822904_55822907delTCTT								USP24 (142142 upstream) : None (None downstream)																							ATTGGTAATATCTTTTGCCTTTCC	0.412													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	57683641	57683641	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57683641delA	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						ggtcccaaggaaaaaaacaca	0.100													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58245621	58245622	+	Intron	INS	-	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58245621_58245622insC	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						CTGACAGTCTGCTTTCCCCACC	0.401													4	2	---	---	---	---	
ITGB3BP	23421	broad.mit.edu	37	1	63922885	63922885	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63922885delT	uc001dba.1	-						ITGB3BP_uc001dbb.1_Intron|ITGB3BP_uc001dbc.1_Intron|ITGB3BP_uc001dbd.1_RNA|ITGB3BP_uc009wak.1_Intron|ITGB3BP_uc001dbe.1_5'Flank	NM_014288	NP_055103	Q13352	CENPR_HUMAN	integrin beta 3 binding protein						apoptosis|cell adhesion|CenH3-containing nucleosome assembly at centromere|induction of apoptosis by extracellular signals|mitotic prometaphase|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome, centromeric region|cytosol|membrane fraction|nucleoplasm	protein C-terminus binding|signal transducer activity				0						TGAAAAATTCTTTTTTTTCAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	64857504	64857504	+	IGR	DEL	G	-	-	rs11329785		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64857504delG								UBE2U (147477 upstream) : CACHD1 (78972 downstream)																							GTCACATCTAGTAGTCTTTTA	0.274													5	3	---	---	---	---	
SGIP1	84251	broad.mit.edu	37	1	67114069	67114070	+	Intron	INS	-	AGTG	AGTG	rs147461319	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67114069_67114070insAGTG	uc001dcr.2	+						SGIP1_uc010opd.1_Intron|SGIP1_uc001dcs.2_Intron|SGIP1_uc001dct.2_Intron	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3						TAATGCTTGCAagtgagtgagt	0.119													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	68337209	68337210	+	Intron	INS	-	CA	CA	rs149088171	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68337209_68337210insCA	uc001deb.1	+						uc001dec.1_Intron					Homo sapiens cDNA FLJ38762 fis, clone KIDNE2013801.																		TCCTTTTCCTTCACACACACAC	0.386													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	68924624	68924626	+	IGR	DEL	AGA	-	-	rs146329678		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68924624_68924626delAGA								RPE65 (8982 upstream) : DEPDC1 (15211 downstream)																							ACAGGAGAAGAGAAGGAGAAAAG	0.320													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	75492599	75492600	+	IGR	INS	-	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75492599_75492600insG								TYW3 (260241 upstream) : LHX8 (101519 downstream)																							aaaaaaaaaaagaccataaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	75637335	75637335	+	IGR	DEL	A	-	-	rs56031657		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75637335delA								LHX8 (10119 upstream) : SLC44A5 (30481 downstream)																							AGCTGCAACCATAACAAAAAT	0.463													4	3	---	---	---	---	
ST6GALNAC5	81849	broad.mit.edu	37	1	77421963	77421963	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77421963delA	uc001dhi.2	+						ST6GALNAC5_uc010ori.1_Intron|ST6GALNAC5_uc009wbw.2_Intron	NM_030965	NP_112227	Q9BVH7	SIA7E_HUMAN	sialyltransferase 7E						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			pancreas(1)|skin(1)	2						CAAGATCCAGAAAAAAAAAAA	0.353													3	3	---	---	---	---	
ST6GALNAC5	81849	broad.mit.edu	37	1	77485699	77485699	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77485699delC	uc001dhi.2	+						ST6GALNAC5_uc010ori.1_Intron|ST6GALNAC5_uc009wbw.2_Intron	NM_030965	NP_112227	Q9BVH7	SIA7E_HUMAN	sialyltransferase 7E						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			pancreas(1)|skin(1)	2						GAAAACCTGTCAGACTGGTTT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	78838504	78838504	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78838504delT								MGC27382 (3359 upstream) : PTGFR (118224 downstream)																							AGTTGCCTCCTTTTTTTTTGT	0.328													3	4	---	---	---	---	
LPHN2	23266	broad.mit.edu	37	1	82119609	82119612	+	Intron	DEL	TTCT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82119609_82119612delTTCT	uc001dis.2	+									O95490	LPHN2_HUMAN	SubName: Full=cDNA FLJ41428 fis, clone BRHIP2005236, highly similar to Latrophilin-2;						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		agagttcagcttctttctttcttt	0.005													4	2	---	---	---	---	
LPHN2	23266	broad.mit.edu	37	1	82445307	82445308	+	Intron	DEL	TA	-	-	rs3215834		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82445307_82445308delTA	uc001dit.3	+						LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Intron|LPHN2_uc001div.2_Intron|LPHN2_uc009wcd.2_Intron|LPHN2_uc001diw.2_Intron|LPHN2_uc009wce.1_Intron	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		TTAGGTTTTCTAATTTATTTAA	0.297													7	4	---	---	---	---	
TTLL7	79739	broad.mit.edu	37	1	84350091	84350092	+	Intron	INS	-	A	A	rs140406313	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84350091_84350092insA	uc001djc.2	-						TTLL7_uc001djb.2_Intron|TTLL7_uc001djd.2_Intron|TTLL7_uc001dje.2_Intron|TTLL7_uc001djf.2_Intron|TTLL7_uc001djg.2_Intron	NM_024686	NP_078962	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7						cell differentiation|nervous system development|protein modification process	cilium|dendrite|microtubule basal body|perikaryon	tubulin-tyrosine ligase activity			ovary(1)	1				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		TTTGAATTCTTAAAAAAATGCC	0.317													4	2	---	---	---	---	
TTLL7	79739	broad.mit.edu	37	1	84392733	84392733	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84392733delA	uc001djc.2	-						TTLL7_uc001djb.2_Intron|TTLL7_uc001djd.2_Intron|TTLL7_uc001dje.2_Intron|TTLL7_uc001djf.2_Intron|TTLL7_uc001djg.2_Intron	NM_024686	NP_078962	Q6ZT98	TTLL7_HUMAN	tubulin tyrosine ligase-like family, member 7						cell differentiation|nervous system development|protein modification process	cilium|dendrite|microtubule basal body|perikaryon	tubulin-tyrosine ligase activity			ovary(1)	1				all cancers(265;0.0126)|Epithelial(280;0.0372)|OV - Ovarian serous cystadenocarcinoma(397;0.16)		TCATCCAAGTAAAAAAAAAGG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	92109905	92109905	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92109905delA								HSP90B3P (571 upstream) : TGFBR3 (35997 downstream)																							TTCCCCTCCTAAAAAAAAATT	0.328													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	97328473	97328473	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97328473delT								PTBP2 (47874 upstream) : DPYD (214829 downstream)																							tcttgctctatgacaagtctg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98520519	98520520	+	IGR	DEL	GA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98520519_98520520delGA								MIR137 (8792 upstream) : SNX7 (606716 downstream)																							TACTGAGGAGGAGAGAGAGAGA	0.441													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98844705	98844706	+	IGR	INS	-	A	A	rs142785612	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98844705_98844706insA								MIR137 (332978 upstream) : SNX7 (282530 downstream)																							TGTTGACTTCTAAAAAAAAAAC	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	99585720	99585720	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99585720delA	uc001dsd.1	+											Homo sapiens cDNA FLJ38225 fis, clone FCBBF2003528.																		AACaaaaaagaaaaaaaaaat	0.249													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	104697029	104697029	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104697029delA								AMY1A (489857 upstream) : None (None downstream)																							ACTTTATGTGAAAAAAAAAAT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	104901343	104901343	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104901343delT								AMY1A (694171 upstream) : None (None downstream)																							ACATGACTCATTTTTTTTCCT	0.294													2	4	---	---	---	---	
WDR47	22911	broad.mit.edu	37	1	109535490	109535490	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109535490delA	uc001dwj.2	-						WDR47_uc001dwl.2_Intron|WDR47_uc001dwi.2_Intron|WDR47_uc001dwk.2_Intron|WDR47_uc010ovf.1_Intron	NM_001142551	NP_001136023	O94967	WDR47_HUMAN	WD repeat domain 47 isoform 3											ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		AATTAAAAGGAAAAAAAAAAG	0.234													3	3	---	---	---	---	
DENND2D	79961	broad.mit.edu	37	1	111749252	111749252	+	5'Flank	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111749252delT	uc001eal.1	-							NM_024901	NP_079177	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D											ovary(1)	1		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		AAAAGGAAACttttttttttt	0.229													4	3	---	---	---	---	
KCND3	3752	broad.mit.edu	37	1	112347848	112347849	+	Intron	INS	-	A	A	rs141874780	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112347848_112347849insA	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)		CCAACAGGGGGAAAAAAAAAGG	0.441													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	114764395	114764395	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114764395delT								SYT6 (67923 upstream) : TRIM33 (171006 downstream)																							ctacacccacttttgcaacaa	0.000													4	2	---	---	---	---	
C1orf203	84852	broad.mit.edu	37	1	116957289	116957289	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116957289delT	uc009whb.2	-						C1orf203_uc001egg.3_Intron|C1orf203_uc001egi.3_Intron|C1orf203_uc001egj.3_Intron|C1orf203_uc001egk.3_Intron	NR_027646				Homo sapiens cDNA, FLJ99430.												0						gctttttttctttttttttaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	119561291	119561291	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119561291delG								TBX15 (29112 upstream) : WARS2 (12550 downstream)																							CCCAGGCTGAGGGGTTGACTC	0.343													4	2	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120607696	120607697	+	Intron	DEL	CC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120607696_120607697delCC	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTCAAAGTGACCTTTATAAATT	0.391			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120826366	120826366	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120826366delA								NOTCH2 (214090 upstream) : FAM72B (12639 downstream)																							CGATGTTAGCAAAAAAAAATG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142633319	142633319	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142633319delG	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		ttatagctctgggggccaagc	0.030													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142672993	142672993	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142672993delC	uc001eiw.1	+						uc001eix.1_Intron|uc001eiz.1_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																		CTGctgaccaccccccactaa	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142787262	142787262	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142787262delC	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		tataccctttccacatggata	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142827025	142827026	+	Intron	DEL	AG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142827025_142827026delAG	uc001eiw.1	+						uc001ejb.2_Intron|uc001ejd.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		TTCATCAGAAAGAGGATCATAA	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143261370	143261371	+	IGR	INS	-	A	A	rs145912009		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143261370_143261371insA								None (None upstream) : LOC100286793 (386268 downstream)																							aaggagaattcaaaaaaccact	0.134													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143397663	143397664	+	IGR	DEL	AA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143397663_143397664delAA								None (None upstream) : LOC100286793 (249975 downstream)																							TTAGAGAAACAAAGAGAAGTAC	0.248													5	8	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144995278	144995278	+	5'Flank	DEL	G	-	-	rs11305863		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144995278delG	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_5'Flank|PDE4DIP_uc001ell.1_5'Flank|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_5'Flank|PDE4DIP_uc001emd.1_5'Flank|PDE4DIP_uc001emg.1_5'Flank|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CAAGAAATAAGGTTGCTATAG	0.423			T	PDGFRB	MPD								5	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145164133	145164133	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145164133delA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						CCACAtggataaaaaagccat	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	146471954	146471954	+	IGR	DEL	A	-	-	rs67168403		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146471954delA								NBPF10 (47859 upstream) : LOC728989 (18941 downstream)																							gattttcagtagagatgaggg	0.010													4	2	---	---	---	---	
BCL9	607	broad.mit.edu	37	1	147090441	147090441	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147090441delA	uc001epq.2	+						BCL9_uc010ozr.1_Intron	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9						Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					CAGTAAGTTTAAAAAAAAAAA	0.388			T	IGH@|IGL@	B-ALL								8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152528591	152528591	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152528591delA								CRCT1 (40111 upstream) : LCE3E (9540 downstream)																							aaactattacaaaaaaaacga	0.000													4	2	---	---	---	---	
ILF2	3608	broad.mit.edu	37	1	153636284	153636284	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153636284delA	uc001fcr.2	-						ILF2_uc010pdy.1_Intron|ILF2_uc009wok.2_Intron	NM_004515	NP_004506	Q12905	ILF2_HUMAN	interleukin enhancer binding factor 2						immune response|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|ribonucleoprotein complex	ATP binding|DNA binding|double-stranded RNA binding|protein binding|transferase activity				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TTGAATATACAAAAAAAAAAA	0.279													4	4	---	---	---	---	
TPM3	7170	broad.mit.edu	37	1	154163103	154163103	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154163103delC	uc001fec.1	-							NM_152263	NP_689476	P06753	TPM3_HUMAN	tropomyosin 3 isoform 1						cellular component movement|muscle filament sliding|regulation of muscle contraction	cytosol|muscle thin filament tropomyosin|stress fiber	actin binding		TPM3/ALK(33)	haematopoietic_and_lymphoid_tissue(22)|soft_tissue(11)|skin(1)	34	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					CTCTCTGCTGCCCTAGGAGCA	0.453			T	NTRK1|ALK	papillary thyroid|ALCL								4	2	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154752036	154752037	+	Intron	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154752036_154752037insT	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron|KCNN3_uc009wox.1_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			TTAAAAAGTTATTTTGCAAGCA	0.421													4	2	---	---	---	---	
FCRL5	83416	broad.mit.edu	37	1	157513771	157513771	+	Intron	DEL	A	-	-	rs68042008		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157513771delA	uc001fqu.2	-						FCRL5_uc009wsm.2_Intron|FCRL5_uc010phv.1_Intron|FCRL5_uc010phw.1_Intron|FCRL5_uc001fqv.1_Intron|FCRL5_uc010phx.1_Intron	NM_031281	NP_112571	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5							integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(2)|central_nervous_system(1)	6	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				GGCCTAGAAGAAAAAAAAATG	0.378													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158414936	158414937	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158414936_158414937insA								OR10K2 (24280 upstream) : OR10K1 (20415 downstream)																							TCTCAGTGTATAGACAAGGGGG	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158484147	158484147	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158484147delG								OR10R2 (33473 upstream) : OR6Y1 (32773 downstream)																							AGTTCTATTTGGGTCATCAAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159087545	159087546	+	IGR	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159087545_159087546delAC								AIM2 (40898 upstream) : CADM3 (53831 downstream)																							AATTTCACTGacacacacacac	0.277													4	3	---	---	---	---	
CADM3	57863	broad.mit.edu	37	1	159154271	159154271	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159154271delT	uc001ftl.2	+						CADM3_uc009wsx.1_Intron|CADM3_uc009wsy.1_Intron|CADM3_uc001ftk.2_Intron	NM_001127173	NP_001120645	Q8N126	CADM3_HUMAN	cell adhesion molecule 3 isoform 2						adherens junction organization|cell junction assembly|heterophilic cell-cell adhesion|homophilic cell adhesion	cell-cell junction|integral to membrane	protein homodimerization activity			ovary(2)	2	all_hematologic(112;0.0429)					CTCAGGGAGCTTTTTTTTTCT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163392607	163392607	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163392607delT								NUF2 (67054 upstream) : None (None downstream)																							TAATTTAATGTTTTTTTTTTC	0.269													3	4	---	---	---	---	
LMX1A	4009	broad.mit.edu	37	1	165236778	165236778	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165236778delA	uc001gcy.1	-						LMX1A_uc001gcz.1_Intron	NM_177398	NP_796372	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(3)|upper_aerodigestive_tract(1)|pancreas(1)	5	all_hematologic(923;0.248)					tcctatacctaggatgaagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166727478	166727478	+	IGR	DEL	A	-	-	rs67646618		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166727478delA								FMO9P (133007 upstream) : POGK (81246 downstream)																							ATGGACATGTAAAAAAAAATT	0.328													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	170056270	170056270	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170056270delT								KIFAP3 (12391 upstream) : METTL11B (58918 downstream)																							GGTGTACGAATTTTTTTTTCC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	171189256	171189257	+	IGR	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171189256_171189257delAC								FMO2 (7434 upstream) : FMO1 (28376 downstream)																							aaaaaaaaaaacagaaaaacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177298597	177298597	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177298597delT								FAM5B (47040 upstream) : SEC16B (598892 downstream)																							AGGAAAGAGGTTTTTTTTTGT	0.328													4	2	---	---	---	---	
TOR1AIP2	163590	broad.mit.edu	37	1	179824149	179824149	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179824149delA	uc001gnk.2	-						TOR1AIP2_uc001gnl.2_Intron	NM_145034	NP_659471	Q8NFQ8	TOIP2_HUMAN	torsin A interacting protein 2							endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1						aaagggaaataatgaattagt	0.000													4	2	---	---	---	---	
CACNA1E	777	broad.mit.edu	37	1	181679712	181679712	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181679712delT	uc001gow.2	+						CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						ttaatcactattGTTATCAAA	0.209													1	5	---	---	---	---	
C1orf26	54823	broad.mit.edu	37	1	185196024	185196024	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185196024delG	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988	Q5T5J6	SWT1_HUMAN	hypothetical protein LOC54823												0						TGGACATTTTGGGACAGTTCC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	187210747	187210747	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187210747delT								PLA2G4A (252642 upstream) : None (None downstream)																							ttccttctgctttacacactg	0.000													4	2	---	---	---	---	
FAM5C	339479	broad.mit.edu	37	1	190310039	190310039	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190310039delT	uc001gse.1	-						FAM5C_uc010pot.1_Intron	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C							extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)					ATACTCATTCTTTTTTTTTCC	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199841904	199841905	+	IGR	INS	-	T	T	rs142422124	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199841904_199841905insT								None (None upstream) : NR5A2 (154865 downstream)																							gtgttccttaattttttctttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	200369053	200369053	+	IGR	DEL	T	-	-	rs115269659	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200369053delT								FAM58B (185410 upstream) : ZNF281 (6373 downstream)																							CAATCATAGGTTTTTTTTTAT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	200687402	200687402	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200687402delA								DDX59 (48276 upstream) : CAMSAP1L1 (21284 downstream)																							gaaaaaacagaaaaagtgaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	203353224	203353224	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203353224delC								FMOD (32935 upstream) : PRELP (91659 downstream)																							ccagccaatgccccagcactc	0.005													4	2	---	---	---	---	
NFASC	23114	broad.mit.edu	37	1	204855155	204855155	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204855155delG	uc001hbj.2	+						NFASC_uc001hbh.2_Intron|NFASC_uc010pqz.1_Intron|NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc009xbg.1_Intron	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			cacattctttgaatatcctca	0.000													4	2	---	---	---	---	
ELK4	2005	broad.mit.edu	37	1	205595700	205595700	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205595700delA	uc001hcy.1	-						ELK4_uc001hcz.2_Intron|SLC45A3_uc010prn.1_Intron|SLC45A3_uc010pro.1_Intron|SLC45A3_uc010prp.1_Intron|ELK4_uc010prq.1_Intron	NM_001973	NP_001964	P28324	ELK4_HUMAN	ELK4 protein isoform a							cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity				0	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			agaaaccaccaaaaaaaaaat	0.179			T	SLC45A3	prostate								4	4	---	---	---	---	
CR2	1380	broad.mit.edu	37	1	207656305	207656305	+	Intron	DEL	G	-	-	rs71851075		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207656305delG	uc001hfw.2	+						CR2_uc001hfv.2_Intron|CR2_uc009xch.2_Intron	NM_001877	NP_001868	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)						complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8						TGCCATTAAAGAAAAAAAAAA	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208951173	208951173	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208951173delG								PLXNA2 (533508 upstream) : LOC642587 (650995 downstream)																							CCGTTCTTTTGGAGGAGTTTA	0.303													4	2	---	---	---	---	
HHAT	55733	broad.mit.edu	37	1	210529728	210529728	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210529728delT	uc009xcx.2	+						HHAT_uc010psq.1_Intron|HHAT_uc001hhz.3_Intron|HHAT_uc010psr.1_Intron|HHAT_uc010pss.1_Intron|HHAT_uc009xcy.2_Intron|HHAT_uc010pst.1_Intron|HHAT_uc010psu.1_Intron	NM_001122834	NP_001116306	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		TGTCACAGGCTTTTTTTTTCA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	211647818	211647818	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211647818delT								C1orf97 (41942 upstream) : RD3 (2046 downstream)																							GTTTGGAGACTTTTTTTTTTT	0.403													4	2	---	---	---	---	
RPS6KC1	26750	broad.mit.edu	37	1	213413821	213413822	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213413821_213413822insA	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide						cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GGTTGTCACTTAAAAAAAAAAT	0.287													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	218780755	218780755	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218780755delG								TGFB2 (162796 upstream) : LYPLAL1 (566437 downstream)																							TTTTGACCCTGGGGTGCCTTG	0.398													4	2	---	---	---	---	
CABC1	56997	broad.mit.edu	37	1	227160504	227160505	+	Intron	INS	-	AGC	AGC	rs137935382	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227160504_227160505insAGC	uc001hqm.1	+						CABC1_uc001hqn.1_Intron|CABC1_uc009xeq.1_Intron|CABC1_uc010pvq.1_Intron|CABC1_uc010pvr.1_Intron	NM_020247	NP_064632	Q8NI60	ADCK3_HUMAN	chaperone, ABC1 activity of bc1 complex like						cell death	mitochondrion	ATP binding|protein serine/threonine kinase activity				0		Prostate(94;0.0771)				atttaaaacaaagcaccacttt	0.000													3	4	---	---	---	---	
OBSCN	84033	broad.mit.edu	37	1	228426312	228426313	+	Intron	DEL	CG	-	-	rs145638349		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228426312_228426313delCG	uc009xez.1	+						OBSCN_uc001hsn.2_Intron	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				tgcactcacacgtatgaatgta	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	231460372	231460375	+	IGR	DEL	AAAC	-	-	rs143715301		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231460372_231460375delAAAC								GNPAT (46654 upstream) : EXOC8 (8108 downstream)																							AAAAGAAAATAAACCATGAAGTGA	0.304													4	5	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	232123036	232123036	+	Intron	DEL	T	-	-	rs35908047		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232123036delT	uc001huz.2	+						TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				CCCTGAAAGATTTTTTTCGCT	0.423													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	234718001	234718010	+	IGR	DEL	GTGTGCATGC	-	-	rs71638500	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234718001_234718010delGTGTGCATGC								TARBP1 (103152 upstream) : IRF2BP2 (22007 downstream)																							gtgcgtacgtgtgtgcatgcgtgtgcatgc	0.319													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	240853922	240853922	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240853922delA								GREM2 (78460 upstream) : RGS7 (77633 downstream)																							accctgtctgaaaaaaaaaaa	0.119													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244446260	244446261	+	IGR	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244446260_244446261delGT								ZNF238 (225484 upstream) : C1orf100 (69676 downstream)																							GATtgtgtgcgtgtgtgtgtct	0.153													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	247570069	247570069	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247570069delA								ZNF496 (74907 upstream) : NLRP3 (9389 downstream)																							tggttcttttaaaaaaattgg	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	249239712	249239713	+	IGR	DEL	AT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249239712_249239713delAT								PGBD2 (26368 upstream) : None (None downstream)																							taatgcacacatgacacccaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	7740545	7740545	+	IGR	DEL	T	-	-	rs67942043		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7740545delT								RNF144A (556238 upstream) : LOC339788 (322013 downstream)																							GTTTGTTTTCTTTTTTTTTTT	0.169													3	4	---	---	---	---	
KIDINS220	57498	broad.mit.edu	37	2	8972817	8972818	+	Intron	INS	-	AA	AA			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8972817_8972818insAA	uc002qzc.2	-						KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Intron|KIDINS220_uc010yiw.1_Intron	NM_020738	NP_065789	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate of 220 kDa						activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ATTTTCAATAGAAAAAAAAATG	0.371													4	2	---	---	---	---	
WDR35	57539	broad.mit.edu	37	2	20180161	20180161	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20180161delA	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGAAATCTGGAAAAAAAAAAA	0.189													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23676676	23676676	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23676676delT								None (None upstream) : KLHL29 (78779 downstream)																							TTGTTTTGTATTTTTTTTTTA	0.333													4	2	---	---	---	---	
NCOA1	8648	broad.mit.edu	37	2	24947774	24947774	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24947774delT	uc002rfk.2	+						NCOA1_uc010eye.2_Intron|NCOA1_uc002rfi.2_Intron|NCOA1_uc002rfj.2_Intron|NCOA1_uc002rfl.2_Intron	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1										PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATTATTTCCCTTTTTTTTTGT	0.303			T	PAX3	alveolar rhadomyosarcoma								4	2	---	---	---	---	
FAM179A	165186	broad.mit.edu	37	2	29209944	29209944	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29209944delT	uc010ezl.2	+						FAM179A_uc010ymm.1_Intron	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186								binding			ovary(3)|skin(1)	4						ctctgtggcctcaacctagtt	0.080													4	2	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29679220	29679221	+	Intron	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29679220_29679221delCA	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	atgtggcacgcacacacacaat	0.000			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	30191017	30191018	+	IGR	INS	-	A	A	rs144489862	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30191017_30191018insA								ALK (46585 upstream) : YPEL5 (178732 downstream)																							GGAGAGAGAGGAAAAAAAAAAC	0.287													5	5	---	---	---	---	
NLRC4	58484	broad.mit.edu	37	2	32484169	32484169	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32484169delA	uc002roi.2	-						NLRC4_uc002roj.1_Intron|NLRC4_uc010ezt.1_Intron	NM_021209	NP_067032	Q9NPP4	NLRC4_HUMAN	caspase recruitment domain protein 12						activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis	cytoplasm	ATP binding|magnesium ion binding|protein homodimerization activity			ovary(3)|large_intestine(1)|lung(1)|skin(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TCCTAACATTAAAACTCtttt	0.234													4	2	---	---	---	---	
BIRC6	57448	broad.mit.edu	37	2	32798266	32798266	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32798266delT	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)					tcagtaaatgttttttgtttg	0.000													4	2	---	---	---	---	
LTBP1	4052	broad.mit.edu	37	2	33492506	33492506	+	Intron	DEL	T	-	-	rs76014413		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33492506delT	uc002ros.2	+						LTBP1_uc002rot.2_Intron|LTBP1_uc002rou.2_Intron|LTBP1_uc002rov.2_Intron|LTBP1_uc010ymz.1_Intron|LTBP1_uc010yna.1_Intron	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				ATGATGGTGATTTTTTTTAAT	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35320024	35320024	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35320024delT								None (None upstream) : None (None downstream)																							gatggctgtcttttttctttg	0.000													4	2	---	---	---	---	
GALM	130589	broad.mit.edu	37	2	38928593	38928593	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38928593delA	uc002rqy.2	+							NM_138801	NP_620156	Q96C23	GALM_HUMAN	galactose mutarotase						hexose metabolic process	cytoplasm	aldose 1-epimerase activity|carbohydrate binding				0		all_hematologic(82;0.248)				TAGCATTAGTAAAATCCCCTC	0.348													4	2	---	---	---	---	
MTA3	57504	broad.mit.edu	37	2	42805491	42805491	+	Intron	DEL	T	-	-	rs143490371	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42805491delT	uc002rso.1	+						MTA3_uc002rsp.1_Intron|MTA3_uc002rsq.2_Intron|MTA3_uc002rsr.2_Intron	NM_020744	NP_065795	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						CATAACTGAATTTTTTTTTGA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45399596	45399596	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45399596delT								SIX2 (163053 upstream) : SRBD1 (216224 downstream)																							AAACTATATGTTTTGGTGAAT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	46730787	46730787	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46730787delA								LOC388946 (19224 upstream) : ATP6V1E2 (8201 downstream)																							GGGGCTTTCCAAAAAAAATGT	0.418													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	47468665	47468665	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47468665delT	uc002rvu.1	-											Homo sapiens cDNA FLJ37024 fis, clone BRACE2010837.									p.?(1)									AATAGATTAGTTTAGGGAAAA	0.169													4	2	---	---	---	---	
MSH2	4436	broad.mit.edu	37	2	47786924	47786924	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47786924delG	uc002rvz.2	+						KCNK12_uc002rwb.2_Intron	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			acaggtctgagggcagtaaga	0.000			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				4	2	---	---	---	---	
LHCGR	3973	broad.mit.edu	37	2	48916863	48916863	+	Intron	DEL	T	-	-	rs74757651		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48916863delT	uc002rwu.3	-						GTF2A1L_uc002rwt.2_Intron	NM_000233	NP_000224	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor						male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|lung(2)|breast(2)|skin(1)	8		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	tctctctctcttttttttttg	0.090									Familial_Male-Limited_Precocious_Puberty				4	2	---	---	---	---	
NRXN1	9378	broad.mit.edu	37	2	50206576	50206576	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50206576delA	uc010fbp.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ATTATCTTCCAAAATATTCCA	0.363													4	2	---	---	---	---	
NRXN1	9378	broad.mit.edu	37	2	50321906	50321907	+	Intron	DEL	AA	-	-	rs34298202		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50321906_50321907delAA	uc010fbp.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			aaaagaaaagaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	59025744	59025745	+	Intron	INS	-	A	A	rs137908171	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59025744_59025745insA	uc002rzy.2	+											Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																		TATCACTGTGCAAATAAAAGTG	0.337													5	6	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61595973	61595973	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61595973delA	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)			tacagaccataaaAACTACAA	0.164													4	2	---	---	---	---	
EHBP1	23301	broad.mit.edu	37	2	62902800	62902800	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62902800delA	uc010fcp.2	+							NM_001142615	NP_001136087	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 3							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TCAATGCTGCAAAAAAAGGCC	0.393									Hereditary_Prostate_Cancer				4	2	---	---	---	---	
C2orf86	51057	broad.mit.edu	37	2	63808204	63808204	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63808204delA	uc002sch.2	-						C2orf86_uc002sci.1_Intron	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0						ataaaagactaaaaaaAATAG	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64717440	64717441	+	IGR	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64717440_64717441delCA								HSPC159 (28929 upstream) : AFTPH (34024 downstream)																							cacacacactcacacacacact	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66049063	66049063	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66049063delA	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																		TTGGCTTTTTAATGGTGTATT	0.303													4	2	---	---	---	---	
MEIS1	4211	broad.mit.edu	37	2	66704034	66704034	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66704034delA	uc002sdu.2	+						MEIS1_uc002sdt.2_Intron|MEIS1_uc002sdv.2_Intron|MEIS1_uc010yqh.1_Intron|MEIS1_uc010yqi.1_Intron|MEIS1_uc002sdw.1_Intron	NM_002398	NP_002389	O00470	MEIS1_HUMAN	Meis homeobox 1								sequence-specific DNA binding transcription factor activity				0						gcatgtaaggaaaaaaaaaat	0.100													4	2	---	---	---	---	
AAK1	22848	broad.mit.edu	37	2	69824155	69824155	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69824155delT	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron|AAK1_uc010fdm.1_Intron	NM_014911	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0						AAATTGGGTCTTTTTTTTTTT	0.393													4	2	---	---	---	---	
TGFA	7039	broad.mit.edu	37	2	70682612	70682612	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70682612delT	uc002sgs.3	-						TGFA_uc010fdq.2_Intron|TGFA_uc010fdr.2_Intron|TGFA_uc002sgt.3_Intron|TGFA_uc002sgu.2_Intron|TGFA_uc002sgv.2_Intron|TGFA_uc002sgw.2_Intron	NM_003236	NP_003227	P01135	TGFA_HUMAN	transforming growth factor, alpha isoform 1						activation of MAPK activity|cell proliferation|positive regulation of cell division|positive regulation of epidermal growth factor receptor activity|positive regulation of epithelial cell proliferation|positive regulation of mitosis	cell surface|extracellular space|integral to membrane|plasma membrane	epidermal growth factor receptor binding|growth factor activity|MAP kinase kinase activity|signal transducer activity			prostate(1)	1						TAACCTACACTGAATTGAATG	0.378													4	2	---	---	---	---	
TGFA	7039	broad.mit.edu	37	2	70683993	70683994	+	Intron	INS	-	T	T	rs72540728	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70683993_70683994insT	uc002sgs.3	-						TGFA_uc010fdq.2_Intron|TGFA_uc010fdr.2_Intron|TGFA_uc002sgt.3_Intron|TGFA_uc002sgu.2_Intron|TGFA_uc002sgv.2_Intron|TGFA_uc002sgw.2_Intron	NM_003236	NP_003227	P01135	TGFA_HUMAN	transforming growth factor, alpha isoform 1						activation of MAPK activity|cell proliferation|positive regulation of cell division|positive regulation of epidermal growth factor receptor activity|positive regulation of epithelial cell proliferation|positive regulation of mitosis	cell surface|extracellular space|integral to membrane|plasma membrane	epidermal growth factor receptor binding|growth factor activity|MAP kinase kinase activity|signal transducer activity			prostate(1)	1						AACCAAATGTGGTTTTCAGACT	0.386													3	3	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71863642	71863642	+	Intron	DEL	G	-	-	rs71403000		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71863642delG	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						ttgagcatctggaaggagaga	0.000													2	5	---	---	---	---	
ALMS1	7840	broad.mit.edu	37	2	73664256	73664256	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73664256delG	uc002sje.1	+						ALMS1_uc002sjf.1_Intron	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1						G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9						agtgtccttaggcttgagctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	74234547	74234547	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74234547delG								DGUOK (48461 upstream) : TET3 (38903 downstream)																							TGGGCTAGCTGGGAAGGGAGC	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	76458993	76458994	+	IGR	INS	-	A	A	rs6729476	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76458993_76458994insA								C2orf3 (520882 upstream) : LRRTM4 (515864 downstream)																							TTTCTTTTTTTTAAAAAAAATT	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	80898255	80898255	+	IGR	DEL	A	-	-	rs79453131		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80898255delA								CTNNA2 (22351 upstream) : None (None downstream)																							AGTCAGGCAGAAAAAAAAAAA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82103143	82103143	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82103143delT								None (None upstream) : None (None downstream)																							CTATTTTGCCTTTTTTAGATG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	84005989	84005990	+	IGR	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84005989_84005990delCA								None (None upstream) : FUNDC2P2 (511816 downstream)																							aaagacttgtcaactctattta	0.045													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87587322	87587326	+	Intron	DEL	ATGAA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87587322_87587326delATGAA	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						atgaaatgagatgaaatgaaataat	0.000													1	8	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87868212	87868213	+	Intron	INS	-	GA	GA			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87868212_87868213insGA	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						tcttcacgccggagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	88957393	88957393	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88957393delT								EIF2AK3 (30399 upstream) : RPIA (33783 downstream)																							CTTTGTTTTGTTTTTTTGTCC	0.418													4	2	---	---	---	---	
FLJ40330	645784	broad.mit.edu	37	2	89073033	89073034	+	Intron	INS	-	TA	TA	rs5832736		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89073033_89073034insTA	uc002stf.2	+						FLJ40330_uc010fhf.2_Intron|FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						TTCTGCATGTGTGTGTGTATCT	0.302													4	3	---	---	---	---	
FLJ40330	645784	broad.mit.edu	37	2	89073040	89073041	+	Intron	INS	-	GTGC	GTGC	rs77574449		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89073040_89073041insGTGC	uc002stf.2	+						FLJ40330_uc010fhf.2_Intron|FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						TGTGTGTGTGTATCTCTGATTA	0.307													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89175806	89175806	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89175806delG	uc010ytr.1	-											Parts of antibodies, mostly variable regions.																		acgtgtgactgaaggttttcc	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89859019	89859020	+	IGR	INS	-	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89859019_89859020insC								FLJ40330 (752894 upstream) : None (None downstream)																							ttcattctaatcattgcaatta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90417010	90417011	+	Intron	INS	-	CGAAA	CGAAA	rs149420300	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90417010_90417011insCGAAA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		ACATGTATCACTGaaatgaaat	0.223													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90451097	90451097	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90451097delT	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		cttggaaatatttttttcata	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91972760	91972760	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91972760delA								GGT8P (2607 upstream) : FKSG73 (156399 downstream)																							tcgcaaggacaaaaaaccaaa	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91979580	91979581	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91979580_91979581insT								GGT8P (9427 upstream) : FKSG73 (149578 downstream)																							TGTAAAATAGATCTTTTCGAGG	0.203													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96524034	96524038	+	Intron	DEL	AAAAT	-	-	rs67685711		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96524034_96524038delAAAAT	uc002sva.1	-						uc002suz.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		tTGATATTAGAAAATAAAACATTCG	0.127													5	4	---	---	---	---	
SNRNP200	23020	broad.mit.edu	37	2	96966501	96966501	+	Intron	DEL	A	-	-	rs79757100		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96966501delA	uc002svu.2	-							NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10						actccgtctcaaaaaaaaaaa	0.104													11	5	---	---	---	---	
CNGA3	1261	broad.mit.edu	37	2	98965729	98965730	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98965729_98965730insA	uc002syt.2	+						CNGA3_uc002syu.2_Intron	NM_001298	NP_001289	Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3 isoform						signal transduction|visual perception	integral to membrane	cGMP binding			ovary(5)|upper_aerodigestive_tract(1)	6						TAGGTGGGGGCAAAAAAAAAAC	0.193													6	3	---	---	---	---	
NPAS2	4862	broad.mit.edu	37	2	101591538	101591540	+	Intron	DEL	CTC	-	-	rs3217562		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101591538_101591540delCTC	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						GCAGTTTATACTCCTCCTTTCCT	0.557													12	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103502114	103502114	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103502114delA								TMEM182 (67978 upstream) : None (None downstream)																							aaggtacaagaaaaaaaaaaa	0.035													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105787510	105787511	+	IGR	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105787510_105787511delCA								MRPS9 (71093 upstream) : GPR45 (70689 downstream)																							cacacacacgcacacacacaca	0.317													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106626929	106626929	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106626929delT								NCK2 (116203 upstream) : C2orf40 (55184 downstream)																							TTGCCCCTAGTTTTTTTTTTC	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108929535	108929535	+	IGR	DEL	C	-	-	rs67742778		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108929535delC								SULT1C2 (3165 upstream) : SULT1C4 (64886 downstream)																							AAAAAAAAAACATTCACTCCA	0.114													4	4	---	---	---	---	
LOC541471	541471	broad.mit.edu	37	2	112175770	112175771	+	Intron	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112175770_112175771delAC	uc002the.2	-						LOC541471_uc010yxl.1_Intron					Homo sapiens hypothetical LOC541471, mRNA (cDNA clone IMAGE:3459303).												0						AAGGTTAGAAACACACACACAC	0.356													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114320684	114320684	+	5'Flank	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114320684delT	uc002tjy.1	+											DQ598479																		ACTGGATTGATTTTTTTTTTT	0.403													4	4	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	116241593	116241593	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116241593delA	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						ATTTTTCTCCAGGGGAAACAT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	123317749	123317749	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123317749delA								TSN (792323 upstream) : None (None downstream)																							ttaagccattaaatttgtggt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131633266	131633266	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131633266delG	uc002try.1	+											Homo sapiens cDNA FLJ45181 fis, clone BRAWH3047644, highly  similar to Homo sapiens Rho guanine nucleotide exchange factor (GEF) 4 (ARHGEF4).																		ctgccatgctggggatcaaat	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133064708	133064709	+	Intron	DEL	TG	-	-	rs4953960		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133064708_133064709delTG	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		TTTTTTGTTTTGTTTTTAGGAT	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133066592	133066592	+	Intron	DEL	G	-	-	rs78544491		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133066592delG	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		AAAAGGAAAAGAATGTGCAGG	0.433													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	135006258	135006265	+	IGR	DEL	TGTGAATG	-	-	rs140741402		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135006258_135006265delTGTGAATG								NCKAP5 (680227 upstream) : MGAT5 (5565 downstream)																							CGCTGTCCTATGTGAATGTGTGAATGTG	0.490													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	137087740	137087740	+	IGR	DEL	G	-	-	rs4464337	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137087740delG								CXCR4 (212015 upstream) : THSD7B (435375 downstream)																							TATTTTTTTTGGCTGACACCA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	139788698	139788698	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139788698delC								NXPH2 (250887 upstream) : None (None downstream)																							ggtactaggtcagctcagccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	140160138	140160138	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140160138delT								NXPH2 (622327 upstream) : LRP1B (828858 downstream)																							TTGGTCATGCTTTTTTTTTCC	0.318													4	2	---	---	---	---	
GTDC1	79712	broad.mit.edu	37	2	144936542	144936542	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144936542delA	uc002tvp.2	-						GTDC1_uc002tvo.2_Intron|GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)		TAAAAACGAGAGTTAGAGAAA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	145723580	145723580	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145723580delT	uc002twc.2	+											Homo sapiens hypothetical gene supported by BC043549; BX648102, mRNA (cDNA clone IMAGE:5172341).																		gtagcctcccttttttggcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	148009053	148009053	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148009053delG								PABPC1P2 (660496 upstream) : ACVR2A (593033 downstream)																							TGAATCTTTTGTTTTGGTGGA	0.284													4	2	---	---	---	---	
MBD5	55777	broad.mit.edu	37	2	149023577	149023578	+	Intron	DEL	GA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149023577_149023578delGA	uc002twm.3	+							NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)		GATTGGGGTGGAGAGAGAGAGA	0.233													4	3	---	---	---	---	
KIF5C	3800	broad.mit.edu	37	2	149663332	149663332	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149663332delC	uc010zbu.1	+							NM_004522	NP_004513	O60282	KIF5C_HUMAN	kinesin family member 5C						microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)		aaaagacatgcccgagactgg	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151026078	151026078	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151026078delA								MMADHC (581748 upstream) : RND3 (298634 downstream)																							agaaagagagaaaaaaaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	153736021	153736024	+	IGR	DEL	ACAT	-	-	rs149683427	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153736021_153736024delACAT								ARL6IP6 (118254 upstream) : RPRM (597828 downstream)																							acacacacacacatacacacacaA	0.255													4	2	---	---	---	---	
WDSUB1	151525	broad.mit.edu	37	2	160113109	160113109	+	Intron	DEL	A	-	-	rs71997428		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160113109delA	uc002uaj.3	-						WDSUB1_uc002uak.3_Intron|WDSUB1_uc002ual.3_Intron|WDSUB1_uc002uam.3_Intron|WDSUB1_uc010foo.2_Intron	NM_152528	NP_689741	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain							ubiquitin ligase complex	ubiquitin-protein ligase activity				0						gaccagtctcaaaaaaaaaaa	0.104													4	4	---	---	---	---	
DPP4	1803	broad.mit.edu	37	2	162930287	162930304	+	Intron	DEL	GCCAGGGTCCTAGCAGAA	-	-	rs3216773		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162930287_162930304delGCCAGGGTCCTAGCAGAA	uc002ubz.2	-						DPP4_uc010fpb.2_Intron|DPP4_uc002uca.1_5'Flank|DPP4_uc002ucb.1_5'Flank	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	AAAGCTCGACGCCAGGGTCCTAGCAGAAGCCAGGGTCC	0.606													6	5	---	---	---	---	
KCNH7	90134	broad.mit.edu	37	2	163694559	163694559	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163694559delT	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	GCTACTACCATTTACATTCTC	0.368													4	2	---	---	---	---	
C2orf77	129881	broad.mit.edu	37	2	170507244	170507245	+	Intron	INS	-	TG	TG	rs140387308	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170507244_170507245insTG	uc002ufe.2	-							NM_001085447	NP_001078916	Q0VFZ6	CB077_HUMAN	hypothetical protein LOC129881												0						TATGTATAATCtgtgtgtgtgt	0.163													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	172858295	172858295	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172858295delT								HAT1 (9696 upstream) : MAP1D (6509 downstream)																							GGACCAAATATTTTAAACCAA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174197706	174197706	+	IGR	DEL	T	-	-	rs139861322		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174197706delT								ZAK (64970 upstream) : CDCA7 (21855 downstream)																							tttagagaactttttttagcc	0.000													3	3	---	---	---	---	
OLA1	29789	broad.mit.edu	37	2	175059968	175059968	+	Intron	DEL	A	-	-	rs67428918		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175059968delA	uc002uih.2	-						OLA1_uc002uii.2_Intron|OLA1_uc010fqq.2_Intron|OLA1_uc002uij.2_Intron|OLA1_uc002uik.2_Intron|OLA1_uc010fqr.2_Intron	NM_013341	NP_037473	Q9NTK5	OLA1_HUMAN	Obg-like ATPase 1 isoform 1						ATP catabolic process	cytoplasm	ATP binding|GTP binding|hydrolase activity|protein binding			ovary(1)|breast(1)	2						TACTATGCTCAAAAAAAAAAT	0.264													7	4	---	---	---	---	
AGPS	8540	broad.mit.edu	37	2	178401139	178401139	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178401139delA	uc002ull.2	+						AGPS_uc010zfb.1_Intron	NM_003659	NP_003650	O00116	ADAS_HUMAN	alkyldihydroxyacetone phosphate synthase						ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			GTAGTTGTTTAAAAAAAAAAA	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181941066	181941066	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181941066delA								UBE2E3 (12916 upstream) : ITGA4 (380553 downstream)																							ACAGTGGTGTAAAGAAGTTCC	0.413													4	2	---	---	---	---	
PDE1A	5136	broad.mit.edu	37	2	183101915	183101916	+	Intron	INS	-	CT	CT			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183101915_183101916insCT	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uor.2_Intron|PDE1A_uc002uou.2_Intron	NM_001003683	NP_001003683	P54750	PDE1A_HUMAN	phosphodiesterase 1A isoform 2						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.061)			TAATTCAAAAACTCTTTAAAAA	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	184483457	184483457	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184483457delT								NUP35 (457050 upstream) : ZNF804A (979636 downstream)																							tgtccaggaatttatccattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	184846820	184846820	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184846820delA								NUP35 (820413 upstream) : ZNF804A (616273 downstream)																							TCCATCTCTGAAATGCCCAGT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	192369099	192369099	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192369099delT								MYO1B (78984 upstream) : OBFC2A (173699 downstream)																							acccagtttcttttttttttt	0.000													3	3	---	---	---	---	
SLC39A10	57181	broad.mit.edu	37	2	196536684	196536684	+	Intron	DEL	T	-	-	rs35307684		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196536684delT	uc002utg.3	+						SLC39A10_uc002uth.3_Intron|SLC39A10_uc010zgp.1_Intron	NM_001127257	NP_001120729	Q9ULF5	S39AA_HUMAN	solute carrier family 39 (zinc transporter),						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			pancreas(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.221)			AGCGGTCATCTTTTTTTTTTT	0.328													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	199546825	199546826	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199546825_199546826insA								PLCL1 (532219 upstream) : SATB2 (587398 downstream)																							gggacagcaataaaacccatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	200694767	200694767	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200694767delA	uc002uvg.2	-											Homo sapiens hypothetical protein LOC348751, mRNA (cDNA clone IMAGE:5311172).																		ATCAAGTAGGAAAAAAAAAAA	0.318													4	3	---	---	---	---	
