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
ESPNP	284729	broad.mit.edu	37	1	17017734	17017734	+	Missense_Mutation	SNP	C	T	T	rs12561805	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17017734C>T	uc001azn.1	-	11	1994	c.1880G>A	c.(1879-1881)CGG>CAG	p.R627Q		NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						CAGCTTCTTCCGCAGGAGGTC	0.647													4	12	---	---	---	---	PASS
HSPG2	3339	broad.mit.edu	37	1	22222714	22222714	+	Silent	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22222714C>T	uc001bfj.2	-	2	193	c.153G>A	c.(151-153)TCG>TCA	p.S51S	HSPG2_uc009vqd.2_Silent_p.S51S|HSPG2_uc009vqe.1_Silent_p.S6S	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	51					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)	CAGAAAGGTACGAATGTGTCC	0.557													16	42	---	---	---	---	PASS
TINAGL1	64129	broad.mit.edu	37	1	32050373	32050373	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32050373G>T	uc001bta.2	+	6	803	c.677G>T	c.(676-678)TGT>TTT	p.C226F	TINAGL1_uc001bsz.2_Missense_Mutation_p.C81F|TINAGL1_uc010ogj.1_Missense_Mutation_p.C195F|TINAGL1_uc010ogk.1_Missense_Mutation_p.C226F	NM_022164	NP_071447	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1	226					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)		CAAGGCAACTGTGCAGGCTCC	0.617													6	17	---	---	---	---	PASS
THRAP3	9967	broad.mit.edu	37	1	36755253	36755253	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36755253C>T	uc001cae.3	+	5	1857	c.1633C>T	c.(1633-1635)CGA>TGA	p.R545*	THRAP3_uc001caf.3_Nonsense_Mutation_p.R545*|THRAP3_uc001cag.1_Nonsense_Mutation_p.R545*	NM_005119	NP_005110	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	545					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(5)|lung(3)|breast(1)	9		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CTCTGAGAGCCGAGACAAGCT	0.498			T	USP6	aneurysmal bone cysts								19	27	---	---	---	---	PASS
BCL10	8915	broad.mit.edu	37	1	85736463	85736463	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85736463T>C	uc001dkz.2	-	3	889	c.184A>G	c.(184-186)AGA>GGA	p.R62G		NM_003921	NP_003912	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	62	CARD.				apoptosis|cellular response to mechanical stimulus|innate immune response|interleukin-6 biosynthetic process|lymphotoxin A biosynthetic process|negative regulation of mature B cell apoptosis|neural tube closure|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 biosynthetic process|positive regulation of mast cell cytokine production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of transcription, DNA-dependent|protein homooligomerization|response to molecule of bacterial origin|T cell receptor signaling pathway	CBM complex|cytosol|lysosome|membrane raft|nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protease binding|protein C-terminus binding|protein kinase B binding|protein self-association|transcription coactivator activity|ubiquitin binding|ubiquitin protein ligase binding			lung(2)	2				all cancers(265;0.0114)|Epithelial(280;0.0311)		GCCCTTTTTCTACTTGATGTT	0.378			T	IGH@	MALT 								5	305	---	---	---	---	PASS
AMPD2	271	broad.mit.edu	37	1	110170727	110170727	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110170727C>G	uc009wfh.1	+	11	1807	c.1265C>G	c.(1264-1266)TCG>TGG	p.S422W	AMPD2_uc009wfg.1_RNA|AMPD2_uc001dyb.1_Missense_Mutation_p.S341W|AMPD2_uc001dyc.1_Missense_Mutation_p.S422W|AMPD2_uc010ovr.1_Missense_Mutation_p.S347W|AMPD2_uc010ovs.1_Missense_Mutation_p.S304W|AMPD2_uc001dyd.1_Missense_Mutation_p.S303W|AMPD2_uc001dye.1_5'Flank	NM_004037	NP_004028	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2 (isoform L)	422					purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|breast(1)	3		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		ATCCATGCCTCGTCCTGCATG	0.607													8	11	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152193684	152193684	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152193684A>G	uc001ezt.1	-	3	497	c.421T>C	c.(421-423)TCC>CCC	p.S141P		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	141	1.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACGTTTCTGGAATAGGAATCA	0.423													7	203	---	---	---	---	PASS