CDK15	65061	broad.mit.edu	37	2	202690227	202690227	+	Intron	DEL	A	-	-	rs11344911		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202690227delA	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc010fto.1_Intron	NM_139158	NP_631897	Q96Q40	CDK15_HUMAN	PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)	aaagagagtgaaaaaaaaaaa	0.100													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	203050461	203050462	+	Intron	DEL	AA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203050461_203050462delAA	uc002uyy.1	+											RecName: Full=Uncharacterized protein KIAA2012;																		cagatttctgaaaaaaaaaaag	0.005													2	4	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	206349592	206349592	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206349592delC	uc002var.1	+						PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		GTCACACTGTCGAGAGGCTAC	0.388													4	2	---	---	---	---	
ZDBF2	57683	broad.mit.edu	37	2	207156128	207156128	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207156128delC	uc002vbp.2	+							NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2								nucleic acid binding|zinc ion binding			ovary(3)	3						tgcttgcctgccgctcacctc	0.000													4	2	---	---	---	---	
PLEKHM3	389072	broad.mit.edu	37	2	208692717	208692717	+	3'UTR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208692717delA	uc002vcl.2	-	8						NM_001080475	NP_001073944	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M,						intracellular signal transduction		metal ion binding			ovary(1)	1						AGACAGAGAGAAAAAAAAAGT	0.358													3	3	---	---	---	---	
IDH1	3417	broad.mit.edu	37	2	209115942	209115942	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209115942delT	uc002vcs.2	-						IDH1_uc002vct.2_Intron|IDH1_uc002vcu.2_Intron	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble						2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity			central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		GATTATATTCTTTTTTTTTTT	0.164			Mis		gliobastoma 								6	3	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	214813196	214813197	+	Intron	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214813196_214813197insT	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		TCACTCTCTAATTTTTTTTGTT	0.337													4	2	---	---	---	---	
MARCH4	57574	broad.mit.edu	37	2	217186819	217186820	+	Intron	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217186819_217186820delTG	uc002vgb.2	-							NM_020814	NP_065865	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4							Golgi membrane|Golgi stack|integral to membrane|trans-Golgi network	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		CTTAAGGGGATGTGTGTGTGTG	0.426													5	4	---	---	---	---	
CDK5R2	8941	broad.mit.edu	37	2	219826020	219826021	+	3'UTR	DEL	CT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219826020_219826021delCT	uc002vjf.2	+	1						NM_003936	NP_003927	Q13319	CD5R2_HUMAN	cyclin-dependent kinase 5, regulatory subunit 2						regulation of cyclin-dependent protein kinase activity	cyclin-dependent protein kinase 5 holoenzyme complex	cyclin-dependent protein kinase 5 activator activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTCTGCATTCctctctctctct	0.371													6	4	---	---	---	---	
RHBDD1	84236	broad.mit.edu	37	2	227724303	227724303	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227724303delG	uc002voi.2	+						RHBDD1_uc010fxc.2_Intron	NM_032276	NP_115652	Q8TEB9	RHBD1_HUMAN	rhomboid domain containing 1							integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		GTGATCCTGTGGTAGCTCTGG	0.229													4	2	---	---	---	---	
COL4A4	1286	broad.mit.edu	37	2	227949592	227949592	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227949592delA	uc010zlt.1	-							NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		tcatgcctgtaatcccagcac	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	228715604	228715607	+	IGR	DEL	CATC	-	-	rs149948339		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228715604_228715607delCATC								CCL20 (33324 upstream) : WDR69 (20720 downstream)																							CCATCATCATcatccatccatcca	0.270													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	229639804	229639804	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229639804delC								SPHKAP (593443 upstream) : PID1 (248886 downstream)																							attttgaaagcagaactaaaa	0.000													4	2	---	---	---	---	
ARMC9	80210	broad.mit.edu	37	2	232215413	232215413	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232215413delA	uc002vrr.1	+							NM_025139		Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9								binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		gaaggtcaggacccttctcag	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232355549	232355551	+	IGR	DEL	AAA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232355549_232355551delAAA								NCL (26344 upstream) : C2orf52 (17586 downstream)																							aaacaaaaacaaaaaacaacaac	0.241													4	2	---	---	---	---	
COPS7B	64708	broad.mit.edu	37	2	232647538	232647538	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232647538delT	uc010fxy.1	+						PDE6D_uc002vse.1_5'Flank|PDE6D_uc002vsf.1_5'Flank|PDE6D_uc010fxx.1_5'Flank	NM_022730	NP_073567	Q9H9Q2	CSN7B_HUMAN	COP9 constitutive photomorphogenic homolog						cullin deneddylation	cytoplasm|signalosome				ovary(1)|liver(1)|skin(1)	3		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GTTAAAAAAGTTTTTTTTTTG	0.244													4	2	---	---	---	---	
DIS3L2	129563	broad.mit.edu	37	2	232854050	232854053	+	Intron	DEL	TGTG	-	-	rs67107718		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232854050_232854053delTGTG	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron	NM_152383	NP_689596	Q8IYB7	DI3L2_HUMAN	DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		TCAGTATAATtgtgtgtgtgtgtg	0.157													4	2	---	---	---	---	
SAG	6295	broad.mit.edu	37	2	234215899	234215899	+	5'Flank	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234215899delA	uc002vuh.2	+						SAG_uc002vug.2_5'Flank|SAG_uc010zmq.1_5'Flank	NM_000541	NP_000532	P10523	ARRS_HUMAN	S-arrestin						rhodopsin mediated phototransduction|rhodopsin mediated signaling pathway		protein phosphatase inhibitor activity			ovary(1)	1		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		aaaacaaaacaaaaaaaagaa	0.239													5	3	---	---	---	---	
TRPM8	79054	broad.mit.edu	37	2	234883629	234883629	+	Intron	DEL	T	-	-	rs115203020	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234883629delT	uc002vvh.2	+						TRPM8_uc010fyj.2_Intron	NM_024080	NP_076985	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel,							integral to membrane				skin(4)	4		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	ACTTACTGAATTTTTTTTGAC	0.393													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	236832526	236832526	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236832526delA	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						TTAAAGGAGGAAAAAAAAAGA	0.239													4	2	---	---	---	---	
LRRFIP1	9208	broad.mit.edu	37	2	238665529	238665529	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238665529delG	uc002vxe.2	+						LRRFIP1_uc002vxc.2_Intron|LRRFIP1_uc010znm.1_Intron|LRRFIP1_uc002vxd.2_Intron|LRRFIP1_uc002vxf.2_Intron	NM_001137552	NP_001131024	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|cytoskeleton|nucleus	DNA binding|double-stranded RNA binding|protein binding			breast(3)	3		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		attatttgatggaacaagcat	0.000													4	2	---	---	---	---	
PER2	8864	broad.mit.edu	37	2	239189036	239189036	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239189036delA	uc002vyc.2	-						PER2_uc010znv.1_Intron|PER2_uc010znw.1_Intron|PER2_uc010fyx.1_5'Flank	NM_022817	NP_073728	O15055	PER2_HUMAN	period 2						circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		gaaagccaacacggggctgtg	0.015													1	6	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	240298927	240298928	+	Intron	INS	-	AGG	AGG	rs147200077	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240298927_240298928insAGG	uc002vyk.3	-						HDAC4_uc010fza.2_Intron	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		TGCCCCAGCTCAGGCGTCGCCA	0.619													11	6	---	---	---	---	
ATG4B	23192	broad.mit.edu	37	2	242608184	242608184	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242608184delT	uc002wbv.2	+						ATG4B_uc002wbu.2_Intron|ATG4B_uc002wbw.2_Intron|ATG4B_uc010zox.1_Intron|ATG4B_uc010zoy.1_Intron|ATG4B_uc010fzp.2_Intron|ATG4B_uc010zoz.1_Intron|ATG4B_uc002wby.2_Intron	NM_013325	NP_037457	Q9Y4P1	ATG4B_HUMAN	APG4 autophagy 4 homolog B isoform a						autophagic vacuole assembly|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		GATTTTTGCGTTTTTTTTTTC	0.507													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	1515008	1515009	+	IGR	DEL	GC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1515008_1515009delGC								CNTN6 (69731 upstream) : CNTN4 (625541 downstream)																							ATACATGCTTGCACACATTTTT	0.307													4	2	---	---	---	---	
GRM7	2917	broad.mit.edu	37	3	7260841	7260841	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7260841delT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)	AGATGCTTTGTTTTTTTCCCG	0.318													4	2	---	---	---	---	
LMCD1	29995	broad.mit.edu	37	3	8570952	8570952	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8570952delT	uc003bqq.2	+						LMCD1_uc011atd.1_Intron|LMCD1_uc011ate.1_Intron	NM_014583	NP_055398	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1						positive regulation of calcineurin-NFAT signaling pathway|regulation of cardiac muscle hypertrophy|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	transcription corepressor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(96;0.124)		CAAATGACTATTTATTGCATT	0.443													4	2	---	---	---	---	
TADA3	10474	broad.mit.edu	37	3	9829229	9829230	+	Intron	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9829229_9829230delAC	uc003bsx.1	-						TADA3_uc010hcn.1_Intron|TADA3_uc003bsy.2_Intron|TADA3_uc003bsw.1_5'UTR	NM_006354	NP_006345	O75528	TADA3_HUMAN	transcriptional adaptor 3 isoform a						estrogen receptor signaling pathway|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex	ligand-dependent nuclear receptor binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity				0						AAGAACTAAGACACACACACAG	0.431													4	2	---	---	---	---	
XPC	7508	broad.mit.edu	37	3	14219361	14219361	+	Intron	DEL	T	-	-	rs36014499		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14219361delT	uc011ave.1	-						XPC_uc011avf.1_Intron|XPC_uc011avg.1_Intron|LSM3_uc003byn.2_5'Flank	NM_004628	NP_004619	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C						nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal	cytoplasm|nucleoplasm|XPC complex	bubble DNA binding|damaged DNA binding|loop DNA binding|protein binding|single-stranded DNA binding			ovary(2)|breast(1)	3						aaatacactcttgaggctgaa	0.000			Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		NER	Xeroderma_Pigmentosum				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	18872454	18872454	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18872454delA								SATB1 (392202 upstream) : KCNH8 (317563 downstream)																							TGTATTAGACAAAAATGGATG	0.279													4	2	---	---	---	---	
RARB	5915	broad.mit.edu	37	3	25235402	25235405	+	Intron	DEL	AGTT	-	-	rs151176102		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25235402_25235405delAGTT	uc011awl.1	+							NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2						embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)	GTAATTAATCAGTTAGTAAGATGA	0.162													4	2	---	---	---	---	
ZCWPW2	152098	broad.mit.edu	37	3	28436736	28436736	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28436736delA	uc003ceh.2	+						ZCWPW2_uc003cei.2_Intron	NM_001040432	NP_001035522	Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2								zinc ion binding			ovary(2)	2						ggctattatcaaaaaaagcag	0.000													4	3	---	---	---	---	
RBMS3	27303	broad.mit.edu	37	3	29849669	29849669	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29849669delT	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)				TTGTTGTTCATTTTTTTTTGT	0.388													1	5	---	---	---	---	
MYRIP	25924	broad.mit.edu	37	3	39952786	39952787	+	Intron	INS	-	AG	AG	rs142311373	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39952786_39952787insAG	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc010hhx.1_Intron	NM_015460	NP_056275	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		ATGTAGAAAAAGGAATCATGCT	0.391													4	3	---	---	---	---	
CCDC13	152206	broad.mit.edu	37	3	42794981	42794982	+	Intron	INS	-	GTG	GTG	rs145035002	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42794981_42794982insGTG	uc003cly.3	-						CCDC13_uc003clz.2_Intron|CCDC13_uc011azq.1_Intron	NM_144719	NP_653320	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13											ovary(1)	1						ttagggattcagtggtggataa	0.079													4	2	---	---	---	---	
ACTR8	93973	broad.mit.edu	37	3	53904826	53904826	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53904826delC	uc003dhd.2	-						ACTR8_uc003dhb.2_Intron|ACTR8_uc003dhc.2_Intron	NM_022899	NP_075050	Q9H981	ARP8_HUMAN	actin-related protein 8						cell division|DNA recombination|DNA repair|mitosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex	protein binding			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		TGCTAACTGACCCCTTTCATC	0.343													4	2	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54730534	54730534	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54730534delT	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		TAGAAGAGGGTTTTTTTTCTC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	55306551	55306551	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55306551delC								CACNA2D3 (197969 upstream) : WNT5A (193193 downstream)																							GAGCTGTAGTCCAGTTGAATC	0.478													4	2	---	---	---	---	
ARHGEF3	50650	broad.mit.edu	37	3	56958088	56958088	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56958088delA	uc003dih.2	-							NM_001128615	NP_001122087	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		TAAACTTTGCAACAAAATCAT	0.448													4	2	---	---	---	---	
FHIT	2272	broad.mit.edu	37	3	60828965	60828965	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60828965delA	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)		TTTTTCTCACAAAAGAGAAGT	0.373			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				4	2	---	---	---	---	
SYNPR	132204	broad.mit.edu	37	3	63264536	63264536	+	Intron	DEL	C	-	-	rs34988753		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63264536delC	uc003dlp.2	+						SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron	NM_001130003	NP_001123475	Q8TBG9	SYNPR_HUMAN	synaptoporin isoform 1							cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)		AACCCTCAAGCCGGGGATTTC	0.602													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	63774418	63774418	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63774418delA								SNTN (123537 upstream) : C3orf49 (30623 downstream)																							aaaaaaaaacaaaaaaaactg	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	64481667	64481667	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64481667delC								PRICKLE2 (270536 upstream) : ADAMTS9 (19666 downstream)																							AAAGGGCTGACCAGAAGATTC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	64775526	64775527	+	Intron	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64775526_64775527delAC	uc003dml.2	+											Homo sapiens cDNA FLJ25194 fis, clone REC04095.																		CAGTTcacagacacacacacac	0.317													4	3	---	---	---	---	
MAGI1	9223	broad.mit.edu	37	3	65528731	65528731	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65528731delA	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hny.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		aatttataagaaaaaaaaaac	0.000													4	2	---	---	---	---	
SUCLG2	8801	broad.mit.edu	37	3	67678416	67678416	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67678416delT	uc003dna.3	-							NM_003848	NP_003839	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming beta subunit						succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	ttagtggtggttttttttgga	0.000													5	3	---	---	---	---	
PDZRN3	23024	broad.mit.edu	37	3	73574972	73574972	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73574972delT	uc003dpl.1	-						PDZRN3_uc011bgh.1_Intron|PDZRN3_uc010hoe.1_Intron	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3								ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		tctcacgtggttttccttgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	76084582	76084582	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76084582delT								ZNF717 (249912 upstream) : None (None downstream)																							TGTTTGTTTGTTTTTTTAATT	0.378													4	2	---	---	---	---	
ROBO2	6092	broad.mit.edu	37	3	77637652	77637653	+	Intron	INS	-	A	A	rs141853385	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77637652_77637653insA	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron|ROBO2_uc003dqa.2_5'Flank	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GATAAATCAACTACGTTGTGAA	0.287													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	83226118	83226119	+	IGR	INS	-	A	A	rs148946552	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83226118_83226119insA								None (None upstream) : None (None downstream)																							atttacaacttacagcgtatgc	0.000													3	3	---	---	---	---	
CADM2	253559	broad.mit.edu	37	3	85502111	85502112	+	Intron	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85502111_85502112delAC	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		agaaaaatatacacacacacac	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	95999264	95999265	+	IGR	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95999264_95999265delTG								None (None upstream) : EPHA6 (534160 downstream)																							tatgtgtgtctgtgtgtgtgtg	0.243													4	2	---	---	---	---	
DCBLD2	131566	broad.mit.edu	37	3	98594769	98594769	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98594769delA	uc003dtd.2	-						DCBLD2_uc003dte.2_Intron|DCBLD2_uc003dtf.1_Intron	NM_080927	NP_563615	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2						cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane				ovary(2)|central_nervous_system(1)	3						atctaaatataaaaaatgaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	98945825	98945825	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98945825delA								DCBLD2 (325292 upstream) : COL8A1 (411629 downstream)																							ttgctgtcttaacagtattat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	102655823	102655823	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102655823delG								ZPLD1 (457138 upstream) : None (None downstream)																							TTTTACTTCTGGGGGTGAATG	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	102960233	102960234	+	IGR	DEL	TG	-	-	rs140963154		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102960233_102960234delTG								ZPLD1 (761548 upstream) : None (None downstream)																							AATAAATAACTGAAACTTGAAA	0.302													2	4	---	---	---	---	
CBLB	868	broad.mit.edu	37	3	105400639	105400639	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105400639delA	uc003dwc.2	-	15	2547	c.2225delT	c.(2224-2226)ATGfs	p.M742fs	CBLB_uc003dwa.2_Frame_Shift_Del_p.M1fs|CBLB_uc011bhi.1_Frame_Shift_Del_p.M764fs|CBLB_uc003dwd.1_Frame_Shift_Del_p.M742fs|CBLB_uc003dwe.1_Frame_Shift_Del_p.M742fs	NM_170662	NP_733762	Q13191	CBLB_HUMAN	Cas-Br-M (murine) ecotropic retroviral	742	Pro-rich.				cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9						TCCATTCAGCATACAGTGACC	0.343			Mis S		AML								260	124	---	---	---	---	
LOC344595	344595	broad.mit.edu	37	3	106982380	106982380	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106982380delG	uc010hpq.2	+							NR_028302				Homo sapiens cDNA FLJ31372 fis, clone NB9N42000281.												0						aaaaaaaaaagaaaaagaaaa	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	107156262	107156262	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107156262delT	uc003dwj.2	+											Homo sapiens cDNA clone IMAGE:5312582.																		CAACCTACGGttttttttttt	0.279													4	2	---	---	---	---	
CD47	961	broad.mit.edu	37	3	107805103	107805103	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107805103delA	uc003dwt.1	-						CD47_uc003dwu.1_Intron|CD47_uc003dwv.1_Intron|CD47_uc003dww.1_Intron	NM_001777	NP_001768	Q08722	CD47_HUMAN	CD47 antigen isoform 1 precursor						blood coagulation|cell adhesion|cell junction assembly|integrin-mediated signaling pathway|leukocyte migration|positive regulation of cell proliferation|positive regulation of cell-cell adhesion|positive regulation of T cell activation	integral to plasma membrane	protein binding|thrombospondin receptor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(3;0.0191)|Epithelial(53;0.118)			TAATTTCAttaaaaaaaaaac	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112755455	112755455	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112755455delA								C3orf17 (16900 upstream) : BOC (174957 downstream)																							aacacagctcaagtcacagag	0.100													4	2	---	---	---	---	
GAP43	2596	broad.mit.edu	37	3	115351804	115351804	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115351804delT	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		TATATATGCGTTTTTTGATTG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117273674	117273674	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117273674delA								LOC285194 (837789 upstream) : None (None downstream)																							TCCAGTAGTCAAAAAAATAGA	0.343													4	2	---	---	---	---	
CHCHD6	84303	broad.mit.edu	37	3	126661824	126661825	+	Intron	DEL	CT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126661824_126661825delCT	uc003ejf.1	+						CHCHD6_uc010hsj.1_Intron	NM_032343	NP_115719	Q9BRQ6	CHCH6_HUMAN	coiled-coil-helix-coiled-coil-helix domain												0						ctttgtagggctctctctctct	0.015													3	3	---	---	---	---	
EEFSEC	60678	broad.mit.edu	37	3	127917676	127917676	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127917676delT	uc003eki.2	+						EEFSEC_uc003ekj.2_Intron	NM_021937	NP_068756	P57772	SELB_HUMAN	eukaryotic elongation factor,							cytoplasm|nucleus	GTP binding|GTPase activity|translation elongation factor activity			ovary(1)	1						AGACtttctgtttttttttct	0.199													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	129125330	129125331	+	Intron	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129125330_129125331delGT	uc003emg.2	-							NM_207307	NP_997190			hypothetical protein LOC90288																		gtgtgTGCACGTGTGTGTGTAT	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	130254385	130254386	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130254385_130254386insT								COL29A1 (50697 upstream) : COL6A6 (24792 downstream)																							TTGAGTGATTCTTTTTTTTTTT	0.366													2	4	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131270994	131270996	+	Intron	DEL	TTA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131270994_131270996delTTA	uc003eok.2	-						CPNE4_uc011blq.1_Intron|CPNE4_uc003eol.2_Intron|CPNE4_uc003eom.2_Intron	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						GAAGTTTCATttattattattat	0.340													4	2	---	---	---	---	
TMEM108	66000	broad.mit.edu	37	3	133035907	133035908	+	Intron	INS	-	T	T	rs146360846	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133035907_133035908insT	uc003eph.2	+						TMEM108_uc003epi.2_Intron|TMEM108_uc003epj.1_Intron|TMEM108_uc003epk.2_Intron	NM_023943	NP_076432	Q6UXF1	TM108_HUMAN	transmembrane protein 108 precursor							integral to membrane				ovary(2)|skin(2)	4						CTTTGTGCTTGTCAAAGTAAGG	0.396													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137183871	137183871	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137183871delA								IL20RB (453951 upstream) : SOX14 (299708 downstream)																							ttttcactagaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137594637	137594637	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137594637delA								SOX14 (110241 upstream) : CLDN18 (123021 downstream)																							tggtctgggcaaaaaaatttt	0.000													4	2	---	---	---	---	
FAIM	55179	broad.mit.edu	37	3	138348258	138348259	+	Intron	INS	-	TAGCAAGTAAAATACC	TAGCAAGTAAAATACC	rs144618719	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138348258_138348259insTAGCAAGTAAAATACC	uc003esr.2	+						FAIM_uc003eso.1_3'UTR|FAIM_uc003esp.2_Intron|FAIM_uc003esq.2_Intron|FAIM_uc003ess.2_Intron	NM_001033032	NP_001028204	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule isoform c						apoptosis	cytoplasm					0						AGGCTCCAGCATAGCAAGTAAA	0.446													18	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	138792420	138792421	+	IGR	INS	-	A	A	rs149027170	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138792420_138792421insA								PRR23C (28686 upstream) : BPESC1 (30606 downstream)																							taaagagggaggggggaaattt	0.035													3	3	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140056832	140056832	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140056832delG	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						tgatagagctggggggaaaca	0.080										HNSCC(16;0.037)			4	2	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140147764	140147764	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140147764delG	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						tcagtcagtaggggggatctt	0.269										HNSCC(16;0.037)			4	2	---	---	---	---	
ZBTB38	253461	broad.mit.edu	37	3	141139784	141139784	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141139784delA	uc003etw.2	+						ZBTB38_uc010hun.2_Intron|ZBTB38_uc010huo.2_Intron|ZBTB38_uc003ety.2_Intron	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38						positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						AGTTTCAGTTAAAAAAAAAAT	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	141182782	141182783	+	IGR	DEL	AG	-	-	rs149366412		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141182782_141182783delAG								ZBTB38 (14157 upstream) : RASA2 (23143 downstream)																							ATGCCAGGACagagagagagag	0.401													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	141447372	141447372	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141447372delA								RASA2 (116175 upstream) : RNF7 (9679 downstream)																							agctgaaatcaagggttcaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144038254	144038255	+	IGR	DEL	AC	-	-	rs111631544		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144038254_144038255delAC								C3orf58 (327045 upstream) : None (None downstream)																							CAGGAAGcatacacacacacac	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	146449854	146449854	+	IGR	DEL	T	-	-	rs71773386		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146449854delT								PLSCR5 (125851 upstream) : ZIC4 (653983 downstream)																							CTGCATTCTATTTTTTTTTGG	0.323													4	2	---	---	---	---	
TM4SF4	7104	broad.mit.edu	37	3	149213962	149213962	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149213962delT	uc003exd.1	+							NM_004617	NP_004608	P48230	T4S4_HUMAN	transmembrane 4 superfamily member 4							integral to membrane					0			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			CCATTTGGGATTTTTTTTTTT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152301133	152301133	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152301133delC								MBNL1 (117565 upstream) : P2RY1 (251603 downstream)																							cagacagtggcccccaaagaa	0.169													4	2	---	---	---	---	
VEPH1	79674	broad.mit.edu	37	3	157019402	157019402	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157019402delA	uc003fbj.1	-						VEPH1_uc003fbk.1_Intron|VEPH1_uc010hvu.1_Intron	NM_024621	NP_078897	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain homolog 1							plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			aaactctattaaaactgctct	0.000													4	2	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	158800325	158800325	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158800325delA	uc003fcq.1	+						IQCJ_uc003fco.2_Intron|IQCJ_uc010hvy.1_Intron|IQCJ_uc003fcp.1_Intron	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			GAGGCCCAGGAAAAAAAAAAT	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161993120	161993120	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161993120delT								OTOL1 (771392 upstream) : None (None downstream)																							AAAACATTGATTTTTTTTTTC	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	167670852	167670852	+	IGR	DEL	A	-	-	rs139529843		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167670852delA								SERPINI1 (127496 upstream) : GOLIM4 (56802 downstream)																							ATATATGTTTAAAAAAAAAAT	0.313													6	3	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	169272014	169272014	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169272014delC	uc011bpj.1	-						MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						aagcctgggtccctgaaaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	172219907	172219907	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172219907delC								GHSR (53704 upstream) : TNFSF10 (3558 downstream)																							ttcctcctaactccatattat	0.000													4	2	---	---	---	---	
SPATA16	83893	broad.mit.edu	37	3	172610680	172610680	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172610680delT	uc003fin.3	-							NM_031955	NP_114161	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16						cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)|skin(1)	3	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			ggcagataaCTTTTTTTGTGT	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177533025	177533027	+	5'Flank	DEL	TCT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177533025_177533027delTCT	uc003fiz.1	+											Homo sapiens cDNA FLJ31690 fis, clone NT2RI2005621.																		cctggttccatcttcttcttctg	0.079													4	2	---	---	---	---	
USP13	8975	broad.mit.edu	37	3	179506683	179506683	+	3'UTR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									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													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184212032	184212033	+	IGR	INS	-	CT	CT	rs77386143		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184212032_184212033insCT								CHRD (104413 upstream) : EPHB3 (67554 downstream)																							CTTTTCCGTGGCaccactccca	0.218													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186416266	186416267	+	IGR	INS	-	A	A	rs139858021	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186416266_186416267insA								HRG (20244 upstream) : KNG1 (18853 downstream)																							ttacatccttcatccaatcaag	0.124													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187291959	187291959	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187291959delA								RTP4 (202592 upstream) : SST (94737 downstream)																							TTAAAGGAGGAAAAAAAATAA	0.383													4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	187933102	187933102	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187933102delA	uc003frs.1	+						LPP_uc011bsg.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		tcagaaaaagaaaaaaaaaaa	0.000			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190627483	190627485	+	IGR	DEL	AAC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190627483_190627485delAAC								SNAR-I (31644 upstream) : OSTN (302837 downstream)																							CAAATGAACAAACAACAACAACA	0.355													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3581398	3581398	+	Intron	DEL	G	-	-	rs5855807		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3581398delG	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																		GTTATTAGAAGGGACAGTTTG	0.303													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3600335	3600336	+	IGR	DEL	AT	-	-	rs35597866		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3600335_3600336delAT								LRPAP1 (66111 upstream) : ADRA2C (167739 downstream)																							aaatgtgcacatgagtatgtgt	0.084													4	3	---	---	---	---	
ZBTB49	166793	broad.mit.edu	37	4	4306671	4306672	+	Intron	INS	-	AGT	AGT	rs149397885	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4306671_4306672insAGT	uc003ghu.2	+						ZBTB49_uc003ghv.2_Intron|ZBTB49_uc010icy.2_Intron|ZBTB49_uc010icz.2_Intron	NM_145291	NP_660334	Q6ZSB9	ZBT49_HUMAN	zinc finger protein 509						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2						tcaattttaaggtgaaggggtc	0.114													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12449143	12449143	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12449143delC								None (None upstream) : HSP90AB2P (885894 downstream)																							CATTTTGGGGCATGTGAGTAG	0.368													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	15173401	15173402	+	IGR	INS	-	T	T	rs142552903	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15173401_15173402insT								CPEB2 (101627 upstream) : C1QTNF7 (168158 downstream)																							ttgtttgtttgttttttttcaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	22622852	22622852	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22622852delA								GPR125 (105180 upstream) : GBA3 (71696 downstream)																							actccagatgaaaaaaaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	26182861	26182862	+	IGR	INS	-	T	T	rs141724204	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26182861_26182862insT								C4orf52 (251361 upstream) : RBPJ (138470 downstream)																							GTTTCTCACTGTAAGTCTGCGT	0.292													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	28199469	28199469	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28199469delT								None (None upstream) : None (None downstream)																							TCAATAAATGTTGATTAAACA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	30441827	30441827	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30441827delA								None (None upstream) : PCDH7 (280210 downstream)																							ttaaaacagcaaaaaaaaata	0.020													4	2	---	---	---	---	
PCDH7	5099	broad.mit.edu	37	4	30907090	30907092	+	Intron	DEL	AAC	-	-	rs142953084	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30907090_30907092delAAC	uc011bxx.1	+						PCDH7_uc011bxw.1_Intron	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						GAAAATGAAAAACAAAAAAAAAC	0.379													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	33177714	33177714	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33177714delA								None (None upstream) : None (None downstream)																							aagcaggtacaaaaaaaaaat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	33842579	33842579	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33842579delA								None (None upstream) : None (None downstream)																							TAAAAGACATAAATAGAAGTA	0.343													3	6	---	---	---	---	
FRYL	285527	broad.mit.edu	37	4	48547095	48547095	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48547095delA	uc003gyh.1	-						FRYL_uc003gyg.1_Intron|FRYL_uc003gyi.1_Intron|FRYL_uc003gyj.1_Intron	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						GCAAGGAGAGAAAGATCTCAT	0.363													22	16	---	---	---	---	
CWH43	80157	broad.mit.edu	37	4	49024700	49024700	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49024700delT	uc003gyv.2	+						CWH43_uc011bzl.1_Intron	NM_025087	NP_079363	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog						GPI anchor biosynthetic process	integral to membrane				skin(2)|ovary(1)	3						gttcctggacttttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49155208	49155209	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49155208_49155209insT								CWH43 (91115 upstream) : None (None downstream)																							attccattccattcattccatt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49213584	49213585	+	IGR	INS	-	A	A	rs141768505		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49213584_49213585insA								CWH43 (149491 upstream) : None (None downstream)																							gggacttgcttaaaaaaaagtc	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49652739	49652739	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49652739delG								CWH43 (588646 upstream) : None (None downstream)																							cgagtgaaatggaatggaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	53344267	53344268	+	IGR	DEL	GA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53344267_53344268delGA								SPATA18 (380810 upstream) : USP46 (112861 downstream)																							tagtgagggcgagagagagaga	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58919466	58919466	+	IGR	DEL	T	-	-	rs5858474		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58919466delT								IGFBP7 (942927 upstream) : None (None downstream)																							TTATAATTGGTGACCAAAGTG	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63039969	63039970	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63039969_63039970insT								LPHN3 (101802 upstream) : None (None downstream)																							tgagggaaatctttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63651750	63651750	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63651750delA								LPHN3 (713583 upstream) : None (None downstream)																							gtgggatcagaaaaaaaaaag	0.194													4	2	---	---	---	---	
UBA6	55236	broad.mit.edu	37	4	68527583	68527584	+	Intron	INS	-	GTGG	GTGG	rs138087607	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68527583_68527584insGTGG	uc003hdg.3	-						UBA6_uc003hdi.2_3'UTR	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0						TATAAGTTTAAGTTAACAAATC	0.124													6	3	---	---	---	---	
UBA6	55236	broad.mit.edu	37	4	68531155	68531156	+	Intron	INS	-	G	G	rs71269059		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68531155_68531156insG	uc003hdg.3	-						UBA6_uc003hdi.2_Intron|UBA6_uc003hdj.2_Intron	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0						gtttgtttttttttttttttAA	0.208													17	14	---	---	---	---	
UBA6	55236	broad.mit.edu	37	4	68561866	68561867	+	Intron	INS	-	ATC	ATC	rs147062332	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68561866_68561867insATC	uc003hdg.3	-						UBA6_uc003hdi.2_Intron|UBA6_uc003hdj.2_Intron	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0						ACAATGAAGTAATATTCTCTAG	0.272													3	4	---	---	---	---	
UGT2B15	7366	broad.mit.edu	37	4	69520182	69520183	+	Intron	INS	-	A	A	rs34449264		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69520182_69520183insA	uc011cal.1	-							NM_001076	NP_001067	P54855	UDB15_HUMAN	UDP glycosyltransferase 2B15 precursor						steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0						TTAAAATGTGCAAAAAAAAGAA	0.228													7	4	---	---	---	---	
UGT2B4	7363	broad.mit.edu	37	4	70364223	70364223	+	5'Flank	DEL	T	-	-	rs112691314		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70364223delT	uc003hek.3	-						UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_5'Flank	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor						estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2						gattttgggcttttttttttt	0.000													3	3	---	---	---	---	
SLC4A4	8671	broad.mit.edu	37	4	72279681	72279682	+	Intron	DEL	TT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72279681_72279682delTT	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron|SLC4A4_uc003hgc.3_Intron|SLC4A4_uc003hga.2_Intron|SLC4A4_uc003hgb.3_Intron	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)			ATGAACTCTGTTTAGAGATCAA	0.376													4	2	---	---	---	---	
SLC4A4	8671	broad.mit.edu	37	4	72352388	72352389	+	Intron	INS	-	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72352388_72352389insC	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron|SLC4A4_uc003hgc.3_Intron|SLC4A4_uc010iid.2_Intron	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)			GTTTTATTTCTTTTTTTTTTGA	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	75497235	75497236	+	IGR	DEL	AG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75497235_75497236delAG								AREG (16604 upstream) : BTC (174212 downstream)																							agatatgattagagagagagat	0.000													4	2	---	---	---	---	
PARM1	25849	broad.mit.edu	37	4	75972628	75972628	+	3'UTR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75972628delC	uc003hih.1	+	4						NM_015393	NP_056208	Q6UWI2	PARM1_HUMAN	prostatic androgen-repressed message-1						positive regulation of telomerase activity	early endosome|endosome membrane|Golgi membrane|integral to membrane|late endosome|plasma membrane				ovary(1)	1						AAATGAGCAACCCTGGGTATA	0.294													4	2	---	---	---	---	
SHROOM3	57619	broad.mit.edu	37	4	77517201	77517201	+	Intron	DEL	T	-	-	rs75064528		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77517201delT	uc011cbx.1	+						uc011cby.1_Intron	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			AAGTGAGGTCTTTTTTTTCAC	0.264													4	2	---	---	---	---	
SEPT11	55752	broad.mit.edu	37	4	77935815	77935815	+	Intron	DEL	A	-	-	rs35467273		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77935815delA	uc003hkj.2	+						SEPT11_uc010ijh.1_Intron|SEPT11_uc011cca.1_Intron|SEPT11_uc003hkk.1_5'Flank	NM_018243	NP_060713	Q9NVA2	SEP11_HUMAN	septin 11						cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0						TCTCTACCCCAAAAAAAAAAA	0.199													7	5	---	---	---	---	
CXCL13	10563	broad.mit.edu	37	4	78493732	78493733	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78493732_78493733insA	uc003hkr.2	+							NM_006419	NP_006410	O43927	CXL13_HUMAN	chemokine (C-X-C motif) ligand 13 (B-cell						activation of Rap GTPase activity|B cell chemotaxis|cell-cell signaling|chronic inflammatory response|defense response to bacterium|elevation of cytosolic calcium ion concentration|endothelial cell chemotaxis to fibroblast growth factor|germinal center formation|lymphocyte chemotaxis across high endothelial venule|negative regulation of apoptosis|positive regulation of cell-cell adhesion mediated by integrin|positive regulation of integrin activation|positive regulation of T cell chemotaxis|regulation of angiogenesis|regulation of humoral immune response	extracellular space|soluble fraction	CCR10 chemokine receptor binding|chemokine activity|CXCR3 chemokine receptor binding|CXCR5 chemokine receptor binding|fibroblast growth factor 2 binding|heparin binding|protein heterodimerization activity|receptor agonist activity				0						attaagaagtcaaaaaaaaata	0.000													4	3	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81342457	81342457	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81342457delA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						tgttttagttagtccttcttc	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84573138	84573139	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84573138_84573139insA								AGPAT9 (46113 upstream) : NKX6-1 (841297 downstream)																							aaaaTTAATACAAAAATATCTA	0.173													4	2	---	---	---	---	
PTPN13	5783	broad.mit.edu	37	4	87720532	87720556	+	Intron	DEL	TCACTACAACCACCACCTCCCCAGT	-	-	rs11732623		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87720532_87720556delTCACTACAACCACCACCTCCCCAGT	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)		cgatctcggctcactacaaccaccacctccccagttcactacaac	0.049													4	2	---	---	---	---	
HERC6	55008	broad.mit.edu	37	4	89325802	89325802	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89325802delT	uc011cdi.1	+						HERC6_uc011cdj.1_Intron|HERC6_uc011cdk.1_Intron|HERC6_uc011cdl.1_Intron	NM_017912	NP_060382	Q8IVU3	HERC6_HUMAN	hect domain and RLD 6 isoform 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytosol	ubiquitin-protein ligase activity			lung(3)|ovary(1)|kidney(1)	5		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		ctgcattcacttttttttttc	0.000													12	6	---	---	---	---	
FAM13A	10144	broad.mit.edu	37	4	89848637	89848638	+	Intron	INS	-	T	T	rs55689709		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89848637_89848638insT	uc003hse.1	-						FAM13A_uc003hsf.1_Intron|FAM13A_uc003hsh.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						ctggttctaggttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	90123913	90123913	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90123913delA								TIGD2 (87863 upstream) : GPRIN3 (41516 downstream)																							TCAGAAAAGTAAAAAAGAAAA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	90549893	90549893	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90549893delA								GPRIN3 (320732 upstream) : SNCA (95358 downstream)																							GATTCTTCCTAAAATAAAAGG	0.348													4	2	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91379511	91379511	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91379511delT	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						ccacaATAAGttttttttttt	0.005													5	4	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91858108	91858109	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91858108_91858109insA	uc003hsv.3	+						FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						TTATGTAAAAGAAAAAAAAAGA	0.168													4	2	---	---	---	---	
PDLIM5	10611	broad.mit.edu	37	4	95471837	95471837	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95471837delT	uc003hti.2	+						PDLIM5_uc003htf.2_Intron|PDLIM5_uc003htg.2_Intron|PDLIM5_uc011cdx.1_Intron|PDLIM5_uc003hth.2_Intron|PDLIM5_uc003htj.2_Intron|PDLIM5_uc003htk.2_Intron|PDLIM5_uc011cdy.1_Intron	NM_006457	NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5 isoform a						regulation of dendritic spine morphogenesis|regulation of synaptogenesis	actin cytoskeleton|cell junction|cytosol|postsynaptic density|postsynaptic membrane|synaptosome	actin binding|actinin binding|protein kinase C binding|zinc ion binding			ovary(1)|skin(1)	2		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		AAAACTCCAATTTTGGAATTC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	97612163	97612163	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97612163delG								PDHA2 (849539 upstream) : C4orf37 (867871 downstream)																							TTTGATAAGTGGATATCTCTG	0.398													4	2	---	---	---	---	
ADH1A	124	broad.mit.edu	37	4	100212942	100212942	+	5'Flank	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100212942delT	uc003hur.1	-						uc003hum.1_Intron|ADH1A_uc011ceg.1_Intron|ADH1A_uc010ilg.1_5'Flank	NM_000667	NP_000658	P07327	ADH1A_HUMAN	class I alcohol dehydrogenase, alpha subunit						ethanol oxidation|transcription, DNA-dependent|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|protein binding|zinc ion binding			large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Fomepizole(DB01213)|NADH(DB00157)	tatAGCACCATTTTAAAGGAC	0.050													4	2	---	---	---	---	
ADH1C	126	broad.mit.edu	37	4	100268753	100268754	+	Intron	INS	-	ATTTAT	ATTTAT	rs141335697	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100268753_100268754insATTTAT	uc003huu.2	-							NM_000669	NP_000660	P00326	ADH1G_HUMAN	class I alcohol dehydrogenase, gamma subunit						ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Fomepizole(DB01213)|NADH(DB00157)	AAAATTTAACAATTTATACTTT	0.243									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				12	12	---	---	---	---	
BANK1	55024	broad.mit.edu	37	4	102706527	102706527	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102706527delT	uc003hvx.3	+							NM_001083907	NP_001077376	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		TCTGCTTGTATTTCCTTTCTT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	105053438	105053438	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105053438delT								TACR3 (412465 upstream) : CXXC4 (339907 downstream)																							TTTGTTTTTATTTTTTTGAAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	105892531	105892531	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105892531delT								CXXC4 (476473 upstream) : TET2 (175412 downstream)																							GATATGTTTGTTTTTTTATGT	0.418													4	2	---	---	---	---	
DKK2	27123	broad.mit.edu	37	4	107992092	107992092	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107992092delT	uc010ilw.1	-									Q9UBU2	DKK2_HUMAN	Homo sapiens dickkopf-2 mRNA, complete cds.						multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		aaacctgaaatttttttcaca	0.045													4	2	---	---	---	---	
COL25A1	84570	broad.mit.edu	37	4	110155531	110155532	+	Intron	DEL	AA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110155531_110155532delAA	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzh.1_Intron	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		CTCTACTCCTAAATGTTTAAAG	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	116638616	116638616	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116638616delT								NDST4 (603584 upstream) : MIR1973 (582265 downstream)																							acagtagtacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	120045607	120045607	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120045607delA								SYNPO2 (63214 upstream) : MYOZ2 (11332 downstream)																							CTTCAAGAAGAAAAACTTTCT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	120702385	120702385	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120702385delA								PDE5A (152404 upstream) : MAD2L1 (278194 downstream)																							AGAGAAATTGAAAGCTGTGTA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	127167100	127167100	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127167100delA								MIR2054 (738638 upstream) : None (None downstream)																							aatcagcaagaaaaaaaaaat	0.000													4	2	---	---	---	---	
C4orf29	80167	broad.mit.edu	37	4	128933140	128933140	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128933140delT	uc003ifr.2	+						C4orf29_uc003ifs.2_Intron|C4orf29_uc003ift.2_Intron|C4orf29_uc003ifu.2_Intron|C4orf29_uc010inz.2_Intron|C4orf29_uc003ifv.2_Intron	NM_001039717	NP_001034806	Q0P651	CD029_HUMAN	hypothetical protein LOC80167 precursor							extracellular region				ovary(1)	1						AAACCCtttcttttttttttt	0.114													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	130820336	130820337	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130820336_130820337insA	uc003igw.1	+											Homo sapiens cDNA clone IMAGE:5170949, partial cds.																		CCTCAAAACAGAAAAAAAAAAA	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	137925939	137925940	+	IGR	INS	-	A	A	rs148224903	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137925939_137925940insA								None (None upstream) : PCDH18 (514136 downstream)																							GATAACCAATTAAAAAAAAACA	0.302													2	4	---	---	---	---	
TBC1D9	23158	broad.mit.edu	37	4	141652926	141652926	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141652926delT	uc010ioj.2	-							NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				GCAGATACAATTTTTTTTACT	0.333													4	2	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	143184620	143184620	+	Intron	DEL	T	-	-	rs79931626	byFrequency	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143184620delT	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_Intron|INPP4B_uc011cho.1_Intron|INPP4B_uc011chp.1_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					TATGAGATAATTTTTAGCTTT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	144686521	144686522	+	IGR	INS	-	A	A	rs140422975	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144686521_144686522insA								LOC441046 (197208 upstream) : GYPE (105498 downstream)																							aacgtctttcctccccacctca	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	145298025	145298026	+	IGR	INS	-	A	A	rs138650975	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145298025_145298026insA								GYPA (236121 upstream) : HHIP (269147 downstream)																							CTATTTTTATTAAAAAAAGGAA	0.302													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	145433699	145433699	+	IGR	DEL	A	-	-	rs71995727		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145433699delA								GYPA (371795 upstream) : HHIP (133474 downstream)																							TCCTGATTATAAAAAAAATTA	0.383													3	3	---	---	---	---	
SH3D19	152503	broad.mit.edu	37	4	152099717	152099718	+	Intron	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152099717_152099718delTG	uc010ipl.1	-						SH3D19_uc003ime.2_Intron|SH3D19_uc010ipm.2_Intron	NM_001009555	NP_001009555	Q5HYK7	SH319_HUMAN	SH3 domain containing 19 isoform a						cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)|skin(1)	2	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				atgacaaccttgtgatgtaggt	0.089													4	2	---	---	---	---	
KIAA0922	23240	broad.mit.edu	37	4	154459705	154459706	+	Intron	INS	-	T	T	rs138323822	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154459705_154459706insT	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				AGCCACTTAGCTTTCTGGTTTA	0.480													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	163494308	163494308	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163494308delA								FSTL5 (409122 upstream) : NAF1 (553552 downstream)																							gtattggaggaaaAAAAAATG	0.154													4	2	---	---	---	---	
KLHL2	11275	broad.mit.edu	37	4	166184761	166184761	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166184761delT	uc003irb.2	+						KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron|KLHL2_uc010ira.2_Intron	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1						intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		GGtttttttgttttttttttt	0.169													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	166277489	166277489	+	IGR	DEL	C	-	-	rs36071551		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166277489delC								SC4MOL (13265 upstream) : CPE (22608 downstream)																							TGAAACACAGCCATAAAGAAA	0.194													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	166577838	166577838	+	IGR	DEL	G	-	-	rs150270351		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166577838delG								CPE (158357 upstream) : TLL1 (216572 downstream)																							TCATTGATCTGGAAAAAAAAA	0.363													3	3	---	---	---	---	
DDX60L	91351	broad.mit.edu	37	4	169341791	169341792	+	Intron	DEL	AT	-	-	rs10598233		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169341791_169341792delAT	uc003irq.3	-						DDX60L_uc003irr.1_Intron|DDX60L_uc003irs.1_Intron	NM_001012967	NP_001012985	Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		acacacacacaTGagatagata	0.153													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	172397894	172397894	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172397894delT								None (None upstream) : GALNTL6 (336681 downstream)																							ctcaatttcattgcagagatg	0.000													4	2	---	---	---	---	
GALNT7	51809	broad.mit.edu	37	4	174126649	174126649	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174126649delT	uc003isz.3	+							NM_017423	NP_059119	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		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;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		tcttgctgtcttttttttatg	0.000													5	4	---	---	---	---	