DCST2	127579	broad.mit.edu	37	1	155002622	155002622	+	Missense_Mutation	SNP	G	A	A	rs138904334		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155002622G>A	uc001fgm.2	-	7	1195	c.1115C>T	c.(1114-1116)ACG>ATG	p.T372M	DCST2_uc009wpb.2_RNA	NM_144622	NP_653223	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	372	Cytoplasmic (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CAGCCCTGCCGTGGAGCGCAC	0.597													6	12	---	---	---	---	PASS
GON4L	54856	broad.mit.edu	37	1	155764938	155764938	+	Silent	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155764938T>C	uc001flz.2	-	12	1747	c.1650A>G	c.(1648-1650)GAA>GAG	p.E550E	GON4L_uc001fly.1_Silent_p.E550E|GON4L_uc009wrh.1_Silent_p.E550E|GON4L_uc001fma.1_Silent_p.E550E|GON4L_uc001fmc.2_Silent_p.E550E|GON4L_uc001fmd.3_Silent_p.E550E|GON4L_uc009wri.2_Silent_p.E136E|GON4L_uc009wrj.1_Silent_p.E65E|GON4L_uc001fme.2_Silent_p.E378E|GON4L_uc001fmf.2_Silent_p.E244E	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	550	Asp-rich.				regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					CATCATCTGCTTCATCTAGGA	0.368													59	86	---	---	---	---	PASS
GON4L	54856	broad.mit.edu	37	1	155764940	155764940	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155764940C>T	uc001flz.2	-	12	1745	c.1648G>A	c.(1648-1650)GAA>AAA	p.E550K	GON4L_uc001fly.1_Missense_Mutation_p.E550K|GON4L_uc009wrh.1_Missense_Mutation_p.E550K|GON4L_uc001fma.1_Missense_Mutation_p.E550K|GON4L_uc001fmc.2_Missense_Mutation_p.E550K|GON4L_uc001fmd.3_Missense_Mutation_p.E550K|GON4L_uc009wri.2_Missense_Mutation_p.E136K|GON4L_uc009wrj.1_Missense_Mutation_p.E65K|GON4L_uc001fme.2_Missense_Mutation_p.E378K|GON4L_uc001fmf.2_Missense_Mutation_p.E244K	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	550	Asp-rich.				regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TCATCTGCTTCATCTAGGAAA	0.363													58	85	---	---	---	---	PASS
C1orf129	80133	broad.mit.edu	37	1	170934396	170934396	+	Silent	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170934396C>T	uc001ghg.2	+	7	610	c.480C>T	c.(478-480)TAC>TAT	p.Y160Y	C1orf129_uc009wvy.2_Translation_Start_Site|C1orf129_uc010plz.1_Silent_p.Y160Y	NM_025063	NP_079339	Q5TGP6	CA129_HUMAN	hypothetical protein LOC80133 isoform 2	160							binding			pancreas(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TCAGAAAATACGTAAGTCACA	0.398													4	195	---	---	---	---	PASS
PSEN2	5664	broad.mit.edu	37	1	227073330	227073330	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227073330G>T	uc009xeo.1	+	6	875	c.448G>T	c.(448-450)GTG>TTG	p.V150L	PSEN2_uc009xep.1_Missense_Mutation_p.V150L|PSEN2_uc001hqk.2_RNA	NM_000447	NP_000438	P49810	PSN2_HUMAN	presenilin 2 isoform 1	150	Helical; (Potential).				amyloid precursor protein catabolic process|anti-apoptosis|apoptosis|beta-amyloid metabolic process|calcium ion transport|induction of apoptosis by extracellular signals|intracellular signal transduction|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity	apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear inner membrane|perinuclear region of cytoplasm|Z disc	aspartic-type endopeptidase activity|protein binding			lung(2)	2		Prostate(94;0.0771)				CAGCGTCATCGTGGTTATGAC	0.597													3	34	---	---	---	---	PASS
GNPAT	8443	broad.mit.edu	37	1	231398532	231398532	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231398532T>C	uc001hup.3	+	4	708	c.502T>C	c.(502-504)TTC>CTC	p.F168L	GNPAT_uc009xfo.1_Missense_Mutation_p.F59L|GNPAT_uc009xfp.2_Missense_Mutation_p.F107L	NM_014236	NP_055051	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	168					ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity			ovary(3)|breast(1)	4	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				TTACATTGACTTCCTCATGTT	0.353													7	471	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235955199	235955199	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235955199A>G	uc001hxj.2	-	12	4518	c.4343T>C	c.(4342-4344)CTT>CCT	p.L1448P	LYST_uc009xgb.1_RNA|LYST_uc010pxs.1_Intron|LYST_uc001hxl.1_Missense_Mutation_p.L1448P	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	1448					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			CCAAGATGAAAGCAGCCGATG	0.498									Chediak-Higashi_syndrome				5	67	---	---	---	---	PASS