GALNT7	51809	broad.mit.edu	37	4	174225552	174225552	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174225552delA	uc003isz.3	+						GALNT7_uc011ckb.1_Intron	NM_017423	NP_059119	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		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;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		cccatctcttaaaaaaaaaaa	0.030													5	3	---	---	---	---	
VEGFC	7424	broad.mit.edu	37	4	177679629	177679630	+	Intron	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177679629_177679630insT	uc003ius.1	-							NM_005429	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C						angiogenesis|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of mast cell chemotaxis|substrate-dependent cell migration|vascular endothelial growth factor receptor signaling pathway	membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity			lung(5)	5		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		GGACATGCACATTTTTTAATCT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	181000829	181000829	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181000829delA								None (None upstream) : None (None downstream)																							CTAATTACTGAAAAAAATTGT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	181075426	181075426	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181075426delA								None (None upstream) : None (None downstream)																							gggagtcctgaaaaaaaaaat	0.000													4	2	---	---	---	---	
CDKN2AIP	55602	broad.mit.edu	37	4	184363057	184363057	+	5'Flank	DEL	C	-	-	rs67379583		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184363057delC	uc003ivp.1	+						CDKN2AIP_uc003ivq.1_5'Flank	NM_017632	NP_060102	Q9NXV6	CARF_HUMAN	CDKN2A interacting protein						negative regulation of cell growth|positive regulation of signal transduction|regulation of protein stability	granular component|nucleoplasm	double-stranded RNA binding|p53 binding				0		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		GACAAGCTGACCACCCCTAGC	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190293416	190293417	+	IGR	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190293416_190293417delAC								None (None upstream) : FRG1 (568557 downstream)																							ACACATGCAAACACACACACAC	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190595397	190595397	+	IGR	DEL	G	-	-	rs11323146		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190595397delG								None (None upstream) : FRG1 (266577 downstream)																							cactgaaaaagtctcaggatg	0.134													6	3	---	---	---	---	
AHRR	57491	broad.mit.edu	37	5	424645	424645	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:424645delG	uc003jav.2	+						AHRR_uc003jaw.2_Intron|AHRR_uc010isy.2_Intron|AHRR_uc010isz.2_Intron|AHRR_uc003jax.2_Intron|AHRR_uc003jay.2_Intron	NM_020731	NP_065782	A9YTQ3	AHRR_HUMAN	arylhydrocarbon receptor repressor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			breast(2)	2			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			TGACGCCTCTGGGCATGCGTG	0.562													4	2	---	---	---	---	
SLC6A19	340024	broad.mit.edu	37	5	1222213	1222214	+	3'UTR	DEL	TG	-	-	rs67714250		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1222213_1222214delTG	uc003jbw.3	+	12						NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19						cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			gcatgggcactgtgtgagtgtg	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1978410	1978410	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1978410delT								IRX4 (95530 upstream) : IRX2 (767871 downstream)																							ttcaatgggcttttttttttc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2263086	2263087	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2263086_2263087insA								IRX4 (380206 upstream) : IRX2 (483194 downstream)																							taggacatcccagatcatccca	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2990750	2990750	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2990750delT								C5orf38 (235238 upstream) : IRX1 (605418 downstream)																							TCTTTGGAAATTAGTGTTCTT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3323990	3323994	+	IGR	DEL	GTATC	-	-	rs148317105	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3323990_3323994delGTATC								C5orf38 (568478 upstream) : IRX1 (272174 downstream)																							gtgtTgtgtggtatctgtggtgtga	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4134205	4134205	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4134205delC								IRX1 (532689 upstream) : LOC340094 (900267 downstream)																							GTCACGTCCTCCCTCAGTGTC	0.537													4	2	---	---	---	---	
KIAA0947	23379	broad.mit.edu	37	5	5454964	5454964	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5454964delA	uc003jdm.3	+							NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379											ovary(1)|central_nervous_system(1)	2						GAGAACCTTCAAAAAAAAACG	0.368													5	3	---	---	---	---	
PAPD7	11044	broad.mit.edu	37	5	6751557	6751558	+	Intron	INS	-	CTTTTCAC	CTTTTCAC			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6751557_6751558insCTTTTCAC	uc003jdx.1	+						PAPD7_uc011cmn.1_Intron|PAPD7_uc010itl.1_Intron	NM_006999	NP_008930	Q5XG87	PAPD7_HUMAN	DNA polymerase sigma						cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding			ovary(1)	1						GGGCCAGGTTGACTGCCTTCCT	0.559													4	4	---	---	---	---	
ADCY2	108	broad.mit.edu	37	5	7440027	7440027	+	Intron	DEL	C	-	-	rs35755966		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7440027delC	uc003jdz.1	+							NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2						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	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						GTGAAGAATTCCGGGGGTGAG	0.473													5	3	---	---	---	---	
LOC285692	285692	broad.mit.edu	37	5	9823132	9823132	+	Intron	DEL	A	-	-	rs139974766		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9823132delA	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0						CCTCTCCACCaaaaaaaaaaa	0.368													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10073314	10073314	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10073314delG								LOC285692 (169378 upstream) : FAM173B (153124 downstream)																							ATGAGGAGGTGGACAGGACGA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	12570212	12570212	+	IGR	DEL	C	-	-	rs67579597		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12570212delC								CTNND2 (666102 upstream) : None (None downstream)																							aaaaaaaaaaCAACTAATTTT	0.134													4	3	---	---	---	---	
TRIO	7204	broad.mit.edu	37	5	14501189	14501189	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14501189delA	uc003jff.2	+						TRIO_uc003jfg.2_Intron	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					taaaaaaaaGAAAAAAAAAAC	0.224													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	16213937	16213938	+	IGR	INS	-	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16213937_16213938insG								MARCH11 (34040 upstream) : ZNF622 (237691 downstream)																							gccccagtagcgactttgtgtg	0.000													7	4	---	---	---	---	
MYO10	4651	broad.mit.edu	37	5	16880363	16880364	+	Intron	INS	-	AA	AA	rs142367955	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16880363_16880364insAA	uc003jft.3	-						MYO10_uc003jfu.2_Intron|MYO10_uc003jfv.2_Intron	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						GATCCATAGTTGTCACTCTTTG	0.342													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20452308	20452308	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20452308delT								CDH18 (464001 upstream) : GUSBP1 (889634 downstream)																							TATAAATCTGTTTCCAAAAAT	0.259													4	2	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21533700	21533700	+	Intron	DEL	G	-	-	rs67891163		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21533700delG	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						TGGCAACTCAGGGGCAGAAAC	0.517													2	4	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21534245	21534246	+	Intron	INS	-	TG	TG	rs143137704		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21534245_21534246insTG	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						GCAGGTGTGTCTGTCACAAACA	0.520													4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22249400	22249400	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22249400delG	uc003jgk.2	-							NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						ATTTGCTACAGGTATACCCAG	0.443										HNSCC(59;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	25424888	25424888	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25424888delA								CDH10 (779977 upstream) : None (None downstream)																							AGACAGAAAGAAAAAAACAAG	0.338													4	2	---	---	---	---	
MTMR12	54545	broad.mit.edu	37	5	32233578	32233579	+	Intron	DEL	AA	-	-	rs35760638		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32233578_32233579delAA	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1						acacacacacaaacacacacac	0.342													5	4	---	---	---	---	
NPR3	4883	broad.mit.edu	37	5	32748539	32748540	+	Intron	INS	-	GCAT	GCAT	rs146034103	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32748539_32748540insGCAT	uc003jhv.2	+						NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Intron	NM_000908	NP_000899	P17342	ANPRC_HUMAN	natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)	aacagcagaaagcattaccacc	0.000													3	4	---	---	---	---	
NIPBL	25836	broad.mit.edu	37	5	36963366	36963366	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36963366delT	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron|NIPBL_uc003jkm.1_Intron	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			ATTTTTGTCCTCCTTAATTAA	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	37896854	37896855	+	IGR	INS	-	G	G	rs137922361	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37896854_37896855insG								GDNF (57072 upstream) : EGFLAM (361678 downstream)																							GATCCAGGCTTGGACTTGCTAT	0.416													1	5	---	---	---	---	
PLCXD3	345557	broad.mit.edu	37	5	41420802	41420802	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41420802delT	uc003jmm.1	-							NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						AGAATTTATCTTTGCATGGCA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	41889029	41889029	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41889029delA								OXCT1 (18238 upstream) : C5orf51 (15441 downstream)																							TCAATTTGACAAAAAAAAGTG	0.378													4	2	---	---	---	---	
CCDC152	100129792	broad.mit.edu	37	5	42771637	42771637	+	Intron	DEL	A	-	-	rs35697985		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42771637delA	uc003jmx.3	+						CCDC152_uc011cpr.1_Intron	NM_001134848	NP_001128320	Q4G0S7	CC152_HUMAN	coiled-coil domain containing 152												0						ggctacactgaaaaaaaaaga	0.000													4	2	---	---	---	---	
MGC42105	167359	broad.mit.edu	37	5	43252224	43252224	+	Intron	DEL	A	-	-	rs78891437		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43252224delA	uc003jno.2	+							NM_153361	NP_699192	Q8IY84	NIM1_HUMAN	serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9						GTGAAAGGACAAAAAAAAAAG	0.363													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	52785735	52785736	+	IGR	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52785735_52785736delTC								FST (3833 upstream) : NDUFS4 (70729 downstream)																							acaaggaaagtctctctctcat	0.005													4	2	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59701846	59701846	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59701846delT	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron	NM_006203	NP_006194	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	CATCTTGCACTTTTTTTTTTC	0.343													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	62424228	62424228	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62424228delA								ISCA1P1 (351058 upstream) : HTR1A (832051 downstream)																							TCCTCTTACTAACCCCCTACC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	65714785	65714785	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65714785delT								SFRS12 (238073 upstream) : MAST4 (177391 downstream)																							ctttcaatagtttttggggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	70081139	70081139	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70081139delA	uc011crh.1	+						uc010iyh.1_Intron|uc003jzx.2_Intron|uc011cro.1_Intron|uc003jzw.2_Intron					Homo sapiens cDNA FLJ36702 fis, clone UTERU2009206.																		attctatctcaaaaaaaaaaa	0.234													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	72002753	72002753	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72002753delT								ZNF366 (199504 upstream) : TNPO1 (109665 downstream)																							tactgacagattttttttttc	0.000													4	3	---	---	---	---	
SSBP2	23635	broad.mit.edu	37	5	80904459	80904459	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80904459delA	uc003kho.2	-						SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		tcaaatgactaaaataaGCAG	0.104													4	2	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	90312826	90312826	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90312826delA	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron|GPR98_uc003kjx.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CCAATGGGAGAACCGTTTATG	0.378													4	2	---	---	---	---	
FAM172A	83989	broad.mit.edu	37	5	93143528	93143528	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93143528delA	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron	NM_032042	NP_114431	Q8WUF8	F172A_HUMAN	hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0						AATTAGGGGGAAAAAAAAGCA	0.338													4	2	---	---	---	---	
MCTP1	79772	broad.mit.edu	37	5	94430014	94430014	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94430014delG	uc003kkx.2	-							NM_024717	NP_078993	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		TTTTCCATTTGGATCTCTATC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	97728480	97728481	+	IGR	INS	-	G	G	rs137919294	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97728480_97728481insG								None (None upstream) : RGMB (376518 downstream)																							CGGGAGTGGCTGTTGTCCATGG	0.550													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	102046937	102046937	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102046937delA								SLCO6A1 (212217 upstream) : PAM (154590 downstream)																							TACGAATGTCAAAAAAAATCC	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	102788516	102788516	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102788516delT								C5orf30 (174155 upstream) : NUDT12 (96041 downstream)																							AAACTCAGAATTTTGTGCATT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	104836099	104836100	+	IGR	DEL	AA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104836099_104836100delAA								RAB9BP1 (400301 upstream) : None (None downstream)																							AAAAACGATTAAAAAAAAAAAA	0.267													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	105317743	105317744	+	IGR	DEL	AG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105317743_105317744delAG								RAB9BP1 (881945 upstream) : None (None downstream)																							agatagagaaagagagagagag	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	105893703	105893704	+	IGR	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105893703_105893704delAC								None (None upstream) : EFNA5 (818887 downstream)																							TCAACCCTTGacacacacacac	0.347													4	2	---	---	---	---	
MAN2A1	4124	broad.mit.edu	37	5	109053037	109053037	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109053037delT	uc003kou.1	+							NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		TAGTGAAGCATTTTTTTTGTG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	109444982	109444983	+	IGR	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109444982_109444983delGT								MAN2A1 (241553 upstream) : TMEM232 (179951 downstream)																							CAAAgtgtgcgtgtgtgtgtgt	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	113239040	113239040	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113239040delA								YTHDC2 (308061 upstream) : KCNN2 (458976 downstream)																							gccttgagctaaGAAAGGGAT	0.090													4	2	---	---	---	---	
DMXL1	1657	broad.mit.edu	37	5	118544543	118544543	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118544543delT	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1											ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		aatccctccatttttttttct	0.000													4	2	---	---	---	---	
SNCAIP	9627	broad.mit.edu	37	5	121727944	121727944	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121727944delT	uc003ksw.1	+						SNCAIP_uc011cwl.1_Intron|SNCAIP_uc010jct.2_Intron|SNCAIP_uc003ksx.1_Intron|SNCAIP_uc003ksy.1_Intron|SNCAIP_uc003ksz.1_Intron|SNCAIP_uc010jcu.2_Intron|SNCAIP_uc011cwm.1_Intron|SNCAIP_uc003kta.1_Intron|SNCAIP_uc010jcv.1_Intron|SNCAIP_uc010jcw.1_Intron|SNCAIP_uc010jcx.1_Intron	NM_005460	NP_005451	Q9Y6H5	SNCAP_HUMAN	synuclein alpha interacting protein						cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		TGGATGAGTCTTTTTTTTTTG	0.323													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123355938	123355941	+	IGR	DEL	TTTG	-	-	rs72427051		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123355938_123355941delTTTG								CSNK1G3 (403476 upstream) : ZNF608 (616669 downstream)																							gacaagggtttttgtttgtttgtt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123460357	123460358	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123460357_123460358insA								CSNK1G3 (507895 upstream) : ZNF608 (512252 downstream)																							TTCTAAAACATAAAAAAAAAGC	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	127585835	127585835	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127585835delA								SLC12A2 (60456 upstream) : FBN2 (7767 downstream)																							GTATGTTGTTAAAAAAAAAAT	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129088472	129088472	+	IGR	DEL	T	-	-	rs148458982		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129088472delT								ADAMTS19 (14096 upstream) : CHSY3 (152051 downstream)																							AATGTGTGTCTTTTTTTTTTT	0.209													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129875235	129875235	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129875235delA								CHSY3 (352909 upstream) : HINT1 (619640 downstream)																							AAAGTCAAGGAAAAAAATGAA	0.303													4	2	---	---	---	---	
CDC42SE2	56990	broad.mit.edu	37	5	130598649	130598649	+	5'Flank	DEL	T	-	-	rs11295428		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130598649delT	uc003kvh.2	+						CDC42SE2_uc003kvi.2_5'Flank|CDC42SE2_uc003kvj.2_5'Flank|CDC42SE2_uc003kvk.2_5'Flank	NM_020240	NP_064625	Q9NRR3	C42S2_HUMAN	CDC42 small effector 2						phagocytosis|regulation of cell shape|regulation of signal transduction	cell projection|cytoplasm|cytoskeleton|phagocytic cup	protein binding|structural molecule activity				0		all_cancers(142;0.0525)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			agatggagaAttttttttttt	0.000													5	3	---	---	---	---	
RAPGEF6	51735	broad.mit.edu	37	5	131008745	131008745	+	Intron	DEL	T	-	-	rs12513562		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131008745delT	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron|FNIP1_uc010jdm.1_Intron	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		CGtttttttgttttttttttt	0.149													9	4	---	---	---	---	
SEPT8	23176	broad.mit.edu	37	5	132087445	132087446	+	3'UTR	DEL	TT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132087445_132087446delTT	uc003kxr.2	-	10					CCNI2_uc003kxq.1_Intron|CCNI2_uc011cxg.1_Intron|CCNI2_uc011cxh.1_Intron	NM_001098811	NP_001092281	Q92599	SEPT8_HUMAN	septin 8 isoform a						cell cycle	septin complex	GTP binding|protein binding			ovary(2)	2		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAAAGCAGACTTTTTTTTTTTT	0.431													7	4	---	---	---	---	
AFF4	27125	broad.mit.edu	37	5	132225028	132225028	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132225028delA	uc003kyd.2	-						AFF4_uc011cxk.1_Intron	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31						transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGTAAACTTTAAAAAAAAAAA	0.169													11	6	---	---	---	---	
AFF4	27125	broad.mit.edu	37	5	132265880	132265880	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132265880delA	uc003kyd.2	-						AFF4_uc011cxk.1_Intron|AFF4_uc003kye.1_Intron|AFF4_uc003kyf.3_Intron	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31						transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACCAAAACCCAAAGGCCAGTG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133362327	133362327	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133362327delG								VDAC1 (21503 upstream) : TCF7 (88075 downstream)																							CGGCTTCCCTGGCCCAGTCTT	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134651932	134651932	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134651932delT	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																		agtccgaggcttttttttttg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	135037568	135037568	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135037568delA								LOC340074 (47944 upstream) : LOC153328 (132797 downstream)																							atttccttctaaaaaattaat	0.109													4	2	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142343830	142343830	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142343830delT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			tttcccaaactttagttttct	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	142937776	142937777	+	IGR	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142937776_142937777delTG								NR3C1 (122699 upstream) : HMHB1 (253949 downstream)																							tgagtatgtttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	143410152	143410152	+	IGR	DEL	T	-	-	rs78490379		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143410152delT								HMHB1 (209870 upstream) : YIPF5 (127579 downstream)																							CAACTATATCTTTTTTTTGCT	0.224													4	2	---	---	---	---	
KCTD16	57528	broad.mit.edu	37	5	143560501	143560501	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143560501delT	uc003lnm.1	+							NM_020768	NP_065819	Q68DU8	KCD16_HUMAN	potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			ttcttttttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	144062238	144062238	+	IGR	DEL	A	-	-	rs77533823		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144062238delA								KCTD16 (205294 upstream) : None (None downstream)																							TTTCCATGATAAAAAAAAAAG	0.269													4	2	---	---	---	---	
SH3RF2	153769	broad.mit.edu	37	5	145337260	145337260	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145337260delA	uc003lnt.2	+						SH3RF2_uc011dbl.1_Intron	NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2								ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTATAACATTAAAAAAAACGT	0.229													4	2	---	---	---	---	
SPINK5	11005	broad.mit.edu	37	5	147468398	147468399	+	Intron	INS	-	A	A	rs139869151		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147468398_147468399insA	uc003lox.2	+						SPINK5_uc010jgq.1_Intron|SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGCTTTGTATAAAAAAAAAAA	0.218													10	12	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148388962	148388963	+	Intron	DEL	TA	-	-	rs71933109		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148388962_148388963delTA	uc003lpu.2	-						SH3TC2_uc003lpp.1_Intron|SH3TC2_uc010jgw.2_Intron|SH3TC2_uc003lps.2_Intron|SH3TC2_uc003lpt.2_Intron|SH3TC2_uc010jgx.2_Intron	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGTCATTTCTATGTTTTTATC	0.297													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	149864867	149864867	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149864867delT								RPS14 (35548 upstream) : NDST1 (12473 downstream)																							GACATTCTAGTAAACAATGAA	0.458													2	5	---	---	---	---	
SLC36A2	153201	broad.mit.edu	37	5	150713094	150713099	+	Intron	DEL	AGGAAT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150713094_150713099delAGGAAT	uc003lty.2	-						GM2A_uc011dcs.1_Intron|SLC36A2_uc003ltz.2_Intron|SLC36A2_uc003lua.2_Intron|SLC36A2_uc010jhv.2_Intron	NM_181776	NP_861441	Q495M3	S36A2_HUMAN	solute carrier family 36, member 2						cellular nitrogen compound metabolic process	cytoplasm|integral to membrane|plasma membrane	glycine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAAGTACTGAAGGAATAGTATTTCAT	0.291													5	7	---	---	---	---	
FAT2	2196	broad.mit.edu	37	5	150909139	150909139	+	Intron	DEL	T	-	-	rs113377880		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150909139delT	uc003lue.3	-						GM2A_uc011dcs.1_Intron|FAT2_uc003lud.3_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor						epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATCTCCCTCATTTTTCTTTAT	0.393													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	153355321	153355321	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153355321delA								GRIA1 (161893 upstream) : FAM114A2 (15950 downstream)																							TGGAAGATACATGTCCAGAGA	0.448													4	2	---	---	---	---	
LARP1	23367	broad.mit.edu	37	5	154111763	154111766	+	Intron	DEL	AAAG	-	-	rs139711421		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154111763_154111766delAAAG	uc003lvo.2	+							NM_015315	NP_056130	Q6PKG0	LARP1_HUMAN	la related protein isoform 1								protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			aaaaaaaaaaaaagaaaGGTGAAT	0.078													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	155004271	155004272	+	IGR	DEL	GA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155004271_155004272delGA								KIF4B (606586 upstream) : SGCD (130791 downstream)																							GGCATATGGggagagagagaga	0.213													4	2	---	---	---	---	
EBF1	1879	broad.mit.edu	37	5	158178387	158178388	+	Intron	INS	-	GACT	GACT	rs143439377	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158178387_158178388insGACT	uc010jip.2	-						EBF1_uc011ddw.1_Intron|EBF1_uc011ddx.1_Intron|EBF1_uc003lxl.3_Intron	NM_024007	NP_076870	Q9UH73	COE1_HUMAN	early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CACATGCCAGGGACTCCTTTAC	0.500			T	HMGA2	lipoma								1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	159106871	159106871	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159106871delA								LOC285627 (213587 upstream) : ADRA1B (236869 downstream)																							aattcacaggaaaaaaaaatt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	160335611	160335611	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160335611delG								ATP10B (56392 upstream) : LOC285629 (23177 downstream)																							AGAGGACCCTGGGGTCAGCCA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	161231535	161231536	+	IGR	DEL	GA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161231535_161231536delGA								GABRA6 (101937 upstream) : GABRA1 (42661 downstream)																							TGTTCCTTGTGAGAGAGAGGGA	0.436													4	2	---	---	---	---	
GABRA1	2554	broad.mit.edu	37	5	161284994	161284995	+	Intron	INS	-	A	A	rs143696381	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161284994_161284995insA	uc010jiw.2	+						GABRA1_uc010jix.2_Intron|GABRA1_uc010jiy.2_Intron|GABRA1_uc003lyx.3_Intron|GABRA1_uc010jiz.2_Intron|GABRA1_uc010jja.2_Intron|GABRA1_uc010jjb.2_Intron	NM_000806	NP_000797	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|pancreas(1)	3	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Alprazolam(DB00404)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Halazepam(DB00801)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Metharbital(DB00463)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Picrotoxin(DB00466)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Zaleplon(DB00962)|Zolpidem(DB00425)	agaaaaaagttaaaaaaaaaag	0.064													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	161897043	161897043	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161897043delC								GABRG2 (314499 upstream) : CCNG1 (967534 downstream)																							aggactgcagcccccatctgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162837504	162837505	+	IGR	INS	-	A	A	rs143696207	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162837504_162837505insA								None (None upstream) : CCNG1 (27072 downstream)																							acaaaaaaaacaaaaaaacaaa	0.045													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163164953	163164953	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163164953delT								MAT2B (218620 upstream) : None (None downstream)																							atcttagtaattttttgtttg	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164600451	164600452	+	IGR	DEL	CC	-	-	rs60535901	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164600451_164600452delCC								None (None upstream) : None (None downstream)																							cacacacacacccccttctgcc	0.000													3	4	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166723446	166723446	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166723446delT	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		ACCAAAATGGTGAATTTATTT	0.398													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168437159	168437159	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168437159delA	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			Acaagaccctaaaaaagtggc	0.139													4	2	---	---	---	---	
DOCK2	1794	broad.mit.edu	37	5	169481042	169481043	+	Intron	INS	-	TT	TT	rs139587348	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169481042_169481043insTT	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron|DOCK2_uc003mah.2_5'Flank	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGGGGGGTGAATTGTTTTCATG	0.470													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173019223	173019223	+	IGR	DEL	C	-	-	rs138713001		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173019223delC								LOC285593 (7149 upstream) : BOD1 (14925 downstream)																							ctgcaatcagccttccattgt	0.020													4	2	---	---	---	---	
HMP19	51617	broad.mit.edu	37	5	173484494	173484495	+	Intron	DEL	TA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173484494_173484495delTA	uc003mcx.2	+							NM_015980	NP_057064	Q9Y328	NSG2_HUMAN	HMP19 protein						dopamine receptor signaling pathway	cytoplasmic vesicle membrane|Golgi cisterna membrane|integral to membrane|multivesicular body membrane	dopamine receptor binding			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00925)|all_lung(126;0.0148)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			AACAAAACACTAAGCTTTATGA	0.436													0	6	---	---	---	---	
MSX2	4488	broad.mit.edu	37	5	174152602	174152616	+	Intron	DEL	AGGGATGGTGGCACC	-	-	rs66988923		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174152602_174152616delAGGGATGGTGGCACC	uc003mcy.2	+							NM_002449	NP_002440	P35548	MSX2_HUMAN	msh homeobox 2						cranial suture morphogenesis|negative regulation of transcription, DNA-dependent|osteoblast differentiation	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0196)|all_lung(126;0.0303)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GATCCCACGAAGGGATGGTGGCACCAGGGATGGTG	0.484													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174299779	174299780	+	IGR	INS	-	AC	AC	rs145533977	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174299779_174299780insAC								MSX2 (141878 upstream) : DRD1 (567896 downstream)																							TTTATCCTGCTacacacacaca	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174967222	174967222	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174967222delC								SFXN1 (11601 upstream) : HRH2 (117818 downstream)																							ATGTCTTTTGCCCCTGGTGGA	0.408													4	2	---	---	---	---	
CLTB	1212	broad.mit.edu	37	5	175845223	175845223	+	5'Flank	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175845223delC	uc003meh.2	-						CLTB_uc003mei.2_5'Flank|CLTB_uc011dfn.1_5'Flank	NM_007097	NP_009028	P09497	CLCB_HUMAN	clathrin, light polypeptide isoform b						intracellular protein transport|vesicle-mediated transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle	protein binding|structural molecule activity				0	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.098)		atagattgagcccaggagttt	0.010													4	2	---	---	---	---	
FAF2	23197	broad.mit.edu	37	5	175935961	175935961	+	3'UTR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175935961delT	uc003mej.3	+	11						NM_014613	NP_055428	Q96CS3	FAF2_HUMAN	UBX domain containing 8						response to unfolded protein	endoplasmic reticulum|lipid particle	protein binding			ovary(1)	1						GAAGTTACGATTTTTTTTTTC	0.438													4	2	---	---	---	---	
RNF130	55819	broad.mit.edu	37	5	179419595	179419595	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179419595delG	uc003mll.1	-						RNF130_uc003mlm.1_Intron	NM_018434	NP_060904	Q86XS8	GOLI_HUMAN	ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			gtgtttttttgggggggtgtc	0.045													3	3	---	---	---	---	
GFPT2	9945	broad.mit.edu	37	5	179734588	179734589	+	Intron	DEL	AG	-	-	rs146202365		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179734588_179734589delAG	uc003mlw.1	-							NM_005110	NP_005101	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	actgaggctcagagaggcaaaA	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	179835693	179835693	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179835693delT								GFPT2 (55378 upstream) : CNOT6 (85724 downstream)																							tatgcaaatgttaggaaagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180540593	180540593	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180540593delT								BTNL9 (52071 upstream) : OR2V2 (41350 downstream)																							GCTCTTCTTGTTATCCTTCCG	0.493													4	2	---	---	---	---	
GNB2L1	10399	broad.mit.edu	37	5	180665830	180665832	+	Intron	DEL	AAC	-	-	rs146950433		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180665830_180665832delAAC	uc003mni.1	-						GNB2L1_uc003mnh.1_Intron|GNB2L1_uc003mnk.1_Intron|GNB2L1_uc003mnj.1_Intron|GNB2L1_uc003mnl.1_Intron|GNB2L1_uc011dhk.1_3'UTR	NM_006098	NP_006089	P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein),						apoptosis|cell cycle|gastrulation|interspecies interaction between organisms|negative regulation of cell growth|negative regulation of phagocytosis|negative regulation of translation|negative regulation of Wnt receptor signaling pathway|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of gastrulation|positive regulation of GTPase activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein homooligomerization|positive regulation of protein phosphorylation|regulation of cell cycle|regulation of cell division|regulation of establishment of cell polarity|regulation of protein localization|rhythmic process	cytoskeleton|dendrite|midbody|nucleus|perikaryon|perinuclear region of cytoplasm|phagocytic cup|small ribosomal subunit	ion channel inhibitor activity|protein kinase C binding|protein phosphatase binding|protein tyrosine kinase inhibitor activity|receptor tyrosine kinase binding|SH2 domain binding				0	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)		caaacaaaaaaacaacaaaaaaa	0.148													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	360710	360710	+	IGR	DEL	A	-	-	rs66515407		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:360710delA								DUSP22 (9357 upstream) : IRF4 (31042 downstream)																							TTCTACTGCCAAAAAAAAATT	0.299													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	2433045	2433045	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2433045delT	uc003mtu.1	+											Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1572223.																		TTCCCATTGGTTTTTTTTTTC	0.423													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	2536554	2536554	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2536554delT								GMDS (290708 upstream) : C6orf195 (86418 downstream)																							TCTCATCTTGTTTTTTTTTTC	0.393													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3714019	3714021	+	IGR	DEL	CTC	-	-	rs72140560		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3714019_3714021delCTC								SLC22A23 (257226 upstream) : C6orf145 (8815 downstream)																							GCTCCACCTTCTCCTCTTCCTTC	0.345													4	2	---	---	---	---	
LYRM4	57128	broad.mit.edu	37	6	5174199	5174199	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5174199delG	uc003mwp.2	-						LYRM4_uc010jnu.2_Intron|LYRM4_uc003mwq.2_Intron|uc003mwn.1_Intron	NM_020408	NP_065141	Q9HD34	LYRM4_HUMAN	LYR motif containing 4 isoform 1							mitochondrion|nucleus					0	Ovarian(93;0.11)	all_hematologic(90;0.0901)				ACTATAGACTGGGGGGCTTTG	0.502													4	2	---	---	---	---	
LY86	9450	broad.mit.edu	37	6	6605071	6605072	+	Intron	INS	-	A	A	rs144792289		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6605071_6605072insA	uc003mwy.1	+						LOC285780_uc003mww.3_Intron|LOC285780_uc003mwx.2_Intron	NM_004271	NP_004262	O95711	LY86_HUMAN	MD-1, RP105-associated precursor						apoptosis|cell proliferation|humoral immune response|inflammatory response|innate immune response	extracellular space|plasma membrane					0	Ovarian(93;0.0377)					accaccaaaggaaaaaaaaaaa	0.109													3	3	---	---	---	---	
LY86	9450	broad.mit.edu	37	6	6635086	6635086	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6635086delG	uc003mwy.1	+							NM_004271	NP_004262	O95711	LY86_HUMAN	MD-1, RP105-associated precursor						apoptosis|cell proliferation|humoral immune response|inflammatory response|innate immune response	extracellular space|plasma membrane					0	Ovarian(93;0.0377)					GGGGAGTGCTGGGAATGCAAT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8495018	8495018	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8495018delT	uc003mye.2	+											Homo sapiens, clone IMAGE:5539086, mRNA.																		ctaatttttcttttttttttc	0.015													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	10213557	10213557	+	5'Flank	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10213557delT	uc003myp.1	-											Homo sapiens clone 958LR MRDS1 protein (MRDS1) mRNA, complete cds.																		cttttttatctttttttttgt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	11620870	11620870	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11620870delG								TMEM170B (37114 upstream) : C6orf105 (93020 downstream)																							TGGATGAACCGATCCAGATCC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	13545891	13545892	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13545891_13545892insT								GFOD1 (58104 upstream) : SIRT5 (28900 downstream)																							tttattttctgttttttttttt	0.000													4	2	---	---	---	---	
SIRT5	23408	broad.mit.edu	37	6	13591181	13591183	+	Intron	DEL	TGT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13591181_13591183delTGT	uc003nay.2	+						SIRT5_uc003naw.2_Intron|SIRT5_uc003nax.2_Intron|SIRT5_uc011dit.1_Intron	NM_012241	NP_036373	Q9NXA8	SIRT5_HUMAN	sirtuin 5 isoform 1						chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial intermembrane space|mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|zinc ion binding			skin(2)|upper_aerodigestive_tract(1)	3	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)		Suramin(DB04786)	tagttgtgtgtgtttagtttgtg	0.000													5	3	---	---	---	---	
RNF182	221687	broad.mit.edu	37	6	13937545	13937545	+	Intron	DEL	T	-	-	rs148992615	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13937545delT	uc003nbe.2	+						RNF182_uc003nbf.2_Intron|RNF182_uc003nbg.2_Intron	NM_152737	NP_689950	Q8N6D2	RN182_HUMAN	ring finger protein 182							cytoplasm|integral to membrane|intracellular membrane-bounded organelle	protein binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3	Breast(50;0.00405)|Ovarian(93;0.0964)	all_hematologic(90;0.135)	Epithelial(50;0.195)			ttcctttgcctttttcagtta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14844656	14844656	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14844656delT								CD83 (707510 upstream) : JARID2 (401078 downstream)																							TACGGTTGTGTTTTTTTTTTT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	15899026	15899026	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15899026delT								DTNBP1 (235755 upstream) : MYLIP (230291 downstream)																							TCTGTCAAAATGTTTTAAGAG	0.463													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	15899033	15899038	+	IGR	DEL	AGAGAT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15899033_15899038delAGAGAT								DTNBP1 (235762 upstream) : MYLIP (230279 downstream)																							AAATGTTTTAAGAGATTCACCACGAT	0.447													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	16089052	16089052	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16089052delT								DTNBP1 (425781 upstream) : MYLIP (40265 downstream)																							TAGGCTTCCCTTTTATGAGAT	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	16202977	16202979	+	IGR	DEL	TGA	-	-	rs71649284		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16202977_16202979delTGA								MYLIP (54501 upstream) : GMPR (35832 downstream)																							aaatcccagctgatttctttgca	0.000													4	2	---	---	---	---	
RNF144B	255488	broad.mit.edu	37	6	18464868	18464868	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18464868delT	uc003ncs.2	+							NM_182757	NP_877434	Q7Z419	R144B_HUMAN	IBR domain containing 2						apoptosis|positive regulation of anti-apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			aagatggccatttttttgctg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	20017120	20017120	+	IGR	DEL	A	-	-	rs34767791		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20017120delA								ID4 (176206 upstream) : MBOAT1 (83815 downstream)																							AGCAGAGTTTAAAAAAAAAAA	0.348													3	3	---	---	---	---	
MBOAT1	154141	broad.mit.edu	37	6	20108025	20108025	+	Intron	DEL	A	-	-	rs112603565		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20108025delA	uc003ncx.1	-						MBOAT1_uc011dji.1_Intron	NM_001080480	NP_001073949	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain						phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			ggcttacaggaaaaaaaaaaa	0.075													4	4	---	---	---	---	
E2F3	1871	broad.mit.edu	37	6	20420670	20420671	+	Intron	DEL	GT	-	-	rs147454226		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20420670_20420671delGT	uc003nda.2	+						E2F3_uc003ncz.2_Intron	NM_001949	NP_001940	O00716	E2F3_HUMAN	E2F transcription factor 3						G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			GCTTTCTCTGgtgtgtgtgtgt	0.153													3	4	---	---	---	---	
CDKAL1	54901	broad.mit.edu	37	6	21148599	21148599	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21148599delA	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron|CDKAL1_uc003ndf.1_Intron	NM_017774	NP_060244	Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			TAATCCTTCTAAAAAAATCCA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	22328616	22328616	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22328616delC								PRL (25534 upstream) : HDGFL1 (241062 downstream)																							GGAGCGATGGCCTGTGTCTGT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	22873850	22873851	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22873850_22873851insT								HDGFL1 (303101 upstream) : None (None downstream)																							ATTTCTCTGGATTTTTTTTAAA	0.366													4	2	---	---	---	---	
LRRC16A	55604	broad.mit.edu	37	6	25405092	25405092	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25405092delA	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						AGGGGAAAGGAAAGCTTGGAA	0.502													4	2	---	---	---	---	
ZNF322A	79692	broad.mit.edu	37	6	26644539	26644539	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26644539delA	uc003nil.3	-							NM_024639	NP_078915	Q6U7Q0	Z322A_HUMAN	zinc finger protein 322A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0						CCTTATCCTTAGGTTAATGGG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27894580	27894580	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27894580delC								OR2B2 (14483 upstream) : OR2B6 (30439 downstream)																							acttttacttccccagccctg	0.000													4	2	---	---	---	---	
GABBR1	2550	broad.mit.edu	37	6	29593757	29593757	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29593757delG	uc003nmt.3	-						GABBR1_uc003nmp.3_Intron|GABBR1_uc003nms.3_Intron|GABBR1_uc003nmu.3_Intron|GABBR1_uc011dlr.1_Intron|GABBR1_uc011dls.1_Intron	NM_001470	NP_001461	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor 1						gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(5)|liver(1)|skin(1)	7					Baclofen(DB00181)|Progabide(DB00837)	TAGGCATTCTGGGGTTAGCTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	30430874	30430874	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30430874delA								TRIM39 (116242 upstream) : HLA-E (26397 downstream)																							TGTTTGCACCACTAGCCTCCA	0.428													4	2	---	---	---	---	
C6orf136	221545	broad.mit.edu	37	6	30619644	30619644	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30619644delA	uc003nqw.3	+						C6orf136_uc003nqx.3_Intron|C6orf136_uc011dmn.1_Intron	NM_001109938	NP_001103408	Q5SQH8	CF136_HUMAN	hypothetical protein LOC221545 isoform 1												0						TGTTAATGTTAAAAAAAAAAT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	30903832	30903832	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30903832delT								SFTA2 (3880 upstream) : DPCR1 (4945 downstream)																							aagttctcccttttttttttt	0.000													5	3	---	---	---	---	
HLA-DPB1	3115	broad.mit.edu	37	6	33073637	33073637	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33073637delA	uc011dqp.1	+							NM_002121	NP_002112	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to membrane|lysosomal membrane|MHC class II protein complex				ovary(1)	1						AATTCACAAGAAAAAAAATGA	0.418													4	2	---	---	---	---	
MLN	4295	broad.mit.edu	37	6	33770784	33770784	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33770784delA	uc003off.1	-						MLN_uc003ofg.1_Intron|MLN_uc011drn.1_Intron	NM_002418	NP_002409	P12872	MOTI_HUMAN	motilin isoform 1 preproprotein						cell-cell signaling|G-protein coupled receptor protein signaling pathway	extracellular region|soluble fraction	hormone activity				0						ACTTTAAATTAAAAAAAAGGC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	37471157	37471157	+	IGR	DEL	T	-	-	rs35304955		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37471157delT								C6orf129 (3457 upstream) : MDGA1 (129127 downstream)																							GAACCTCCTATTGGGGGTTTT	0.299													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	40902562	40902565	+	IGR	DEL	GGTC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40902562_40902565delGGTC								LRFN2 (347436 upstream) : UNC5CL (92207 downstream)																							taggaggtgaggtcatgaactgaa	0.029													4	2	---	---	---	---	
TRERF1	55809	broad.mit.edu	37	6	42306630	42306630	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42306630delT	uc003osd.2	-						TRERF1_uc003osb.2_Intron|TRERF1_uc003osc.2_Intron|TRERF1_uc003ose.2_Intron|TRERF1_uc010jxu.1_Intron	NM_033502	NP_277037	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1						cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TATCTTTATATTTTTTTCACA	0.373													6	3	---	---	---	---	
KIAA0240	23506	broad.mit.edu	37	6	42756351	42756351	+	Intron	DEL	G	-	-	rs56976798	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42756351delG	uc003osn.1	+						KIAA0240_uc003osm.1_Intron|KIAA0240_uc011duw.1_Intron	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506											ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)			gacaaagaatgggggcacaag	0.000													4	2	---	---	---	---	
PEX6	5190	broad.mit.edu	37	6	42931628	42931631	+	3'UTR	DEL	TTTA	-	-	rs3831134		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42931628_42931631delTTTA	uc003otf.2	-	17					uc003ote.1_5'Flank|PEX6_uc010jya.2_RNA	NM_000287	NP_000278	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6						protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			ATGCATTGTGTTTATTTATGTCAG	0.529													4	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	49693004	49693004	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49693004delA								CRISP2 (11705 upstream) : CRISP3 (2088 downstream)																							aagtataattaaaaaaaaaaG	0.005													3	3	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51831942	51831942	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51831942delA	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					TATGTCATAGAAAAAAAAAAT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	52980472	52980473	+	IGR	INS	-	CTCT	CTCT	rs147645220	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52980472_52980473insCTCT								FBXO9 (14804 upstream) : GCM1 (11289 downstream)																							GACCTTCTCACCACTCTGTCTG	0.450													4	2	---	---	---	---	
LRRC1	55227	broad.mit.edu	37	6	53705261	53705261	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53705261delT	uc003pcd.1	+							NM_018214	NP_060684	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1							cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		tggtatgtactttttttttca	0.000													4	3	---	---	---	---	
C6orf142	90523	broad.mit.edu	37	6	54038121	54038121	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54038121delT	uc003pcg.3	+						C6orf142_uc003pcf.2_Intron|C6orf142_uc003pch.3_Intron|C6orf142_uc011dxa.1_Intron	NM_138569	NP_612636	Q5VWP3	MLIP_HUMAN	hypothetical protein LOC90523							nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)					TCTTTAAATATTTTATCCATT	0.303													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57293417	57293418	+	Intron	INS	-	T	T	rs149853195	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57293417_57293418insT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TAATATAATTGTTCTTTTGATG	0.272													2	6	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57382856	57382857	+	Intron	INS	-	TT	TT	rs150444876		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57382856_57382857insTT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		tgtcctggatctttccaagtaa	0.030													5	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57432145	57432146	+	Intron	INS	-	A	A	rs66859328		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57432145_57432146insA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		tatgcacctctaaaaaaaatag	0.030													1	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57443408	57443414	+	Intron	DEL	GAATATA	-	-	rs66695644		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57443408_57443414delGAATATA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ACTAGATTCTGAATATAGCCTCTGCTG	0.333													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57511048	57511049	+	Intron	INS	-	TA	TA	rs10643529		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57511048_57511049insTA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AGGTTTTTAAGTCTGACTTACT	0.213													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57512916	57512917	+	Splice_Site	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57512916_57512917insT	uc003pdx.2	+	16	1839	c.1752_splice	c.e16+1			NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ttttttttcaattttttttgta	0.000													6	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57512930	57512931	+	Splice_Site	INS	-	GT	GT	rs143949713		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57512930_57512931insGT	uc003pdx.2	+	17	1854	c.1767_splice	c.e17+1			NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		tttttgtagagggggggtctcc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57522595	57522595	+	IGR	DEL	C	-	-	rs111414309		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57522595delC								PRIM2 (9220 upstream) : GUSBL2 (723564 downstream)																							caacttccttccctttcTCTT	0.005													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57538130	57538131	+	IGR	DEL	TG	-	-	rs67422833		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57538130_57538131delTG								PRIM2 (24755 upstream) : GUSBL2 (708028 downstream)																							CGAGTTTGACTGTTTTGGTTAG	0.386													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57559922	57559922	+	IGR	DEL	A	-	-	rs76419512		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57559922delA								PRIM2 (46547 upstream) : GUSBL2 (686237 downstream)																							ggtggttaccaggggctgggg	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57563746	57563746	+	IGR	DEL	C	-	-	rs113591131		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57563746delC								PRIM2 (50371 upstream) : GUSBL2 (682413 downstream)																							tctttgtcttccctgccatgc	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57576631	57576632	+	IGR	INS	-	TGT	TGT	rs139864615	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57576631_57576632insTGT								PRIM2 (63256 upstream) : GUSBL2 (669527 downstream)																							agtccattttgtgttgtaacag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58514560	58514560	+	IGR	DEL	A	-	-	rs5876726		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58514560delA								GUSBL2 (226836 upstream) : None (None downstream)																							ATCATGTGATATTTTTTGAAA	0.303													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58682320	58682320	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58682320delC								GUSBL2 (394596 upstream) : None (None downstream)																							TTCTTATCCACCCCATGCCAC	0.413													4	2	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	66276284	66276285	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66276284_66276285insA	uc011dxu.1	-						EYS_uc003peq.2_Intron|EYS_uc003per.1_Intron|EYS_uc010kaj.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						acaagacctcgaaaaaaaaaag	0.000													4	2	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69493535	69493535	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69493535delA	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				GAATTTTCATAAGAGAAAAGC	0.398													2	5	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69999845	69999845	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69999845delA	uc003pev.3	+						BAI3_uc010kak.2_Intron|BAI3_uc011dxx.1_Intron|BAI3_uc003pex.1_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				AGTTGTGAGGAAAGGAGGATT	0.473													4	2	---	---	---	---	
COL19A1	1310	broad.mit.edu	37	6	70880058	70880058	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70880058delT	uc003pfc.1	+							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						GAAATACACATTTAGTGTACA	0.398													4	2	---	---	---	---	