XPO1	7514	broad.mit.edu	37	2	61720125	61720125	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61720125G>C	uc002sbj.2	-	13	2037	c.1309C>G	c.(1309-1311)CAA>GAA	p.Q437E	XPO1_uc010fcl.2_Missense_Mutation_p.Q433E|XPO1_uc010ypn.1_Missense_Mutation_p.Q433E|XPO1_uc002sbk.2_Translation_Start_Site|XPO1_uc002sbh.2_Missense_Mutation_p.Q84E	NM_003400	NP_003391	O14980	XPO1_HUMAN	exportin 1	437	HEAT 3.|Necessary for HTLV-1 Rex-mediated mRNA export.|Interaction with RANBP3.|Interaction with Ran and nuclear export complex formation.			VLVVENDQGEVVREFMK->DEDEENDQGEDEEEDDD: Partially restores Ran binding activity in presence of cargo.|EEVLVVENDQGEVVREFMKD->QQVLVVQNNQGQVVRQFMK N: Abolishes Ran binding activity in absence of cargo and abolishes partially Ran binding activity in presence of cargo.	intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			ACTTCTCCTTGATCATTCTCT	0.318													8	575	---	---	---	---	PASS
CEP68	23177	broad.mit.edu	37	2	65300044	65300044	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65300044C>A	uc002sdl.3	+	3	2028	c.1814C>A	c.(1813-1815)CCA>CAA	p.P605Q	CEP68_uc002sdj.2_Missense_Mutation_p.P605Q|CEP68_uc010yqb.1_Missense_Mutation_p.P605Q|CEP68_uc002sdk.3_Intron|CEP68_uc010yqc.1_Missense_Mutation_p.P605Q|CEP68_uc010yqd.1_Missense_Mutation_p.P605Q	NM_015147	NP_055962	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	605					centrosome organization	centrosome				skin(1)	1						TTCTCAGACCCAGATGTTGAA	0.557													9	50	---	---	---	---	PASS
ANKRD23	200539	broad.mit.edu	37	2	97505515	97505515	+	Silent	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97505515T>C	uc002sxa.2	-	8	800	c.771A>G	c.(769-771)AAA>AAG	p.K257K	ANKRD23_uc002sxb.2_RNA|ANKRD23_uc002sxc.2_Silent_p.K215K	NM_144994	NP_659431	Q86SG2	ANR23_HUMAN	diabetes related ankyrin repeat protein	257	ANK 4.					nucleus				ovary(1)	1						GCTTCATGGCTTTGTAGCTGC	0.677													3	6	---	---	---	---	PASS
UNC50	25972	broad.mit.edu	37	2	99226122	99226122	+	Intron	SNP	G	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99226122G>T	uc002szc.3	+						C2orf64_uc002syz.2_5'Flank|C2orf64_uc002sza.2_Intron|UNC50_uc002szb.2_5'UTR|UNC50_uc010yvl.1_5'UTR	NM_014044	NP_054763	Q53HI1	UNC50_HUMAN	unc-50 homolog						protein transport	Golgi membrane|integral to membrane|nuclear inner membrane	RNA binding				0						GAAGAACATGGAAAGTGACCT	0.468													6	30	---	---	---	---	PASS
PASK	23178	broad.mit.edu	37	2	242072498	242072498	+	Intron	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242072498C>T	uc002wao.1	-						PASK_uc010zol.1_Intron|PASK_uc010zom.1_Intron|PASK_uc010fzl.1_Intron|PASK_uc010zon.1_Intron|PASK_uc002wap.2_5'UTR|PASK_uc002waq.2_Intron	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase						regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|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;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		CTCCCTAAAACGAATCTGCTC	0.353													20	26	---	---	---	---	PASS
STT3B	201595	broad.mit.edu	37	3	31667559	31667559	+	Silent	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31667559T>C	uc011axe.1	+	13	2013	c.2013T>C	c.(2011-2013)GAT>GAC	p.D671D		NM_178862	NP_849193	Q8TCJ2	STT3B_HUMAN	source of immunodominant MHC-associated	671					protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0						CTGGTGATGATATCAACAAAT	0.373													6	536	---	---	---	---	PASS
MLH1	4292	broad.mit.edu	37	3	37038191	37038191	+	Silent	SNP	C	A	A	rs61751642	byFrequency	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37038191C>A	uc003cgl.2	+	2	258	c.198C>A	c.(196-198)ACC>ACA	p.T66T	MLH1_uc011aye.1_5'UTR|MLH1_uc011ayb.1_Intron|MLH1_uc010hge.2_Silent_p.T66T|MLH1_uc003cgn.3_5'UTR|MLH1_uc011ayc.1_5'UTR|MLH1_uc011ayd.1_5'UTR|MLH1_uc003cgo.2_5'UTR	NM_000249	NP_000240	P40692	MLH1_HUMAN	MutL protein homolog 1	66					mismatch repair|somatic hypermutation of immunoglobulin genes	chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|protein binding			large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1)	77						ACAATGGCACCGGGATCAGGG	0.428		1	D|Mis|N|F|S		colorectal|endometrial|ovarian|CNS	colorectal|endometrial|ovarian|CNS		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				5	300	---	---	---	---	PASS
CDC25A	993	broad.mit.edu	37	3	48215854	48215854	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48215854G>T	uc003csh.1	-	9	1214	c.850C>A	c.(850-852)CCA>ACA	p.P284T	CDC25A_uc003csi.1_Missense_Mutation_p.P244T	NM_001789	NP_001780	P30304	MPIP1_HUMAN	cell division cycle 25A isoform a	284					cell cycle checkpoint|cell division|cell proliferation|cellular response to UV|DNA replication|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle	cytosol|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(3)|kidney(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000685)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		CTTCCAGGTGGAGACTCCTCT	0.517													105	26	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52441261	52441261	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52441261A>C	uc003ddx.2	-	7	624	c.509T>G	c.(508-510)TTT>TGT	p.F170C	BAP1_uc010hmh.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	170					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	p.E166fs*13(1)		pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		ATAGCTGACAAAGTGGAACGC	0.582			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								28	8	---	---	---	---	PASS
CRYBG3	131544	broad.mit.edu	37	3	97611768	97611768	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97611768C>G	uc003drx.2	+	8	1725	c.1661C>G	c.(1660-1662)TCT>TGT	p.S554C		NM_153605	NP_705833			beta-gamma crystallin domain containing 3												0						CATATAGATTCTGTTCCTAAT	0.279													8	299	---	---	---	---	PASS
OR5H1	26341	broad.mit.edu	37	3	97851659	97851659	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97851659A>T	uc011bgt.1	+	1	118	c.118A>T	c.(118-120)ATG>TTG	p.M40L		NM_001005338	NP_001005338	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H,	40	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2						CATCACCATCATGGGGAATCT	0.413													8	114	---	---	---	---	PASS
OR5H1	26341	broad.mit.edu	37	3	97851661	97851661	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97851661G>T	uc011bgt.1	+	1	120	c.120G>T	c.(118-120)ATG>ATT	p.M40I		NM_001005338	NP_001005338	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H,	40	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2						TCACCATCATGGGGAATCTTG	0.413													8	117	---	---	---	---	PASS
OR5H1	26341	broad.mit.edu	37	3	97851689	97851689	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97851689T>C	uc011bgt.1	+	1	148	c.148T>C	c.(148-150)TGG>CGG	p.W50R		NM_001005338	NP_001005338	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H,	50	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2						TGCTGTCATCTGGAAAGACCC	0.418													8	137	---	---	---	---	PASS
PLXND1	23129	broad.mit.edu	37	3	129308262	129308262	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129308262C>T	uc003emx.2	-	2	1520	c.1420G>A	c.(1420-1422)GTG>ATG	p.V474M		NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1 precursor	474	Extracellular (Potential).|Sema.				axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1						GCCACGGCCACGGAGGTGAGG	0.662													4	15	---	---	---	---	PASS
TXNDC6	347736	broad.mit.edu	37	3	138023808	138023808	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138023808G>C	uc003esg.2	-	9	726	c.698C>G	c.(697-699)ACC>AGC	p.T233S	TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Missense_Mutation_p.T148S|TXNDC6_uc003ese.1_Missense_Mutation_p.T172S	NM_178130	NP_835231	Q86XW9	TXND6_HUMAN	thioredoxin domain containing 6	233	NDK.				cell redox homeostasis|CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	cytoplasm|cytoskeleton	ATP binding|nucleoside diphosphate kinase activity			breast(3)|ovary(1)|pancreas(1)	5						CTCAGTCCTGGTGAGGATCAG	0.597													20	28	---	---	---	---	PASS
ATR	545	broad.mit.edu	37	3	142188266	142188266	+	Silent	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142188266T>C	uc003eux.3	-	38	6587	c.6465A>G	c.(6463-6465)GAA>GAG	p.E2155E	ATR_uc003euy.1_Silent_p.E41E	NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	2155	FAT.				cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						CAACAAAAACTTCATCGTGAG	0.353								Other_conserved_DNA_damage_response_genes					8	597	---	---	---	---	PASS
ZBBX	79740	broad.mit.edu	37	3	167000169	167000169	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167000169G>A	uc003fep.2	-	19	2317	c.1994C>T	c.(1993-1995)TCA>TTA	p.S665L	ZBBX_uc011bpc.1_Missense_Mutation_p.S704L|ZBBX_uc003feq.2_Missense_Mutation_p.S636L	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	665	Ser-rich.					intracellular	zinc ion binding			ovary(2)	2						TCTAGATGATGATTGAGCAGC	0.378													119	418	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511283	195511283	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511283C>T	uc011bto.1	-	2	7628	c.7168G>A	c.(7168-7170)GCT>ACT	p.A2390T	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)		GCTGAGGAAGCGTCGGTGACA	0.592													6	73	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195515059	195515059	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195515059G>A	uc011bto.1	-	2	3852	c.3392C>T	c.(3391-3393)ACA>ATA	p.T1131I	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	1008	Ser-rich.|Repeat.				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)		GGCGTGACCTGTGGATGCTGA	0.562													12	16	---	---	---	---	PASS