FAM135A	57579	broad.mit.edu	37	6	71236468	71236469	+	Intron	DEL	AT	-	-	rs111717563		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71236468_71236469delAT	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfl.2_Intron|FAM135A_uc003pfn.2_Intron|FAM135A_uc003pfo.1_Intron|FAM135A_uc010kan.1_5'Flank	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1						acacacacacatacacacacac	0.218													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	75227369	75227369	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75227369delT	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																		tagaggaaccttttggttaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	77572175	77572175	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77572175delA								IMPG1 (789840 upstream) : HTR1B (599773 downstream)																							AGTAAAAGAGAAAAAAAAAGT	0.358													6	3	---	---	---	---	
SH3BGRL2	83699	broad.mit.edu	37	6	80351086	80351087	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80351086_80351087insA	uc003piz.1	+							NM_031469	NP_113657	Q9UJC5	SH3L2_HUMAN	SH3 domain binding glutamic acid-rich protein							nucleus	SH3 domain binding				0		all_cancers(76;0.00188)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.174)		BRCA - Breast invasive adenocarcinoma(397;0.0278)		GCTTACTAGCCAAAATAAATGT	0.401													4	2	---	---	---	---	
BCKDHB	594	broad.mit.edu	37	6	80995238	80995239	+	Intron	DEL	TT	-	-	rs72564121		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80995238_80995239delTT	uc003pjd.2	+						BCKDHB_uc003pje.2_Intron	NM_000056	NP_000047	P21953	ODBB_HUMAN	branched chain keto acid dehydrogenase E1 beta						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|carboxy-lyase activity|protein binding				0		all_cancers(76;1.38e-05)|Acute lymphoblastic leukemia(125;1.15e-05)|all_hematologic(105;0.00118)|all_epithelial(107;0.0149)		BRCA - Breast invasive adenocarcinoma(397;0.0291)		ATGGATACTCTTATATCTGTTC	0.391													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82237810	82237811	+	IGR	DEL	TA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82237810_82237811delTA								None (None upstream) : FAM46A (217637 downstream)																							tcttcctgattatatatatagc	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	83014547	83014547	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83014547delT								IBTK (57099 upstream) : TPBG (58376 downstream)																							agccaggctctttttTTTTTT	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	86684612	86684612	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86684612delG								SNHG5 (296161 upstream) : HTR1E (962412 downstream)																							CCAGTGAGGTGGAGATGACAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	88680610	88680610	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88680610delT								AKIRIN2 (268625 upstream) : SPACA1 (76897 downstream)																							AGTCAGAGTGTTAGGAATGTT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	91805406	91805406	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91805406delT								MAP3K7 (508499 upstream) : None (None downstream)																							TAATAACCACTTTTTTTTCCC	0.284													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	97064952	97064952	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97064952delC								FHL5 (440 upstream) : GPR63 (180937 downstream)																							AGTGAGAAGTCCATCACCAGG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	98796996	98796996	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98796996delC								MIR2113 (324499 upstream) : POU3F2 (485584 downstream)																							ctaactggaacccacaagagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	99531137	99531137	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99531137delT								FBXL4 (135288 upstream) : C6orf168 (189657 downstream)																							CTCAGGTAAATTTTTAGTCCT	0.358													4	2	---	---	---	---	
USP45	85015	broad.mit.edu	37	6	99913209	99913209	+	Intron	DEL	G	-	-	rs72192308		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99913209delG	uc003ppx.2	-						USP45_uc003ppv.2_5'Flank|USP45_uc003ppw.2_Intron|USP45_uc003ppy.2_Intron|USP45_uc010kcq.1_Intron	NM_001080481	NP_001073950	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|breast(1)	2		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		ATCAGTGAATGGTGATCCAAT	0.259													10	7	---	---	---	---	
SIM1	6492	broad.mit.edu	37	6	100853615	100853615	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100853615delA	uc003pqj.3	-						SIM1_uc010kcu.2_Intron	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		CCCACCCCCCAAAAAAAGTTA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	106311853	106311853	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106311853delT								PREP (460884 upstream) : PRDM1 (222342 downstream)																							AGTCCCCCTCTTTCTGGTATT	0.453													4	2	---	---	---	---	
LACE1	246269	broad.mit.edu	37	6	108809175	108809175	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108809175delG	uc003psj.2	+							NM_145315	NP_660358	Q8WV93	LACE1_HUMAN	lactation elevated 1								ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)		TAATGTTTTAGGAAGATTAAC	0.408													4	2	---	---	---	---	
AKD1	221264	broad.mit.edu	37	6	109819575	109819575	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109819575delT	uc003ptn.2	-						AKD1_uc011eas.1_Intron	NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1						atacatggcctttaatgtcac	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	110288358	110288359	+	IGR	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110288358_110288359delGT								FIG4 (141724 upstream) : GPR6 (11150 downstream)																							AATATGTAGCGTGTGTGTGTGT	0.252													3	4	---	---	---	---	
WASF1	8936	broad.mit.edu	37	6	110423574	110423574	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110423574delA	uc003ptv.1	-						WASF1_uc003ptw.1_Intron|WASF1_uc003ptx.1_Intron|WASF1_uc003pty.1_Intron	NM_003931	NP_003922	Q92558	WASF1_HUMAN	Wiskott-Aldrich syndrome protein family member						actin filament polymerization|cellular component movement	actin cytoskeleton	actin binding				0		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)		CAGTATTTAGAAAAAAAAAAA	0.279													11	5	---	---	---	---	
RSPH4A	345895	broad.mit.edu	37	6	116948512	116948513	+	Intron	INS	-	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116948512_116948513insC	uc003pxe.2	+						RSPH4A_uc010kee.2_Intron	NM_001010892	NP_001010892	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A isoform 1						cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0						acaggcacgcaccaccatgtcc	0.000									Kartagener_syndrome				2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	119770144	119770144	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119770144delG								MAN1A1 (99218 upstream) : None (None downstream)																							gccatctgttggccttattct	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	119964607	119964607	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119964607delA								MAN1A1 (293681 upstream) : None (None downstream)																							CCATTAGAAGAAAAAGGGATT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	122259529	122259530	+	IGR	INS	-	A	A	rs138923349	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122259529_122259530insA								GJA1 (488657 upstream) : HSF2 (461166 downstream)																							ttttgctcattaaaaaaatggt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	124010876	124010876	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124010876delT								TRDN (52934 upstream) : NKAIN2 (114193 downstream)																							aagctcattattttttttgaa	0.055													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	130993087	130993088	+	IGR	INS	-	G	G	rs141522495		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130993087_130993088insG								TMEM200A (228879 upstream) : LOC285733 (155236 downstream)																							AGGATTTGTTTGGGGGGGGCGG	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	132452958	132452958	+	5'Flank	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132452958delC	uc003qdc.2	+						uc003qdd.2_5'Flank					Homo sapiens full length insert cDNA clone ZC30H06.																		CCTCAACAGTCCAAGGTTTGT	0.433											OREG0003884	type=REGULATORY REGION|Gene=AK098583|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	133462393	133462393	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133462393delT								LOC285735 (34683 upstream) : EYA4 (99343 downstream)																							TTTTCTTTTCTTTTTTTTAAA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134806785	134806786	+	Intron	INS	-	TATGC	TATGC	rs144479946		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134806785_134806786insTATGC	uc003qet.1	+						uc003qeu.1_Intron					Homo sapiens cDNA FLJ30604 fis, clone CD34C2000152.																		caatgaagtcttataTGCAATA	0.109													4	2	---	---	---	---	
PDE7B	27115	broad.mit.edu	37	6	136336879	136336879	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136336879delA	uc003qgp.2	+						uc003qgq.1_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)	GCAATACTTGAAAAAAAATTT	0.388													4	2	---	---	---	---	
IFNGR1	3459	broad.mit.edu	37	6	137543564	137543564	+	5'Flank	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137543564delG	uc003qho.2	-						IFNGR1_uc011edn.1_5'Flank	NM_000416	NP_000407	P15260	INGR1_HUMAN	interferon gamma receptor 1 precursor						regulation of interferon-gamma-mediated signaling pathway|response to virus	integral to plasma membrane	interferon-gamma receptor activity			upper_aerodigestive_tract(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	aaattggggtggagcgtagat	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138386293	138386294	+	IGR	INS	-	T	T	rs56196713		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138386293_138386294insT								TNFAIP3 (181848 upstream) : PERP (23348 downstream)																							agttttttgtgttttttttttt	0.000													4	2	---	---	---	---	
ECT2L	345930	broad.mit.edu	37	6	139143691	139143692	+	Intron	INS	-	ATAAATAA	ATAAATAA			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139143691_139143692insATAAATAA	uc003qif.1	+						ECT2L_uc011edq.1_Intron	NM_001077706	NP_001071174	Q008S8	ECT2L_HUMAN	epithelial cell transforming sequence 2						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0						gagaccctgtcataaataaata	0.109													4	2	---	---	---	---	
REPS1	85021	broad.mit.edu	37	6	139253597	139253597	+	Intron	DEL	C	-	-	rs72196387		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139253597delC	uc003qii.2	-						REPS1_uc003qig.3_Intron|REPS1_uc011edr.1_Intron|REPS1_uc003qij.2_Intron|REPS1_uc003qik.2_Intron	NM_031922	NP_114128	Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1							coated pit|plasma membrane	calcium ion binding|SH3 domain binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		gtattccttacccccccccac	0.000													9	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	140890453	140890453	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140890453delA								None (None upstream) : None (None downstream)																							CCTAAATAAGAAAAATGGTGA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	142106119	142106119	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142106119delC	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																		AAAcagcagtccccaaccttt	0.139													4	2	---	---	---	---	
UTRN	7402	broad.mit.edu	37	6	144906126	144906127	+	Intron	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144906126_144906127insT	uc003qkt.2	+							NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ATAAAGCTTTCTTTTTTTTAAG	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	147160605	147160608	+	IGR	DEL	TGGA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147160605_147160608delTGGA								C6orf103 (24010 upstream) : STXBP5 (364900 downstream)																							catatgtatgtggatggatggatg	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	148372769	148372770	+	IGR	DEL	AG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148372769_148372770delAG								SAMD5 (481612 upstream) : SASH1 (290959 downstream)																							tcatgaggaaagagagagagag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	150411388	150411389	+	IGR	DEL	TG	-	-	rs143649978		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150411388_150411389delTG								ULBP3 (21105 upstream) : PPP1R14C (52799 downstream)																							CTTGACTGGCTGTGTCCCTTCT	0.396													5	3	---	---	---	---	
MTHFD1L	25902	broad.mit.edu	37	6	151204174	151204174	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151204174delT	uc003qob.2	+						MTHFD1L_uc011een.1_Intron|MTHFD1L_uc011eeo.1_Intron|MTHFD1L_uc003qoc.2_Intron|MTHFD1L_uc003qoa.1_Intron|MTHFD1L_uc010kil.1_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)		GTCTATAGGAttttttttttt	0.124													11	5	---	---	---	---	
TIAM2	26230	broad.mit.edu	37	6	155230532	155230533	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155230532_155230533insA	uc003qqb.2	+							NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GCACCTCTACCAAATTTGATAT	0.391													4	2	---	---	---	---	
TCP1	6950	broad.mit.edu	37	6	160209788	160209788	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160209788delA	uc003qsr.2	-						TCP1_uc003qss.2_Intron|TCP1_uc010kjz.2_Intron|TCP1_uc003qst.2_Intron|TCP1_uc010kka.1_RNA|MRPL18_uc010kkb.2_5'Flank|MRPL18_uc003qsw.3_5'Flank	NM_030752	NP_110379	P17987	TCPA_HUMAN	T-complex protein 1 isoform a						'de novo' posttranslational protein folding|tubulin complex assembly	cell junction|Golgi apparatus	ATP binding|unfolded protein binding			breast(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		TTTGTTTACGAAAAAAATTAG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164610970	164610971	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164610970_164610971insT								QKI (616078 upstream) : None (None downstream)																							AAGGATCATACttttttttttt	0.248													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165519331	165519331	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165519331delC								None (None upstream) : C6orf118 (173824 downstream)																							CAGTCCAATGCCCAGTTGAAA	0.443													4	2	---	---	---	---	
RNASET2	8635	broad.mit.edu	37	6	167398449	167398450	+	Intron	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167398449_167398450insT	uc003qvh.2	-									O00584	RNT2_HUMAN	Homo sapiens mRNA for extra-cellular ribonuclease (RNASE6PL gene).						RNA catabolic process	extracellular region	ribonuclease T2 activity|RNA binding				0		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)		cttagtggctattttttatttt	0.000													3	3	---	---	---	---	
SMOC2	64094	broad.mit.edu	37	6	169004404	169004405	+	Intron	DEL	AC	-	-	rs146630696		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169004404_169004405delAC	uc003qws.1	+						SMOC2_uc003qwr.1_Intron	NM_022138	NP_071421	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2						signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		aaaaaaaaaaaccagtaatcca	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169715645	169715646	+	IGR	INS	-	AC	AC			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169715645_169715646insAC								THBS2 (61508 upstream) : WDR27 (141661 downstream)																							catactcatttacacacacaca	0.094													6	3	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	946101	946101	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:946101delA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						aagggaaaggagaaaggagaa	0.000													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	4137318	4137318	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4137318delG	uc003smx.2	+						SDK1_uc010kso.2_Intron	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)		ATCTGGGGCTGGGGATTTCTC	0.488													4	2	---	---	---	---	
COL28A1	340267	broad.mit.edu	37	7	7398638	7398641	+	Intron	DEL	ATTA	-	-	rs150938485		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7398638_7398641delATTA	uc003src.1	-						COL28A1_uc011jxe.1_Intron	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	collagen, type XXVIII precursor						cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			skin(3)	3		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		GCTACTAGATATTAATTCTTTTGA	0.328													13	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	8133899	8133899	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8133899delA								GLCCI1 (5192 upstream) : ICA1 (18918 downstream)																							CTCACACTGTAAGGTAAGCAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	8928737	8928737	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8928737delC								NXPH1 (136145 upstream) : PER4 (745163 downstream)																							cctgcttccacccatccttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	10153906	10153906	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10153906delA								PER4 (478459 upstream) : NDUFA4 (818909 downstream)																							acaaacaaacaaaaaaaacaa	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	12783397	12783397	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12783397delG								ARL4A (52841 upstream) : None (None downstream)																							tcaagtgaaaggaagagttgc	0.000													4	2	---	---	---	---	
ETV1	2115	broad.mit.edu	37	7	13980642	13980643	+	Intron	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13980642_13980643delGT	uc011jxq.1	-						ETV1_uc011jxn.1_Intron|ETV1_uc011jxo.1_Intron|ETV1_uc011jxp.1_Intron|ETV1_uc003ssw.3_Intron|ETV1_uc003ssx.2_Intron|ETV1_uc011jxr.1_Intron|ETV1_uc011jxs.1_Intron|ETV1_uc010ktv.2_Intron	NM_004956	NP_004947	P50549	ETV1_HUMAN	ets variant gene 1 isoform a						transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		TMPRSS2/ETV1(24)|EWSR1/ETV1(7)	prostate(24)|soft_tissue(4)|bone(3)|lung(2)|central_nervous_system(1)|ovary(1)	35						TTTTAATGTAGTGTGTGTGTGT	0.292			T	EWSR1|TMPRSS2|SLC45A3|C15orf21|HNRNPA2B1. ACSL3	Ewing sarcoma|prostate								4	2	---	---	---	---	
DGKB	1607	broad.mit.edu	37	7	14737282	14737282	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14737282delA	uc003ssz.2	-						DGKB_uc011jxt.1_Intron|DGKB_uc003sta.2_Intron|DGKB_uc011jxu.1_Intron|DGKB_uc011jxv.1_Intron	NM_004080	NP_004071	Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)	CAGACAAGAGAAAAAAAAAGA	0.164													4	2	---	---	---	---	
TMEM195	392636	broad.mit.edu	37	7	15317158	15317158	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15317158delT	uc003stb.1	-							NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						ttggattggattttttttttc	0.000													6	3	---	---	---	---	
TMEM195	392636	broad.mit.edu	37	7	15567949	15567949	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15567949delA	uc003stb.1	-							NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						tctaggaaacaaaaaaaattg	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17723038	17723039	+	IGR	INS	-	AC	AC			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17723038_17723039insAC								AHR (337263 upstream) : SNX13 (107347 downstream)																							CATATGCACAGACACACACACA	0.391													4	2	---	---	---	---	
ABCB5	340273	broad.mit.edu	37	7	20743238	20743239	+	Intron	INS	-	T	T	rs142830215	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20743238_20743239insT	uc003suw.3	+						ABCB5_uc010kuh.2_Intron	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5						regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6						GTAAGCCAAGATTTTTTTGTTC	0.436													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	21447724	21447726	+	IGR	DEL	AAG	-	-	rs34586013		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21447724_21447726delAAG								RPL23P8 (580285 upstream) : SP4 (19963 downstream)																							GATTTGAAGAAAGAAGGAGGGAT	0.478													10	7	---	---	---	---	
DNAH11	8701	broad.mit.edu	37	7	21757807	21757808	+	Intron	INS	-	T	T	rs59449964		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21757807_21757808insT	uc003svc.2	+							NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						tgttttactgatttttttttag	0.059									Kartagener_syndrome				5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24595368	24595369	+	IGR	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24595368_24595369delGT								NPY (263891 upstream) : MPP6 (17716 downstream)																							ATTACAAAAGGTGTGTGTGTGT	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25275110	25275111	+	IGR	INS	-	G	G	rs145591295	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25275110_25275111insG								NPVF (7005 upstream) : MIR148A (714428 downstream)																							GTTTTCTTTTTGGGGGGGGGCA	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25317811	25317811	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25317811delA								NPVF (49706 upstream) : MIR148A (671728 downstream)																							GAAGCTAATGAAAAAAAAAAA	0.348													3	3	---	---	---	---	
SNX10	29887	broad.mit.edu	37	7	26331080	26331080	+	5'Flank	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26331080delT	uc003sxx.2	+						SNX10_uc011jzg.1_5'Flank|SNX10_uc010kuu.2_5'Flank	NM_013322	NP_037454	Q9Y5X0	SNX10_HUMAN	sorting nexin 10						cell communication|endosome organization|protein transport	extrinsic to endosome membrane	1-phosphatidylinositol binding				0						TCAGGTGCCATTTGGGAAATG	0.333													4	2	---	---	---	---	
SCRN1	9805	broad.mit.edu	37	7	30000335	30000336	+	Intron	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30000335_30000336delCA	uc010kvp.2	-						SCRN1_uc011jzy.1_Intron|SCRN1_uc003tak.2_Intron|SCRN1_uc011jzz.1_Intron|SCRN1_uc011kaa.1_Intron|SCRN1_uc011jzx.1_Intron	NM_001145515	NP_001138987	Q12765	SCRN1_HUMAN	secernin 1 isoform c						exocytosis|proteolysis	cytoplasm|nuclear membrane	dipeptidase activity			ovary(2)	2						cacacacatccacacacacaca	0.347													4	2	---	---	---	---	
PDE1C	5137	broad.mit.edu	37	7	32293668	32293668	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32293668delA	uc003tco.1	-							NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C						activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)			AGTGAATCCCAAAGGGTCTCA	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36883281	36883284	+	IGR	DEL	GAGT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36883281_36883284delGAGT								AOAH (119128 upstream) : ELMO1 (10677 downstream)																							GTGAGAGAAGGAGTGAGATGAGAG	0.500													4	2	---	---	---	---	
ELMO1	9844	broad.mit.edu	37	7	36998304	36998305	+	Intron	INS	-	T	T	rs111588384	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36998304_36998305insT	uc003tfk.1	-						ELMO1_uc003tfi.1_Intron|ELMO1_uc003tfj.1_Intron|ELMO1_uc011kbb.1_Intron|ELMO1_uc011kbc.1_Intron|ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						tcgtggcactacaaacgccaca	0.000													4	2	---	---	---	---	
GLI3	2737	broad.mit.edu	37	7	42030204	42030204	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42030204delT	uc011kbh.1	-						GLI3_uc011kbg.1_Intron	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						ATAATCATAGTTACAATAAAA	0.264									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				4	2	---	---	---	---	
HECW1	23072	broad.mit.edu	37	7	43570452	43570453	+	Intron	INS	-	C	C	rs142428537	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43570452_43570453insC	uc003tid.1	+						HECW1_uc011kbi.1_Intron	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						CTCCAAATCTGCCccctcctaa	0.238													4	2	---	---	---	---	
SUN3	256979	broad.mit.edu	37	7	48047096	48047096	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48047096delA	uc003tof.2	-						SUN3_uc010kyq.2_Intron|SUN3_uc003tog.2_Intron|SUN3_uc011kcf.1_Intron	NM_152782	NP_689995	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 1							integral to membrane				central_nervous_system(1)	1						ACGCTTCACTAAAAAAAAAAC	0.483													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	49177581	49177581	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49177581delT								CDC14C (210532 upstream) : VWC2 (635676 downstream)																							aacttagccattttagtaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	49213000	49213000	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49213000delT								CDC14C (245951 upstream) : VWC2 (600257 downstream)																							GCTTAGGGAATTTTTTTTTCT	0.264													4	2	---	---	---	---	
VWC2	375567	broad.mit.edu	37	7	49914453	49914454	+	Intron	DEL	AG	-	-	rs80051560		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49914453_49914454delAG	uc003tot.1	+							NM_198570	NP_940972	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2						negative regulation of BMP signaling pathway|positive regulation of neuron differentiation	basement membrane|extracellular space					0						TTCAGAATTCAGAGAGTATGGC	0.431													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	51630362	51630363	+	IGR	INS	-	C	C	rs139681584	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51630362_51630363insC								COBL (245847 upstream) : None (None downstream)																							ccttctgagaacctacgtccat	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53987539	53987539	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53987539delT								POM121L12 (882922 upstream) : HPVC1 (281378 downstream)																							ATTCACTAGGTTTTTTTTTTT	0.338													4	2	---	---	---	---	
VSTM2A	222008	broad.mit.edu	37	7	54636355	54636355	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54636355delA	uc010kzf.2	+						VSTM2A_uc003tqc.3_Intron|uc003tqd.2_5'Flank	NM_182546	NP_872352	Q8TAG5	VTM2A_HUMAN	V-set and transmembrane domain containing 2							extracellular region					0			STAD - Stomach adenocarcinoma(5;0.0525)			ATGCAGTAGGAAAAAAAAAAA	0.428													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57929464	57929464	+	IGR	DEL	G	-	-	rs76511107		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57929464delG								ZNF716 (396199 upstream) : None (None downstream)																							AGGACCTTTCGAAATAAAATG	0.423													3	3	---	---	---	---	
ZNF679	168417	broad.mit.edu	37	7	63721651	63721651	+	Intron	DEL	T	-	-	rs145025661		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63721651delT	uc003tsx.2	+							NM_153363	NP_699194	Q8IYX0	ZN679_HUMAN	zinc finger protein 679						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						CCATTAAAAATTTTTTTTTGC	0.224													0	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65223470	65223470	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65223470delT	uc003tud.1	-						CCT6P1_uc003tug.2_Intron|CCT6P1_uc003tuh.2_Intron|CCT6P1_uc003tui.2_Intron|uc003tuk.1_5'Flank					Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																		atctctaggattttttttatc	0.030													4	2	---	---	---	---	
TPST1	8460	broad.mit.edu	37	7	65716781	65716781	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65716781delT	uc003tuw.2	+						TPST1_uc010kzy.2_Intron|TPST1_uc010kzz.2_Intron|TPST1_uc010laa.2_Intron	NM_003596	NP_003587	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1						inflammatory response|peptidyl-tyrosine sulfation	Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity				0						ggtcaggttcttttttttttt	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	66324903	66324903	+	IGR	DEL	C	-	-	rs76810689		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66324903delC								LOC729156 (15090 upstream) : C7orf42 (61300 downstream)																							AAGCTCAGATCCTACCCCATC	0.428													8	8	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71265108	71265109	+	Intron	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71265108_71265109delTG	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)				ACAGGAACGCTGTGACTTCAGC	0.510													4	2	---	---	---	---	
SPDYE7P	441251	broad.mit.edu	37	7	72339825	72339826	+	5'Flank	DEL	TG	-	-	rs3973815	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72339825_72339826delTG	uc010lal.1	-							NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0						TTCTTTTTTttgttgttgttgt	0.257													7	4	---	---	---	---	
HIP1	3092	broad.mit.edu	37	7	75175502	75175502	+	Intron	DEL	A	-	-	rs72194830		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75175502delA	uc003uds.1	-						HIP1_uc011kfz.1_Intron	NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8						TGAATACATTAAAAAAAAATA	0.318			T	PDGFRB	CMML								4	2	---	---	---	---	
ABCB4	5244	broad.mit.edu	37	7	87038329	87038329	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87038329delT	uc003uiv.1	-						ABCB4_uc003uiw.1_Intron|ABCB4_uc003uix.1_Intron	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4						cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					TGGTTTTCCCTTTTTTTTTTA	0.269													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	88071908	88071908	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88071908delA								STEAP4 (135699 upstream) : ZNF804B (316845 downstream)																							TTGCACAACCAGGAATATCAG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	89722945	89722945	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89722945delA								ZNF804B (756601 upstream) : DPY19L2P4 (25769 downstream)																							cccatggaggaaaaaaaagtt	0.080													4	2	---	---	---	---	
STEAP1	26872	broad.mit.edu	37	7	89791614	89791614	+	Intron	DEL	T	-	-	rs112025068	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89791614delT	uc003ujx.2	+							NM_012449	NP_036581	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the						electron transport chain|ion transport|iron ion homeostasis	cell-cell junction|endosome membrane|integral to plasma membrane	channel activity|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	all_hematologic(106;0.112)					ATATTCtttgttttttttttt	0.149													7	6	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	92000490	92000490	+	Intron	DEL	T	-	-	rs67457943		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92000490delT	uc003ulw.2	+						ANKIB1_uc010lew.1_5'Flank	NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AATATGTTGCttttttttttt	0.279													5	4	---	---	---	---	
GNGT1	2792	broad.mit.edu	37	7	93264074	93264074	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93264074delG	uc003umx.1	+									P63211	GBG1_HUMAN	Homo sapiens guanine nucleotide binding protein gamma 1 (GNG1) mRNA, complete cds.						G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|signal transducer activity				0	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			GATGGGGTGTGGGATGATTGC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	97131384	97131384	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97131384delT								ACN9 (320311 upstream) : TAC1 (229887 downstream)																							TCCTCAAGTATTTTAGAGTAT	0.403													4	2	---	---	---	---	
TRRAP	8295	broad.mit.edu	37	7	98509398	98509398	+	Intron	DEL	A	-	-	rs113146131		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98509398delA	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	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)			tcaaaatctcaaaaaaaaaaa	0.164													4	2	---	---	---	---	
ZCWPW1	55063	broad.mit.edu	37	7	100004129	100004130	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100004129_100004130insA	uc003uut.2	-						ZCWPW1_uc011kjq.1_Intron|ZCWPW1_uc003uur.2_Intron|ZCWPW1_uc003uus.2_Intron|ZCWPW1_uc011kjr.1_Intron|ZCWPW1_uc003uuu.1_Intron|ZCWPW1_uc011kjp.1_Intron	NM_017984	NP_060454	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1								zinc ion binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GAAGGGGACTGAAAAAAAAAAT	0.485													5	3	---	---	---	---	
MLL5	55904	broad.mit.edu	37	7	104661668	104661668	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104661668delA	uc003vcm.2	+						MLL5_uc010lja.1_Intron|MLL5_uc010ljb.1_Intron|MLL5_uc003vcl.2_Intron|MLL5_uc010ljc.2_Intron	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5						cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3						TCTTACCCAGAAAATAAGTCT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	106036334	106036335	+	IGR	DEL	GA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106036334_106036335delGA								NAMPT (110696 upstream) : FLJ36031 (262815 downstream)																							gcaagcaggtgagagagagaga	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	106159650	106159651	+	Intron	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106159650_106159651delCA	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																		cacacacacgcacacacacaca	0.000													4	2	---	---	---	---	
COG5	10466	broad.mit.edu	37	7	107088809	107088809	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107088809delT	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4						TCTTTCTTTCTTTTTTTTGGC	0.308													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	108468635	108468637	+	IGR	DEL	AGG	-	-	rs149468509		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108468635_108468637delAGG								DNAJB9 (253343 upstream) : C7orf66 (55403 downstream)																							ttgagtaattaggatgtcatggg	0.025													4	2	---	---	---	---	
IMMP2L	83943	broad.mit.edu	37	7	110854842	110854842	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110854842delA	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		ATAACCATGTAAAAAAAAAAA	0.274													4	2	---	---	---	---	
DOCK4	9732	broad.mit.edu	37	7	111518337	111518337	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111518337delA	uc003vfx.2	-						DOCK4_uc003vfw.2_5'Flank|DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4						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)				CCGACTTTTTAAAAATCTGTA	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	113107305	113107305	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113107305delA								LOC401397 (348668 upstream) : PPP1R3A (409577 downstream)																							aatttttgtcaaAAAATAAAT	0.144													4	2	---	---	---	---	
MDFIC	29969	broad.mit.edu	37	7	114614976	114614976	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114614976delT	uc003vhf.2	+							NM_199072	NP_951038	Q9P1T7	MDFIC_HUMAN	MyoD family inhibitor domain containing protein						activation of JUN kinase activity|interspecies interaction between organisms|negative regulation of protein import into nucleus|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|regulation of Wnt receptor signaling pathway|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleolus|nucleolus|nucleus	cyclin binding|Tat protein binding			ovary(1)	1						GTCAGCAATGTTTTTTTTTTT	0.303													4	2	---	---	---	---	
TSPAN12	23554	broad.mit.edu	37	7	120480558	120480559	+	Intron	INS	-	G	G	rs72584337	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120480558_120480559insG	uc003vjk.2	-							NM_012338	NP_036470	O95859	TSN12_HUMAN	transmembrane 4 superfamily member 12						angiogenesis|cell surface receptor linked signaling pathway|regulation of angiogenesis|retina layer formation	integral to plasma membrane|membrane fraction					0	all_neural(327;0.117)					aaaaagtcacaagttaatttaa	0.015													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124877922	124877922	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124877922delT	uc010lky.1	-											Homo sapiens chromosome 7 isolate HA_003154 mRNA sequence.																		actttctctattttttttttt	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	125194256	125194257	+	IGR	INS	-	TG	TG	rs79226791		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125194256_125194257insTG								POT1 (624219 upstream) : GRM8 (884395 downstream)																							AAGTTTTTTTTTGTGTGTGTGT	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	125712797	125712797	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125712797delG								None (None upstream) : GRM8 (365855 downstream)																							AGCTTGTAAAGGGGGAAAAAA	0.214													4	2	---	---	---	---	
SND1	27044	broad.mit.edu	37	7	127292573	127292574	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127292573_127292574insA	uc003vmi.2	+							NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						TTGACTCCACCTTCCGCCAGCC	0.624													4	2	---	---	---	---	
SND1	27044	broad.mit.edu	37	7	127292577	127292578	+	Intron	INS	-	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127292577_127292578insG	uc003vmi.2	+							NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						CTCCACCTTCCGCCAGCCTGCT	0.619													4	2	---	---	---	---	
SND1	27044	broad.mit.edu	37	7	127539012	127539012	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127539012delT	uc003vmi.2	+						SND1_uc010lle.2_Intron	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						ACAAACCTCATTTTTTTGCCC	0.433													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133391822	133391822	+	Intron	DEL	T	-	-	rs76290083		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133391822delT	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				TTAAGTGGCCTTTTTTTTTTT	0.308													1	5	---	---	---	---	
LUZP6	767558	broad.mit.edu	37	7	135661289	135661290	+	Intron	INS	-	T	T	rs140823578	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135661289_135661290insT	uc003vte.3	-						LUZP6_uc010lmv.2_Intron	NM_145808	NP_665807	Q538Z0	LUZP6_HUMAN	myotrophin												0						TTTCGGTACTCTTTTCACGGTC	0.386													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	136800485	136800486	+	Intron	INS	-	G	G	rs1425073	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136800485_136800486insG	uc003vtp.1	-											Homo sapiens clone N1 NTera2D1 teratocarcinoma mRNA.																		attttgaaagcaggaaagaaga	0.243													4	2	---	---	---	---	
AKR1D1	6718	broad.mit.edu	37	7	137731317	137731318	+	Intron	INS	-	A	A	rs138190915		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137731317_137731318insA	uc011kqb.1	+						AKR1D1_uc011kqc.1_Intron|AKR1D1_uc011kqd.1_Intron	NM_005989	NP_005980	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1						ccacagacattaaaaaaaaatg	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	143720793	143720794	+	IGR	INS	-	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143720793_143720794insC								OR6B1 (18768 upstream) : OR2A5 (26701 downstream)																							TTGAGAAGTTTCCCCTTTTGAC	0.371													4	2	---	---	---	---	
TPK1	27010	broad.mit.edu	37	7	144183890	144183890	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144183890delA	uc003weq.2	-						TPK1_uc003weo.2_Intron|TPK1_uc003wep.2_Intron|TPK1_uc003wer.2_Intron|TPK1_uc003wes.2_Intron	NM_022445	NP_071890	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1 isoform a						thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)	gacattatgtattacatgttt	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	145072689	145072689	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145072689delT								TPK1 (539543 upstream) : CNTNAP2 (740764 downstream)																							atgagaagagtttttttaaaa	0.000													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147687152	147687153	+	Intron	INS	-	G	G	rs139079055	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147687152_147687153insG	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			actacaaatttggggttgctac	0.000										HNSCC(39;0.1)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148331052	148331052	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148331052delG								C7orf33 (18101 upstream) : CUL1 (63954 downstream)																							TCTGGGACGTGGGACTTTGAG	0.428													4	2	---	---	---	---	
ZNF775	285971	broad.mit.edu	37	7	150074011	150074011	+	5'Flank	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150074011delA	uc003whf.1	+							NM_173680	NP_775951	Q96BV0	ZN775_HUMAN	zinc finger protein 775						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.0173)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACTGGGGAGGACTGCCTGGGT	0.502													4	2	---	---	---	---	
GIMAP8	155038	broad.mit.edu	37	7	150155230	150155231	+	Intron	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150155230_150155231delGT	uc003whj.2	+							NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8							endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		gatgtgtgtggtgtgtgtgtgt	0.079													3	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151944708	151944708	+	Intron	DEL	T	-	-	rs113407913		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151944708delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		ACTAAAAGAATTTTTAAAGTT	0.264			N		medulloblastoma								7	7	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151971455	151971456	+	Intron	DEL	AC	-	-	rs143729499	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151971455_151971456delAC	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		ACAGAAAAAAACACAAAACTAC	0.292			N		medulloblastoma								4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151981593	151981593	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151981593delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		caagcaaagattttttaataa	0.000			N		medulloblastoma								2	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152105810	152105810	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152105810delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		gtgctccccctggggtctgtg	0.030			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153293719	153293719	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153293719delT								ACTR3B (741256 upstream) : DPP6 (290700 downstream)																							AGGACCCTTGTTTTTTTCACC	0.438													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153905855	153905855	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153905855delA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GAATTGAAGTAAAAAAAAAAA	0.368													5	3	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	154576618	154576618	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154576618delT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TTCTGTGCCCTTTCCTGCCTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155357645	155357645	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155357645delA								CNPY1 (31106 upstream) : RBM33 (79558 downstream)																							tcgagtggtcaaacccacaga	0.000													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157637940	157637940	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157637940delA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CAGCTGTAGGAAAAAAATGCA	0.448													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157747098	157747099	+	Intron	INS	-	TG	TG	rs147462231	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157747098_157747099insTG	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		tgcctgtgtactgtgtgtgctg	0.030													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158133963	158133964	+	Intron	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158133963_158133964delCA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CATTCACACCCACACTCTCACC	0.525													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1124972	1124973	+	IGR	INS	-	T	T	rs141645265	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1124972_1124973insT								ERICH1 (443746 upstream) : DLGAP2 (324596 downstream)																							CCCCTTTCTAGTTCCCCCAAGA	0.376													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1955226	1955227	+	IGR	INS	-	A	A	rs147688685	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1955226_1955227insA								KBTBD11 (118 upstream) : MYOM2 (37931 downstream)																							TCCTGCCCGTTAAGTGAGGAAC	0.594													3	3	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3432693	3432693	+	Intron	DEL	A	-	-	rs71850597		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3432693delA	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TAATCACAGTAAAAAAAAAAA	0.383													7	5	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	4832283	4832283	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4832283delT	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TAGAAGGTGATTTTTTGAGCC	0.353													4	2	---	---	---	---	
PPP1R3B	79660	broad.mit.edu	37	8	9000575	9000575	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9000575delT	uc003wsn.3	-						PPP1R3B_uc003wso.3_Intron	NM_024607	NP_078883	Q86XI6	PPR3B_HUMAN	protein phosphatase 1, regulatory (inhibitor)						glycogen metabolic process					ovary(1)|skin(1)	2				COAD - Colon adenocarcinoma(149;0.0717)|READ - Rectum adenocarcinoma(644;0.241)		ctagttgtggttttttgagga	0.000													4	2	---	---	---	---	
TDH	157739	broad.mit.edu	37	8	11202759	11202759	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11202759delA	uc003wtq.1	+						TDH_uc003wts.1_5'Flank	NR_001578				Homo sapiens mRNA for hypothetical protein (ORF1), clone vir17.												0						GACAGAAGCCAAAGGGTCTGA	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	12430286	12430288	+	Intron	DEL	TGG	-	-	rs75911783		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12430286_12430288delTGG	uc003wvy.3	-						uc003wwa.2_5'Flank					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		aagtatggattggacctggtgag	0.044													4	2	---	---	---	---	
DLC1	10395	broad.mit.edu	37	8	13242776	13242778	+	Intron	DEL	AAC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13242776_13242778delAAC	uc003wwm.2	-						DLC1_uc003wwn.2_Intron|DLC1_uc011kxy.1_Intron	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						caacaacagtaacaacaacaaca	0.246													4	2	---	---	---	---	
DLC1	10395	broad.mit.edu	37	8	13364718	13364718	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13364718delC	uc003wwm.2	-						DLC1_uc003wwn.2_Intron|DLC1_uc011kxy.1_Intron	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						TGGGCGCCTTCCCACTGGCAC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	13488946	13488946	+	IGR	DEL	A	-	-	rs74519945		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13488946delA								C8orf48 (63150 upstream) : SGCZ (458428 downstream)																							tatggtcatgagagagagaga	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	13488948	13488948	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13488948delA								C8orf48 (63152 upstream) : SGCZ (458426 downstream)																							tggtcatgagagagagagaga	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	15304563	15304563	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15304563delA								SGCZ (208771 upstream) : TUSC3 (93167 downstream)																							AATGCAGAAGAAAAAAAAAAT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	15379122	15379122	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15379122delC								SGCZ (283330 upstream) : TUSC3 (18608 downstream)																							taggtaattaccccccccaaa	0.000													4	4	---	---	---	---	
MSR1	4481	broad.mit.edu	37	8	16025580	16025580	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16025580delA	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron|MSR1_uc003wxb.2_Intron|MSR1_uc011kxz.1_Intron	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		ACTTACAAATAAAAAAAAAAA	0.323													4	2	---	---	---	---	
ZDHHC2	51201	broad.mit.edu	37	8	17022106	17022106	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17022106delA	uc003wxe.2	+							NM_016353	NP_057437	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2							integral to membrane	acyltransferase activity|zinc ion binding				0				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		ACTAAACAATAAAAAAAAAAA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20762644	20762644	+	IGR	DEL	T	-	-	rs34313346		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20762644delT								LZTS1 (649841 upstream) : GFRA2 (786886 downstream)																							ATTCTCATTCTTTTTTTTTTT	0.383													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	24130968	24130969	+	IGR	INS	-	TG	TG	rs143275653	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24130968_24130969insTG								STC1 (418648 upstream) : ADAM28 (20611 downstream)																							AACATCTGATAtgtgtgtgtgt	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	26903958	26903958	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26903958delA								ADRA1A (181036 upstream) : MIR548H-4 (2412 downstream)																							actctgtctcaaaaaaaaagg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	27537044	27537044	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27537044delA								SCARA3 (2758 upstream) : CCDC25 (53791 downstream)																							caacagcaacaaaaaAATTTA	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	30834555	30834555	+	IGR	DEL	A	-	-	rs72018292		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30834555delA								TEX15 (88333 upstream) : PURG (18766 downstream)																							ATTGCATCGGAAAAAAAAAAG	0.353													4	2	---	---	---	---	
UNC5D	137970	broad.mit.edu	37	8	35155295	35155296	+	Intron	INS	-	T	T	rs142770412	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35155295_35155296insT	uc003xjr.1	+							NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor						apoptosis|axon guidance	integral to membrane	receptor activity			upper_aerodigestive_tract(2)|ovary(2)|pancreas(1)|skin(1)	6				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		AGATGTTATGATTTTTTTTTTA	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	40862005	40862005	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40862005delA								ZMAT4 (106662 upstream) : SFRP1 (257474 downstream)																							CCACTGACCTAACAGTTATTA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	41051008	41051008	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41051008delG								ZMAT4 (295665 upstream) : SFRP1 (68471 downstream)																							ATGAGTAATTGGCAAGAGCAG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	41276511	41276512	+	IGR	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41276511_41276512delAC								SFRP1 (109531 upstream) : GOLGA7 (71569 downstream)																							aaacacacatacacacacacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	42602796	42602796	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42602796delT								CHRNB3 (10587 upstream) : CHRNA6 (4986 downstream)																							TGTGATTCCCTTTTTTTTTTC	0.363													6	3	---	---	---	---	
SNTG1	54212	broad.mit.edu	37	8	50988859	50988860	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50988859_50988860insA	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				GAAACAAAAACAAAAAAAAACC	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	53866145	53866146	+	IGR	INS	-	A	A	rs141852572	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53866145_53866146insA								NPBWR1 (12692 upstream) : OPRK1 (272130 downstream)																							ATAAGAATAAGAAAAAAATGCG	0.163													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54303880	54303880	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54303880delA								OPRK1 (139686 upstream) : ATP6V1H (324236 downstream)																							aaatggagccaaaaaaaaaag	0.055													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58262723	58262724	+	Intron	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58262723_58262724delTG	uc003xth.2	+											Homo sapiens cDNA clone IMAGE:5267652.																		tgaggtgccctgtgtgtgtgtg	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58592210	58592210	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58592210delT								C8orf71 (394922 upstream) : FAM110B (314903 downstream)																							TTGTTTTACCTTTTTTTGTGA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58719188	58719191	+	IGR	DEL	TTAT	-	-	rs6150598		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58719188_58719191delTTAT								C8orf71 (521900 upstream) : FAM110B (187922 downstream)																							ACTGTCTTAATTATTTCTTAAGAC	0.343													5	3	---	---	---	---	
SDCBP	6386	broad.mit.edu	37	8	59494739	59494739	+	3'UTR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59494739delT	uc003xtn.2	+	9					SDCBP_uc003xto.2_3'UTR|SDCBP_uc003xtr.2_3'UTR|SDCBP_uc003xtp.2_3'UTR|SDCBP_uc003xtq.2_3'UTR|SDCBP_uc003xts.2_3'UTR|SDCBP_uc011led.1_3'UTR	NM_005625	NP_005616	O00560	SDCB1_HUMAN	syntenin isoform 1						actin cytoskeleton organization|axon guidance|positive regulation of phosphorylation|protein targeting to membrane|substrate-dependent cell migration, cell extension|synaptic transmission	cytoskeleton|cytosol|endoplasmic reticulum membrane|focal adhesion|interleukin-5 receptor complex|melanosome|nucleus	cytoskeletal adaptor activity|frizzled binding|interleukin-5 receptor binding|protein heterodimerization activity|protein N-terminus binding|syndecan binding				0		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				TTGCCTTTGATTTTTTTTTTA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	62790193	62790194	+	IGR	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62790193_62790194delGT								ASPH (162994 upstream) : NKAIN3 (371307 downstream)																							gtttgtaggggtgtgtgtgtgt	0.139													4	2	---	---	---	---	
NKAIN3	286183	broad.mit.edu	37	8	63825469	63825469	+	Intron	DEL	A	-	-	rs111620337		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63825469delA	uc010lyq.1	+							NM_173688	NP_775959	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)				actctgtctcaaaaaaaaaag	0.000													2	5	---	---	---	---	
GGH	8836	broad.mit.edu	37	8	63929777	63929777	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63929777delA	uc003xuw.2	-							NM_003878	NP_003869	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase precursor						glutamine metabolic process	extracellular space|lysosome|melanosome	gamma-glutamyl-peptidase activity				0	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|L-Glutamic Acid(DB00142)	aaaAGAAACCAAAAAAAAAAC	0.179													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65274885	65274886	+	IGR	DEL	TA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65274885_65274886delTA								None (None upstream) : MIR124-2 (16820 downstream)																							AATTCATGTGTATATATATATG	0.381													4	2	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	69002479	69002480	+	Intron	INS	-	TTA	TTA			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69002479_69002480insTTA	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						TATGTTTCTGGTCTTCTCATTT	0.287													3	4	---	---	---	---	
SULF1	23213	broad.mit.edu	37	8	70535957	70535972	+	Intron	DEL	CACTGCCAGGCAATGG	-	-	rs11273366		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70535957_70535972delCACTGCCAGGCAATGG	uc010lza.1	+						SULF1_uc003xyd.2_Intron|SULF1_uc003xye.2_Intron|SULF1_uc003xyf.2_Intron|SULF1_uc003xyg.2_Intron|SULF1_uc003xyh.1_Intron	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor						apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			tcatccatcacactgccaggcaatggcaCTGCCAGG	0.269													4	6	---	---	---	---	
SLCO5A1	81796	broad.mit.edu	37	8	70650620	70650620	+	Intron	DEL	T	-	-	rs72442955		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70650620delT	uc003xyl.2	-						SLCO5A1_uc010lzb.2_Intron|SLCO5A1_uc011lfa.1_Intron|SLCO5A1_uc003xyk.2_Intron|SLCO5A1_uc010lzc.2_Intron	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,							integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			TTTTCTTTTGTTTTTTTTTTT	0.308													12	6	---	---	---	---	
CRISPLD1	83690	broad.mit.edu	37	8	75919679	75919679	+	Intron	DEL	A	-	-	rs68020850		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75919679delA	uc003yan.2	+						CRISPLD1_uc011lfk.1_Intron|CRISPLD1_uc011lfl.1_Intron	NM_031461	NP_113649	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain							extracellular region				ovary(1)|central_nervous_system(1)	2	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			GTGGGAGCTCAACTCATGTTT	0.353													4	4	---	---	---	---	