USO1	8615	broad.mit.edu	37	4	76721828	76721828	+	Silent	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76721828A>G	uc003hiu.2	+	15	1915	c.1740A>G	c.(1738-1740)AAA>AAG	p.K580K	USO1_uc003hiv.2_Silent_p.K422K|USO1_uc003hiw.2_Silent_p.K415K	NM_003715	NP_003706	O60763	USO1_HUMAN	USO1 homolog, vesicle docking protein	580	Globular head.				intracellular protein transport|vesicle fusion with Golgi apparatus	cytosol|Golgi membrane	protein binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TCATAGAGAAACTAGGATTTA	0.343													7	323	---	---	---	---	PASS
NAAA	27163	broad.mit.edu	37	4	76836107	76836107	+	Missense_Mutation	SNP	C	A	A	rs112900017		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76836107C>A	uc003hjb.2	-	10	1094	c.1030G>T	c.(1030-1032)GGT>TGT	p.G344C	NAAA_uc003hja.2_Intron	NM_014435	NP_055250	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase isoform 1	344					lipid metabolic process	lysosome	hydrolase activity			skin(1)	1						TCTGGGCTACCGGCGCTCATT	0.413													6	212	---	---	---	---	PASS
ABCG2	9429	broad.mit.edu	37	4	89020488	89020488	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89020488A>T	uc003hrg.2	-	12	1973	c.1480T>A	c.(1480-1482)TAC>AAC	p.Y494N	ABCG2_uc003hrh.2_Missense_Mutation_p.Y494N|ABCG2_uc003hrf.2_Missense_Mutation_p.Y362N	NM_004827	NP_004818	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G, member 2	494	ABC transmembrane type-2.|Helical; (Potential).				cellular iron ion homeostasis|urate metabolic process	integral to membrane|plasma membrane	ATP binding|heme transporter activity|protein homodimerization activity|xenobiotic-transporting ATPase activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Imatinib(DB00619)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nitrendipine(DB01054)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Topotecan(DB01030)	AACATGAAGTACACTATACAG	0.358													5	208	---	---	---	---	PASS
C4orf21	55345	broad.mit.edu	37	4	113506734	113506734	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113506734G>T	uc003iau.2	-	14	4275	c.4064C>A	c.(4063-4065)GCA>GAA	p.A1355E	C4orf21_uc003iav.2_RNA	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	177						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		GACAAGTTTTGCAGGTTGACT	0.373													7	362	---	---	---	---	PASS
SORBS2	8470	broad.mit.edu	37	4	186599615	186599615	+	5'UTR	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186599615C>T	uc003iyl.2	-	4					SORBS2_uc003iyh.2_5'UTR|SORBS2_uc011ckw.1_Missense_Mutation_p.V42I|SORBS2_uc003iyi.2_Missense_Mutation_p.V59I|SORBS2_uc011ckx.1_Missense_Mutation_p.V19I|SORBS2_uc003iyk.2_Missense_Mutation_p.V59I|SORBS2_uc003iym.2_Missense_Mutation_p.V73I|SORBS2_uc003iyn.1_Missense_Mutation_p.V19I|SORBS2_uc011cky.1_Missense_Mutation_p.V36I|SORBS2_uc003iyp.2_Missense_Mutation_p.V73I|SORBS2_uc003iyd.2_5'UTR|SORBS2_uc003iye.2_5'UTR|SORBS2_uc003iya.2_5'UTR|SORBS2_uc003iyb.2_5'UTR|SORBS2_uc003iyc.2_5'UTR|SORBS2_uc003iyg.2_Missense_Mutation_p.V59I|SORBS2_uc003iyf.2_Missense_Mutation_p.V36I	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TTTGGTCGAACGCTTCTAAAA	0.413													72	294	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13727702	13727702	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13727702G>A	uc003jfd.2	-	70	11989	c.11947C>T	c.(11947-11949)CTT>TTT	p.L3983F	DNAH5_uc003jfc.2_Missense_Mutation_p.L151F	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3983					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)					GCATTTGGAAGAGGTTCCTCC	0.413									Kartagener_syndrome				7	411	---	---	---	---	PASS
PCDHA11	56138	broad.mit.edu	37	5	140250599	140250599	+	Silent	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140250599C>T	uc003lia.2	+	1	2769	c.1911C>T	c.(1909-1911)GAC>GAT	p.D637D	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Silent_p.D637D	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	637	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGCCCTGGACGAGGCAGACT	0.662													3	12	---	---	---	---	PASS
PCDHAC2	56134	broad.mit.edu	37	5	140390965	140390965	+	3'UTR	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140390965C>T	uc003lii.2	+	4					PCDHA1_uc003lha.2_3'UTR|PCDHA1_uc003lhb.2_3'UTR|PCDHA2_uc003lhd.2_3'UTR|PCDHA3_uc003lhf.2_3'UTR|PCDHA4_uc003lhi.2_3'UTR|PCDHA4_uc003lhh.1_3'UTR|PCDHA5_uc003lhk.1_3'UTR|PCDHA5_uc003lhl.2_3'UTR|PCDHA6_uc003lhn.2_3'UTR|PCDHA6_uc003lho.2_3'UTR|PCDHA7_uc003lhq.2_3'UTR|PCDHA8_uc003lhs.2_3'UTR|PCDHA9_uc003lhu.2_3'UTR|PCDHA10_uc003lhw.2_3'UTR|PCDHA10_uc003lhx.2_3'UTR|PCDHA11_uc003lia.2_3'UTR|PCDHA12_uc003lic.2_3'UTR|PCDHA13_uc003lie.1_3'UTR|PCDHA13_uc003lif.2_3'UTR|PCDHAC1_uc003lih.2_3'UTR	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTAAGACTCCTGAAATATA	0.318													223	266	---	---	---	---	PASS
GCNT2	2651	broad.mit.edu	37	6	10529145	10529145	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10529145A>G	uc010joo.2	+	3	552	c.1A>G	c.(1-3)ATG>GTG	p.M1V	GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_5'UTR|GCNT2_uc010jon.2_5'UTR	NM_145649	NP_663624	Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2,	1	Cytoplasmic (Potential).					Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		CTGGTTGTGAATGATGGGCTC	0.373													8	399	---	---	---	---	PASS
HLA-C	3107	broad.mit.edu	37	6	31237140	31237140	+	Silent	SNP	A	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31237140A>T	uc003nsy.2	-	7	1078	c.1071T>A	c.(1069-1071)TCT>TCA	p.S357S	HLA-C_uc011dnj.1_Silent_p.S329S|HLA-C_uc003nsx.2_Silent_p.S236S|HLA-C_uc003nsz.2_Silent_p.S363S|HLA-C_uc010jsl.2_Missense_Mutation_p.L356Q|HLA-C_uc003nta.2_Intron|HLA-C_uc003ntb.2_RNA|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_RNA	NM_002117	NP_002108	Q9TNN7	1C05_HUMAN	major histocompatibility complex, class I, C	357	Cytoplasmic (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex					0						GAGACTCATCAGAGCCCTGGG	0.527													3	14	---	---	---	---	PASS
RIMS1	22999	broad.mit.edu	37	6	72892128	72892128	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72892128G>T	uc003pga.2	+	6	1031	c.954G>T	c.(952-954)AGG>AGT	p.R318S	RIMS1_uc011dyb.1_5'UTR|RIMS1_uc003pgc.2_5'UTR|RIMS1_uc003pgb.3_5'UTR	NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	318					calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)				AAAGCCGAAGGCTTGAGAAAG	0.582													4	28	---	---	---	---	PASS
SNAP91	9892	broad.mit.edu	37	6	84302945	84302945	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84302945G>A	uc011dze.1	-	18	2047	c.1730C>T	c.(1729-1731)GCG>GTG	p.A577V	SNAP91_uc011dzd.1_Missense_Mutation_p.A80V|SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Missense_Mutation_p.A575V|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Missense_Mutation_p.A575V	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog	577	Ala-rich.				clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		TGGCTTAGGCGCTGCAGCAAC	0.413													88	132	---	---	---	---	PASS
HIVEP2	3097	broad.mit.edu	37	6	143093080	143093080	+	Silent	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143093080C>T	uc003qjd.2	-	5	3539	c.2796G>A	c.(2794-2796)GCG>GCA	p.A932A		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	932					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)		GCAACTTCTCCGCGGGGAGCT	0.562													76	74	---	---	---	---	PASS
C1GALT1	56913	broad.mit.edu	37	7	7278252	7278252	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7278252G>A	uc010ktn.2	+	3	810	c.587G>A	c.(586-588)AGA>AAA	p.R196K	C1GALT1_uc003sra.2_Missense_Mutation_p.R196K|C1GALT1_uc010kto.1_Missense_Mutation_p.R196K	NM_020156	NP_064541	Q9NS00	C1GLT_HUMAN	core 1 synthase,	196	Lumenal (Potential).				angiogenesis|cell differentiation|kidney development	integral to membrane	glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity|metal ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (126;0.177)		TACTTTGGGAGAAGATTTAAG	0.383													6	300	---	---	---	---	PASS
FAM126A	84668	broad.mit.edu	37	7	22999886	22999886	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22999886C>T	uc003svm.3	-	10	1235	c.980G>A	c.(979-981)TGG>TAG	p.W327*	FAM126A_uc003svn.3_Nonsense_Mutation_p.W183*	NM_032581	NP_115970	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	327						cytoplasm|membrane	signal transducer activity			central_nervous_system(1)	1						ATGTCTTTTCCACCTATGACC	0.358													6	437	---	---	---	---	PASS