HNF4G	3174	broad.mit.edu	37	8	76472319	76472320	+	Intron	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76472319_76472320insT	uc003yaq.2	+						HNF4G_uc003yar.2_Intron	NM_004133	NP_004124	Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma						endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			GGCAGCGAACCTAATGATTCCA	0.371													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	76606191	76606192	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76606191_76606192insT								HNF4G (127132 upstream) : LOC100192378 (916923 downstream)																							TTTTCTCTCTCTTTTTTTTTTT	0.287													4	2	---	---	---	---	
LOC100192378	100192378	broad.mit.edu	37	8	77527331	77527332	+	Intron	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77527331_77527332delCA	uc003yas.3	-							NR_024360				Homo sapiens cDNA clone IMAGE:4811567.												0						CACACAATGCCACACACACTGC	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	78702048	78702048	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78702048delG								PEX2 (789524 upstream) : PKIA (726288 downstream)																							tgttgttcctgggcaggcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79310717	79310717	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79310717delT								None (None upstream) : PKIA (117619 downstream)																							gtagaactggtttgctagcaa	0.005													4	2	---	---	---	---	
TPD52	7163	broad.mit.edu	37	8	81064410	81064410	+	Intron	DEL	C	-	-	rs35354946		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81064410delC	uc003ybs.1	-						TPD52_uc010lzs.1_Intron|TPD52_uc003ybt.1_Intron	NM_001025253	NP_001020424	P55327	TPD52_HUMAN	tumor protein D52 isoform 2						anatomical structure morphogenesis|B cell differentiation|secretion	endoplasmic reticulum|perinuclear region of cytoplasm	calcium ion binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)			GCCTTTCATGCCCCCCCGACC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	84573912	84573912	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84573912delT								None (None upstream) : RALYL (521541 downstream)																							AAGCTACTTCTTTTTTTTCTG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	86427862	86427863	+	IGR	DEL	TG	-	-	rs66903875		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86427862_86427863delTG								CA2 (34141 upstream) : REXO1L1 (140701 downstream)																							gcataACCTCtgtgtgtgtgtg	0.183													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	87024895	87024895	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87024895delT								REXO1L1 (449627 upstream) : PSKH2 (35798 downstream)																							GAATGCCAACTTTTTTCACAC	0.303													4	2	---	---	---	---	
CALB1	793	broad.mit.edu	37	8	91094033	91094034	+	Intron	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91094033_91094034delTC	uc003yel.1	-						CALB1_uc003yem.1_Intron|CALB1_uc011lge.1_5'Flank	NM_004929	NP_004920	P05937	CALB1_HUMAN	calbindin 1							nucleus	calcium ion binding|vitamin D binding			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.00953)			gtccctcccttctctctctctc	0.193													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94103379	94103380	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94103379_94103380insA								C8orf83 (73478 upstream) : FAM92A1 (609393 downstream)																							TTTGAGATTTTAAAAAAAACTG	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96782083	96782083	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96782083delG								C8orf37 (500646 upstream) : GDF6 (372477 downstream)																							ctttggttttgtatctagaaa	0.000													4	2	---	---	---	---	
NIPAL2	79815	broad.mit.edu	37	8	99297962	99297962	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99297962delT	uc003yil.1	-						NIPAL2_uc003yim.1_Intron	NM_024759	NP_079035	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2							integral to membrane					0						tctttctttcttttttttttg	0.144													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102008251	102008252	+	IGR	INS	-	TG	TG	rs146231389	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102008251_102008252insTG								YWHAZ (42628 upstream) : ZNF706 (201016 downstream)																							cactttgtttctgtgtgtgtgt	0.005													4	3	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	102946896	102946897	+	Intron	INS	-	T	T	rs149586436	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102946896_102946897insT	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			gttttattagatatgacaggaa	0.074													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103494863	103494863	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103494863delG								UBR5 (70368 upstream) : ODF1 (68985 downstream)																							ggcagattgtgggacttcatc	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103733879	103733879	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103733879delC								KLF10 (65896 upstream) : AZIN1 (104658 downstream)																							ATGATTTTTTCCCAACATTTC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103963545	103963545	+	IGR	DEL	A	-	-	rs72222713		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103963545delA								AZIN1 (87148 upstream) : ATP6V1C1 (69703 downstream)																							acactgtctcaaaaaaaaaag	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	104297369	104297370	+	Intron	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104297369_104297370insT	uc003ylf.2	-											Homo sapiens cDNA FLJ43745 fis, clone TESTI2019648.																		CCAATTGTGTGTTTTTTTTTAA	0.356													4	2	---	---	---	---	
FZD6	8323	broad.mit.edu	37	8	104331760	104331760	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104331760delT	uc003ylh.2	+						FZD6_uc003yli.2_Intron|FZD6_uc003ylj.2_Intron|FZD6_uc011lhn.1_Intron|FZD6_uc011lho.1_Intron|FZD6_uc011lhp.1_Intron	NM_003506	NP_003497	O60353	FZD6_HUMAN	frizzled 6 isoform a precursor						angiogenesis|axonogenesis|cell proliferation in midbrain|establishment of planar polarity|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|neural tube closure|non-canonical Wnt receptor signaling pathway	apical part of cell|apicolateral plasma membrane|cytoplasm|integral to plasma membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			GCAGTTTCTGTTAGGAATCCA	0.517													4	2	---	---	---	---	
RIMS2	9699	broad.mit.edu	37	8	104759660	104759660	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104759660delA	uc003ylp.2	+							NM_001100117	NP_001093587	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			cgttttgaccaaaaaaaaaat	0.000										HNSCC(12;0.0054)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	106304928	106304928	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106304928delA								LRP12 (703708 upstream) : ZFPM2 (26219 downstream)																							ACAATGCTTTAAAAAAAAATG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	106916964	106916965	+	IGR	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106916964_106916965delTC								ZFPM2 (100199 upstream) : OXR1 (365508 downstream)																							TGTGAGCCCTTCTCTCTCCTCT	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	108226964	108226965	+	IGR	INS	-	T	T	rs147137547	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108226964_108226965insT								ABRA (444492 upstream) : ANGPT1 (34746 downstream)																							TCTGCAAACACTTTCTAGATca	0.064													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	112323726	112323726	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112323726delT								None (None upstream) : CSMD3 (911435 downstream)																							TCCTGTTTTGTTTTTTTTTTC	0.299													3	3	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	114287047	114287048	+	Intron	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114287047_114287048delAC	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.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						ACATTCAGCTACACACACACAC	0.168										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			6	3	---	---	---	---	
TRPS1	7227	broad.mit.edu	37	8	116445121	116445121	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116445121delT	uc003ynz.2	-						TRPS1_uc011lhy.1_Intron|TRPS1_uc003yny.2_Intron|TRPS1_uc010mcy.2_Intron	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1						negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			TGAACTTGACTTTTTTTTTTT	0.323									Langer-Giedion_syndrome				3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	117477971	117477971	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117477971delC								TRPS1 (796743 upstream) : EIF3H (179085 downstream)																							GCACCTGTTTCCAAAACCACA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120038152	120038152	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120038152delC								TNFRSF11B (73769 upstream) : COLEC10 (41272 downstream)																							ttagtttatgcctgcatcatg	0.100													4	2	---	---	---	---	
FER1L6	654463	broad.mit.edu	37	8	125045737	125045737	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125045737delT	uc003yqw.2	+						uc003yqx.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			ACTTACTTGATTTTTTTTTTT	0.363													3	4	---	---	---	---	
MTSS1	9788	broad.mit.edu	37	8	125658340	125658340	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125658340delA	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TTTTAAAGGCATTCCTGGGCC	0.343													1	5	---	---	---	---	
PVT1	5820	broad.mit.edu	37	8	128808723	128808723	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128808723delT	uc003ysj.2	+						PVT1_uc010mdq.2_Intron|PVT1_uc010mdp.1_Intron					Human proto-oncogene myc mRNA, 5' end, clone DMmyc.												0						TCTTTAGTTGTTTTTTTTTTC	0.488													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129443344	129443344	+	IGR	DEL	C	-	-	rs34605452		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129443344delC								MIR1208 (280910 upstream) : None (None downstream)																							agccaagtcaccagccatgta	0.000													7	5	---	---	---	---	
ADCY8	114	broad.mit.edu	37	8	131984612	131984612	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131984612delT	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TTGCTAAACCTTAATGTTCCA	0.348										HNSCC(32;0.087)			4	2	---	---	---	---	
ST3GAL1	6482	broad.mit.edu	37	8	134529074	134529074	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134529074delT	uc003yuk.2	-						ST3GAL1_uc003yum.2_Intron	NM_173344	NP_775479	Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			CCCTCACTGATTATGAGATTT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137944564	137944565	+	IGR	INS	-	AC	AC	rs150354269	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137944564_137944565insAC								None (None upstream) : None (None downstream)																							GGACCTTCTGTacacacacaca	0.153													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138949416	138949416	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138949416delC								None (None upstream) : FAM135B (192852 downstream)																							CTCACCTTTTCCGGTTGAATA	0.383													4	2	---	---	---	---	
FAM135B	51059	broad.mit.edu	37	8	139238103	139238103	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139238103delG	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			gcagctggcagggtggtggtg	0.264										HNSCC(54;0.14)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140304752	140304754	+	IGR	DEL	TGT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140304752_140304754delTGT								COL22A1 (378516 upstream) : KCNK9 (308328 downstream)																							TTCCCTTGTGTGTTGTTGTTGTT	0.419													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141130938	141130941	+	Intron	DEL	CATC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141130938_141130941delCATC	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						atccatccatcatccatccatcca	0.000													4	4	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141389507	141389508	+	Intron	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141389507_141389508delGT	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						tcttgtgaaggtgtgtgtgtgg	0.050													4	2	---	---	---	---	
TSNARE1	203062	broad.mit.edu	37	8	143446964	143446965	+	Intron	DEL	CA	-	-	rs34247548		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143446964_143446965delCA	uc003ywk.2	-						TSNARE1_uc003ywl.3_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					catgcacacgcacacacacaca	0.000													4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	9849353	9849353	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9849353delA	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		GGCATCAAATAAAAAAAAATT	0.323										TSP Lung(15;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	11138518	11138519	+	IGR	INS	-	AA	AA	rs143892489	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11138518_11138519insAA								PTPRD (525795 upstream) : None (None downstream)																							TAGACACTGAGAAAAAAAAAAG	0.317													3	3	---	---	---	---	
TYRP1	7306	broad.mit.edu	37	9	12693762	12693762	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12693762delA	uc003zkv.3	+							NM_000550	NP_000541	P17643	TYRP1_HUMAN	tyrosinase-related protein 1 precursor						melanin biosynthetic process	clathrin-coated endocytic vesicle membrane|endosome membrane|integral to membrane|melanosome membrane	copper ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen|protein heterodimerization activity|protein homodimerization activity			lung(1)	1		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		TTTTAAAGGTAAAATTTGTGT	0.308									Oculocutaneous_Albinism				5	3	---	---	---	---	
TYRP1	7306	broad.mit.edu	37	9	12693768	12693780	+	Intron	DEL	TGTGTGAAATGTC	-	-	rs59527529		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12693768_12693780delTGTGTGAAATGTC	uc003zkv.3	+							NM_000550	NP_000541	P17643	TYRP1_HUMAN	tyrosinase-related protein 1 precursor						melanin biosynthetic process	clathrin-coated endocytic vesicle membrane|endosome membrane|integral to membrane|melanosome membrane	copper ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen|protein heterodimerization activity|protein homodimerization activity			lung(1)	1		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		AGGTAAAATTTGTGTGAAATGTCACACTTTTAT	0.305									Oculocutaneous_Albinism				5	3	---	---	---	---	
ZDHHC21	340481	broad.mit.edu	37	9	14614076	14614076	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14614076delA	uc003zlg.1	-						uc003zlh.1_RNA			Q8IVQ6	ZDH21_HUMAN	Homo sapiens HSPC097 mRNA, partial cds.						nitric oxide metabolic process|regulation of nitric-oxide synthase activity	Golgi membrane|integral to membrane	palmitoyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(50;4.31e-06)		AGATAAGGCTAAAATGATTAC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16991990	16991990	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16991990delA								BNC2 (121204 upstream) : CNTLN (143048 downstream)																							TCTAGAACACAATGAAACCAC	0.274													4	2	---	---	---	---	
ADAMTSL1	92949	broad.mit.edu	37	9	18859833	18859833	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18859833delT	uc003zne.3	+						ADAMTSL1_uc003znf.3_Intron	NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)		ATGGTGCTGATTTttttttta	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	19956610	19956611	+	IGR	DEL	AG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19956610_19956611delAG								SLC24A2 (167802 upstream) : MLLT3 (388357 downstream)																							gcagcaggcaagagagagagct	0.000													4	2	---	---	---	---	
MLLT3	4300	broad.mit.edu	37	9	20349532	20349532	+	Intron	DEL	A	-	-	rs11303969		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20349532delA	uc003zoe.2	-						MLLT3_uc011lne.1_Intron|MLLT3_uc011lnf.1_Intron	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		GGCTTGAATTAAAAAAAAAAA	0.328			T	MLL	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	26412846	26412846	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26412846delT								TUSC1 (733990 upstream) : C9orf82 (427838 downstream)																							GGTTTTTGTGTTTTTTTTTTG	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	26687457	26687458	+	IGR	INS	-	GA	GA	rs142760750	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26687457_26687458insGA								None (None upstream) : C9orf82 (153226 downstream)																							ATGAAGAAAGTGAGAGAGCTGG	0.431													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	35788919	35788919	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35788919delA								MSMP (34647 upstream) : NPR2 (3487 downstream)																							GTGTGTTAATAAAAAACCTCA	0.294													4	2	---	---	---	---	
LOC92973	92973	broad.mit.edu	37	9	35857540	35857540	+	5'Flank	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35857540delA	uc003zyp.3	+							NR_024006				Homo sapiens clone 23583 mRNA sequence.												0						ggcatagtggaaaatcaggct	0.129													4	2	---	---	---	---	
RECK	8434	broad.mit.edu	37	9	36092866	36092866	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36092866delA	uc003zyv.2	+						RECK_uc003zyw.2_Intron|RECK_uc003zyx.2_Intron	NM_021111	NP_066934	O95980	RECK_HUMAN	RECK protein precursor							anchored to membrane|peripheral to membrane of membrane fraction|plasma membrane	metalloendopeptidase inhibitor activity|serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)	3			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			atattgaaggaaaaaaaaaat	0.000													5	3	---	---	---	---	
FBXO10	26267	broad.mit.edu	37	9	37584083	37584083	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37584083delT	uc004aac.2	-						FBXO10_uc004aad.2_Intron|TOMM5_uc004aae.3_RNA	NM_012166	NP_036298	Q9UK96	FBX10_HUMAN	F-box protein 10							ubiquitin ligase complex	ubiquitin-protein ligase activity			lung(5)	5				GBM - Glioblastoma multiforme(29;0.0107)		GATAAAGCAGTTTTTTTTTTT	0.373													3	3	---	---	---	---	
CNTNAP3	79937	broad.mit.edu	37	9	39138474	39138475	+	Intron	INS	-	AA	AA			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39138474_39138475insAA	uc004abi.2	-						CNTNAP3_uc004abj.2_Intron|CNTNAP3_uc011lqr.1_Intron|CNTNAP3_uc004abk.1_Intron|CNTNAP3_uc011lqs.1_Intron|CNTNAP3_uc004abl.1_Intron	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3 precursor						cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		caaaacaaaacaagaaaacaaa	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44109097	44109098	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44109097_44109098insA								FAM75A6 (478367 upstream) : FAM27C (881138 downstream)																							ATAAAGGTCTCAAAAATCCAGA	0.347													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44764413	44764414	+	IGR	INS	-	T	T	rs142987641	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44764413_44764414insT								None (None upstream) : FAM27C (225822 downstream)																							TAGGCAACATATTCTAGGACTA	0.337													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	47202619	47202619	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:47202619delA								KGFLP1 (454234 upstream) : None (None downstream)																							AAACTTCTCCAAAAAAAAAGT	0.443													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66465026	66465027	+	Intron	INS	-	G	G	rs145447612		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66465026_66465027insG	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		CAGCAGGCTGAGGGATCCAAGG	0.381													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66480779	66480779	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66480779delT								FAM74A4 (986393 upstream) : LOC442421 (15691 downstream)																							gtcctggatatttttttgttg	0.000													8	4	---	---	---	---	
LOC442421	442421	broad.mit.edu	37	9	66496197	66496197	+	5'Flank	DEL	G	-	-	rs79383207		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66496197delG	uc004aee.1	+						LOC442421_uc004aed.1_5'Flank					Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).												0						agttttgtttgtttttttttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67301383	67301384	+	IGR	INS	-	G	G	rs144184994		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67301383_67301384insG								AQP7P1 (11891 upstream) : FAM27B (491546 downstream)																							GGAGCATGTTTGGGCATCAGTG	0.569													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67791249	67791250	+	5'Flank	DEL	AC	-	-	rs74992488		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67791249_67791250delAC	uc004aes.1	+											Homo sapiens cDNA FLJ36039 fis, clone TESTI2017311.																		agaatgggagacacacacacac	0.064													5	6	---	---	---	---	
ANKRD20A3	441425	broad.mit.edu	37	9	67935111	67935111	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67935111delT	uc004aeu.2	+						ANKRD20A3_uc010mnn.2_Intron	NM_001012419	NP_001012419	Q5VUR7	A20A3_HUMAN	ankyrin repeat domain 20 family, member A3												0						GTTTTATTAAttttttttttt	0.119													7	19	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69808158	69808158	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69808158delC								LOC100133920 (143209 upstream) : FOXD4L5 (367551 downstream)																							TAGTATTTTTCCAGCAGATGG	0.289													4	2	---	---	---	---	
MAMDC2	256691	broad.mit.edu	37	9	72835679	72835679	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72835679delT	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron|uc004ahq.1_Intron	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						ATAATCCTCATTGGCCTGAAG	0.104													4	2	---	---	---	---	
TLE4	7091	broad.mit.edu	37	9	82317974	82317975	+	Intron	DEL	AA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82317974_82317975delAA	uc004ald.2	+						TLE4_uc004alc.2_Intron|TLE4_uc010mpr.2_Intron|TLE4_uc004ale.2_Intron|TLE4_uc011lsq.1_Intron|TLE4_uc010mps.2_Intron|TLE4_uc004alf.2_Intron	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4											lung(2)|ovary(1)|breast(1)|skin(1)	5						AAGATAAAGCAAAAAAAAAAAC	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82420750	82420751	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82420750_82420751insT								TLE4 (79093 upstream) : None (None downstream)																							tcatcattacattttttttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85597301	85597310	+	IGR	DEL	TTTCTTTTCT	-	-	rs10538467		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85597301_85597310delTTTCTTTTCT								FLJ46321 (987131 upstream) : RASEF (7 downstream)																							GAGCATGTGAtttcttttcttttctttttt	0.314													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	88452106	88452107	+	Intron	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88452106_88452107delAC	uc004aog.1	+						uc004aoh.1_Intron					Homo sapiens cDNA FLJ42532 fis, clone BRACE3003004.																		ATATACACAAACACACACACAC	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	89110389	89110389	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89110389delT								ZCCHC6 (141011 upstream) : GAS1 (448890 downstream)																							cttgctgagattttttttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91868143	91868144	+	IGR	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91868143_91868144delGT								SHC3 (74461 upstream) : CKS2 (57969 downstream)																							GTAGTGTGGGgtgtgtgtgtgt	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92175927	92175927	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92175927delT								SEMA4D (63039 upstream) : GADD45G (44000 downstream)																							AAATGTTACGttagcgtgatg	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93544896	93544896	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93544896delC								DIRAS2 (139788 upstream) : SYK (19116 downstream)																							ctgtcctgcacccccagagct	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	94233940	94233940	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94233940delC								NFIL3 (47796 upstream) : ROR2 (91433 downstream)																							tgctatccctccccccaagtc	0.000													4	2	---	---	---	---	
C9orf3	84909	broad.mit.edu	37	9	97663418	97663418	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97663418delT	uc004ava.2	+						C9orf3_uc004aux.1_Intron|C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron	NM_032823	NP_116212	Q8N6M6	AMPO_HUMAN	aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		ATCAAAACAATTAGAATGTGT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98296665	98296665	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98296665delA								PTCH1 (17418 upstream) : C9orf130 (271707 downstream)																							aggaatcaataaccccttcct	0.015													4	2	---	---	---	---	
GABBR2	9568	broad.mit.edu	37	9	101201382	101201382	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101201382delA	uc004ays.2	-							NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	tatctgccttaaaaaaaaaac	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	104091150	104091151	+	IGR	INS	-	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104091150_104091151insG								LPPR1 (3734 upstream) : BAAT (31549 downstream)																							tggtgagtaaaggggaaaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	105272262	105272262	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105272262delA								GRIN3A (771400 upstream) : CYLC2 (485331 downstream)																							tgtggaatctaaaacagtcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	106948744	106948744	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106948744delT								SMC2 (45051 upstream) : OR13F1 (317800 downstream)																							cacattaacatttggtattgt	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107907613	107907613	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107907613delT								ABCA1 (217177 upstream) : SLC44A1 (99316 downstream)																							ACCAAGGTTCTTTATAGCTTA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111005745	111005745	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111005745delT								KLF4 (753698 upstream) : ACTL7B (611126 downstream)																							TTATGTGCCATTTTAACATCA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111487274	111487274	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111487274delA								None (None upstream) : ACTL7B (129597 downstream)																							tcatagctttaaaaaaaacct	0.025													4	2	---	---	---	---	
C9orf5	23731	broad.mit.edu	37	9	111871717	111871717	+	Intron	DEL	A	-	-	rs72286087		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111871717delA	uc004bdt.3	-						C9orf5_uc004bds.3_5'Flank|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		gaaccttgccaaaaaaaaaag	0.000													4	2	---	---	---	---	
SUSD1	64420	broad.mit.edu	37	9	114823787	114823787	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114823787delA	uc004bfu.2	-						SUSD1_uc010mui.2_Intron|SUSD1_uc010muj.2_Intron	NM_022486	NP_071931	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1 precursor							integral to membrane	calcium ion binding				0						CCACAAGGGTAAGCTGTCATT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	115858896	115858897	+	IGR	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115858896_115858897delTC								ZFP37 (39900 upstream) : C9orf110 (8109 downstream)																							tgtctgtctgtctctctctctC	0.282													4	2	---	---	---	---	
C9orf43	257169	broad.mit.edu	37	9	116178963	116178963	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116178963delT	uc004bho.3	+						C9orf43_uc004bhp.2_Intron	NM_152786	NP_689999	Q8TAL5	CI043_HUMAN	hypothetical protein LOC257169												0						cTTAACTAGGTTTTTTTTTTT	0.035													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	116545999	116546000	+	IGR	INS	-	TTGG	TTGG	rs79958641		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116545999_116546000insTTGG								RGS3 (185982 upstream) : ZNF618 (92562 downstream)																							atgatggatgattgagtgagtg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	118571176	118571176	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118571176delA								DEC1 (406253 upstream) : C9orf27 (79370 downstream)																							GCCAGGGGCCAAGGAGGCAGA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	118901442	118901442	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118901442delT								C9orf27 (214065 upstream) : PAPPA (14629 downstream)																							ctccaactcctacgttcaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120250762	120250762	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120250762delA								ASTN2 (73445 upstream) : TLR4 (215698 downstream)																							TTCAGATGGGAAAAAAAAAAG	0.318													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120898009	120898009	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120898009delT								TLR4 (418245 upstream) : None (None downstream)																							CTCTGGTGGGTTCCAGTAGCC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	121634771	121634772	+	IGR	INS	-	A	A	rs73536475	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121634771_121634772insA								None (None upstream) : DBC1 (294136 downstream)																							attctcttcttaaaaaaaaaat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122262626	122262626	+	IGR	DEL	G	-	-	rs16908454		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122262626delG								DBC1 (130887 upstream) : MIR147 (744631 downstream)																							TTGGACAAAAGCTATGATTCA	0.562													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	123503945	123503946	+	IGR	INS	-	A	A	rs112945103		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123503945_123503946insA								MEGF9 (27333 upstream) : FBXW2 (15308 downstream)																							actatATAACTAAAAAAAAAAA	0.129													4	2	---	---	---	---	
CEP110	11064	broad.mit.edu	37	9	123924715	123924715	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123924715delT	uc004bkx.1	+						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						TCCTTCTAGCTTTTTTTTTTT	0.209													11	10	---	---	---	---	
MORN5	254956	broad.mit.edu	37	9	124944529	124944529	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124944529delC	uc004blw.2	+						MORN5_uc011lyo.1_Intron	NM_198469	NP_940871	Q5VZ52	MORN5_HUMAN	MORN repeat containing 5												0						tcatgtattgccccagcacag	0.000													4	2	---	---	---	---	
NR6A1	2649	broad.mit.edu	37	9	127354022	127354022	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127354022delT	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron	NM_033334	NP_201591	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3						TCTATCAGGCTTTTCAAAATA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	128496100	128496101	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128496100_128496101insA								MAPKAP1 (26587 upstream) : PBX3 (13516 downstream)																							TGTACCAGCTTAAAAAAAATCT	0.342													4	2	---	---	---	---	
WDR34	89891	broad.mit.edu	37	9	131409563	131409564	+	Intron	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131409563_131409564delGT	uc004bvq.1	-						WDR34_uc004bvs.1_Intron|WDR34_uc004bvr.1_Intron	NM_052844	NP_443076	Q96EX3	WDR34_HUMAN	WD repeat domain 34							cytoplasm				central_nervous_system(2)|skin(1)	3						ATGCCAGGCAGTGTGTGACTAG	0.559													4	2	---	---	---	---	
CEL	1056	broad.mit.edu	37	9	135942772	135942772	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135942772delT	uc010naa.1	+							NM_001807	NP_001798	P19835	CEL_HUMAN	carboxyl ester lipase precursor						cholesterol catabolic process|fatty acid catabolic process|intestinal cholesterol absorption|intestinal lipid catabolic process|pancreatic juice secretion|protein esterification	cytosol|extracellular space	acylglycerol lipase activity|carboxylesterase activity|heparin binding|sterol esterase activity|triglyceride lipase activity			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CCGtttcttctttttttttga	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	139596864	139596865	+	IGR	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139596864_139596865delCA								AGPAT2 (14953 upstream) : FAM69B (10159 downstream)																							cacccatgtgcacacacacaca	0.252													4	2	---	---	---	---	
CACNA1B	774	broad.mit.edu	37	9	140968697	140968697	+	Intron	DEL	T	-	-	rs78547363		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140968697delT	uc004cog.2	+						CACNA1B_uc004coi.2_Intron|CACNA1B_uc004cok.1_5'Flank|CACNA1B_uc010ncp.1_5'Flank	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,						membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)	tttcttactcttttttttttt	0.020													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2530971	2530971	+	IGR	DEL	T	-	-	rs11316425		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2530971delT								ADARB2 (751253 upstream) : PFKP (578781 downstream)																							TACAGCTGCCTTTTTTTTTTT	0.413													5	4	---	---	---	---	
PRKCQ	5588	broad.mit.edu	37	10	6528954	6528954	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6528954delA	uc001ijj.1	-						PRKCQ_uc009xim.1_Intron|PRKCQ_uc001iji.1_Intron|PRKCQ_uc009xin.1_Intron|PRKCQ_uc010qax.1_Intron	NM_006257	NP_006248	Q04759	KPCT_HUMAN	protein kinase C, theta						axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6						CTCAGCTTTGAAAAAAAAATC	0.517													4	2	---	---	---	---	
UPF2	26019	broad.mit.edu	37	10	12076804	12076805	+	Intron	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12076804_12076805insT	uc001ila.2	-						UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron|UPF2_uc009xiz.1_Intron	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				attccgtctcaaaataaataaa	0.134													4	2	---	---	---	---	
FAM107B	83641	broad.mit.edu	37	10	14561157	14561158	+	3'UTR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14561157_14561158insT	uc001imx.1	-	4					FAM107B_uc001ina.1_3'UTR|FAM107B_uc010qbu.1_RNA|FAM107B_uc009xjg.1_3'UTR|FAM107B_uc001imy.1_3'UTR|FAM107B_uc001imz.1_3'UTR	NM_031453	NP_113641	Q9H098	F107B_HUMAN	hypothetical protein LOC83641											breast(4)	4						TCTTAAGTAACTTTTTTTTTTT	0.356													4	2	---	---	---	---	
OLAH	55301	broad.mit.edu	37	10	15104113	15104113	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15104113delT	uc001inu.2	+						ACBD7_uc010qby.1_Intron|OLAH_uc001int.2_Intron	NM_001039702	NP_001034791	Q9NV23	SAST_HUMAN	oleoyl-ACP hydrolase isoform 2						fatty acid biosynthetic process		myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity				0						ATTCTATTTATTTTTGAAATA	0.234													4	2	---	---	---	---	
CUBN	8029	broad.mit.edu	37	10	17165193	17165193	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17165193delT	uc001ioo.2	-							NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CTTACTTAACTTTTTTTTTTA	0.338													4	2	---	---	---	---	
ST8SIA6	338596	broad.mit.edu	37	10	17432861	17432861	+	Intron	DEL	T	-	-	rs146797949		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17432861delT	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron|uc001ipe.2_Intron|uc001ipf.1_Intron	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						TTTGAAGACCttttttttttt	0.144													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	18409016	18409016	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18409016delA								SLC39A12 (76795 upstream) : CACNB2 (20590 downstream)																							GTGAGAAGAGAAAAAAATAGA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	19614969	19614969	+	IGR	DEL	T	-	-	rs67982527		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19614969delT								ARL5B (648029 upstream) : PLXDC2 (490403 downstream)																							AATTTTAGAATTTTTTTTATA	0.254													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	20872552	20872552	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20872552delG								PLXDC2 (303437 upstream) : NEBL (196353 downstream)																							ggtaaagtgtgtttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	22449359	22449361	+	IGR	DEL	ACA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22449359_22449361delACA								DNAJC1 (156709 upstream) : COMMD3 (155938 downstream)																							ttctgaactcacaacaacaacaa	0.108													4	2	---	---	---	---	
SPAG6	9576	broad.mit.edu	37	10	22635970	22635971	+	Intron	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22635970_22635971delGT	uc001iri.2	+						SPAG6_uc001irj.2_Intron|SPAG6_uc010qct.1_Intron|SPAG6_uc009xkh.2_Intron	NM_012443	NP_036575	O75602	SPAG6_HUMAN	sperm associated antigen 6 isoform 1						cell projection organization|spermatid development	axoneme|cilium|cytoplasm|flagellum|microtubule	binding			breast(1)	1						ttaattgttcgtgtgtgtgtgt	0.000													3	3	---	---	---	---	
MYO3A	53904	broad.mit.edu	37	10	26457274	26457274	+	Intron	DEL	T	-	-	rs141340923		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26457274delT	uc001isn.2	+						MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA						protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						ATTTTTTTAATTTGGGAAATA	0.254													4	2	---	---	---	---	
ANKRD26	22852	broad.mit.edu	37	10	27295462	27295462	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27295462delG	uc001ith.2	-						ANKRD26_uc001itg.2_Intron|ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						TAGTGAGTCTGGGGTCTTTGG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	27626050	27626050	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27626050delA								LOC387646 (84815 upstream) : PTCHD3 (61067 downstream)																							CACCAAGGCTAAAAGGAAGGA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29427530	29427530	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29427530delA								BAMBI (455662 upstream) : LYZL1 (150460 downstream)																							TTTGACCACTAAACTAGCAAA	0.348													4	2	---	---	---	---	
SVIL	6840	broad.mit.edu	37	10	29844274	29844275	+	Intron	DEL	TG	-	-	rs1547171		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29844274_29844275delTG	uc001iut.1	-						SVIL_uc001iuu.1_Intron|SVIL_uc009xld.1_Intron	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2						cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)				cacacacacatggacacacCCT	0.223													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30931927	30931928	+	IGR	INS	-	TGTT	TGTT	rs150764284	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30931927_30931928insTGTT								LYZL2 (13280 upstream) : ZNF438 (201639 downstream)																							AGATGCGTCTCTGCCACCAGCA	0.515													3	3	---	---	---	---	
NRP1	8829	broad.mit.edu	37	10	33487690	33487691	+	Intron	INS	-	G	G	rs148626522	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33487690_33487691insG	uc001iwx.3	-						NRP1_uc001iwv.3_Intron|NRP1_uc009xlz.2_Intron|NRP1_uc001iww.3_Intron|NRP1_uc001iwy.3_Intron|NRP1_uc001iwz.2_Intron|NRP1_uc001ixa.2_Intron	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a						axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)	TAAGATGCTATGGTTCCTCCTC	0.436													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45378631	45378631	+	Intron	DEL	A	-	-	rs72030365		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45378631delA	uc001jbk.1	-						uc001jbl.2_Intron					Homo sapiens cDNA FLJ31956 fis, clone NT2RP7007359.																		ACGGGCACAGAAAAAAATGGA	0.428													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47090757	47090758	+	Intron	DEL	AG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47090757_47090758delAG	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						gtagatattcagagtccttgtt	0.153													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	50426424	50426424	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50426424delC								C10orf128 (30017 upstream) : C10orf71 (80763 downstream)																							GCCCTGGTAGCCCCCTGGGAA	0.483													4	2	---	---	---	---	
CHAT	1103	broad.mit.edu	37	10	50891421	50891421	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50891421delT	uc010qgs.1	+						C10orf53_uc001jib.2_Intron|C10orf53_uc001jic.1_Intron|C10orf53_uc001jid.1_Intron	NM_020986	NP_066266	P28329	CLAT_HUMAN	choline acetyltransferase isoform 1						neurotransmitter biosynthetic process|neurotransmitter secretion	cytosol|nucleus	choline O-acetyltransferase activity			central_nervous_system(3)	3		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)	tgggttgcacttttttttgtt	0.000													4	2	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53136846	53136846	+	Intron	DEL	A	-	-	rs35935908		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53136846delA	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		GTTAGCAGTTAAAAAAAAAAA	0.294													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	59442962	59442963	+	IGR	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59442962_59442963delTG								None (None upstream) : IPMK (512655 downstream)																							TGAAATTAAATGTGTGTGTGTG	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	60641919	60641919	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60641919delA								BICC1 (53074 upstream) : PHYHIPL (294429 downstream)																							aatgtagtctaatgttgaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	61733444	61733444	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61733444delT								C10orf40 (12773 upstream) : ANK3 (54716 downstream)																							taagtttttgtttttttccta	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64497309	64497310	+	IGR	DEL	CA	-	-	rs35606743		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64497309_64497310delCA								ZNF365 (65538 upstream) : ADO (67206 downstream)																							gctcctcagtcacacacacaca	0.015													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	71439208	71439209	+	IGR	INS	-	CTC	CTC	rs140038469	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71439208_71439209insCTC								C10orf35 (45861 upstream) : COL13A1 (122435 downstream)																							GCTTCCTTAAGCTCCACATTTG	0.455													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	72572134	72572135	+	IGR	INS	-	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72572134_72572135insG								C10orf27 (26977 upstream) : SGPL1 (3569 downstream)																							gagaacagcatgggggaaacca	0.000													4	2	---	---	---	---	
CDH23	64072	broad.mit.edu	37	10	73403316	73403317	+	Intron	INS	-	C	C	rs150881254	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73403316_73403317insC	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc001jry.2_5'Flank|CDH23_uc001jrz.2_5'Flank	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						AGGAGCCCTTGCCCCCCCCTCA	0.594													6	6	---	---	---	---	
ADK	132	broad.mit.edu	37	10	76050736	76050738	+	Intron	DEL	AAT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76050736_76050738delAAT	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron	NM_006721	NP_006712	P55263	ADK_HUMAN	adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)	GTCTGTAGCAAATAATAATAATA	0.310													4	2	---	---	---	---	
C10orf11	83938	broad.mit.edu	37	10	77684218	77684218	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77684218delA	uc001jxi.2	+							NM_032024	NP_114413	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)					ATGGCTTGTCAAAAAAAATAA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	79545933	79545934	+	IGR	INS	-	AAACAAAC	AAACAAAC	rs142231133	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79545933_79545934insAAACAAAC								KCNMA1 (148356 upstream) : DLG5 (4617 downstream)																							gaccaaggcaaaaacaaacaaa	0.000													7	4	---	---	---	---	
ZMIZ1	57178	broad.mit.edu	37	10	80944994	80944994	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80944994delC	uc001kaf.2	+						ZMIZ1_uc001kae.2_Intron	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17						transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			TGTTAAGACGCCCCCCTCCCC	0.537													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81270425	81270426	+	Intron	INS	-	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81270425_81270426insG	uc010qls.1	-						EIF5AL1_uc009xrx.2_5'Flank					SubName: Full=cDNA FLJ60964, weakly similar to Homo sapiens dentin sialophosphoprotein (DSPP), mRNA;																		CCAGTTGTTGAGGCCTTTCTTG	0.465													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85597919	85597919	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85597919delC								NRG3 (850984 upstream) : GHITM (301266 downstream)																							GGTTCCAAGTCCTGGGCCCTC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85764837	85764837	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85764837delA								None (None upstream) : GHITM (134348 downstream)																							atgtagaatcaaaaaaaaaaa	0.119													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	88288609	88288610	+	IGR	DEL	TT	-	-	rs72057964		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88288609_88288610delTT								WAPAL (7068 upstream) : OPN4 (125704 downstream)																							aaaaaatgaattttttttttgt	0.000													4	2	---	---	---	---	
LIPA	3988	broad.mit.edu	37	10	90981910	90981910	+	Intron	DEL	A	-	-	rs67421550		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90981910delA	uc001kga.3	-						LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|LIPA_uc010qnf.1_Intron|LIPA_uc009xtq.2_Intron|LIPA_uc009xtr.1_Intron	NM_000235	NP_000226	P38571	LICH_HUMAN	lipase A precursor						lipid catabolic process	lysosome	lipase activity|sterol esterase activity				0		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		ACACAGAAATAAAAAAAATCT	0.234													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91565578	91565581	+	IGR	DEL	CACA	-	-	rs74773941		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91565578_91565581delCACA								KIF20B (30878 upstream) : HTR7 (934997 downstream)																							ACTATACACCCACACACACACACC	0.422													4	2	---	---	---	---	
ALDH18A1	5832	broad.mit.edu	37	10	97406814	97406814	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97406814delT	uc001kkz.2	-						ALDH18A1_uc001kky.2_Intron|ALDH18A1_uc010qog.1_Intron|ALDH18A1_uc010qoh.1_Intron	NM_002860	NP_002851	P54886	P5CS_HUMAN	pyrroline-5-carboxylate synthetase isoform 1						proline biosynthetic process	mitochondrial inner membrane	ATP binding|glutamate 5-kinase activity|glutamate-5-semialdehyde dehydrogenase activity			pancreas(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)	L-Glutamic Acid(DB00142)	CTTTCTTTTCTTTTTTTTTCC	0.408													5	3	---	---	---	---	
NFKB2	4791	broad.mit.edu	37	10	104158973	104158973	+	Intron	DEL	A	-	-	rs146186127		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104158973delA	uc001kvb.2	+						NFKB2_uc001kva.2_Intron|NFKB2_uc001kvd.2_Intron|NFKB2_uc009xxc.2_Intron	NM_001077494	NP_001070962	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|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	Bcl3/NF-kappaB2 complex|cytosol|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			lung(3)	3		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)		actccgtctcaaaaaaaaaaa	0.264			T	IGH@	B-NHL								7	5	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	106571984	106571984	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106571984delC	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)		ACTAGCTAGGCCCCATCCTTA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	107377104	107377104	+	IGR	DEL	C	-	-	rs5787594		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107377104delC								SORCS3 (352111 upstream) : SORCS1 (956318 downstream)																							aggaagggagcgatgagcgaa	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	111507385	111507385	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111507385delA								None (None upstream) : XPNPEP1 (117139 downstream)																							CTCACACAGGAAAAAAAAAAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113239565	113239565	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113239565delC								ADRA2A (398905 upstream) : GPAM (670057 downstream)																							GTTCCCCCCTCCCCCAACCCT	0.403													4	2	---	---	---	---	
GPAM	57678	broad.mit.edu	37	10	113914740	113914740	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113914740delA	uc009xxy.1	-						GPAM_uc001kzp.2_Intron	NM_020918	NP_065969	Q9HCL2	GPAT1_HUMAN	mitochondrial glycerol 3-phosphate						phospholipid biosynthetic process|triglyceride biosynthetic process	integral to membrane|mitochondrial outer membrane	glycerol-3-phosphate O-acyltransferase activity			ovary(1)|skin(1)	2				Epithelial(162;0.0306)|all cancers(201;0.123)		agaaatacctaaaacatccat	0.184													4	2	---	---	---	---	
ATRNL1	26033	broad.mit.edu	37	10	116858027	116858027	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116858027delT	uc001lcg.2	+						ATRNL1_uc001lce.2_Intron|ATRNL1_uc001lcf.2_Intron|ATRNL1_uc009xyq.2_Intron	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor							integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		atttggcccctttagctgatt	0.129													4	2	---	---	---	---	
PNLIP	5406	broad.mit.edu	37	10	118319680	118319680	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118319680delA	uc001lcm.2	+							NM_000936	NP_000927	P16233	LIPP_HUMAN	pancreatic lipase precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	extracellular region	retinyl-palmitate esterase activity|triglyceride lipase activity			ovary(1)|central_nervous_system(1)|skin(1)	3				all cancers(201;0.0131)	Bentiromide(DB00522)|Orlistat(DB01083)	CCTTGGCTTGAAAAAAAATCT	0.303													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	120239684	120239685	+	IGR	INS	-	C	C	rs148359620	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120239684_120239685insC								C10orf84 (137845 upstream) : PRLHR (113231 downstream)																							ctcctccttttcctttcttctc	0.322													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	121224790	121224790	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121224790delG								GRK5 (9660 upstream) : RGS10 (34550 downstream)																							aaggaagcaaggatgggtagg	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122440619	122440619	+	IGR	DEL	T	-	-	rs11324175		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122440619delT								PPAPDC1A (91252 upstream) : WDR11 (170076 downstream)																							TGTCCCATGGTTGGCTGCCAG	0.264													2	4	---	---	---	---	
FGFR2	2263	broad.mit.edu	37	10	123309490	123309490	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123309490delT	uc010qtk.1	-						FGFR2_uc010qtg.1_Intron|FGFR2_uc010qth.1_Intron|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Intron|FGFR2_uc010qtl.1_Intron|FGFR2_uc010qtm.1_Intron|FGFR2_uc001lfl.3_Intron|FGFR2_uc001lfm.2_Intron|FGFR2_uc001lfn.3_Intron|FGFR2_uc010qtn.1_Intron|FGFR2_uc010qto.1_Intron|FGFR2_uc001lfo.1_Intron|FGFR2_uc010qtp.1_Intron|FGFR2_uc010qtq.1_Intron	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1						angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)	cagcaacaggtaactaataTG	0.169		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				4	2	---	---	---	---	
CPXM2	119587	broad.mit.edu	37	10	125519459	125519459	+	Intron	DEL	A	-	-	rs74578712		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125519459delA	uc001lhk.1	-						CPXM2_uc001lhj.2_Intron	NM_198148	NP_937791	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2						cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		AATGAGTGagaaaaaaaatgg	0.318													4	2	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127580326	127580327	+	Intron	DEL	CT	-	-	rs138246554		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127580326_127580327delCT	uc001ljg.1	-							NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GCATGAACTCCTCAGGAGTAGG	0.257													4	3	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127626952	127626952	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127626952delA	uc001ljh.3	+						FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				ctcagttgctaaatatatttc	0.015													4	2	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	128784591	128784592	+	Intron	INS	-	AA	AA	rs147558545	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128784591_128784592insAA	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		AATCGTGAGCCAGTCAGGGTTC	0.545													2	5	---	---	---	---	
CLRN3	119467	broad.mit.edu	37	10	129683748	129683748	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129683748delT	uc001lka.1	-						CLRN3_uc001ljz.1_5'Flank	NM_152311	NP_689524	Q8NCR9	CLRN3_HUMAN	clarin 3							integral to membrane				skin(1)	1		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				ACAGCCCACATTTCTGGAGTA	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130502761	130502761	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130502761delT								MKI67 (578293 upstream) : MGMT (762693 downstream)																							cttttttttctttttttttct	0.000													4	2	---	---	---	---	
MGMT	4255	broad.mit.edu	37	10	131544612	131544612	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131544612delT	uc001lkh.2	+							NM_002412	NP_002403	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase											ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)		tatctctctcttttttttatc	0.000								Direct_reversal_of_damage					4	2	---	---	---	---	
AP2A2	161	broad.mit.edu	37	11	944389	944389	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:944389delC	uc001lss.2	+						AP2A2_uc001lst.1_Intron|AP2A2_uc009yco.1_Intron	NM_012305	NP_036437	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2						axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|cytosol	lipid binding|protein transporter activity				0		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		ccaggcacttcccaggattct	0.134													4	2	---	---	---	---	
NUP98	4928	broad.mit.edu	37	11	3723555	3723567	+	Intron	DEL	TCTCTCTCTCTCT	-	-	rs150064304	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3723555_3723567delTCTCTCTCTCTCT	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyg.2_Intron	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1						carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		tctctctctctctctctctctctctctctctct	0.225			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								9	8	---	---	---	---	
HBB	3043	broad.mit.edu	37	11	5249283	5249283	+	5'Flank	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5249283delT	uc001mae.1	-							NM_000518	NP_000509	P68871	HBB_HUMAN	beta globin						blood coagulation|hydrogen peroxide catabolic process|nitric oxide transport|positive regulation of cell death|positive regulation of nitric oxide biosynthetic process|protein heterooligomerization|regulation of blood pressure|regulation of blood vessel size	haptoglobin-hemoglobin complex|hemoglobin complex	heme binding|hemoglobin binding|oxygen binding|oxygen transporter activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Iron Dextran(DB00893)	TTTAAAATCATTTCCTTGATT	0.353									Sickle_Cell_Trait				4	2	---	---	---	---	