SRPK2	6733	broad.mit.edu	37	7	104844182	104844182	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104844182G>C	uc003vct.2	-	2	276	c.89C>G	c.(88-90)CCA>CGA	p.P30R	SRPK2_uc003vcu.2_Missense_Mutation_p.P30R|SRPK2_uc003vcv.2_Missense_Mutation_p.P41R|SRPK2_uc003vcw.1_Missense_Mutation_p.P30R	NM_182691	NP_872633	P78362	SRPK2_HUMAN	serine/arginine-rich protein-specific kinase 2	30					angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6						tggtggtggtggtggcggtgg	0.443													30	76	---	---	---	---	PASS
WNT2	7472	broad.mit.edu	37	7	116918296	116918296	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116918296G>C	uc003viz.2	-	5	1296	c.996C>G	c.(994-996)TGC>TGG	p.C332W	WNT2_uc003vja.2_Missense_Mutation_p.C236W	NM_003391	NP_003382	P09544	WNT2_HUMAN	wingless-type MMTV integration site family	332					atrial cardiac muscle tissue morphogenesis|canonical Wnt receptor signaling pathway|cardiac epithelial to mesenchymal transition|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|dorsal/ventral axis specification|iris morphogenesis|labyrinthine layer blood vessel development|lens development in camera-type eye|lung induction|mammary gland epithelium development|neuron differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of fibroblast proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|proteinaceous extracellular matrix	cytokine activity|frizzled binding|frizzled-2 binding|signal transducer activity			breast(2)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	7	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		AGCGCACGGCGCAGCACCAGT	0.602													11	45	---	---	---	---	PASS
AKR1B10	57016	broad.mit.edu	37	7	134212620	134212620	+	Translation_Start_Site	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134212620G>A	uc003vrr.2	+	1	277	c.-43G>A	c.(-45--41)ACGTG>ACATG			NM_020299	NP_064695	O60218	AK1BA_HUMAN	aldo-keto reductase family 1, member B10						cellular aldehyde metabolic process|digestion|steroid metabolic process	cytoplasm	aldo-keto reductase (NADP) activity|protein binding			skin(5)	5						AGAGCAGGACGTGAGACTTCT	0.323													17	110	---	---	---	---	PASS
ERI1	90459	broad.mit.edu	37	8	8887690	8887690	+	Intron	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8887690A>G	uc011kwu.1	+						ERI1_uc003wsk.2_3'UTR	NM_153332	NP_699163	Q8IV48	ERI1_HUMAN	three prime histone mRNA exonuclease 1						gene silencing by RNA|rRNA 3'-end processing	cytoplasm|histone pre-mRNA 3'end processing complex|nucleolus	3'-5' exonuclease activity|histone pre-mRNA stem-loop binding|metal ion binding|ribosome binding|rRNA binding				0					Adenosine monophosphate(DB00131)	AGATACATGTATGTGAACAGA	0.343													3	2	---	---	---	---	PASS
SH2D4A	63898	broad.mit.edu	37	8	19218719	19218719	+	Silent	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19218719A>G	uc003wzb.2	+	6	936	c.600A>G	c.(598-600)AAA>AAG	p.K200K	SH2D4A_uc011kym.1_Silent_p.K155K|SH2D4A_uc003wzc.2_Silent_p.K200K	NM_022071	NP_071354	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	200						cytoplasm|nucleus	protein binding				0				Colorectal(111;0.0732)		AACAGAAGAAAGAATCTATGA	0.313													6	280	---	---	---	---	PASS
RRS1	23212	broad.mit.edu	37	8	67341565	67341565	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67341565G>C	uc003xwa.2	+	1	303	c.199G>C	c.(199-201)GAC>CAC	p.D67H		NM_015169	NP_055984	Q15050	RRS1_HUMAN	homolog of yeast ribosome biogenesis regulatory	67					mitotic metaphase plate congression|ribosome biogenesis	condensed nuclear chromosome|nucleolus					0		Lung NSC(129;0.197)	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			CCTGGCGCGGGACAACACGCA	0.716											OREG0018806	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	PASS
STAU2	27067	broad.mit.edu	37	8	74440017	74440017	+	Intron	SNP	C	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74440017C>A	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Missense_Mutation_p.S414I	NM_014393	NP_055208	Q9NUL3	STAU2_HUMAN	staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			CTCTTTGCCACTTTGTCTATC	0.443													89	130	---	---	---	---	PASS