ILK	3611	broad.mit.edu	37	11	6627032	6627034	+	Intron	DEL	ATG	-	-	rs139352397		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6627032_6627034delATG	uc001mee.2	+						RRP8_uc001med.2_5'Flank|ILK_uc001mef.2_Intron|ILK_uc010rap.1_Intron|ILK_uc010raq.1_Intron|ILK_uc001meg.2_Intron|ILK_uc001meh.2_Intron	NM_001014794	NP_001014794	Q13418	ILK_HUMAN	integrin-linked kinase						cell junction assembly|cell proliferation|cell-matrix adhesion|integrin-mediated signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent	cytosol|focal adhesion	ATP binding|protein serine/threonine kinase activity			central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)		TTAAGGCACTATGATGAACACCT	0.365													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	11800160	11800160	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11800160delT								GALNTL4 (156599 upstream) : USP47 (62810 downstream)																							TCCCTGCCCATAACTGACCTC	0.338													4	2	---	---	---	---	
TEAD1	7003	broad.mit.edu	37	11	12881846	12881846	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12881846delT	uc001mkj.3	+						TEAD1_uc009ygk.2_Intron	NM_021961	NP_068780	P28347	TEAD1_HUMAN	TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		aatgggctacttCCTCAATTT	0.219													4	2	---	---	---	---	
TEAD1	7003	broad.mit.edu	37	11	12885665	12885665	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12885665delT	uc001mkj.3	+						TEAD1_uc009ygk.2_Intron	NM_021961	NP_068780	P28347	TEAD1_HUMAN	TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		TCCATTTCTCTTTGAGATCTA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	14962346	14962346	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14962346delT								CYP2R1 (48595 upstream) : CALCA (25870 downstream)																							agactggatgttacccaccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15323103	15323104	+	IGR	INS	-	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15323103_15323104insC								INSC (54351 upstream) : SOX6 (664892 downstream)																							caaaaaacaaaaaaaaaaacaa	0.015													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	17269105	17269105	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17269105delT								PIK3C2A (39575 upstream) : NUCB2 (12782 downstream)																							tctctgtgtctttttatattt	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	17708696	17708696	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17708696delA								USH1C (142733 upstream) : MYOD1 (32414 downstream)																							tccagagcccaaatcttcact	0.164													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21249405	21249406	+	Intron	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21249405_21249406delTG	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						CTACCTCTGTTGTGTGTGTGTG	0.332													5	4	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21457327	21457328	+	Intron	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21457327_21457328delTG	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						gtctgtactttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21460614	21460615	+	Intron	INS	-	ATAG	ATAG	rs142502112	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21460614_21460615insATAG	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						AACTGCAGGTAATAGAGGTGTG	0.406													2	4	---	---	---	---	
SLC17A6	57084	broad.mit.edu	37	11	22360359	22360360	+	Intron	DEL	GT	-	-	rs71861548		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22360359_22360360delGT	uc001mqk.2	+							NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent						sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4						AACCTGTCTGgtgtgtgtgtgt	0.332													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	30158562	30158565	+	IGR	DEL	GATA	-	-	rs148218429		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30158562_30158565delGATA								KCNA4 (120074 upstream) : FSHB (93998 downstream)																							gattgtctgggatagactgagtag	0.000													2	4	---	---	---	---	
DNAJC24	120526	broad.mit.edu	37	11	31440820	31440820	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31440820delT	uc001msx.2	+						DNAJC24_uc009yjm.2_Intron	NM_181706	NP_859057	Q6P3W2	DJC24_HUMAN	zinc finger, CSL domain containing 3						protein folding		heat shock protein binding|metal ion binding|unfolded protein binding			breast(2)	2						GGGGGGTATGTTTTTTTTGGT	0.348													4	2	---	---	---	---	
DEPDC7	91614	broad.mit.edu	37	11	33050568	33050569	+	Intron	INS	-	A	A	rs137881581	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33050568_33050569insA	uc001mub.2	+						DEPDC7_uc001muc.2_Intron	NM_001077242	NP_001070710	Q96QD5	DEPD7_HUMAN	novel 58.3 KDA protein isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|skin(1)	2						CACATTAAGTGAAAAAAAAATG	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	33501622	33501622	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33501622delA								HIPK3 (125683 upstream) : C11orf41 (62255 downstream)																							ACGCGTGCttaaaatagcttt	0.164													4	2	---	---	---	---	
TRIM44	54765	broad.mit.edu	37	11	35737553	35737553	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35737553delG	uc001mwi.2	+							NM_017583	NP_060053	Q96DX7	TRI44_HUMAN	DIPB protein							intracellular	protein binding|zinc ion binding			skin(1)	1	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				tcaacattgtggattacaatt	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37355798	37355798	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37355798delA								C11orf74 (659408 upstream) : None (None downstream)																							ATTGATAGTGAAAGCTGTGCT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44002646	44002647	+	IGR	INS	-	AAAC	AAAC	rs142235852	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44002646_44002647insAAAC								AG2 (37214 upstream) : ACCSL (66884 downstream)																							atggggcaggaaaacaaacaaa	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	45040590	45040590	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45040590delC								LOC221122 (41014 upstream) : PRDM11 (74974 downstream)																							CTTTCTGTTACCAGGAttgat	0.204													4	2	---	---	---	---	
AMBRA1	55626	broad.mit.edu	37	11	46567012	46567012	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46567012delA	uc010rgu.1	-						AMBRA1_uc010rgt.1_5'Flank|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		accctgtctcaaaaaaaaaaT	0.219													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48382931	48382932	+	IGR	INS	-	GTCCAGGGAG	GTCCAGGGAG	rs140231387	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48382931_48382932insGTCCAGGGAG								OR4C45 (8932 upstream) : OR4A47 (127413 downstream)																							ttaacaaaccaagcaatgtaga	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	57290363	57290370	+	IGR	DEL	TTTGTTTG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57290363_57290370delTTTGTTTG								SLC43A1 (7204 upstream) : TIMM10 (5566 downstream)																							CTTTAGATCTtttgtttgtttgtttgtt	0.226													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	58801697	58801698	+	Intron	INS	-	TT	TT	rs35671089		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58801697_58801698insTT	uc001nng.1	-											Homo sapiens cDNA FLJ34127 fis, clone FCBBF3010124.																		aaatttcagggttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	63726083	63726083	+	IGR	DEL	C	-	-	rs320123	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63726083delC								NAA40 (1639 upstream) : COX8A (15996 downstream)																							ATGTCCCCAGCGGGAGGGACG	0.582													4	2	---	---	---	---	
CPT1A	1374	broad.mit.edu	37	11	68605299	68605299	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68605299delA	uc001oog.3	-						CPT1A_uc001oof.3_Intron	NM_001876	NP_001867	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A liver isoform						carnitine shuttle|fatty acid beta-oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			skin(2)	2	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		L-Carnitine(DB00583)|Perhexiline(DB01074)	gtcactaaagaaaaaaaaaga	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69796910	69796910	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69796910delA								FGF3 (162718 upstream) : ANO1 (127498 downstream)																							TCACCACAATAAAAAAAAGTG	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71605479	71605480	+	IGR	INS	-	GTGA	GTGA			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71605479_71605480insGTGA								DEFB108B (56872 upstream) : RNF121 (34288 downstream)																							TTCTTGTGTGGGTAAGGGCAAC	0.441													4	2	---	---	---	---	
FCHSD2	9873	broad.mit.edu	37	11	72574328	72574328	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72574328delA	uc009ytl.2	-						FCHSD2_uc010rrg.1_Intron|FCHSD2_uc001oth.3_Intron|FCHSD2_uc001oti.2_Intron	NM_014824	NP_055639	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			aaggacagttaaaaaaaaaag	0.000													4	2	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	78440269	78440269	+	Intron	DEL	G	-	-	rs35235071		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78440269delG	uc001ozl.3	-							NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						CATTCTTTTAGGTCCTGGCCA	0.448													7	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	82372333	82372333	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82372333delA								None (None upstream) : FAM181B (70720 downstream)																							taattacaagaaaaaaatgtt	0.000													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83307862	83307862	+	Intron	DEL	T	-	-	rs67073467		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83307862delT	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc010rsw.1_Intron|DLG2_uc010rsx.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				TCTTTTTCTGTTTTTTTTCTG	0.303													4	5	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83902955	83902955	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83902955delA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				GCTGAAACTTAAAAAAAAAAA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	89820328	89820328	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89820328delT								UBTFL1 (30 upstream) : NAALAD2 (47490 downstream)																							AGCttccttgttttttttttt	0.378													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	90555191	90555191	+	IGR	DEL	T	-	-	rs79761703		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90555191delT								CHORDC1 (598659 upstream) : MIR1261 (47098 downstream)																							CACTATTTCCTTTTTTTTTTT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	95266132	95266132	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95266132delC								SESN3 (300427 upstream) : FAM76B (235974 downstream)																							cctggaaatgccaatgtgagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	101094948	101094948	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101094948delG								PGR (94404 upstream) : TRPC6 (227348 downstream)																							ttacgcacatggtggtttggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107141962	107141962	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107141962delT								GUCY1A2 (252791 upstream) : CWF19L2 (55112 downstream)																							AATAGCAACATTTTAGAAAAT	0.383													4	2	---	---	---	---	
RDX	5962	broad.mit.edu	37	11	110122062	110122062	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110122062delC	uc001pku.2	-						RDX_uc009yxx.1_Intron|RDX_uc009yxy.2_Intron|RDX_uc009yxz.2_Intron|RDX_uc009yya.2_Intron|RDX_uc010rwe.1_Intron	NM_002906	NP_002897	P35241	RADI_HUMAN	radixin						actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		AAAAACATATCCAACTTAGTT	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	110233198	110233198	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110233198delT	uc001pkv.1	+						uc001pkw.1_Intron					Homo sapiens cDNA FLJ36798 fis, clone ADRGL2007283.																		taaaaccacatttttataggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	110906155	110906155	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110906155delA								ARHGAP20 (322243 upstream) : C11orf53 (220552 downstream)																							TCAGAGATAGAAAACAAGTCT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	111201192	111201193	+	IGR	DEL	CA	-	-	rs10606945		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111201192_111201193delCA								C11orf93 (21839 upstream) : POU2AF1 (21790 downstream)																							ctcAGTACATCACATTCAGGCC	0.277													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112616527	112616527	+	IGR	DEL	C	-	-	rs35986478		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112616527delC								PTS (475850 upstream) : NCAM1 (215468 downstream)																							AAATGCAGATCCCCACATGCA	0.473													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119822871	119822871	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119822871delA								PVRL1 (223436 upstream) : TRIM29 (159124 downstream)																							TTGgacttctagctaaacatg	0.134													4	2	---	---	---	---	
SORL1	6653	broad.mit.edu	37	11	121490263	121490263	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121490263delG	uc001pxx.2	+						SORL1_uc010rzp.1_Intron|SORL1_uc010rzq.1_Intron	NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class						cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		GGGGATTTCTGGAAGGAAGCA	0.264													4	2	---	---	---	---	
LOC399959	399959	broad.mit.edu	37	11	122178308	122178309	+	Intron	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122178308_122178309delTC	uc009zbb.1	-											Homo sapiens cDNA FLJ34394 fis, clone HCHON2000676.												0						CTGCCAGTCAtctctctctctc	0.347													4	2	---	---	---	---	
PKNOX2	63876	broad.mit.edu	37	11	125117764	125117764	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125117764delT	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron	NM_022062	NP_071345	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		tcccaaagtctttttttgctc	0.134													4	2	---	---	---	---	
ACRV1	56	broad.mit.edu	37	11	125550958	125550959	+	5'Flank	INS	-	A	A	rs35513824		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125550958_125550959insA	uc001qcs.2	-						ACRV1_uc001qck.2_5'Flank|ACRV1_uc001qcl.2_5'Flank|ACRV1_uc001qcm.2_5'Flank|ACRV1_uc001qcn.2_5'Flank|ACRV1_uc001qco.2_5'Flank|ACRV1_uc001qcp.2_5'Flank|ACRV1_uc001qcq.2_5'Flank|ACRV1_uc001qcr.2_5'Flank	NM_001612	NP_001603	P26436	ASPX_HUMAN	acrosomal vesicle protein 1 isoform a precursor						multicellular organismal development	acrosomal vesicle					0	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0179)|Lung NSC(97;0.0185)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0713)		GCCCTATCTTTAAAAAAAAAAA	0.327													4	3	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131368019	131368020	+	Intron	INS	-	A	A	rs151152115	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131368019_131368020insA	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						gccttgctgataaacttttgcc	0.050													3	3	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131697198	131697198	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131697198delT	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						CAGTGTGAGATTTTTAAGAAT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134609428	134609429	+	IGR	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134609428_134609429delTG								B3GAT1 (327616 upstream) : None (None downstream)																							gagtatgtgttgtgtgtgtgta	0.223													4	2	---	---	---	---	
NTF3	4908	broad.mit.edu	37	12	5600307	5600308	+	5'Flank	DEL	AG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5600307_5600308delAG	uc001qnl.3	+						NTF3_uc001qnk.3_Intron	NM_002527	NP_002518	P20783	NTF3_HUMAN	neurotrophin 3 isoform 2 preproprotein						signal transduction	extracellular region	growth factor activity|neurotrophin receptor binding			pancreas(1)	1						gtctgaccttagacagctcact	0.198													4	2	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6062399	6062399	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6062399delA	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	ctcaagaaagaaaaaaaaaaG	0.159													3	3	---	---	---	---	
SCNN1A	6337	broad.mit.edu	37	12	6470910	6470910	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6470910delA	uc001qnx.2	-						SCNN1A_uc001qnv.2_Intron|SCNN1A_uc001qnw.2_Intron|SCNN1A_uc010sfb.1_Intron	NM_001038	NP_001029	P37088	SCNNA_HUMAN	sodium channel, nonvoltage-gated 1 alpha isoform						excretion|response to stimulus|sensory perception of taste	apical plasma membrane	WW domain binding				0					Amiloride(DB00594)|Triamterene(DB00384)	actccatctcaaaaaaaagaa	0.214													4	2	---	---	---	---	
C1S	716	broad.mit.edu	37	12	7168292	7168292	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7168292delA	uc001qsj.2	+						C1S_uc001qsk.2_Intron|C1S_uc001qsl.2_Intron|C1S_uc009zfr.2_Intron|C1S_uc009zfs.2_5'Flank	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent						complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	AAGGCAGCATAAAAAAAGGCA	0.458											OREG0021646	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
C1S	716	broad.mit.edu	37	12	7169575	7169575	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7169575delA	uc001qsj.2	+						C1S_uc001qsk.2_Intron|C1S_uc001qsl.2_Intron|C1S_uc009zfr.2_Intron|C1S_uc009zfs.2_Intron	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent						complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	aacctgtctcaaaaaaaaaaa	0.219													4	3	---	---	---	---	
CLEC1B	51266	broad.mit.edu	37	12	10149204	10149204	+	Intron	DEL	T	-	-	rs67059054		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10149204delT	uc001qwu.2	-						CLEC1B_uc009zhd.2_Intron	NM_016509	NP_057593	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B isoform						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	protein binding|sugar binding|transmembrane receptor activity				0						TGACCCACTATGTACCTGAGC	0.408													5	4	---	---	---	---	
MANSC1	54682	broad.mit.edu	37	12	12482819	12482819	+	3'UTR	DEL	C	-	-	rs61922021		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12482819delC	uc001rai.1	-	4					MANSC1_uc010shm.1_3'UTR|MANSC1_uc001raj.1_3'UTR|MANSC1_uc009zht.1_3'UTR	NM_018050	NP_060520	Q9H8J5	MANS1_HUMAN	MANSC domain containing 1 precursor							integral to membrane					0		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		gactctgtctccaaaaaaaaa	0.189													6	4	---	---	---	---	
PIK3C2G	5288	broad.mit.edu	37	12	18734005	18734005	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18734005delA	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				ATGACATAGGAAAAGCACTTA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	20061923	20061923	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20061923delT								AEBP2 (386750 upstream) : PDE3A (460274 downstream)																							TTCAGTGCCCTTCCTCTTTTT	0.393													4	2	---	---	---	---	
SLCO1B3	28234	broad.mit.edu	37	12	21217430	21217430	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21217430delG	uc010sil.1	+						LST-3TM12_uc010sim.1_Intron|LST-3TM12_uc010sin.1_Intron			Q9NPD5	SO1B3_HUMAN	SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					ttttaaaagtgggtactgatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	23362767	23362767	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23362767delA								ETNK1 (519160 upstream) : SOX5 (322465 downstream)																							ggagaagaagaaAAAAAAAAC	0.333													4	2	---	---	---	---	
STK38L	23012	broad.mit.edu	37	12	27417208	27417209	+	Intron	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27417208_27417209delGT	uc001rhr.2	+						STK38L_uc001rhs.2_Intron|STK38L_uc010sjm.1_Intron	NM_015000	NP_055815	Q9Y2H1	ST38L_HUMAN	serine/threonine kinase 38 like						intracellular protein kinase cascade|regulation of cellular component organization	actin cytoskeleton|cytoplasm	actin binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|kidney(1)	5	Colorectal(261;0.0847)					TTGAATGCTGGTAAGTAATGTT	0.391													4	2	---	---	---	---	
LRRK2	120892	broad.mit.edu	37	12	40664342	40664342	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40664342delT	uc001rmg.3	+						LRRK2_uc001rmh.1_Intron	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2						activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				taaaatattgtttttttttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	44070426	44070427	+	IGR	INS	-	A	A	rs148436819		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44070426_44070427insA								ADAMTS20 (124702 upstream) : PUS7L (51987 downstream)																							gaaactacattaaaaaaaaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47846434	47846435	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47846434_47846435insA								FAM113B (215993 upstream) : RPAP3 (209281 downstream)																							CATTGATTCAGAAAAAAAAAAT	0.292													5	3	---	---	---	---	
DHH	50846	broad.mit.edu	37	12	49486674	49486674	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49486674delT	uc001rtf.2	-							NM_021044	NP_066382	O43323	DHH_HUMAN	desert hedgehog preproprotein						cell-cell signaling|proteolysis	extracellular space|plasma membrane	calcium ion binding|peptidase activity|zinc ion binding			lung(1)|breast(1)	2						GGAATGCCCCTTTTCCCATCT	0.507													4	2	---	---	---	---	
SLC4A8	9498	broad.mit.edu	37	12	51877257	51877257	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51877257delT	uc001rys.1	+						SLC4A8_uc001rym.2_Intron|SLC4A8_uc001ryn.2_Intron|SLC4A8_uc001ryo.2_Intron|SLC4A8_uc010snj.1_Intron|SLC4A8_uc001ryr.2_Intron	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate						bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)		ttcttttctcttttttttttt	0.274													4	2	---	---	---	---	
KRT75	9119	broad.mit.edu	37	12	52824979	52824979	+	Intron	DEL	T	-	-	rs11336732		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52824979delT	uc001saj.2	-							NM_004693	NP_004684	O95678	K2C75_HUMAN	keratin 75							keratin filament	structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.192)		ACAGCTTGCCTTTTTTTTTTT	0.488													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	52955674	52955674	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52955674delT								KRT71 (8743 upstream) : KRT74 (3929 downstream)																							TTAAGCAAGATTTTGGGTGTC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54159840	54159840	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54159840delA								CALCOCO1 (38533 upstream) : HOXC13 (172736 downstream)																							GATACTCCCTAATCTTGCCAA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	56069060	56069060	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56069060delA								OR10P1 (37444 upstream) : METTL7B (6270 downstream)																							acccaagactaaacccaaaga	0.000													4	2	---	---	---	---	
METTL7B	196410	broad.mit.edu	37	12	56074953	56074953	+	5'Flank	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56074953delC	uc010spr.1	+							NM_152637	NP_689850	Q6UX53	MET7B_HUMAN	methyltransferase like 7B precursor								methyltransferase activity				0						gtccaacttaccccattcccc	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	57255299	57255300	+	IGR	INS	-	A	A	rs139092727	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57255299_57255300insA								HSD17B6 (73725 upstream) : SDR9C7 (62319 downstream)																							ATGGAAGAAGGAAaaaaaaata	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	58300638	58300638	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58300638delA								CTDSP2 (59891 upstream) : XRCC6BP1 (34807 downstream)																							AAACCTGGAGAGTGTGTGGAG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	58300640	58300640	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58300640delT								CTDSP2 (59893 upstream) : XRCC6BP1 (34805 downstream)																							ACCTGGAGAGTGTGTGGAGTG	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	60647158	60647158	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60647158delT								SLC16A7 (471751 upstream) : None (None downstream)																							gcttatttactttctgtcatt	0.095													4	2	---	---	---	---	
FAM19A2	338811	broad.mit.edu	37	12	62126509	62126510	+	Intron	INS	-	T	T	rs146382537	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62126509_62126510insT	uc001sqw.2	-						FAM19A2_uc001sqv.2_Intron|FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		TGAGCAAGTGATTTTTtgtgtg	0.332													3	3	---	---	---	---	
PPM1H	57460	broad.mit.edu	37	12	63119615	63119615	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63119615delA	uc001srk.3	-							NM_020700	NP_065751	Q9ULR3	PPM1H_HUMAN	protein phosphatase 1H (PP2C domain containing)								phosphoprotein phosphatase activity			lung(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		cagatatgttaaaaaaaaaca	0.164													5	3	---	---	---	---	
DPY19L2	283417	broad.mit.edu	37	12	63995114	63995115	+	Intron	INS	-	TGT	TGT	rs147561427	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63995114_63995115insTGT	uc001srp.1	-						DPY19L2_uc009zqk.1_Intron	NM_173812	NP_776173	Q6NUT2	D19L2_HUMAN	dpy-19-like 2						multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		TGAGGCTTCTGTGTTGTTGTTG	0.347													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	64141215	64141216	+	IGR	DEL	TG	-	-	rs67143557		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64141215_64141216delTG								DPY19L2 (78861 upstream) : TMEM5 (32421 downstream)																							AAATATTTTTTGTTCTCTTAAA	0.233													3	4	---	---	---	---	
LEMD3	23592	broad.mit.edu	37	12	65601199	65601199	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65601199delA	uc001ssl.1	+						LEMD3_uc009zqo.1_Intron	NM_014319	NP_055134	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3						negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway	integral to nuclear inner membrane|membrane fraction	DNA binding|nucleotide binding|protein binding			central_nervous_system(3)|ovary(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		GTAGTACATTACTGAGATTCT	0.448													4	2	---	---	---	---	
MSRB3	253827	broad.mit.edu	37	12	65832602	65832603	+	Intron	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65832602_65832603delCA	uc001ssn.2	+						MSRB3_uc001ssm.2_Intron|MSRB3_uc009zqp.2_Intron	NM_198080	NP_932346	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		TGTTTGTGAGCACACACACACA	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	67973855	67973855	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67973855delG								CAND1 (265467 upstream) : DYRK2 (68657 downstream)																							ATGTTTTTTTGGGGGGGTGGG	0.383													4	2	---	---	---	---	
LGR5	8549	broad.mit.edu	37	12	71973777	71973777	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71973777delT	uc001swl.2	+						LGR5_uc001swm.2_Intron|LGR5_uc001swn.1_Intron	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9						CTTAGCAGCCTTTTTTTTAAC	0.294													4	2	---	---	---	---	
C12orf26	84190	broad.mit.edu	37	12	82857069	82857069	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82857069delT	uc001szq.2	+							NM_032230	NP_115606	Q8N6Q8	CL026_HUMAN	hypothetical protein LOC84190												0						ggagattaactttttttttcc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	83566473	83566473	+	IGR	DEL	A	-	-	rs72007703		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83566473delA								TMTC2 (38410 upstream) : None (None downstream)																							GTCAAAAAGGAAAAAAAAAAA	0.343													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	87773787	87773788	+	IGR	INS	-	TA	TA	rs138048259	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87773787_87773788insTA								MGAT4C (541106 upstream) : C12orf50 (600028 downstream)																							taagcatctcttatgtttactg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	87840959	87840959	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87840959delC								MGAT4C (608278 upstream) : C12orf50 (532857 downstream)																							TCTCTtgtggcaaaaagagtg	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92559087	92559088	+	Intron	INS	-	T	T	rs144615475	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92559087_92559088insT	uc001tca.2	+											Homo sapiens cDNA clone IMAGE:4828106.																		TTTGTTCAATGTTTTTTTTCTG	0.277													4	2	---	---	---	---	
CCDC38	120935	broad.mit.edu	37	12	96334353	96334353	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96334353delT	uc001tek.1	-						AMDHD1_uc001tel.1_5'Flank|AMDHD1_uc009zth.1_5'Flank	NM_182496	NP_872302	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38											skin(1)	1						TGCCCTTCCATTTTTTTTTCC	0.433													5	3	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99760624	99760625	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99760624_99760625insA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		ttcaactacttaaaaaaaagaa	0.000													4	2	---	---	---	---	
UHRF1BP1L	23074	broad.mit.edu	37	12	100492518	100492518	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100492518delA	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2						catctctactaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	101076620	101076627	+	IGR	DEL	CTTCATCC	-	-	rs143357791		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101076620_101076627delCTTCATCC								GAS2L3 (57937 upstream) : ANO4 (34677 downstream)																							ccaTTCCCCACTTCATCCCTTCATCCCC	0.115													3	3	---	---	---	---	
CCDC53	51019	broad.mit.edu	37	12	102440083	102440083	+	Intron	DEL	T	-	-	rs71877323		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102440083delT	uc010svw.1	-						CCDC53_uc010svx.1_Intron|CCDC53_uc010svy.1_Intron|CCDC53_uc010svz.1_Intron	NM_016053	NP_057137	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53							WASH complex	protein binding				0						TCTCAGtttcttttttttttg	0.139													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102734269	102734269	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102734269delT								PMCH (142655 upstream) : IGF1 (55376 downstream)																							TTCAGGGCCATTTTTTTTTCC	0.338													4	2	---	---	---	---	
LOC253724	253724	broad.mit.edu	37	12	104308157	104308157	+	3'UTR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104308157delA	uc009zuh.2	-	2					LOC253724_uc010swf.1_Intron					RecName: Full=Tetratricopeptide repeat protein GNN;          Short=TPR repeat protein GNN; AltName: Full=Grp94-neighboring nucleotidase;												0						tcatactttTAAAAAAAAAgg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106314441	106314441	+	IGR	DEL	C	-	-	rs34285476		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106314441delC								C12orf75 (549146 upstream) : NUAK1 (142684 downstream)																							TCAGTGGGGACCGTTTGCATA	0.463													5	3	---	---	---	---	
UBE3B	89910	broad.mit.edu	37	12	109957694	109957695	+	Intron	INS	-	A	A	rs71297464		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109957694_109957695insA	uc001top.2	+						UBE3B_uc001toq.2_Intron|UBE3B_uc001tos.2_Intron|UBE3B_uc001too.1_Intron|UBE3B_uc009zvj.1_Intron	NM_130466	NP_569733	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			ovary(2)|lung(2)	4						ACCCCTGAATCGGGGCACCATA	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	111387432	111387432	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111387432delT								MYL2 (29028 upstream) : CUX2 (84397 downstream)																							TTACCACTAAttttttttttt	0.174													6	5	---	---	---	---	
ALDH2	217	broad.mit.edu	37	12	112231390	112231390	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112231390delT	uc001tst.2	+						ALDH2_uc010syi.1_Intron|ALDH2_uc009zvy.2_Intron	NM_000690	NP_000681	P05091	ALDH2_HUMAN	mitochondrial aldehyde dehydrogenase 2						carbohydrate metabolic process|ethanol oxidation|neurotransmitter biosynthetic process|xenobiotic metabolic process	mitochondrial matrix	aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase|electron carrier activity			skin(2)|ovary(1)|central_nervous_system(1)	4					Disulfiram(DB00822)|Guanidine(DB00536)|NADH(DB00157)|Nitroglycerin(DB00727)	tatattcgggttttttttttt	0.000			T	HMGA2	leiomyoma								4	2	---	---	---	---	
TMEM116	89894	broad.mit.edu	37	12	112376702	112376703	+	Intron	INS	-	TAT	TAT	rs149021849	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112376702_112376703insTAT	uc001ttc.1	-						TMEM116_uc001ttd.1_Intron|TMEM116_uc001tte.1_Intron|TMEM116_uc001ttf.1_Intron|TMEM116_uc001ttg.1_Intron|TMEM116_uc001tth.1_Intron|TMEM116_uc001tti.1_Intron	NM_138341	NP_612350	Q8NCL8	TM116_HUMAN	transmembrane protein 116							integral to membrane				ovary(1)	1						GATAGAAAACATATATTTGGAA	0.292													2	5	---	---	---	---	
C12orf51	283450	broad.mit.edu	37	12	112709560	112709560	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112709560delT	uc009zwc.2	-						C12orf51_uc010syk.1_Intron|C12orf51_uc001tts.2_Intron|C12orf51_uc001ttt.3_Intron	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						ggaatttccatttttttttgt	0.000													4	2	---	---	---	---	
CCDC42B	387885	broad.mit.edu	37	12	113589599	113589599	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113589599delA	uc010sys.1	+							NM_001144872	NP_001138344	A6NFT4	CC42B_HUMAN	coiled-coil domain containing 42B												0						aacaagtctcaaaaaaaaaaa	0.234													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115742007	115742007	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115742007delT								TBX3 (620038 upstream) : MED13L (654376 downstream)																							TCACCCTACCTTTTTTTTTAA	0.418													4	2	---	---	---	---	
CCDC60	160777	broad.mit.edu	37	12	119921440	119921440	+	Intron	DEL	A	-	-	rs115670270	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119921440delA	uc001txe.2	+						uc001txf.2_Intron	NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60											ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CTTGTAAAAGAAAAAAAAATG	0.433													4	2	---	---	---	---	
HIP1R	9026	broad.mit.edu	37	12	123343572	123343573	+	Intron	INS	-	GC	GC	rs139779747	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123343572_123343573insGC	uc001udj.1	+						HIP1R_uc001udk.1_Intron	NM_003959	NP_003950	O75146	HIP1R_HUMAN	huntingtin interacting protein-1-related						receptor-mediated endocytosis	clathrin coated vesicle membrane|coated pit|perinuclear region of cytoplasm	actin binding|phosphatidylinositol binding			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		GCCTGTCGGTGGGGGGGGCTCC	0.668													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	124712339	124712339	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124712339delC								ZNF664 (212372 upstream) : FAM101A (61371 downstream)																							AATTCCTCTGCCCACACAAGC	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128079842	128079843	+	IGR	INS	-	TAGCT	TAGCT	rs150704328	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128079842_128079843insTAGCT								None (None upstream) : TMEM132C (819448 downstream)																							TGTTCGACAAATAGCCCTTGCG	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128801047	128801047	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128801047delG								None (None upstream) : TMEM132C (98244 downstream)																							AACTGAGTGAGGGCCCACTGT	0.468													4	2	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	130112674	130112674	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130112674delA	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)		ATCATTTGGTAAATGAGAGAA	0.274													4	2	---	---	---	---	
PIWIL1	9271	broad.mit.edu	37	12	130856458	130856458	+	3'UTR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130856458delA	uc001uik.2	+	21						NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1						gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|P granule	mRNA binding|piRNA binding|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		ATGTGTTTGGAGATTTACTTA	0.289													6	3	---	---	---	---	
POLE	5426	broad.mit.edu	37	12	133222387	133222388	+	Intron	DEL	CA	-	-	rs10553413		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133222387_133222388delCA	uc001uks.1	-						POLE_uc001ukr.1_Intron|POLE_uc010tbq.1_Intron|POLE_uc009zyu.1_Intron	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon						base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)		cacacacacccacacacacaca	0.149								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	20370779	20370780	+	IGR	DEL	CT	-	-	rs149055817		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20370779_20370780delCT								PSPC1 (13696 upstream) : ZMYM5 (26844 downstream)																							ggactaatagctCttttttttt	0.005													4	2	---	---	---	---	
ZDHHC20	253832	broad.mit.edu	37	13	22019907	22019908	+	Intron	INS	-	CT	CT	rs141564899	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22019907_22019908insCT	uc001uob.2	-						ZDHHC20_uc001uod.2_Intron|ZDHHC20_uc001uoc.2_Intron|ZDHHC20_uc001uoe.2_Intron|ZDHHC20_uc010tcs.1_Intron	NM_153251	NP_694983	Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		tgaatatacgactggagagaaa	0.045													5	4	---	---	---	---	
MIPEP	4285	broad.mit.edu	37	13	24346447	24346448	+	Intron	INS	-	T	T	rs151167752	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24346447_24346448insT	uc001uox.3	-							NM_005932	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase precursor						protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		GTTTTTAGCAATTTTTTTTTAA	0.337													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	26979240	26979240	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26979240delA								CDK8 (671 upstream) : WASF3 (152600 downstream)																							ATTTTTGAGGAAAAAAAAACC	0.318													3	3	---	---	---	---	
BRCA2	675	broad.mit.edu	37	13	32930373	32930373	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32930373delT	uc001uub.1	+							NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset						cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		cttttatatattttttttttg	0.000			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	37846672	37846672	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37846672delG								CSNK1A1L (166871 upstream) : POSTN (290048 downstream)																							gctgtctcctggaccacattg	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	40618482	40618482	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40618482delA								COG6 (252680 upstream) : LOC646982 (302791 downstream)																							cccacttatcaccaatggctt	0.035													4	2	---	---	---	---	
KIAA0564	23078	broad.mit.edu	37	13	42338477	42338477	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42338477delT	uc001uyj.2	-						KIAA0564_uc001uyk.2_Intron	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)		cctcccttcgtttctccctct	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	43407961	43407961	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43407961delT								C13orf30 (42278 upstream) : EPSTI1 (54161 downstream)																							gtggaatcgattttgggactt	0.000													4	2	---	---	---	---	
CDADC1	81602	broad.mit.edu	37	13	49830268	49830268	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49830268delA	uc001vcu.2	+						CDADC1_uc001vcs.1_Intron|CDADC1_uc001vct.1_Intron|CDADC1_uc010tgk.1_Intron|CDADC1_uc001vcv.2_Intron	NM_030911	NP_112173	Q9BWV3	CDAC1_HUMAN	cytidine and dCMP deaminase domain containing 1								hydrolase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		Lung NSC(96;0.000705)|Breast(56;0.0011)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;1.06e-08)|COAD - Colon adenocarcinoma(199;0.216)		ATCTTGCTTTAAAAAAAAAAA	0.179													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	51865497	51865497	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51865497delT								FAM124A (9881 upstream) : SERPINE3 (49671 downstream)																							AAAAAAGCCCTTTTCCCAGAc	0.234													4	2	---	---	---	---	
SERPINE3	647174	broad.mit.edu	37	13	51912194	51912194	+	5'Flank	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51912194delC	uc001vfh.2	+						SERPINE3_uc010tgp.1_5'Flank	NM_001101320	NP_001094790	A8MV23	SERP3_HUMAN	nexin-related serine protease inhibitor						regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)	2						TAGCATTTTTCCCGAAGGATG	0.199													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	55088288	55088288	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55088288delA								MIR1297 (202105 upstream) : None (None downstream)																							ATAAAAAAGCAAAAAAAAGAA	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	57667995	57667996	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57667995_57667996insT								None (None upstream) : PRR20C (47056 downstream)																							cctggtgctaattagactgcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63630823	63630826	+	IGR	DEL	TAAT	-	-	rs149444684		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63630823_63630826delTAAT								None (None upstream) : OR7E156P (680742 downstream)																							CCATCTGTTATAATTAATTACCAT	0.176													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63662346	63662346	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63662346delT								None (None upstream) : OR7E156P (649222 downstream)																							ctccaatacctttctgtgcct	0.085													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	64796578	64796578	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64796578delT								OR7E156P (479877 upstream) : None (None downstream)																							TTCTTAACTCTTTTTTTTCTA	0.279													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	70252531	70252531	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70252531delT								None (None upstream) : KLHL1 (22195 downstream)																							TTCTCTACTATTTCAGAAGTT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71953995	71953995	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71953995delT								None (None upstream) : DACH1 (58103 downstream)																							CTCCCAACTCTTAGGATCCCC	0.378													4	2	---	---	---	---	
DACH1	1602	broad.mit.edu	37	13	72023463	72023463	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72023463delA	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937	Q9UI36	DACH1_HUMAN	dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		ctcaaaaaagaaaaaaaaaga	0.129													4	2	---	---	---	---	
DACH1	1602	broad.mit.edu	37	13	72324430	72324430	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72324430delT	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937	Q9UI36	DACH1_HUMAN	dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		CAATAATTGCTTTTTTTGAAT	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75296282	75296282	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75296282delT								KLF12 (587888 upstream) : LOC647288 (515608 downstream)																							aaaacaaggcttttttttttt	0.010													3	5	---	---	---	---	
LMO7	4008	broad.mit.edu	37	13	76377952	76377953	+	Intron	DEL	TT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76377952_76377953delTT	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc001vjt.1_Intron|LMO7_uc010thw.1_Intron|LMO7_uc001vjw.1_5'Flank|LMO7_uc001vju.1_Intron	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		TACAAGCTTGTTTTTTTTTTTC	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	77385524	77385525	+	IGR	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77385524_77385525delTC								LMO7 (951520 upstream) : KCTD12 (68779 downstream)																							tctcaatctgtctctctctctc	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	77554890	77554890	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77554890delA								BTF3L1 (51667 upstream) : CLN5 (11169 downstream)																							GCTGGAGGACAAAAAAAAAAT	0.453											OREG0022450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	80322779	80322779	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80322779delT								NDFIP2 (192574 upstream) : SPRY2 (587335 downstream)																							attttatgggttttttttttG	0.224													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85760818	85760818	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85760818delT								None (None upstream) : SLITRK6 (606104 downstream)																							TGATTGATAGTTTTTTAATTG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	86917555	86917555	+	IGR	DEL	T	-	-	rs67555327		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86917555delT								SLITRK6 (544072 upstream) : None (None downstream)																							acttttccagtttttcctatg	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	88703342	88703342	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88703342delA								SLITRK5 (371474 upstream) : None (None downstream)																							ctgtgggaataagaatggtag	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	90588235	90588235	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90588235delA								None (None upstream) : MIR622 (295201 downstream)																							CAGTGGACATAATTTGTGCTT	0.373													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94277710	94277710	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94277710delC	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				TGAGATCCTACCTCCTTGGAT	0.488													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94419232	94419232	+	Intron	DEL	T	-	-	rs80001617		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94419232delT	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				ATGCACTTAATTTTTTTTTTT	0.388													4	3	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94903985	94903985	+	Intron	DEL	C	-	-	rs1473755	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94903985delC	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				AAAACAAAAACAAAACAAACT	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	95338291	95338291	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95338291delA								GPR180 (56347 upstream) : SOX21 (23591 downstream)																							tttaccaaagaaaaaaaaaaa	0.015													4	2	---	---	---	---	
FARP1	10160	broad.mit.edu	37	13	99092704	99092705	+	Intron	INS	-	CCTT	CCTT	rs145107071	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99092704_99092705insCCTT	uc001vnj.2	+						FARP1_uc001vnh.2_Intron	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1						regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CCGGCATTTACCCTTGTCCAGG	0.520													7	4	---	---	---	---	
ZIC5	85416	broad.mit.edu	37	13	100621654	100621657	+	Intron	DEL	GTGA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100621654_100621657delGTGA	uc001vom.1	-							NM_033132	NP_149123	Q96T25	ZIC5_HUMAN	zinc finger protein of the cerebellum 5						cell differentiation	nucleus	DNA binding|zinc ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TGTAAATGATGTGAGTGTGAGGAC	0.554													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105086521	105086521	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105086521delA								None (None upstream) : None (None downstream)																							AATATACTTTAAAAAAAAAAC	0.413													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106655755	106655755	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106655755delT								DAOA (512373 upstream) : EFNB2 (486343 downstream)																							TGTTGAAGGATTTTTTTTTTT	0.373													4	3	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109845451	109845452	+	Intron	DEL	CT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109845451_109845452delCT	uc001vqt.1	+						MYO16_uc010agk.1_Intron	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TTCATACATActctctctctct	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	110020584	110020584	+	IGR	DEL	T	-	-	rs113571535		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110020584delT								MYO16 (160229 upstream) : IRS2 (385602 downstream)																							AATGGGCCTCTTTTTTTTTTT	0.398													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	21003069	21003069	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21003069delT								RNASE10 (23755 upstream) : RNASE9 (21184 downstream)																							gtttttagcctttttttgaaa	0.000													4	2	---	---	---	---	
MRPL52	122704	broad.mit.edu	37	14	23298107	23298107	+	5'Flank	DEL	G	-	-	rs1028648	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23298107delG	uc001wgw.3	+						MRPL52_uc001wgx.3_5'Flank|MRPL52_uc001wgy.3_5'Flank|MRPL52_uc001wgz.3_5'Flank|MRPL52_uc001wha.3_5'Flank|MRPL52_uc001whb.3_5'Flank	NM_178336	NP_848026	Q86TS9	RM52_HUMAN	mitochondrial ribosomal protein L52 isoform a						translation	mitochondrial large ribosomal subunit	structural constituent of ribosome				0	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)		TTGATTGTCTGtttttttttt	0.174													4	2	---	---	---	---	
IRF9	10379	broad.mit.edu	37	14	24632007	24632007	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24632007delA	uc001wmq.2	+						RNF31_uc001wmp.2_Intron|IRF9_uc010alj.2_5'Flank	NM_006084	NP_006075	Q00978	IRF9_HUMAN	interferon-stimulated transcription factor 3,						interferon-gamma-mediated signaling pathway|response to virus|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|nucleoplasm	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00853)		actctgtctcaaaaaaaaaaa	0.000													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26147574	26147574	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26147574delA								STXBP6 (628403 upstream) : NOVA1 (767516 downstream)																							ATACTTGGGTAATTTGTATCC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26839108	26839108	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26839108delT								None (None upstream) : NOVA1 (75982 downstream)																							CTCATATAGCTTTTTTTTCTT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	27431048	27431049	+	IGR	INS	-	T	T	rs79134153	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27431048_27431049insT								NOVA1 (364088 upstream) : None (None downstream)																							AACAATACTAATTTTTTTTTAC	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	30802974	30802974	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30802974delA								PRKD1 (406075 upstream) : G2E3 (225355 downstream)																							TGTATGGGTCAAAAAAGCTCA	0.418													4	2	---	---	---	---	
STRN3	29966	broad.mit.edu	37	14	31455517	31455518	+	Intron	INS	-	T	T	rs147681005	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31455517_31455518insT	uc001wqu.2	-						STRN3_uc001wqv.2_Intron|STRN3_uc010tpj.1_Intron	NM_001083893	NP_001077362	Q13033	STRN3_HUMAN	nuclear autoantigen isoform 1						negative regulation of estrogen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus	cytoplasm|dendrite|Golgi apparatus|neuronal cell body|nucleoplasm|nucleus|plasma membrane|protein complex	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		AGAGAAATACGTATTTTTATTT	0.351													4	2	---	---	---	---	
NUBPL	80224	broad.mit.edu	37	14	32268669	32268669	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32268669delT	uc001wrk.3	+						NUBPL_uc010amj.2_Intron|NUBPL_uc010tpl.1_Intron	NM_025152	NP_079428	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like						mitochondrial respiratory chain complex I assembly|mitochondrion morphogenesis	mitochondrion	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding				0	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		CTCCATCTTGTTACATAAAAT	0.129													4	2	---	---	---	---	
NUBPL	80224	broad.mit.edu	37	14	32318868	32318868	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32318868delT	uc001wrk.3	+						NUBPL_uc010amj.2_Intron|NUBPL_uc010tpl.1_Intron	NM_025152	NP_079428	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like						mitochondrial respiratory chain complex I assembly|mitochondrion morphogenesis	mitochondrion	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding				0	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		TGACCAGTTCTTTGAGCTCAC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	34648175	34648175	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34648175delT								EGLN3 (227888 upstream) : C14orf147 (253970 downstream)																							TTGTTCATAGTTTTTTTTTTC	0.348													8	5	---	---	---	---	
C14orf147	171546	broad.mit.edu	37	14	34908685	34908685	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34908685delA	uc001wsc.2	-							NM_138288	NP_612145	Q969W0	SSPTA_HUMAN	hypothetical protein LOC171546						sphingolipid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	protein binding				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.000389)|Lung(238;0.000887)|Epithelial(34;0.143)	GBM - Glioblastoma multiforme(112;0.0195)		ctctaccaagaaaaaaaataa	0.169													4	2	---	---	---	---	
SNX6	58533	broad.mit.edu	37	14	35073916	35073917	+	Intron	INS	-	T	T	rs147978719	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35073916_35073917insT	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419	Q9UNH7	SNX6_HUMAN	sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		TATGggttgagtatccctaccc	0.144													0	9	---	---	---	---	
KIAA0391	9692	broad.mit.edu	37	14	35694094	35694094	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35694094delT	uc001wsy.1	+						KIAA0391_uc010tps.1_Intron|KIAA0391_uc001wsz.1_Intron|KIAA0391_uc001wta.2_Intron|KIAA0391_uc001wtb.1_Intron|KIAA0391_uc001wtc.1_Intron	NM_014672	NP_055487	O15091	MRRP3_HUMAN	mitochondrial RNase P protein 3 precursor						tRNA processing	mitochondrion					0	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		AATGAACTCCTTTTTTTTTTG	0.368													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35835096	35835096	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35835096delT								KIAA0391 (48423 upstream) : NFKBIA (35621 downstream)																							GTTTGGTTTCTTTTTTTTTTT	0.423													14	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	36858596	36858596	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36858596delA								MBIP (68714 upstream) : SFTA3 (83900 downstream)																							GCTGTACTATAAAAAAACAGT	0.284													6	3	---	---	---	---	
SLC25A21	89874	broad.mit.edu	37	14	37187715	37187716	+	Intron	DEL	TC	-	-	rs71873540		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37187715_37187716delTC	uc001wtz.1	-							NM_030631	NP_085134	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial						lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		TAACTCAACTTCTCTCTCTCTC	0.366													5	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	41000968	41000968	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41000968delA								None (None upstream) : None (None downstream)																							TATATTAGTTAAAAAAAAAAG	0.294													3	3	---	---	---	---	
FSCB	84075	broad.mit.edu	37	14	44977462	44977462	+	5'Flank	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44977462delA	uc001wvn.2	-							NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein							cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		CATATCACTCAAGAATTTTAC	0.284													4	2	---	---	---	---	
FANCM	57697	broad.mit.edu	37	14	45628666	45628666	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45628666delT	uc001wwd.3	+						FANCM_uc001wwc.2_Intron|FANCM_uc010anf.2_Intron|FANCM_uc001wwe.3_Intron	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M						DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7						GTTTTGGAACTTTTTTTTTTT	0.139								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	46211124	46211125	+	IGR	INS	-	AAA	AAA	rs149863630	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46211124_46211125insAAA								C14orf106 (488519 upstream) : RPL10L (909097 downstream)																							TCTTTTCTATCAAAAAAAAaac	0.089													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	46359037	46359037	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46359037delA								C14orf106 (636432 upstream) : RPL10L (761185 downstream)																							gagttataggaaaaaaatcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49378378	49378379	+	IGR	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49378378_49378379delTC								None (None upstream) : SDCCAG1 (654648 downstream)																							CTTCTTTTCTTCTCTCTCTCTC	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	50004794	50004795	+	IGR	INS	-	A	A	rs146176545	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50004794_50004795insA								None (None upstream) : SDCCAG1 (28232 downstream)																							TGTCCACACTTACTCAGAAATG	0.248													6	3	---	---	---	---	
FRMD6	122786	broad.mit.edu	37	14	52116088	52116089	+	5'Flank	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52116088_52116089insT	uc001wzd.2	+						FRMD6_uc001wzb.2_Intron|FRMD6_uc001wzc.2_5'Flank	NM_152330	NP_689543	Q96NE9	FRMD6_HUMAN	FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)					CTTAAACACACTTTTTTTTTTA	0.277													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	53466518	53466518	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53466518delA								FERMT2 (48703 upstream) : DDHD1 (36941 downstream)																							TTGGAAACTGAAAAAAAAAAA	0.264													4	2	---	---	---	---	
CDKN3	1033	broad.mit.edu	37	14	54866955	54866956	+	Intron	INS	-	ATAATATAGA	ATAATATAGA	rs143586415	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54866955_54866956insATAATATAGA	uc001xap.2	+						CDKN3_uc001xar.2_Intron|CDKN3_uc001xaq.2_Intron|CDKN3_uc010aoi.1_Intron|CDKN3_uc001xas.1_Intron|CDKN3_uc010aoj.1_Intron	NM_005192	NP_005183	Q16667	CDKN3_HUMAN	cyclin-dependent kinase inhibitor 3 isoform 1						cell cycle arrest|G1/S transition of mitotic cell cycle|negative regulation of cell proliferation|regulation of cyclin-dependent protein kinase activity	perinuclear region of cytoplasm	protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0						ATTTACTCTTTATAAGACCCTT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57546896	57546896	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57546896delT								OTX2 (269712 upstream) : EXOC5 (122300 downstream)																							CAATATTGCATTTTTTTTTCA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	61622532	61622532	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61622532delA								SLC38A6 (72082 upstream) : PRKCH (31755 downstream)																							ACTCCGTGGTAAAAAAAAATC	0.269													8	4	---	---	---	---	
SNAPC1	6617	broad.mit.edu	37	14	62252201	62252201	+	Intron	DEL	C	-	-	rs137954144	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62252201delC	uc001xft.2	+							NM_003082	NP_003073	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		tctaCtgagaccccagaatat	0.005													4	2	---	---	---	---	
SYT16	83851	broad.mit.edu	37	14	62496499	62496499	+	Intron	DEL	A	-	-	rs35272199		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62496499delA	uc001xfu.1	+						SYT16_uc010tsd.1_Intron	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like											central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GTCTAGTTGGAAAAAAAAAAA	0.343													4	2	---	---	---	---	
KCNH5	27133	broad.mit.edu	37	14	63407970	63407970	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63407970delG	uc001xfx.2	-						KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_Intron	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GCTGTTTTCTGGGGAAAGTCA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	64838978	64838979	+	IGR	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64838978_64838979delAC								ESR2 (33710 upstream) : MTHFD1 (15780 downstream)																							acatacacatacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	66221625	66221628	+	IGR	DEL	TTGA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66221625_66221628delTTGA								FUT8 (11664 upstream) : C14orf53 (731481 downstream)																							tcactgcagtttgattgaatgaat	0.225													2	5	---	---	---	---	
GALNTL1	57452	broad.mit.edu	37	14	69800666	69800667	+	Intron	INS	-	GCTGGGA	GCTGGGA	rs144003189	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69800666_69800667insGCTGGGA	uc010aqu.1	+						GALNTL1_uc001xla.1_Intron|GALNTL1_uc001xlb.1_Intron	NM_020692	NP_065743	Q8N428	GLTL1_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)	2				all cancers(60;0.00793)|BRCA - Breast invasive adenocarcinoma(234;0.0174)|OV - Ovarian serous cystadenocarcinoma(108;0.0656)		CTACCAGCAAGGCTGGGAGGTG	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	70320232	70320232	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70320232delC								SLC10A1 (56226 upstream) : SMOC1 (25911 downstream)																							GAAGTTATGTCCCACTGTGGG	0.468													4	2	---	---	---	---	
MAP3K9	4293	broad.mit.edu	37	14	71271410	71271411	+	Intron	DEL	AA	-	-	rs5809497		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71271410_71271411delAA	uc001xmm.2	-						MAP3K9_uc001xml.2_Intron	NM_033141	NP_149132	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		TTGAAAAAATAAATGCAGGGAG	0.401													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	72394157	72394157	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72394157delA								SIPA1L1 (188039 upstream) : RGS6 (4999 downstream)																							TTGCAAAGAGAAAAAAAAATC	0.368													4	2	---	---	---	---	
TMED8	283578	broad.mit.edu	37	14	77816652	77816652	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77816652delC	uc001xto.1	-						TMED8_uc010ast.1_Intron	NM_213601	NP_998766	Q6PL24	TMED8_HUMAN	transmembrane emp24 protein transport domain						transport	integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		ctgtccacttcccccactaga	0.144													4	2	---	---	---	---	
SEL1L	6400	broad.mit.edu	37	14	81976563	81976563	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81976563delT	uc010tvv.1	-						SEL1L_uc001xvo.3_Intron	NM_005065	NP_005056	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like precursor						Notch signaling pathway	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0299)		gaagagtagatttagcagtct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82227091	82227091	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82227091delT								SEL1L (226886 upstream) : None (None downstream)																							tcattaggcattcaccttgcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	83483778	83483779	+	IGR	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83483778_83483779delCA								None (None upstream) : None (None downstream)																							cacacacgtgcacacacacaca	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	83766357	83766358	+	IGR	INS	-	GT	GT	rs147357491	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83766357_83766358insGT								None (None upstream) : None (None downstream)																							CATACTCCCAAGTGTGTGTGTG	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	85314362	85314362	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85314362delG								None (None upstream) : FLRT2 (682126 downstream)																							gattctcagtggcatacagtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	85769763	85769763	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85769763delA								None (None upstream) : FLRT2 (226725 downstream)																							agacaaaatgaaaaacaatca	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	87860106	87860106	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87860106delT								None (None upstream) : GALC (444058 downstream)																							CTTAGGACAATTTTTTTTTCT	0.259													4	2	---	---	---	---	
SMEK1	55671	broad.mit.edu	37	14	91941910	91941914	+	Intron	DEL	AAAAC	-	-	rs71989693		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91941910_91941914delAAAAC	uc001xzn.2	-						SMEK1_uc001xzm.2_Intron|SMEK1_uc001xzo.2_Intron|SMEK1_uc010atz.2_Intron|SMEK1_uc001xzp.1_Intron|SMEK1_uc001xzq.1_3'UTR	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1							microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		CTTCAGAATTaaaacaaaacaaaac	0.259													6	6	---	---	---	---	
SMEK1	55671	broad.mit.edu	37	14	91944295	91944296	+	Intron	INS	-	ATTTT	ATTTT	rs145163618	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91944295_91944296insATTTT	uc001xzn.2	-						SMEK1_uc001xzm.2_Intron|SMEK1_uc001xzo.2_Intron|SMEK1_uc010atz.2_Intron|SMEK1_uc001xzp.1_Intron|SMEK1_uc001xzq.1_Intron	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1							microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		gctcgaccAAGATTTTAATTAC	0.188													4	3	---	---	---	---	
TC2N	123036	broad.mit.edu	37	14	92258466	92258466	+	Intron	DEL	G	-	-	rs6575218		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92258466delG	uc001xzu.3	-						TC2N_uc001xzt.3_Intron|TC2N_uc010auc.2_Intron|TC2N_uc001xzv.3_Intron	NM_001128595	NP_001122067	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear							nucleus				upper_aerodigestive_tract(1)	1				COAD - Colon adenocarcinoma(157;0.218)		ccatctcaaagaaaaaaagaa	0.134													6	3	---	---	---	---	
DICER1	23405	broad.mit.edu	37	14	95573120	95573120	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95573120delA	uc001ydw.2	-						DICER1_uc010avh.1_5'Flank|DICER1_uc001ydv.2_Intron|DICER1_uc001ydx.2_Intron|DICER1_uc001ydy.1_5'Flank	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1						negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		TAAAATAAGGAAAAAAATCAT	0.229			Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				4	2	---	---	---	---	
CLMN	79789	broad.mit.edu	37	14	95662150	95662150	+	Intron	DEL	A	-	-	rs35172170		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95662150delA	uc001yef.2	-							NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)		TGACGATGAGAGAGGGGAGAG	0.473													0	6	---	---	---	---	
CLMN	79789	broad.mit.edu	37	14	95662152	95662152	+	Intron	DEL	A	-	-	rs34187978		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95662152delA	uc001yef.2	-							NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)		ACGATGAGAGAGGGGAGAGAC	0.478													0	6	---	---	---	---	
EML1	2009	broad.mit.edu	37	14	100345171	100345174	+	Intron	DEL	CTGT	-	-	rs55988713		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100345171_100345174delCTGT	uc001ygs.2	+						EML1_uc010avt.1_Intron|EML1_uc010tww.1_Intron|EML1_uc001ygq.2_Intron|EML1_uc001ygr.2_Intron	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				GGTGGAAAAACTGTCACTCAGATT	0.441													5	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101678701	101678702	+	IGR	INS	-	CA	CA	rs147442886	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101678701_101678702insCA								MIR656 (145563 upstream) : DIO3OS (339858 downstream)																							CAacacacacgcacacacacac	0.139													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106230050	106230050	+	Intron	DEL	G	-	-	rs144270909		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106230050delG	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron					Parts of antibodies, mostly variable regions.												0						tgctgagacaggatgaatgta	0.020													3	4	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106955142	106955142	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106955142delT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						atgttgagcatttttttcatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20109593	20109594	+	IGR	DEL	AT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20109593_20109594delAT								None (None upstream) : GOLGA6L6 (627500 downstream)																							gacatataacatattaaatatg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20444449	20444450	+	IGR	INS	-	CCTGGGCAATAGGGCAAGAC	CCTGGGCAATAGGGCAAGAC	rs142410977		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20444449_20444450insCCTGGGCAATAGGGCAAGAC								None (None upstream) : GOLGA6L6 (292644 downstream)																							ctgcaaaccagcctgTCTTTAA	0.183													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20555036	20555036	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20555036delC								None (None upstream) : GOLGA6L6 (182058 downstream)																							CCTACCTGTACCCCCAGGGTA	0.612													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20848462	20848462	+	IGR	DEL	T	-	-	rs56862210		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20848462delT								GOLGA8C (67436 upstream) : BCL8 (21594 downstream)																							CCCATACCCCTAAAACAAACT	0.468													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22686246	22686246	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22686246delT								MIR1268 (172966 upstream) : GOLGA8DP (16039 downstream)																							TTGTTTTGGGTttttttaata	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24039435	24039435	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24039435delT								NDN (106985 upstream) : PWRN2 (370491 downstream)																							ATTTTTCACATTTTTTTTTTC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	25029842	25029846	+	IGR	DEL	AAGTT	-	-	rs146180342		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25029842_25029846delAAGTT								C15orf2 (101250 upstream) : SNRPN (38948 downstream)																							cagctggcagaagttaagtccttga	0.000													11	5	---	---	---	---	
SNRPN	6638	broad.mit.edu	37	15	25078862	25078862	+	Intron	DEL	A	-	-	rs76080163		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25078862delA	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		aggaggcaggaagcagacatt	0.000									Prader-Willi_syndrome				3	5	---	---	---	---	
UBE3A	7337	broad.mit.edu	37	15	25598663	25598663	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25598663delA	uc001zaq.2	-						uc001zae.2_Intron|UBE3A_uc001zar.2_Intron|UBE3A_uc001zas.2_Intron|UBE3A_uc001zat.2_Intron	NM_000462	NP_000453	Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A isoform 2						brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		cttagttgagaaaaaaaatct	0.035													4	2	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	33780651	33780651	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33780651delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CAGTCTTGCCTTTTTTTTTTT	0.333													5	3	---	---	---	---	
RASGRP1	10125	broad.mit.edu	37	15	38797815	38797816	+	Intron	INS	-	A	A	rs138560908	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38797815_38797816insA	uc001zke.3	-						RASGRP1_uc010bbe.2_Intron|RASGRP1_uc010bbf.2_Intron|RASGRP1_uc010bbg.2_Intron|RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		TCACTGGTCACACATTAGGCTT	0.376													18	20	---	---	---	---	
RASGRP1	10125	broad.mit.edu	37	15	38798329	38798330	+	Intron	INS	-	ATCTC	ATCTC	rs142542643	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38798329_38798330insATCTC	uc001zke.3	-						RASGRP1_uc010bbe.2_Intron|RASGRP1_uc010bbf.2_Intron|RASGRP1_uc010bbg.2_Intron|RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		ATTTTGGACATAGGATGCCCTC	0.337													7	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	38994247	38994247	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38994247delC								C15orf53 (2008 upstream) : C15orf54 (548638 downstream)																							gagtgtatttccccaGcaggg	0.005													4	2	---	---	---	---	
EIF2AK4	440275	broad.mit.edu	37	15	40242952	40242953	+	Intron	DEL	AT	-	-	rs147851683		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40242952_40242953delAT	uc001zkm.1	+						EIF2AK4_uc001zkl.2_Intron	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha						translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		gttcacacacatgtgagatacg	0.124													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	40639241	40639241	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40639241delC								C15orf52 (6073 upstream) : PHGR1 (3993 downstream)																							AGGGGAGTGGCGGTGGCTTTT	0.567													5	3	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40899519	40899519	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40899519delT	uc010bbs.1	+						CASC5_uc010ucq.1_Intron|CASC5_uc001zme.2_Intron|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)		atcAGTATTCTTTTTTTTCAG	0.189													4	2	---	---	---	---	
DNAJC17	55192	broad.mit.edu	37	15	41095952	41095953	+	Intron	INS	-	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41095952_41095953insC	uc001zms.1	-						DNAJC17_uc010bbz.1_Intron|DNAJC17_uc010bca.1_Intron|DNAJC17_uc010bcb.1_Intron	NM_018163	NP_060633	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17						protein folding		heat shock protein binding|nucleotide binding|RNA binding|unfolded protein binding				0		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		CGTGAATCTTGCCCCCCCATTA	0.480													4	2	---	---	---	---	
INO80	54617	broad.mit.edu	37	15	41332567	41332567	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41332567delA	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						gcactggttcaaggatagtca	0.000													4	2	---	---	---	---	
JMJD7-PLA2G4B	8681	broad.mit.edu	37	15	42132468	42132482	+	Intron	DEL	GAGGAGGAGGGTGCT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42132468_42132482delGAGGAGGAGGGTGCT	uc010bco.2	+						JMJD7-PLA2G4B_uc001zoo.3_Intron|JMJD7-PLA2G4B_uc010bcn.2_Intron|JMJD7-PLA2G4B_uc001zoq.3_Intron|JMJD7-PLA2G4B_uc001zor.1_5'Flank	NM_001114633	NP_001108105	P0C869	PA24B_HUMAN	phospholipase A2, group IVB						arachidonic acid metabolic process|calcium-mediated signaling|glycerophospholipid catabolic process|inflammatory response|parturition	cytosol|early endosome membrane|extracellular region|mitochondrial membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|calcium-dependent phospholipid binding|lysophospholipase activity			large_intestine(1)	1						TGGGCTGAGGGAGGAGGAGGGTGCTGAGGAGGAGG	0.670													8	5	---	---	---	---	
SORD	6652	broad.mit.edu	37	15	45323011	45323022	+	Intron	DEL	CCTGGTGAGGAC	-	-	rs71967134		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45323011_45323022delCCTGGTGAGGAC	uc001zul.3	+						SORD_uc010uel.1_Intron|SORD_uc001zum.3_Intron|SORD_uc010bdz.2_Intron	NM_003104	NP_003095	Q00796	DHSO_HUMAN	sorbitol dehydrogenase						fructose biosynthetic process|glucose metabolic process|L-xylitol catabolic process|sorbitol catabolic process|sperm motility	cilium|extracellular space|flagellum|membrane fraction|mitochondrial membrane|soluble fraction	L-iditol 2-dehydrogenase activity|NAD binding|sugar binding|zinc ion binding				0		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)	NADH(DB00157)	acctctccagcctggtgaggacaggggaggct	0.245													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	47402758	47402759	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47402758_47402759insT								None (None upstream) : SEMA6D (73644 downstream)																							aatacttgtgattttttcacat	0.000													4	3	---	---	---	---	
ATP8B4	79895	broad.mit.edu	37	15	50355561	50355561	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50355561delA	uc001zxu.2	-						ATP8B4_uc010ber.2_Intron|ATP8B4_uc010ufd.1_Intron|ATP8B4_uc010ufe.1_Intron	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		ggggagctttaaaaaaaaaaa	0.080													4	2	---	---	---	---	
SLC27A2	11001	broad.mit.edu	37	15	50487039	50487040	+	Intron	INS	-	A	A	rs150751800	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50487039_50487040insA	uc001zxw.2	+						SLC27A2_uc010bes.2_Intron|SLC27A2_uc001zxx.2_Intron	NM_003645	NP_003636	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid						bile acid biosynthetic process|fatty acid alpha-oxidation	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity|phytanate-CoA ligase activity|pristanate-CoA ligase activity			ovary(1)|skin(1)	2		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)		TGGGGCAAaagaaaaaaaaaga	0.173													4	2	---	---	---	---	
MYO5A	4644	broad.mit.edu	37	15	52806703	52806703	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52806703delA	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010uge.1_Intron	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GTAATCCAGGAAGGGGAATGC	0.289													4	2	---	---	---	---	
RAB27A	5873	broad.mit.edu	37	15	55516498	55516499	+	Intron	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55516498_55516499delCA	uc002aco.2	-						RAB27A_uc002acr.2_Intron|RAB27A_uc002acp.2_Intron|RAB27A_uc002acq.2_Intron	NM_183234	NP_899057	P51159	RB27A_HUMAN	Ras-related protein Rab-27A						small GTPase mediated signal transduction	dendrite|exocytic vesicle|late endosome|lysosome|melanosome	GTP binding|GTPase activity			ovary(1)	1				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		cacacatatgcacacacacaca	0.317													4	2	---	---	---	---	
ALDH1A2	8854	broad.mit.edu	37	15	58471708	58471709	+	Intron	INS	-	TGTG	TGTG	rs147605496	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58471708_58471709insTGTG	uc010ugw.1	-						AQP9_uc010ugx.1_Intron|AQP9_uc002aez.2_Intron	NM_170697	NP_733798	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 3						negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	TTGTGGTATGAtgtgtgtgtgt	0.307													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	61847403	61847403	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61847403delA								RORA (325901 upstream) : VPS13C (297189 downstream)																							AAGAGACTCCAAGGGGGGTCG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62853938	62853939	+	IGR	INS	-	T	T	rs151210571	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62853938_62853939insT								C2CD4B (396456 upstream) : MGC15885 (75432 downstream)																							TGGTCTTCAGACCCCACCCTGG	0.550													3	6	---	---	---	---	
ANP32A	8125	broad.mit.edu	37	15	69097186	69097186	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69097186delG	uc002arl.2	-						hsa-mir-4312|MI0015842_5'Flank|C15orf28_uc010uka.1_RNA	NM_006305	NP_006296	P39687	AN32A_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32						intracellular signal transduction|mRNA metabolic process|nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleoplasm|perinuclear region of cytoplasm	protein binding				0						GAAAAACAGTGGGCATGAAAT	0.259													4	2	---	---	---	---	
PML	5371	broad.mit.edu	37	15	74297934	74297935	+	Intron	INS	-	T	T	rs113972054		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74297934_74297935insT	uc002awv.2	+						PML_uc002awm.2_Intron|PML_uc002awl.2_Intron|PML_uc002awj.1_Intron|PML_uc002awk.2_Intron|PML_uc002awn.2_Intron|PML_uc002awo.2_Intron|PML_uc002awp.2_Intron|PML_uc002awq.2_Intron|PML_uc002awr.2_Intron|PML_uc002aws.2_Intron|PML_uc002awt.2_Intron|PML_uc002awu.2_Intron|PML_uc010ule.1_Intron|PML_uc002aww.1_Intron	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1						cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5						CCCCAGCAATCTTTTTTTTTTT	0.421			T	RARA|PAX5	APL|ALL								10	8	---	---	---	---	
SCAPER	49855	broad.mit.edu	37	15	77022629	77022629	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77022629delT	uc002bby.2	-						SCAPER_uc010bkr.2_5'Flank|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron|SCAPER_uc002bca.1_Intron|SCAPER_uc002bcb.1_Intron	NM_020843	NP_065894	Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3						TATTTCTTTCTTTTTTTTTTG	0.423													3	3	---	---	---	---	
IREB2	3658	broad.mit.edu	37	15	78785945	78785945	+	Intron	DEL	T	-	-	rs5813921		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78785945delT	uc002bdr.2	+						IREB2_uc010unb.1_Intron	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2								4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		attattgtgattttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	86402567	86402567	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86402567delC								KLHL25 (64378 upstream) : AGBL1 (282675 downstream)																							TACCCTTGCACCCCCAAACAG	0.388											OREG0023429	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	86683482	86683482	+	5'Flank	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86683482delT	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						ttactgtgggttttttttttt	0.229													3	3	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	87175989	87175990	+	Intron	INS	-	A	A	rs140457963	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87175989_87175990insA	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						CCACTGCTCTTAAGATGCATGT	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87740233	87740234	+	IGR	INS	-	ATG	ATG	rs77056534		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87740233_87740234insATG								AGBL1 (167950 upstream) : NCRNA00052 (379926 downstream)																							TCATCAGTCTTATATTAGCCCC	0.490													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	92205323	92205323	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92205323delT								SV2B (366675 upstream) : SLCO3A1 (191615 downstream)																							ATCCTGCTGGTTTTTTTTTTT	0.323													2	4	---	---	---	---	
MCTP2	55784	broad.mit.edu	37	15	94984230	94984230	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94984230delT	uc002btj.2	+						MCTP2_uc010boj.2_Intron|MCTP2_uc010bok.2_Intron|MCTP2_uc002btl.2_Intron	NM_018349	NP_060819	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2 isoform 1						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			ATTTGTAGGCTTTTTTTTTAT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96123093	96123094	+	IGR	DEL	GA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96123093_96123094delGA								LOC145820 (72019 upstream) : NR2F2 (746063 downstream)																							GTTTGTGTGTGAGAGAGAGAGA	0.376													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98741810	98741810	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98741810delT								ARRDC4 (224743 upstream) : FAM169B (238581 downstream)																							CCATGGCTGATTAGCCTCCCA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98915164	98915164	+	IGR	DEL	A	-	-	rs138768253		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98915164delA								ARRDC4 (398097 upstream) : FAM169B (65227 downstream)																							tacccagtgtaaacatcctgt	0.000													2	4	---	---	---	---	
UNKL	64718	broad.mit.edu	37	16	1451537	1451537	+	Intron	DEL	A	-	-	rs111930031	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1451537delA	uc010bro.1	-						UNKL_uc002clq.2_Intron	NM_001037125	NP_001032202	Q9H9P5	UNKL_HUMAN	unkempt homolog (Drosophila)-like isoform 2							cytoplasm|nucleus	ligase activity|nucleic acid binding|zinc ion binding				0		Hepatocellular(780;0.0893)				CGCCCCCCCCACCACCGCCCT	0.567													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8438639	8438639	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8438639delA								A2BP1 (675299 upstream) : TMEM114 (180864 downstream)																							ctggagatttaaaaaaaaaaa	0.000													12	8	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12487249	12487250	+	Intron	INS	-	CATGCATG	CATGCATG	rs8049579		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12487249_12487250insCATGCATG	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						attcattcattcatgcatgcat	0.317													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	16739366	16739367	+	IGR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16739366_16739367insT								LOC339047 (294929 upstream) : XYLT1 (456816 downstream)																							ttctttcctgcttttttttccc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17719495	17719495	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17719495delG								XYLT1 (154757 upstream) : NOMO2 (791688 downstream)																							acttgaacctggggggcagag	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	18479961	18479961	+	5'Flank	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18479961delC	uc010vak.1	-											DQ596229																		GTGGCTGAGACCCAGCTGACT	0.637													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	19339542	19339542	+	IGR	DEL	G	-	-	rs56281786		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19339542delG								LOC728276 (23826 upstream) : TMC5 (82319 downstream)																							aaaacaaaatgtacactaata	0.000													1	6	---	---	---	---	
ACSM2A	123876	broad.mit.edu	37	16	20489924	20489925	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20489924_20489925insC	uc010bwe.2	+	11	1445_1446	c.1206_1207insC	c.(1204-1209)CTGCCCfs	p.L402fs	ACSM2A_uc010vax.1_Frame_Shift_Ins_p.L323fs|ACSM2A_uc002dhf.3_Frame_Shift_Ins_p.L402fs|ACSM2A_uc002dhg.3_Frame_Shift_Ins_p.L402fs|ACSM2A_uc010vay.1_Frame_Shift_Ins_p.L323fs|ACSM2A_uc002dhh.3_Frame_Shift_Ins_p.L32fs	NM_001010845	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member	402_403					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			skin(2)|breast(1)	3						GCAACGTCCTGCCCCCCGGCAC	0.505													209	129	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21536332	21536333	+	Intron	INS	-	CA	CA	rs113987115		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21536332_21536333insCA	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																		catgtgtgaactatctgttcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22393708	22393708	+	5'Flank	DEL	T	-	-	rs11298487		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22393708delT	uc002dko.1	+											DQ596887																		AATTTTAACCTTTTTTTTTTT	0.383													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22654097	22654097	+	IGR	DEL	G	-	-	rs5816181		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22654097delG								LOC653786 (65911 upstream) : HS3ST2 (171763 downstream)																							CATAGATTTTGTGGGAGCTTC	0.453													5	3	---	---	---	---	
PRKCB	5579	broad.mit.edu	37	16	23956854	23956854	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23956854delA	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	GCTGAATGAGAAAATGAGGAG	0.537													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	24620906	24620907	+	IGR	DEL	AG	-	-	rs71804038		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24620906_24620907delAG								RBBP6 (36725 upstream) : TNRC6A (120142 downstream)																							agagagagacagagagagagag	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25493148	25493148	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25493148delC								ZKSCAN2 (224293 upstream) : HS3ST4 (210199 downstream)																							CCCACATTGTCCCAGCAACTT	0.478													4	2	---	---	---	---	
HS3ST4	9951	broad.mit.edu	37	16	26073693	26073693	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26073693delG	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)		CACTGTGATTGGGGCACATTA	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26587353	26587354	+	IGR	DEL	TC	-	-	rs112166324		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26587353_26587354delTC								HS3ST4 (438345 upstream) : C16orf82 (490865 downstream)																							tctctctctttctctctctctc	0.257													3	4	---	---	---	---	
EIF3CL	728689	broad.mit.edu	37	16	28429364	28429364	+	Intron	DEL	C	-	-	rs138118162		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28429364delC	uc010byc.2	-							NM_001099661	NP_001093131	B5ME19	B5ME19_HUMAN	eukaryotic translation initiation factor 3,							eukaryotic translation initiation factor 3 complex	translation initiation factor activity				0						gactctgtctcaaaaaaaaaa	0.194													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28604332	28604332	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28604332delA	uc010vct.1	-						SULT1A2_uc002dqg.1_Intron|SULT1A2_uc002dqh.1_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		actttgtctcaaaaaaaaaaG	0.294													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32345646	32345651	+	IGR	DEL	ATTTCA	-	-	rs145195301		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32345646_32345651delATTTCA								HERC2P4 (181772 upstream) : TP53TG3B (339190 downstream)																							tttcaattttatttcaatttcatttt	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32549299	32549299	+	IGR	DEL	T	-	-	rs148533555		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32549299delT								HERC2P4 (385425 upstream) : TP53TG3B (135542 downstream)																							tattcagcagtttggaaacac	0.000													7	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33521131	33521133	+	IGR	DEL	AAT	-	-	rs35351557		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33521131_33521133delAAT								SLC6A10P (624668 upstream) : MIR1826 (444375 downstream)																							gctgtacaacaatgacaggtaat	0.074													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33535455	33535456	+	IGR	INS	-	G	G			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33535455_33535456insG								SLC6A10P (638992 upstream) : MIR1826 (430052 downstream)																							TCTTAAACAAAGGGGAAGGAGG	0.351													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33918554	33918554	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33918554delT								None (None upstream) : MIR1826 (46954 downstream)																							agggaatatcttcacataaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33976749	33976749	+	IGR	DEL	G	-	-	rs111283986		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33976749delG								MIR1826 (11157 upstream) : UBE2MP1 (427053 downstream)																							ggcctatggtgaaaaaaggaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	35238933	35238933	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35238933delA								LOC146481 (523966 upstream) : None (None downstream)																							tgaggcctatagtggaaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46611689	46611689	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46611689delT								ANKRD26P1 (8680 upstream) : SHCBP1 (2784 downstream)																							tggccTGTGAttttttttttt	0.010													3	3	---	---	---	---	
PHKB	5257	broad.mit.edu	37	16	47630056	47630056	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47630056delT	uc002eev.3	+						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)				gatctgatggttttgtaaatg	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	50558948	50558948	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50558948delT								BRD7 (156119 upstream) : NKD1 (23293 downstream)																							cagttgttgatttggagctcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51102969	51102969	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51102969delA								CYLD (267123 upstream) : SALL1 (66917 downstream)																							AGACATACAGAAAAAAAATCC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52233367	52233368	+	IGR	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52233367_52233368delCA								None (None upstream) : TOX3 (238550 downstream)																							TTTacatacgcacacacacaca	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52265668	52265668	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52265668delA								None (None upstream) : TOX3 (206250 downstream)																							ATGATATGACATGACATAAAG	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52949696	52949696	+	IGR	DEL	G	-	-	rs113150891		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52949696delG								TOX3 (367982 upstream) : CHD9 (139249 downstream)																							Ggttttgtttgttttttgttt	0.179													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	53396844	53396844	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53396844delC								CHD9 (35431 upstream) : RBL2 (71507 downstream)																							TTGGTTTTTGCCCACAGCCAC	0.418													4	2	---	---	---	---	
FTO	79068	broad.mit.edu	37	16	54086188	54086188	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54086188delT	uc002ehr.2	+						FTO_uc010vha.1_Intron|FTO_uc010cbz.2_Intron|FTO_uc002ehs.2_Intron	NM_001080432	NP_001073901	Q9C0B1	FTO_HUMAN	fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						ACATCTTGACTTTTTTTTAAT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54763534	54763539	+	IGR	DEL	TTCCTT	-	-	rs71146766		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54763534_54763539delTTCCTT								IRX3 (443156 upstream) : IRX5 (201572 downstream)																							ccttccttccttccttccccctctct	0.010													4	2	---	---	---	---	
NLRC5	84166	broad.mit.edu	37	16	57077811	57077811	+	Intron	DEL	T	-	-	rs5817086		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57077811delT	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_Intron|NLRC5_uc002ekq.1_Intron|NLRC5_uc002ekr.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)				TTTTTTAGGATttttttttta	0.199													4	2	---	---	---	---	
CNOT1	23019	broad.mit.edu	37	16	58604789	58604792	+	Intron	DEL	TAAC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58604789_58604792delTAAC	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002enx.2_Intron|CNOT1_uc002enz.1_Intron	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		aatatctatttaacagtaagacag	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59000257	59000257	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59000257delT								GOT2 (232011 upstream) : None (None downstream)																							TATCGCTTCATTGAAATGATT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59193526	59193526	+	IGR	DEL	A	-	-	rs57563929		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59193526delA								GOT2 (425280 upstream) : None (None downstream)																							ctttgttggcaggggtgaggg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	61311017	61311018	+	IGR	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61311017_61311018delCA								None (None upstream) : CDH8 (376217 downstream)																							AAGACACAAGCACACACACACA	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	61662041	61662042	+	IGR	DEL	GT	-	-	rs147470530	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61662041_61662042delGT								None (None upstream) : CDH8 (25193 downstream)																							ATGTGTGTGCGTGTGTGTGTGA	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	62300185	62300185	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62300185delG								CDH8 (230149 upstream) : None (None downstream)																							aacacctctaggcatcccaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66058790	66058793	+	IGR	DEL	TCCA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66058790_66058793delTCCA								LOC283867 (448587 upstream) : CDH5 (341732 downstream)																							catccatccctccatccatccatc	0.049													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	71351766	71351767	+	IGR	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71351766_71351767delGT								FTSJD1 (28253 upstream) : CALB2 (40859 downstream)																							TAAATCTCTCGTGTGTGTGTGT	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	71446749	71446749	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71446749delC								CALB2 (22410 upstream) : ZNF23 (34764 downstream)																							TTCTGCGATTCCCATCTCTCT	0.552											OREG0023922	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	71860637	71860637	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71860637delA								AP1G1 (17661 upstream) : ATXN1L (19262 downstream)																							gctacagaggaaaaaaaaaat	0.000													4	2	---	---	---	---	
PKD1L3	342372	broad.mit.edu	37	16	71984637	71984637	+	Intron	DEL	T	-	-	rs145525687		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71984637delT	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0						tatttctctcttttttttttt	0.139													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	72401243	72401243	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72401243delT								PMFBP1 (194894 upstream) : ZFHX3 (415545 downstream)																							catacttagcttttttttaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	72742127	72742127	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72742127delT	uc002fcj.1	+											Homo sapiens cDNA FLJ11501 fis, clone HEMBA1002100.																		tttgttattgttttttttttt	0.124													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73598455	73598455	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73598455delC								HTA (470785 upstream) : PSMD7 (732226 downstream)																							TGCCTCTCTTCCACCCATCTT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73841007	73841007	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73841007delG								HTA (713337 upstream) : PSMD7 (489674 downstream)																							GAAAGGGAGTGGCCACATCCA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	76165891	76165891	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76165891delT								TERF2IP (474563 upstream) : CNTNAP4 (145285 downstream)																							AGCCCATCTCTTTTAATCAAA	0.383													4	2	---	---	---	---	
CNTNAP4	85445	broad.mit.edu	37	16	76532271	76532272	+	Intron	DEL	AG	-	-	rs145551640		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76532271_76532272delAG	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						cctgggagacagagtgagaccc	0.119													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79612995	79612996	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79612995_79612996insA								WWOX (366432 upstream) : MAF (14750 downstream)																							TAGGGGGAAAGAAAAAAAAAGT	0.366													4	2	---	---	---	---	
CMIP	80790	broad.mit.edu	37	16	81498101	81498104	+	Intron	DEL	TCAT	-	-	rs66489725		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81498101_81498104delTCAT	uc002fgp.2	+							NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0						AGTGAAGGTCtcattcattcattc	0.270													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	83954505	83954506	+	IGR	INS	-	GATG	GATG	rs111265343		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83954505_83954506insGATG								MLYCD (4720 upstream) : OSGIN1 (28166 downstream)																							gaaggaaggaagatggatggat	0.010													4	4	---	---	---	---	
OSGIN1	29948	broad.mit.edu	37	16	83984144	83984149	+	Intron	DEL	ACACAC	-	-	rs12932950		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83984144_83984149delACACAC	uc002fha.2	+						OSGIN1_uc002fhb.2_Intron|OSGIN1_uc002fhc.2_5'Flank	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1						cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						gcacacacgtacacacacatgcacac	0.000													6	5	---	---	---	---	
OSGIN1	29948	broad.mit.edu	37	16	83984346	83984347	+	Intron	INS	-	CA	CA			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83984346_83984347insCA	uc002fha.2	+						OSGIN1_uc002fhb.2_Intron|OSGIN1_uc002fhc.2_5'Flank	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1						cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						atacatactggcacacgtacac	0.030													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	84233700	84233701	+	IGR	INS	-	CTCCGTC	CTCCGTC	rs147791434	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84233700_84233701insCTCCGTC								ADAD2 (2928 upstream) : KCNG4 (22124 downstream)																							CCATCCCGTCACTTCCTCCTGC	0.530													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87158694	87158696	+	Intron	DEL	CAC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87158694_87158696delCAC	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																		cacacaagcacaccacacacatc	0.020													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88489156	88489163	+	IGR	DEL	ATGGATGG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88489156_88489163delATGGATGG								BANP (378233 upstream) : ZNF469 (4716 downstream)																							ggatgagtgaatggatggatggatggat	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	89142920	89142921	+	IGR	INS	-	TG	TG			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89142920_89142921insTG								CBFA2T3 (99519 upstream) : ACSF3 (17333 downstream)																							gtgcatgtgaatgtgtgtgtgt	0.000													6	5	---	---	---	---	
ANKRD11	29123	broad.mit.edu	37	16	89491490	89491490	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89491490delA	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		caaactatttaaaaaaaaaaa	0.060													3	4	---	---	---	---	
VPS53	55275	broad.mit.edu	37	17	512755	512755	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:512755delA	uc002frn.2	-						VPS53_uc002frk.2_Intron|VPS53_uc010cjo.1_Intron|VPS53_uc002frl.2_Intron|VPS53_uc002frm.2_Intron|VPS53_uc002fro.2_Intron|VPS53_uc010cjp.1_Intron	NM_018289	NP_060759	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 2						protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		atgTGTAATTAAAAAAAAAGA	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5965857	5965857	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5965857delA								NLRP1 (478025 upstream) : WSCD1 (6580 downstream)																							acagacaaacaaaaaaaAAGC	0.184													4	2	---	---	---	---	
PITPNM3	83394	broad.mit.edu	37	17	6400344	6400345	+	Intron	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6400344_6400345delAC	uc002gdd.3	-						PITPNM3_uc010cln.2_Intron	NM_031220	NP_112497	Q9BZ71	PITM3_HUMAN	PITPNM family member 3 isoform 1						phosphatidylinositol metabolic process	endomembrane system|integral to membrane	calcium ion binding|lipid binding|phosphatidylinositol transporter activity|receptor tyrosine kinase binding			ovary(2)|central_nervous_system(2)	4				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		CCAAGCAGAGACACACACACAC	0.500													4	4	---	---	---	---	
DULLARD	23399	broad.mit.edu	37	17	7147350	7147351	+	3'UTR	INS	-	C	C	rs147084197	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7147350_7147351insC	uc002gfd.2	-	8					GABARAP_uc002gfb.2_5'Flank|DULLARD_uc002gfe.2_3'UTR|DULLARD_uc002gff.2_3'UTR|DULLARD_uc002gfc.2_Intron	NM_001143775	NP_001137247	O95476	CNEP1_HUMAN	dullard homolog						nuclear envelope organization|protein dephosphorylation	endoplasmic reticulum membrane|integral to membrane|nuclear membrane	protein serine/threonine phosphatase activity				0						CCATCCAGACTCCAAGTGGAGT	0.614													3	6	---	---	---	---	
PIK3R6	146850	broad.mit.edu	37	17	8732819	8732820	+	Intron	DEL	AC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8732819_8732820delAC	uc002glq.1	-						PIK3R6_uc002glr.1_Intron|PIK3R6_uc002gls.1_Intron	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6						platelet activation	cytosol					0						acacacactgacacacactcat	0.000													13	8	---	---	---	---	
MYH3	4621	broad.mit.edu	37	17	10547483	10547486	+	Intron	DEL	AAAC	-	-	rs147605554		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10547483_10547486delAAAC	uc002gmq.1	-							NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,						muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7						caaaaaaaaaaaacaaacaaaaaa	0.201													18	10	---	---	---	---	
COX10	1352	broad.mit.edu	37	17	14058186	14058187	+	Intron	DEL	TG	-	-	rs146887565		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14058186_14058187delTG	uc002gof.3	+						COX10_uc010vvs.1_Intron|COX10_uc010vvt.1_Intron	NM_001303	NP_001294	Q12887	COX10_HUMAN	heme A:farnesyltransferase precursor						heme a biosynthetic process|heme O biosynthetic process|respiratory chain complex IV assembly	integral to membrane|mitochondrial membrane	protoheme IX farnesyltransferase activity				0		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		CAGTTTGCTCTGTTCCTGAGAT	0.381													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	15258164	15258165	+	IGR	INS	-	A	A	rs72535808	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15258164_15258165insA								TEKT3 (13206 upstream) : CDRT4 (81173 downstream)																							CAGTTTTGAACGCTTCTTCTTT	0.317													3	3	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21217017	21217017	+	Intron	DEL	C	-	-	rs67245637		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21217017delC	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|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	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		ATACCTGGCTCCCTCCTCCCT	0.393													21	10	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21217021	21217022	+	Intron	DEL	CC	-	-	rs67362606		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21217021_21217022delCC	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|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	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CTGGCTCCCTCCTCCCTCCTTC	0.381													19	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21248150	21248151	+	IGR	INS	-	C	C	rs142379650		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21248150_21248151insC								MAP2K3 (29601 upstream) : KCNJ12 (31548 downstream)																							ACAACAGTGGTCatacctctgg	0.228													4	3	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21313451	21313451	+	Intron	DEL	C	-	-	rs147481555		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21313451delC	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	CTGGCAGTGTCCCCCAGGAGT	0.657										Prostate(3;0.18)			6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21555332	21555332	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21555332delC								C17orf51 (77601 upstream) : FAM27L (270038 downstream)																							aaaaaataaaCAAACTATTGG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21566064	21566065	+	IGR	INS	-	T	T	rs142859905	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21566064_21566065insT								C17orf51 (88333 upstream) : FAM27L (259305 downstream)																							TCTTCAAGAAATGTTCTCCTTC	0.356													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	29337856	29337856	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29337856delT								RNF135 (10931 upstream) : NF1 (84139 downstream)														p.?(1)									GAAAGTGAACTTTTTTTTTTT	0.308													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	30735662	30735662	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30735662delA								ZNF207 (27687 upstream) : PSMD11 (35840 downstream)																							aaagaaaaaGAAAAAAAAAAA	0.164													4	2	---	---	---	---	
LIG3	3980	broad.mit.edu	37	17	33330326	33330326	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33330326delT	uc002hik.1	+							NM_013975	NP_039269	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent isoform alpha						base-excision repair|cell division|DNA ligation involved in DNA repair|DNA replication|reciprocal meiotic recombination|spermatogenesis	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|protein binding|zinc ion binding			skin(3)|lung(2)|ovary(2)|large_intestine(1)|pancreas(1)	9		Ovarian(249;0.17)			Bleomycin(DB00290)	TGAGCAAttcttttttttttt	0.249								Other_BER_factors					4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36148053	36148053	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36148053delT								HNF1B (42957 upstream) : LOC284100 (54520 downstream)																							GATGGACTGCTTttttttttt	0.209													4	2	---	---	---	---	
MLLT6	4302	broad.mit.edu	37	17	36867156	36867156	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36867156delC	uc002hqi.3	+						MLLT6_uc010wdr.1_Intron|MLLT6_uc010cvm.1_Intron	NM_005937	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent	nucleus	protein binding|zinc ion binding			breast(3)|prostate(1)|lung(1)|skin(1)	6	Breast(7;4.43e-21)					GCAGGAGACACCATGTGGAGA	0.433			T	MLL	AL								4	2	---	---	---	---	
BRCA1	672	broad.mit.edu	37	17	41267519	41267519	+	Intron	DEL	A	-	-	rs35149296		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41267519delA	uc002icq.2	-						BRCA1_uc010whp.1_Intron|BRCA1_uc010whl.1_Intron|BRCA1_uc010whm.1_Intron|BRCA1_uc002icp.3_Intron|BRCA1_uc002icu.2_Intron|BRCA1_uc010cyx.2_Intron|BRCA1_uc002ict.2_Intron|BRCA1_uc010whn.1_Intron|BRCA1_uc010who.1_Intron|BRCA1_uc002idc.1_Intron|BRCA1_uc010whr.1_Intron|BRCA1_uc002idd.2_Intron|BRCA1_uc010cyy.1_Intron|BRCA1_uc010whs.1_Intron|BRCA1_uc010cyz.2_Intron|BRCA1_uc010cza.2_Intron|BRCA1_uc010wht.1_Intron	NM_007294	NP_009225	P38398	BRCA1_HUMAN	breast cancer 1, early onset isoform 1						androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)	52		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		actttgtctcaaaaaaaaaaa	0.124			D|Mis|N|F|S		ovarian	breast|ovarian		Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_BRCA1_type	TCGA Ovarian(2;0.000030)			2	4	---	---	---	---	
ARHGAP27	201176	broad.mit.edu	37	17	43499100	43499100	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43499100delA	uc002iix.2	-							NM_199282	NP_954976	Q6ZUM4	RHG27_HUMAN	Rho GTPase activating protein 27 isoform a						positive regulation of Cdc42 GTPase activity|receptor-mediated endocytosis|signal transduction	cytoplasm|membrane	Rac GTPase activator activity|SH3 domain binding				0	Renal(3;0.0405)					GATCAGAGGGAAAAAAACTGC	0.294													4	2	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44107957	44107957	+	3'UTR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44107957delA	uc002ikb.2	-	14					KIAA1267_uc002ikc.2_3'UTR|KIAA1267_uc002ikd.2_3'UTR|KIAA1267_uc010dav.2_3'UTR|KIAA1267_uc010wkb.1_3'UTR|KIAA1267_uc010wkc.1_3'UTR	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				AATCAGAGGGAAAAAAAAAAA	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48298986	48298986	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48298986delA								COL1A1 (19986 upstream) : TMEM92 (52851 downstream)																							TTCCTCAAGTAAAGTTGTTAG	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53776878	53776878	+	IGR	DEL	T	-	-	rs76490471		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53776878delT								MMD (277537 upstream) : TMEM100 (20112 downstream)																							GCAGAATTGATTTTTTTTTCC	0.463													9	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	54818415	54818416	+	IGR	INS	-	T	T	rs149974788	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54818415_54818416insT								NOG (145464 upstream) : C17orf67 (50859 downstream)																							GCTGATGCTGATTTttttttat	0.243													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	55125181	55125185	+	IGR	DEL	AAGAC	-	-	rs71363885		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55125181_55125185delAAGAC								RNF126P1 (1026 upstream) : AKAP1 (37368 downstream)																							agcgctgaataagacaagacaagac	0.112													3	4	---	---	---	---	
VEZF1	7716	broad.mit.edu	37	17	56054168	56054168	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56054168delG	uc002ivf.1	-							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						ACCAAATAGAGGAGTACACCG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	56120846	56120846	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56120846delG								SFRS1 (36139 upstream) : DYNLL2 (39934 downstream)																							TCTCATGTGCGGGGCTGGGCT	0.453													4	2	---	---	---	---	
MTMR4	9110	broad.mit.edu	37	17	56571107	56571107	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56571107delA	uc002iwj.2	-							NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4							cytoplasm|membrane	metal ion binding|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ggccttttacaaaaaaaaaaa	0.169													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	58490409	58490409	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58490409delA								USP32 (20823 upstream) : C17orf64 (9456 downstream)																							TTGCTACAGGAAAAAAAAAGT	0.333													4	2	---	---	---	---	
PPM1D	8493	broad.mit.edu	37	17	58683929	58683929	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58683929delA	uc002iyt.1	+						PPM1D_uc010ddm.1_Intron	NM_003620	NP_003611	O15297	PPM1D_HUMAN	protein phosphatase 1D						negative regulation of cell proliferation|protein dephosphorylation|response to radiation	nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein binding|protein serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			cttttgtattAAAAAAAAAAA	0.149													3	4	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	59045928	59045928	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59045928delT	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyx.1_Intron|BCAS3_uc002iyy.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			agttgttgccttttttttttg	0.000													3	4	---	---	---	---	
INTS2	57508	broad.mit.edu	37	17	59944674	59944674	+	3'UTR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59944674delA	uc002izn.2	-	25					INTS2_uc002izm.2_3'UTR	NM_020748	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3						TTCCCAGTGGAAAAAAAAAAA	0.343													6	5	---	---	---	---	
TLK2	11011	broad.mit.edu	37	17	60677123	60677123	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60677123delT	uc010ddp.2	+						TLK2_uc002izx.3_Intron|TLK2_uc002izz.3_Intron|TLK2_uc002jaa.3_Intron|TLK2_uc010wpd.1_Intron	NM_006852	NP_006843	Q86UE8	TLK2_HUMAN	tousled-like kinase 2 isoform A						cell cycle|chromatin modification|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|kidney(1)	2						gttcaggtggtttttttttcc	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	63330065	63330065	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63330065delA								RGS9 (106246 upstream) : AXIN2 (194620 downstream)																							TAATTTTAAGAAAAAAATCCA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	64884169	64884169	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64884169delA								CACNG5 (2813 upstream) : CACNG4 (76844 downstream)																							CAAGCACTGTAAAAAAATGGG	0.343													4	2	---	---	---	---	
PITPNC1	26207	broad.mit.edu	37	17	65566008	65566009	+	Intron	DEL	GA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65566008_65566009delGA	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			CAAGAAGAGGGAGAGAGAGATA	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	69222633	69222633	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69222633delT								None (None upstream) : SOX9 (894528 downstream)																							TTCAGGGTGATTTTTTTTTTC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	70514341	70514341	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70514341delA	uc002jix.2	-						uc002jiz.1_Intron					Homo sapiens cDNA FLJ20470 fis, clone KAT06815.																		cagaaccttgaagctattatg	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	74366087	74366087	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74366087delG								PRPSAP1 (15808 upstream) : SPHK1 (6655 downstream)																							ctccaagtgaggaccacccag	0.000													4	2	---	---	---	---	
MGAT5B	146664	broad.mit.edu	37	17	74927723	74927723	+	Intron	DEL	T	-	-	rs67886757		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74927723delT	uc002jti.2	+						MGAT5B_uc002jth.2_Intron	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN	N-acetylglucosaminyltranferase VB isoform 2							Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)|skin(1)	3						TCGGGCGGACTTTGGCATATG	0.328													3	8	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75308585	75308586	+	Intron	INS	-	G	G	rs147100318	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75308585_75308586insG	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			TAGCTGACTCAGTGACTTTGGG	0.594													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75636486	75636487	+	IGR	DEL	CT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75636486_75636487delCT								SEPT9 (139810 upstream) : FLJ45079 (238622 downstream)																							GGTCCAGTGCCTCTCTCCTCCT	0.540													4	2	---	---	---	---	
SGSH	6448	broad.mit.edu	37	17	78187722	78187723	+	Intron	DEL	AG	-	-	rs34029730		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78187722_78187723delAG	uc002jxz.3	-						SGSH_uc002jya.3_Intron|SGSH_uc002jxy.2_3'UTR|SGSH_uc010wue.1_Intron	NM_000199	NP_000190	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase precursor						proteoglycan metabolic process	lysosome	metal ion binding|N-sulfoglucosamine sulfohydrolase activity|sulfuric ester hydrolase activity			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TAGAACAGACAGACCGGGGGAG	0.663													8	7	---	---	---	---	
RNF213	57674	broad.mit.edu	37	17	78331222	78331223	+	Intron	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78331222_78331223delTC	uc002jyh.1	+						uc002jyi.1_Intron|RNF213_uc010dhw.1_Intron	NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213											ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			catccacctgtctatcAGACAC	0.228													4	2	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78665245	78665246	+	Intron	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78665245_78665246delTG	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						atgtgagtgatgtgtgtgtgtg	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	80446257	80446257	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80446257delT								NARF (116 upstream) : FOXK2 (31337 downstream)																							tttttttttcttttttttttt	0.224													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	519582	519582	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:519582delT								COLEC12 (18853 upstream) : CETN1 (60787 downstream)																							TGCAGGTTTATTTTGAATGTG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5362735	5362735	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5362735delT								ZFP161 (66696 upstream) : EPB41L3 (29653 downstream)																							CATTTTGACCTAGATTCTGAA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	7376511	7376511	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7376511delA								LRRC30 (144470 upstream) : PTPRM (190803 downstream)																							cccacccgtcaaaaaaaaaag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10259609	10259610	+	IGR	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10259609_10259610delGT								VAPA (299592 upstream) : APCDD1 (195015 downstream)																							TTTGATCACCGTGTGTGTGTGG	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	13822648	13822651	+	IGR	DEL	GCTG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13822648_13822651delGCTG								RNMT (58094 upstream) : MC5R (3114 downstream)																							GTTCTTTTTTGCTGGAGTAAGGAA	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	22979677	22979677	+	IGR	DEL	A	-	-	rs111501714		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22979677delA								ZNF521 (47463 upstream) : SS18 (616542 downstream)																							aaatgctcttaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	25242073	25242076	+	IGR	DEL	AAAG	-	-	rs72404172		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25242073_25242076delAAAG								C18orf16 (471423 upstream) : CDH2 (288854 downstream)																							AAaaaaaaaaaaagaaagaaagaa	0.284													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	25293375	25293375	+	IGR	DEL	C	-	-	rs34760545		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25293375delC								C18orf16 (522725 upstream) : CDH2 (237555 downstream)																							TGGAGGATGACCCAGATCATT	0.274													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	25344139	25344139	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25344139delA								C18orf16 (573489 upstream) : CDH2 (186791 downstream)																							GTGTCTCAGGAAAAAAAAAAA	0.328													4	2	---	---	---	---	
CDH2	1000	broad.mit.edu	37	18	25736005	25736005	+	Intron	DEL	T	-	-	rs140395191		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25736005delT	uc002kwg.2	-							NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4						CTTGCATGGGTTTTTTAACTC	0.244													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	26687747	26687748	+	IGR	DEL	AC	-	-	rs35889383		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26687747_26687748delAC								CDH2 (930302 upstream) : None (None downstream)																							gtgcatgtatacacacacacat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	27630358	27630359	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27630358_27630359insA								None (None upstream) : MIR302F (248517 downstream)																							AAACTAAACAGAAAAAAAAAAT	0.208													4	3	---	---	---	---	
KLHL14	57565	broad.mit.edu	37	18	30353205	30353206	+	5'Flank	DEL	TC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30353205_30353206delTC	uc002kxm.1	-							NM_020805	NP_065856	Q9P2G3	KLH14_HUMAN	kelch-like 14							cytosol|endoplasmic reticulum membrane				ovary(1)	1						ccctctctcttctctctctctA	0.361													4	2	---	---	---	---	
C18orf34	374864	broad.mit.edu	37	18	30737570	30737570	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30737570delT	uc002kxn.2	-						C18orf34_uc010dme.1_Intron|C18orf34_uc010xbr.1_Intron|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Intron|C18orf34_uc002kxp.2_Intron	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1											ovary(1)	1						TACACAGACATAGTATTTTAC	0.299													4	2	---	---	---	---	
ASXL3	80816	broad.mit.edu	37	18	31241861	31241862	+	Intron	INS	-	AA	AA	rs146967011	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31241861_31241862insAA	uc010dmg.1	+						ASXL3_uc002kxq.2_Intron	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						TAATCTGTGATAAAAAAAAACT	0.302													14	9	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34190919	34190919	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34190919delA	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron|FHOD3_uc002kzu.1_Intron|FHOD3_uc010dmz.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				TGTATAAGATAAAGGGCTTGC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35222231	35222231	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35222231delA								CELF4 (76231 upstream) : None (None downstream)																							TCTCCCCATTAAAAAATTTCC	0.368													4	2	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	36805981	36805982	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36805981_36805982insA	uc002lak.1	-						LOC647946_uc010xcj.1_Intron|LOC647946_uc002lal.1_Intron					Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						TCAAAAATTGGAAAAAAAAATT	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	37500217	37500217	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37500217delA								LOC647946 (119935 upstream) : None (None downstream)																							CAATAACAGGAAAAAAAAGGA	0.249													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38671300	38671300	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38671300delA								None (None upstream) : KC6 (388938 downstream)																							TCGTCAAGATAAAAAGGGTAT	0.323													4	2	---	---	---	---	
RIT2	6014	broad.mit.edu	37	18	40480941	40480942	+	Intron	INS	-	T	T	rs142199561	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40480941_40480942insT	uc002lav.2	-						RIT2_uc010dnf.2_Intron	NM_002930	NP_002921	Q99578	RIT2_HUMAN	Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1						ttttatttggctttttttttac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	41982512	41982512	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41982512delT	uc002lax.3	-											Homo sapiens cDNA clone IMAGE:5265929.																		gttttgtttgttttttttttc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	42048026	42048026	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42048026delT	uc002lax.3	-											Homo sapiens cDNA clone IMAGE:5265929.																		CTTTTTTTAATTTTTTTTTTc	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	52637486	52637486	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52637486delA								CCDC68 (10747 upstream) : TCF4 (252076 downstream)																							AGAACAGAAGACATTAACCTT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	52793084	52793085	+	5'Flank	INS	-	G	G	rs144217323	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52793084_52793085insG	uc002lfu.1	-											Homo sapiens cDNA FLJ36621 fis, clone TRACH2016651.																		GGTCGGGGGTTGGGGGTGACTC	0.450													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	54925552	54925552	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54925552delA								WDR7 (228516 upstream) : ST8SIA3 (94169 downstream)																							TAAGCCTATTAAGAGATTCAT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	55696413	55696413	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55696413delA								ATP8B1 (297374 upstream) : NEDD4L (15206 downstream)																							actgacttggaggtctgggac	0.000													4	2	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	55820465	55820466	+	Intron	INS	-	T	T	rs142976900	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55820465_55820466insT	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lha.1_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						AGAACACACAGTTGTAGAGGGA	0.381													1	6	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	55826148	55826149	+	Intron	DEL	GA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55826148_55826149delGA	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lha.1_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						gtaagctcctgagagagagaga	0.149													4	2	---	---	---	---	
ZNF532	55205	broad.mit.edu	37	18	56632365	56632365	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56632365delA	uc002lho.2	+						ZNF532_uc002lhp.2_Intron|ZNF532_uc010xeg.1_Intron|ZNF532_uc002lhr.2_Intron|ZNF532_uc002lhs.2_Intron|ZNF532_uc010xeh.1_Intron	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN	zinc finger protein 532						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2						AACTTTTTTTAATGTAAGGCT	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57856934	57856934	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57856934delT								PMAIP1 (285396 upstream) : MC4R (181630 downstream)																							agcctcaacctttaaagctga	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58086429	58086429	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58086429delA								MC4R (46428 upstream) : CDH20 (914559 downstream)																							gaacattggcaaaaaatggaa	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	60061145	60061145	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60061145delC								TNFRSF11A (7643 upstream) : ZCCHC2 (129513 downstream)																							ccagactggtcccctttttag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65042571	65042572	+	IGR	INS	-	A	A	rs150098817		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65042571_65042572insA								CDH19 (771355 upstream) : DSEL (131247 downstream)																							ATATTACCAGTAAAAAAAAAAA	0.337													4	2	---	---	---	---	
DOK6	220164	broad.mit.edu	37	18	67171592	67171592	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67171592delA	uc002lkl.2	+							NM_152721	NP_689934	Q6PKX4	DOK6_HUMAN	docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				ACAGTTCCTTAAAAAAAAAGC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71590609	71590609	+	IGR	DEL	C	-	-	rs35731287		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71590609delC								None (None upstream) : FBXO15 (149979 downstream)																							cctgctttcactacctgctcc	0.199													1	6	---	---	---	---	
ZNF516	9658	broad.mit.edu	37	18	74196747	74196747	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74196747delT	uc002lme.2	-									Q92618	ZN516_HUMAN	Synthetic construct DNA, clone: pF1KSDA0222, Homo sapiens ZNF516 gene for zinc finger protein 516, complete cds, without stop codon, in Flexi system.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		TATGTAAATATTAGGAAAATC	0.299													4	2	---	---	---	---	
GNG7	2788	broad.mit.edu	37	19	2679783	2679784	+	Intron	INS	-	TCAT	TCAT	rs139310596	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2679783_2679784insTCAT	uc002lwd.2	-							NM_052847	NP_443079	O60262	GBG7_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTCACCTTACTCATTGTATTA	0.460													5	3	---	---	---	---	
KANK3	256949	broad.mit.edu	37	19	8387500	8387501	+	3'UTR	DEL	AG	-	-	rs4147654		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8387500_8387501delAG	uc010dwa.2	-	11					NDUFA7_uc002mjm.1_5'Flank	NM_198471	NP_940873	Q6NY19	KANK3_HUMAN	ankyrin repeat domain 47												0						AAGAAGTTTCAGAGAGTGGGTG	0.515													4	5	---	---	---	---	
HNRNPM	4670	broad.mit.edu	37	19	8538344	8538344	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8538344delA	uc010dwe.2	+						HNRNPM_uc010dwc.1_Intron|HNRNPM_uc010xke.1_Intron|HNRNPM_uc010dwd.2_Intron|HNRNPM_uc002mka.2_Intron	NM_005968	NP_005959	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M						alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0						tactgtgtttaaaaaaaaaaa	0.119													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	10455434	10455437	+	IGR	DEL	AAAC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10455434_10455437delAAAC								ICAM3 (5089 upstream) : TYK2 (5768 downstream)																							aacgtctcaaaaacaaacaaacaa	0.113													4	2	---	---	---	---	
NFIX	4784	broad.mit.edu	37	19	13177550	13177551	+	Intron	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13177550_13177551delTG	uc010xmx.1	+						NFIX_uc002mwd.2_Intron|NFIX_uc002mwe.2_Intron|NFIX_uc002mwf.2_Intron|NFIX_uc002mwg.1_Intron			Q14938	NFIX_HUMAN	RecName: Full=Nuclear factor 1;						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			tgtgtgtgcatgtgtgtgtgtg	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	15464238	15464239	+	IGR	DEL	AA	-	-	rs72572477		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15464238_15464239delAA								BRD4 (20896 upstream) : AKAP8 (102 downstream)																							TTTTTGCCTTAAGAGAACAAGC	0.366													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	15890943	15890944	+	5'Flank	DEL	AG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15890943_15890944delAG	uc002nbo.2	-											Homo sapiens cDNA FLJ60024 complete cds, highly similar to Cytochrome P450 4F12 (EC 1.14.14.1).																		AGAAAGGAGAAGAGAGAGAGAG	0.525													3	4	---	---	---	---	
MYO9B	4650	broad.mit.edu	37	19	17188380	17188380	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17188380delG	uc010eak.2	+						HAUS8_uc002nfe.2_5'Flank|HAUS8_uc002nff.2_5'Flank|HAUS8_uc002nfg.1_5'Flank|HAUS8_uc002nfh.1_5'Flank|MYO9B_uc002nfi.2_Intron	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1						actin filament-based movement	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1						AGGGTCTTGTGGGGGGAGCAC	0.552													4	2	---	---	---	---	
FAM129C	199786	broad.mit.edu	37	19	17662889	17662890	+	Intron	INS	-	T	T	rs34537214		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17662889_17662890insT	uc010xpr.1	+							NM_173544	NP_775815	Q86XR2	NIBL2_HUMAN	B-cell novel protein 1 isoform a												0						ctttattttaattttttttttt	0.000													14	7	---	---	---	---	
CCDC124	115098	broad.mit.edu	37	19	18053698	18053699	+	Intron	DEL	AG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18053698_18053699delAG	uc010xpz.1	+						CCDC124_uc002nhs.2_Intron	NM_001136203	NP_001129675	Q96CT7	CC124_HUMAN	coiled-coil domain containing 124								DNA binding				0						TGCCCACTGCAGAGGCAGTGGA	0.678													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	20385711	20385711	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20385711delA								LOC284441 (15208 upstream) : ZNF826 (65367 downstream)																							CCAGGCCCAGAAAAAAAAAAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	20787831	20787832	+	IGR	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20787831_20787832insA								ZNF737 (39205 upstream) : ZNF626 (14913 downstream)																							CATGAGTAGGGACATAACCTCT	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	22213061	22213061	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22213061delG								ZNF208 (19316 upstream) : ZNF257 (22205 downstream)																							aatccctcctgggggctggac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	23316634	23316637	+	Intron	DEL	CTTA	-	-	rs151192543		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23316634_23316637delCTTA	uc002nrb.1	+											Homo sapiens cDNA FLJ16640 fis, clone TESTI4028938, moderately similar to Zinc finger protein 85.																		GTGTTCATGTCTTACTTCATCATC	0.304													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24052483	24052483	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24052483delG								RPSAP58 (41566 upstream) : ZNF254 (163764 downstream)																							tggattgcttggcatggagca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29046800	29046800	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29046800delA	uc002nsa.1	-											Homo sapiens cDNA clone IMAGE:5297319, with apparent retained intron.																		GCTAAGCTGTAAAACCTTAAG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30825544	30825544	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30825544delG								C19orf2 (318933 upstream) : ZNF536 (37784 downstream)																							TAAGGACTGTGATCATGCTGT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	35297551	35297552	+	IGR	INS	-	ACTC	ACTC	rs137993281	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35297551_35297552insACTC								ZNF599 (33417 upstream) : ZNF30 (120255 downstream)																							agaatagacttatcagatgagt	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36012138	36012138	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36012138delC								DMKN (7578 upstream) : SBSN (2133 downstream)																							GCAGGCCCCTCCCCTTGCCGG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	39706049	39706051	+	IGR	DEL	TTG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39706049_39706051delTTG								SYCN (11143 upstream) : IL28B (28222 downstream)																							ataatttcctttgttgttgttgt	0.000													4	2	---	---	---	---	
AXL	558	broad.mit.edu	37	19	41731740	41731741	+	Intron	DEL	GT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41731740_41731741delGT	uc010ehj.2	+						CYP2F1_uc010xvw.1_Intron|AXL_uc010ehi.1_Intron|AXL_uc010ehk.2_Intron	NM_021913	NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase isoform 1							integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13						TTCATTGTGAGTGTGTGTGTGG	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	43125330	43125331	+	Intron	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43125330_43125331delTG	uc010eif.1	+						uc010eig.1_Intron|uc010eih.1_Intron					Homo sapiens cDNA FLJ39530 fis, clone PUAEN2004400.																		CGTATATATAtgtgtgtgtgtg	0.238													4	2	---	---	---	---	
ZNF235	9310	broad.mit.edu	37	19	44807360	44807361	+	Intron	DEL	AT	-	-	rs147186620		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44807360_44807361delAT	uc002oza.3	-						ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron|ZNF235_uc002ozb.3_Intron|ZNF235_uc010xwx.1_Intron	NM_004234	NP_004225	Q14590	ZN235_HUMAN	zinc finger protein 93 homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)	3		Prostate(69;0.0352)|all_neural(266;0.116)				AAATTAACAGATATATATATAT	0.158													3	6	---	---	---	---	
KLC3	147700	broad.mit.edu	37	19	45852954	45852955	+	Intron	INS	-	GGGGTG	GGGGTG	rs144670186	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45852954_45852955insGGGGTG	uc002pbf.1	+						KLC3_uc010ejy.1_Intron|KLC3_uc002pbg.1_Intron	NM_177417	NP_803136	Q6P597	KLC3_HUMAN	kinesin light chain 3							cytoplasm|kinesin complex|microtubule	microtubule motor activity			ovary(1)	1		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		AACGTGAGGGTGGGGGGGGGCC	0.653													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	46940069	46940069	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46940069delT								CCDC8 (23150 upstream) : PNMAL1 (29680 downstream)																							TTTAGCTTAatttttttccat	0.030													4	2	---	---	---	---	
PRKD2	25865	broad.mit.edu	37	19	47178640	47178640	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47178640delT	uc002pfh.2	-						PRKD2_uc002pfd.2_Intron|PRKD2_uc010eks.2_Intron|PRKD2_uc010ekt.2_Intron|PRKD2_uc002pfe.2_Intron|PRKD2_uc002pff.2_Intron|PRKD2_uc002pfg.2_Intron|PRKD2_uc002pfi.2_Intron|PRKD2_uc002pfj.2_Intron|PRKD2_uc010xye.1_Intron|PRKD2_uc002pfk.2_Intron	NM_001079881	NP_001073350	Q9BZL6	KPCD2_HUMAN	protein kinase D2 isoform A						cell death|intracellular signal transduction|positive regulation of transcription from RNA polymerase II promoter|protein autophosphorylation|T cell receptor signaling pathway	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein kinase C activity			ovary(2)|central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)	7		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		CTATGTCACCTTTTTTTTTCT	0.294													3	3	---	---	---	---	
SNAR-A4	100169956	broad.mit.edu	37	19	50627135	50627135	+	5'Flank	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50627135delA	uc010ybw.1	-							NR_024242				Homo sapiens small ILF3/NF90-associated RNA A3 (SNAR-A3), non-coding RNA.												0						acaaacaaacaaaaaaaaaaa	0.005													4	2	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50752588	50752590	+	Intron	DEL	CTT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50752588_50752590delCTT	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		tctctgtccccttctctctctgg	0.010													9	7	---	---	---	---	
CEACAM18	729767	broad.mit.edu	37	19	51979530	51979530	+	5'Flank	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51979530delA	uc002pwv.1	+							NM_001080405	NP_001073874	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion							integral to membrane				skin(1)	1		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		ctctgtctggaaaaaaaaaaa	0.005													4	4	---	---	---	---	
NLRP2	55655	broad.mit.edu	37	19	55502268	55502269	+	Intron	INS	-	T	T	rs143396187	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55502268_55502269insT	uc002qij.2	+						NLRP2_uc010yfp.1_Intron|NLRP2_uc010esn.2_Intron|NLRP2_uc010eso.2_Intron|NLRP2_uc010esp.2_Intron	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2						apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TGGTTTTCGGGttttttttttc	0.198													6	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57457340	57457340	+	IGR	DEL	A	-	-	rs67908325		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57457340delA								MIMT1 (97418 upstream) : USP29 (174169 downstream)																							AGTGGGGATTAAAAAAAAAAG	0.443													4	3	---	---	---	---	
ZNF587	84914	broad.mit.edu	37	19	58333949	58333949	+	Intron	DEL	A	-	-	rs34939568		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58333949delA	uc002qqb.2	+						uc002qqh.1_Intron|ZNF587_uc010yhh.1_Intron|ZNF587_uc002qqi.1_Intron	NM_032828	NP_116217	Q96SQ5	ZN587_HUMAN	zinc finger protein 587						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		tggtattgacaacaatattca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	1235305	1235306	+	IGR	INS	-	T	T	rs142754247	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1235305_1235306insT								RAD21L1 (160 upstream) : SNPH (11654 downstream)																							ATTCTGTTTTGTTTTtttttgt	0.168													8	4	---	---	---	---	
SIRPB1	10326	broad.mit.edu	37	20	1558417	1558417	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1558417delA	uc010gai.2	-						SIRPB1_uc002wfk.3_Intron	NM_006065	NP_006056	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1 isoform 1						cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding			ovary(1)	1						AGATTAAATTAAAAAAAAAAA	0.378													4	3	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9389981	9389981	+	Intron	DEL	A	-	-	rs112519707	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9389981delA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						GGTGAGAAATAAAAAAAAAAA	0.348													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12546644	12546644	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12546644delA								BTBD3 (639402 upstream) : SPTLC3 (442983 downstream)																							ACCTTATGAGAAAAAAAAATC	0.358													4	2	---	---	---	---	
SEL1L2	80343	broad.mit.edu	37	20	13841811	13841811	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13841811delT	uc010gcf.2	-						SEL1L2_uc002woq.3_Intron|SEL1L2_uc010zrl.1_Intron|SEL1L2_uc002wor.2_Intron	NM_025229	NP_079505	Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 precursor							integral to membrane	binding			ovary(2)	2						caggatgatctttttttttat	0.000													4	2	---	---	---	---	
KIF16B	55614	broad.mit.edu	37	20	16455971	16455971	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16455971delA	uc002wpg.1	-						KIF16B_uc010gch.1_Intron|KIF16B_uc010gci.1_Intron|KIF16B_uc010gcj.1_Intron	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23						cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						acccatcaggaagctgaagtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	18483142	18483143	+	IGR	INS	-	TATT	TATT	rs151288578	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18483142_18483143insTATT								RBBP9 (5255 upstream) : SEC23B (5045 downstream)																							aaattgagaaatagagtaacaa	0.000													4	3	---	---	---	---	
RALGAPA2	57186	broad.mit.edu	37	20	20528770	20528773	+	Intron	DEL	CACA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20528770_20528773delCACA	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						GCAAAATCTCcacacacacacaca	0.201													4	2	---	---	---	---	
XRN2	22803	broad.mit.edu	37	20	21324475	21324475	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21324475delT	uc002wsf.1	+						XRN2_uc002wsg.1_Intron|XRN2_uc010zsk.1_Intron	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2						cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1						CTTCAGAAACTTTTTTTTTTG	0.249													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23531770	23531770	+	IGR	DEL	G	-	-	rs5840998		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23531770delG								CSTT (9117 upstream) : CST9L (13602 downstream)																							AGGAGTAAAAGTGCTGTGAGT	0.398													3	5	---	---	---	---	
CST5	1473	broad.mit.edu	37	20	23861813	23861813	+	5'Flank	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23861813delA	uc002wtr.1	-							NM_001900	NP_001891	P28325	CYTD_HUMAN	cystatin D precursor							extracellular region	cysteine-type endopeptidase inhibitor activity|protein binding				0						taaaatgcctaattgtatgtg	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26209149	26209150	+	IGR	DEL	AA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26209149_26209150delAA								MIR663 (20235 upstream) : None (None downstream)																							TTTGTATTTTAAAAGATACTTA	0.198													4	2	---	---	---	---	
TM9SF4	9777	broad.mit.edu	37	20	30753553	30753554	+	3'UTR	INS	-	T	T			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30753553_30753554insT	uc002wxj.2	+	18					TM9SF4_uc010zts.1_3'UTR|TM9SF4_uc002wxk.2_3'UTR|TM9SF4_uc010gdz.2_3'UTR	NM_014742	NP_055557	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4							integral to membrane				central_nervous_system(1)|pancreas(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TCTGGTTTGGATTTTTTTTTCC	0.416													4	2	---	---	---	---	
MMP24	10893	broad.mit.edu	37	20	33836576	33836576	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33836576delG	uc002xbu.2	+						EDEM2_uc010zuv.1_Intron	NM_006690	NP_006681	Q9Y5R2	MMP24_HUMAN	matrix metalloproteinase 24 preproprotein						proteolysis	integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00252)			TTGGCCCCGTGGTCTCCAGAG	0.512													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	34664142	34664142	+	IGR	DEL	T	-	-	rs113482157		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34664142delT								LOC647979 (25260 upstream) : EPB41L1 (15284 downstream)																							TTCACCCAACTTTTTTTTTTC	0.418													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	39094432	39094433	+	IGR	DEL	TG	-	-	rs67018430		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39094432_39094433delTG								None (None upstream) : MAFB (220086 downstream)																							TGTTTTAAATtgtgtgtgtgtg	0.287													4	2	---	---	---	---	
ZMYND8	23613	broad.mit.edu	37	20	45978592	45978592	+	Intron	DEL	A	-	-	rs5841687		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45978592delA	uc002xta.1	-						ZMYND8_uc010ghr.1_5'Flank|ZMYND8_uc002xst.1_5'Flank|ZMYND8_uc002xsu.1_5'Flank|ZMYND8_uc002xsv.1_5'Flank|ZMYND8_uc002xsw.1_5'Flank|ZMYND8_uc002xsx.1_5'Flank|ZMYND8_uc002xsy.1_5'Flank|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc010ghs.1_5'Flank|ZMYND8_uc002xth.2_Intron|uc002xtj.2_5'Flank	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			GAACTGAGCCAAAAAAAACCC	0.398													3	3	---	---	---	---	
ZMYND8	23613	broad.mit.edu	37	20	45982368	45982368	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45982368delA	uc002xta.1	-						ZMYND8_uc002xsz.1_5'Flank|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc002xth.2_Intron|uc002xti.1_5'Flank|uc002xtj.2_RNA	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			GTCTTGAAGGAAAAAAAAGGA	0.453													4	2	---	---	---	---	
SULF2	55959	broad.mit.edu	37	20	46375825	46375826	+	Intron	INS	-	TGCTGG	TGCTGG	rs146110947	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46375825_46375826insTGCTGG	uc002xto.2	-						SULF2_uc002xtr.2_Intron|SULF2_uc002xtq.2_Intron|SULF2_uc010ghv.1_Intron	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor						bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6						GTGCTCACTGCTGCTGGTGGCA	0.337													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49078670	49078670	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49078670delT								CEBPB (269458 upstream) : PTPN1 (48221 downstream)																							ggtgaacacctttttccccta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49586277	49586277	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49586277delT								MOCS3 (8457 upstream) : KCNG1 (33917 downstream)																							CTTGGGGCACtttttttttga	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49940718	49940727	+	IGR	DEL	TTGGCCCAGC	-	-	rs67157158		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49940718_49940727delTTGGCCCAGC								KCNG1 (301043 upstream) : NFATC2 (67039 downstream)																							tagggttgatttggcccagcttggcttggg	0.267													4	2	---	---	---	---	
NFATC2	4773	broad.mit.edu	37	20	50150643	50150643	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50150643delT	uc002xwd.2	-						NFATC2_uc002xwc.2_Intron|NFATC2_uc010zyv.1_Intron|NFATC2_uc010zyw.1_Intron|NFATC2_uc010zyx.1_Intron|NFATC2_uc010zyy.1_Intron|NFATC2_uc010zyz.1_Intron|NFATC2_uc002xwe.2_Intron	NM_173091	NP_775114	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells,						B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)					ctctctgcagtttacataaac	0.080													4	2	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51929282	51929282	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51929282delA	uc002xwo.2	+							NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			CCTAGATTTTAAAAAAGGAAA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53443203	53443204	+	IGR	DEL	GT	-	-	rs57958827		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53443203_53443204delGT								DOK5 (175494 upstream) : None (None downstream)																							AATTACCCCAGTAACAAATTAC	0.218													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53443206	53443219	+	IGR	DEL	ACAAATTACCCCAG	-	-	rs71196471		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53443206_53443219delACAAATTACCCCAG								DOK5 (175497 upstream) : None (None downstream)																							TACCCCAGTAACAAATTACCCCAGTAACAAATCA	0.206													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	62604379	62604380	+	IGR	INS	-	GTATTTGT	GTATTTGT	rs142567120	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62604379_62604380insGTATTTGT								ZNF512B (3161 upstream) : SAMD10 (1086 downstream)																							TCTGCATGCTAGTATTTGTGTA	0.475													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9544374	9544374	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9544374delT								None (None upstream) : None (None downstream)																							ctcctggcactgaccttgccc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10725157	10725157	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10725157delC								None (None upstream) : TPTE (181586 downstream)																							atttccttttccatgataggc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10738981	10738981	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10738981delA								None (None upstream) : TPTE (167762 downstream)																							gattacatttattgatttgca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10745931	10745931	+	IGR	DEL	T	-	-	rs111734254		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10745931delT								None (None upstream) : TPTE (160812 downstream)																							gagttaaacctttttttttga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10772829	10772830	+	IGR	INS	-	GAA	GAA	rs148229481		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10772829_10772830insGAA								None (None upstream) : TPTE (133913 downstream)																							agtttttatttgaagatatttc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10780119	10780123	+	IGR	DEL	TGGAA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10780119_10780123delTGGAA								None (None upstream) : TPTE (126620 downstream)																							tgaagtggagtggaatggagtggaa	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11037605	11037606	+	Intron	INS	-	A	A			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11037605_11037606insA	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AAATAACTGTCAAGGAAAATAC	0.322													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11076421	11076422	+	Intron	INS	-	T	T	rs56216079		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11076421_11076422insT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tttttctgacctttagttttat	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14361863	14361864	+	IGR	INS	-	C	C	rs146825566		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14361863_14361864insC								None (None upstream) : C21orf99 (48623 downstream)																							ctccatccaaaaaaagttcaac	0.000													5	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14362623	14362623	+	IGR	DEL	T	-	-	rs151299636		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14362623delT								None (None upstream) : C21orf99 (47864 downstream)																							tgtgaggatatttccttttct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14363273	14363275	+	IGR	DEL	TTC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14363273_14363275delTTC								None (None upstream) : C21orf99 (47212 downstream)																							tttctcaggattcttctgtctag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	15205585	15205585	+	IGR	DEL	C	-	-	rs145626753		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15205585delC								POTED (191679 upstream) : C21orf15 (9870 downstream)																							GGCTGCAAAACTTTTGTTGGT	0.348													4	3	---	---	---	---	
ABCC13	150000	broad.mit.edu	37	21	15684782	15684783	+	Intron	DEL	GA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15684782_15684783delGA	uc002yjs.2	+											Homo sapiens ATP-binding cassette protein C13 (ABCC13) mRNA, complete cds.												0						cacaaagagggagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	17041758	17041758	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17041758delC								NRIP1 (604632 upstream) : USP25 (60738 downstream)																							CAAGCTCTTTCCAAAGTAAGA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	21865146	21865146	+	IGR	DEL	T	-	-	rs143565469		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21865146delT								None (None upstream) : C21orf131 (249768 downstream)																							tcattttctcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	32234671	32234671	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32234671delT								KRTAP7-1 (32620 upstream) : KRTAP11-1 (18295 downstream)																							CACAACTAGCTTATTAAAAAC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	32400618	32400618	+	IGR	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32400618delA								KRTAP11-1 (146744 upstream) : KRTAP19-8 (9861 downstream)																							acaaactgggaaaaaaaatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	34474026	34474027	+	IGR	DEL	AC	-	-	rs149260698		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34474026_34474027delAC								OLIG1 (29299 upstream) : C21orf54 (63750 downstream)																							AGAGAGAGAGACAAAGACTCAA	0.658													2	4	---	---	---	---	
TMEM50B	757	broad.mit.edu	37	21	34824151	34824152	+	Intron	INS	-	AG	AG	rs144166041	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34824151_34824152insAG	uc002yrt.1	-						TMEM50B_uc002yrs.1_Intron|TMEM50B_uc010gmb.1_Intron	NM_006134	NP_006125	P56557	TM50B_HUMAN	transmembrane protein 50B							endoplasmic reticulum|integral to membrane|plasma membrane				ovary(1)|skin(1)	2						aggccaagaacagctttaagag	0.000													4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36741316	36741316	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36741316delA	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						GCCTTCTTTTAGGAAAAAACA	0.209			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	37495874	37495874	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37495874delA	uc011aea.1	-											Homo sapiens cDNA FLJ59082 complete cds.																		actcagttttaaaataactaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40211861	40211861	+	IGR	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40211861delG								ETS2 (14985 upstream) : PSMG1 (335529 downstream)																							GCACACCTctggggccctccc	0.194													4	2	---	---	---	---	
BRWD1	54014	broad.mit.edu	37	21	40673403	40673403	+	Intron	DEL	C	-	-	rs35684385		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40673403delC	uc002yxk.1	-						BRWD1_uc002yxl.2_Intron|BRWD1_uc002yxm.2_Intron	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				gaaactgaggccctcagtcaa	0.000													4	6	---	---	---	---	
LCA5L	150082	broad.mit.edu	37	21	40812462	40812462	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40812462delA	uc002yxu.2	-						LCA5L_uc002yxv.2_Intron|LCA5L_uc002yxw.1_Intron|LCA5L_uc002yxx.1_Intron|LCA5L_uc002yxy.2_5'Flank	NM_152505	NP_689718	O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like												0		Prostate(19;1.2e-06)				accctgtctcaaaaaaaaaca	0.035													4	2	---	---	---	---	
SH3BGR	6450	broad.mit.edu	37	21	40842993	40842993	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40842993delT	uc002yya.2	+						SH3BGR_uc002yxz.2_Intron	NM_007341	NP_031367	P55822	SH3BG_HUMAN	SH3-binding domain and glutamic acid-rich						protein complex assembly	cytosol	SH3 domain binding|SH3/SH2 adaptor activity				0		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)		ggaaactttgttttttcctTT	0.050													4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	41867120	41867120	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41867120delA	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				aaattattttaaaaagtctaa	0.000													4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	41993019	41993019	+	Intron	DEL	A	-	-	rs112718296	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41993019delA	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				taaaaatgacaaaaaaggggc	0.000													4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	42099320	42099320	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42099320delA	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AGTACTTCAGAAAAAAATTAA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44584551	44584552	+	IGR	INS	-	T	T	rs144926590	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44584551_44584552insT								U2AF1 (56863 upstream) : CRYAA (4589 downstream)																							tgagttcagtgttagtgaatca	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	46770602	46770603	+	IGR	DEL	CA	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46770602_46770603delCA								LOC642852 (53334 upstream) : COL18A1 (54494 downstream)																							aatgcattcccacacacaccat	0.000													4	2	---	---	---	---	
LSS	4047	broad.mit.edu	37	21	47620479	47620479	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47620479delA	uc002zij.2	-						LSS_uc011afv.1_Intron|LSS_uc002zil.2_Intron|LSS_uc002zik.2_Intron	NM_001001438	NP_001001438	P48449	ERG7_HUMAN	lanosterol synthase isoform 1						cholesterol biosynthetic process	endoplasmic reticulum membrane	lanosterol synthase activity				0	Breast(49;0.214)					gagacaccagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17653996	17653996	+	IGR	DEL	C	-	-	rs11363838		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17653996delC								CECR4 (7662 upstream) : CECR1 (6196 downstream)																							atttgggattccggaatgggt	0.189													4	2	---	---	---	---	
BID	637	broad.mit.edu	37	22	18237539	18237539	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18237539delT	uc002znd.1	-						BID_uc002znc.1_Intron|BID_uc002zne.1_Intron|BID_uc010gra.1_Intron|BID_uc002znf.1_Intron|BID_uc010grb.1_Intron|BID_uc010grc.1_Intron	NM_001196	NP_001187	P55957	BID_HUMAN	BH3 interacting domain death agonist isoform 2						activation of pro-apoptotic gene products|establishment of protein localization in membrane|induction of apoptosis by intracellular signals|induction of apoptosis via death domain receptors|neuron apoptosis|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|release of cytochrome c from mitochondria	cytosol|membrane fraction|mitochondrial outer membrane	death receptor binding				0		all_epithelial(15;0.198)		Lung(27;0.0419)		tttgtttgtgttttttttgga	0.174													4	2	---	---	---	---	
GGT3P	2679	broad.mit.edu	37	22	18771547	18771548	+	5'Flank	INS	-	T	T	rs149629602		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18771547_18771548insT	uc010gri.1	-						GGT3P_uc011ago.1_Intron|GGT3P_uc011agp.1_Intron|GGT3P_uc002zob.1_Intron					Homo sapiens cDNA clone IMAGE:5761295, **** WARNING: chimeric clone ****.												0						TTTTTGttttgttttttttttc	0.203													4	2	---	---	---	---	
PI4KA	5297	broad.mit.edu	37	22	21178398	21178398	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21178398delA	uc002zsz.3	-						PI4KA_uc010gsq.1_Intron	NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			TAGaaaaaagaaaaaaaaaaa	0.383													11	5	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22419634	22419634	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22419634delG	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						TCTGTCCTCTGGCTCTATGGC	0.463													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22657422	22657422	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22657422delT	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_Intron|LOC96610_uc010gto.2_Intron					Parts of antibodies, mostly variable regions.												0						AAATACTAACTGTTTTACGAA	0.403													4	7	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26373252	26373263	+	Intron	DEL	TGTATTTGTATT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26373252_26373263delTGTATTTGTATT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron|MYO18B_uc010gva.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						TTCCAACTCCtgtatttgtatttgtatttgta	0.349													2	4	---	---	---	---	
TTC28	23331	broad.mit.edu	37	22	28532846	28532846	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28532846delT	uc003adp.3	-							NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28								binding				0						TGGCCTCACATTTTATCAGCC	0.458													4	2	---	---	---	---	
DEPDC5	9681	broad.mit.edu	37	22	32266255	32266255	+	Intron	DEL	G	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32266255delG	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alu.2_Intron|DEPDC5_uc003alv.2_Intron|DEPDC5_uc011alw.1_Intron|DEPDC5_uc003alw.2_Intron|DEPDC5_uc011alx.1_Intron|DEPDC5_uc010gwk.2_Intron|DEPDC5_uc011aly.1_Intron	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8						TGTGGTTTGAGGCAGGTGCTG	0.473													4	2	---	---	---	---	
BPIL2	254240	broad.mit.edu	37	22	32827620	32827620	+	Intron	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32827620delT	uc003amn.2	-						BPIL2_uc010gwo.2_Intron|BPIL2_uc011amb.1_Intron	NM_174932	NP_777592	Q8NFQ6	BPIL2_HUMAN	bactericidal/permeability-increasing							extracellular region	lipopolysaccharide binding|phospholipid binding			ovary(1)|skin(1)	2						CTCCTTTGAATTTTTTTTTTC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	34700635	34700636	+	IGR	INS	-	AAA	AAA	rs150984411	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34700635_34700636insAAA								LARGE (382051 upstream) : ISX (761493 downstream)																							ACAACCACAACAAAAGCAAGAG	0.416													3	3	---	---	---	---	
TOM1	10043	broad.mit.edu	37	22	35739336	35739337	+	Intron	INS	-	CA	CA	rs144221305		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35739336_35739337insCA	uc003ann.2	+						TOM1_uc011ami.1_Intron|TOM1_uc011amj.1_Intron|TOM1_uc003ans.2_Intron|TOM1_uc011amk.1_Intron|TOM1_uc003anp.2_Intron|TOM1_uc011aml.1_Intron|TOM1_uc003ano.2_Intron|TOM1_uc003anq.2_Intron|TOM1_uc003anr.2_Intron	NM_005488	NP_005479	O60784	TOM1_HUMAN	target of myb1 isoform 1						endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1						cacacacacaccacacacatct	0.000													3	3	---	---	---	---	
CACNG2	10369	broad.mit.edu	37	22	37025554	37025555	+	Intron	DEL	TG	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37025554_37025555delTG	uc003aps.1	-							NM_006078	NP_006069	Q9Y698	CCG2_HUMAN	voltage-dependent calcium channel gamma-2						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0						tgtgtgtgtttgtgtgtgtgtg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	37719214	37719215	+	IGR	INS	-	TTGT	TTGT	rs145112558	by1000genomes	TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37719214_37719215insTTGT								CYTH4 (7826 upstream) : ELFN2 (44764 downstream)																							gggtttttttgttgtttgtttg	0.000													2	5	---	---	---	---	
ZC3H7B	23264	broad.mit.edu	37	22	41735630	41735630	+	Intron	DEL	A	-	-	rs66971293		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41735630delA	uc003azw.2	+						ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B						interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1						actccgtctcaaaaaaaaaaa	0.249													12	7	---	---	---	---	
ZC3H7B	23264	broad.mit.edu	37	22	41749841	41749841	+	Intron	DEL	T	-	-	rs60656030		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41749841delT	uc003azw.2	+						ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B						interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1						CTGCCCTCCATCAGTCTCCTG	0.567													4	4	---	---	---	---	
TCF20	6942	broad.mit.edu	37	22	42585255	42585255	+	Intron	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42585255delC	uc003bcj.1	-						TCF20_uc003bck.1_Intron|TCF20_uc003bnt.2_Intron	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5						TGACACATGGCCAGGGGGTCT	0.522													4	2	---	---	---	---	
TBC1D22A	25771	broad.mit.edu	37	22	47528164	47528168	+	Intron	DEL	CTGCT	-	-	rs5845773		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47528164_47528168delCTGCT	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)		CCGCCCCGCCCTGCTGTCTCTGGCC	0.610													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47733425	47733426	+	IGR	INS	-	TT	TT			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47733425_47733426insTT								TBC1D22A (163703 upstream) : None (None downstream)																							agccatttgtattttctttttt	0.094													4	2	---	---	---	---	
USP9X	8239	broad.mit.edu	37	X	41091472	41091473	+	Intron	INS	-	TTTTTG	TTTTTG	rs71955511		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41091472_41091473insTTTTTG	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						TTTCAAGCCTTtttttgttttt	0.332													8	9	---	---	---	---	
LAS1L	81887	broad.mit.edu	37	X	64738891	64738891	+	Intron	DEL	A	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64738891delA	uc004dwa.1	-						LAS1L_uc004dwc.1_Intron|LAS1L_uc004dwd.1_Intron|LAS1L_uc004dvy.1_5'UTR|LAS1L_uc004dvz.1_5'UTR	NM_031206	NP_112483	Q9Y4W2	LAS1L_HUMAN	LAS1-like							MLL1 complex|nucleolus	protein binding			ovary(3)|large_intestine(1)	4						GGAGGAAAAGAAAAAAAAAGC	0.537													4	2	---	---	---	---	
ARMCX5	64860	broad.mit.edu	37	X	101857839	101857841	+	In_Frame_Del	DEL	CTC	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101857839_101857841delCTC	uc004ejg.2	+	6	1651_1653	c.770_772delCTC	c.(769-774)ACTCCT>ACT	p.P258del	ARMCX5_uc004ejh.2_In_Frame_Del_p.P258del	NM_022838	NP_073749	Q6P1M9	ARMX5_HUMAN	armadillo repeat containing, X-linked 5	258							binding			ovary(1)	1						TTGATTGAAACTCCTCTGGGGAT	0.473													71	59	---	---	---	---	
SPANXC	64663	broad.mit.edu	37	X	140446532	140446533	+	Intron	INS	-	CT	CT			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140446532_140446533insCT	uc004fbl.2	-									Q9NY87	SPNXC_HUMAN	Homo sapiens nuclear-associated protein SPAN-Xa (SPANX) mRNA, complete cds.							cytoplasm|nucleus					0	Acute lymphoblastic leukemia(192;7.65e-05)					gtagctgagcactctctctaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	149449757	149449757	+	IGR	DEL	C	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149449757delC								MIR2114 (53439 upstream) : MAMLD1 (80079 downstream)																							ATTCCCTTCTCCCTTTCCCTT	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9992165	9992167	+	IGR	DEL	CTC	-	-	rs112314725		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9992165_9992167delCTC								TTTY22 (341311 upstream) : None (None downstream)																							ttttcttctactcctccccacct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13272775	13272776	+	IGR	DEL	TT	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13272775_13272776delTT								None (None upstream) : None (None downstream)																							ttcttttttctttttttttttt	0.168													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28661514	28661514	+	IGR	DEL	T	-	-			TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28661514delT								None (None upstream) : None (None downstream)																							GCCACAGAGATTTTTTTTTTT	0.388													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58977825	58977826	+	IGR	INS	-	TCCAT	TCCAT	rs111257567		TCGA-CW-5581-01A-02D-1534-10	TCGA-CW-5581-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58977825_58977826insTCCAT								None (None upstream) : None (None downstream)																							ttccactaaactcgactccact	0.064													5	3	---	---	---	---	