CBWD1	55871	broad.mit.edu	37	9	173364	173364	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:173364T>C	uc003zga.3	-	3	350	c.244A>G	c.(244-246)AGT>GGT	p.S82G	CBWD1_uc003zgb.3_Missense_Mutation_p.S46G|CBWD1_uc003zgc.3_Missense_Mutation_p.S82G|CBWD1_uc011llr.1_Missense_Mutation_p.S46G|CBWD1_uc003zgd.2_Missense_Mutation_p.S82G	NM_018491	NP_060961	Q9BRT8	CBWD1_HUMAN	COBW domain containing 1 isoform 1	82							ATP binding|protein binding			ovary(1)	1	all_lung(41;0.218)	all_cancers(5;3.04e-16)|all_epithelial(5;4.68e-12)|all_lung(10;1.94e-10)|Lung NSC(10;3.61e-10)|Acute lymphoblastic leukemia(5;0.00439)|Breast(48;0.0148)|all_hematologic(5;0.024)|Prostate(43;0.122)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		TCCAGCGCACTTCCTAGAATA	0.413													7	311	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68412892	68412892	+	RNA	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68412892G>A	uc004aew.1	+	2		c.1054G>A			uc004aex.2_5'Flank					Homo sapiens cDNA, FLJ98602.																		atctcactctgtctctgttcc	0.129													4	4	---	---	---	---	PASS
ANP32B	10541	broad.mit.edu	37	9	100774735	100774735	+	Silent	SNP	A	G	G	rs146318630		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100774735A>G	uc004aya.2	+	6	1018	c.669A>G	c.(667-669)GAA>GAG	p.E223E		NM_006401	NP_006392	Q92688	AN32B_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32	223	Asp/Glu-rich (highly acidic).					cytoplasm|nucleus					0		Acute lymphoblastic leukemia(62;0.0559)				AAGAAGATGAAGATGAGGATG	0.318													9	666	---	---	---	---	PASS
CNNM2	54805	broad.mit.edu	37	10	104687140	104687140	+	Intron	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104687140A>G	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron|CNNM2_uc001kwl.2_3'UTR	NM_017649	NP_060119	Q9H8M5	CNNM2_HUMAN	cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CCAACACTGAAAAGAAGAGAC	0.338													7	531	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	30921891	30921891	+	Splice_Site	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30921891A>G	uc001mss.1	-	11		c.1757_splice	c.e11+1		uc009yjk.1_Splice_Site_p.A1000_splice|uc009yjj.1_Splice_Site					Homo sapiens mRNA for KIAA1493 protein, partial cds.																		CAAAAAAGTTACCATTTGGAG	0.343													37	146	---	---	---	---	PASS
NANOG	79923	broad.mit.edu	37	12	7947298	7947298	+	Silent	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7947298C>T	uc009zfy.1	+	4	741	c.525C>T	c.(523-525)CCC>CCT	p.P175P		NM_024865	NP_079141	Q9H9S0	NANOG_HUMAN	Nanog homeobox	175					cell proliferation|embryo development|somatic stem cell maintenance	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				Kidney(36;0.0872)		CTACCTACCCCAGCCTTTACT	0.517													63	75	---	---	---	---	PASS
SLC38A4	55089	broad.mit.edu	37	12	47173425	47173425	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47173425G>T	uc001rpi.2	-	10	1085	c.686C>A	c.(685-687)TCT>TAT	p.S229Y	SLC38A4_uc001rpj.2_Missense_Mutation_p.S229Y|SLC38A4_uc009zkl.2_Missense_Mutation_p.S229Y	NM_018018	NP_060488	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	229	Helical; (Potential).				cellular nitrogen compound metabolic process|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Lung SC(27;0.192)|Renal(347;0.236)					GCAGGTAAGAGAAAATCCACT	0.363													7	312	---	---	---	---	PASS
LARP4	113251	broad.mit.edu	37	12	50831576	50831576	+	Silent	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50831576T>C	uc001rwp.1	+	6	738	c.594T>C	c.(592-594)CGT>CGC	p.R198R	LARP4_uc001rwo.1_Silent_p.R204R|LARP4_uc001rwq.1_Silent_p.R198R|LARP4_uc001rwr.1_Silent_p.R198R|LARP4_uc001rws.1_Silent_p.R197R|LARP4_uc009zlr.1_Silent_p.R17R|LARP4_uc001rwm.2_Silent_p.R198R|LARP4_uc001rwn.2_Silent_p.R128R	NM_052879	NP_443111	Q71RC2	LARP4_HUMAN	c-Mpl binding protein isoform a	198	HTH La-type RNA-binding.						nucleotide binding|RNA binding			ovary(1)	1						GTCATAAGCGTTGTATTGTAA	0.333													17	327	---	---	---	---	PASS
LRRIQ1	84125	broad.mit.edu	37	12	85449781	85449781	+	Missense_Mutation	SNP	G	A	A	rs142901418		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85449781G>A	uc001tac.2	+	8	1321	c.1210G>A	c.(1210-1212)GGA>AGA	p.G404R	LRRIQ1_uc001tab.1_Missense_Mutation_p.G404R|LRRIQ1_uc001taa.1_Missense_Mutation_p.G379R	NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	404										ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)		AAAGAAGAGCGGATATAATAA	0.313													4	120	---	---	---	---	PASS
EIF2B1	1967	broad.mit.edu	37	12	124116921	124116921	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124116921G>A	uc001ufm.2	-	2	229	c.86C>T	c.(85-87)ACG>ATG	p.T29M	GTF2H3_uc001ufo.1_5'Flank|GTF2H3_uc010tau.1_5'Flank|EIF2B1_uc001ufn.2_Missense_Mutation_p.T29M|EIF2B1_uc010tat.1_Missense_Mutation_p.T29M	NM_001414	NP_001405	Q14232	EI2BA_HUMAN	eukaryotic translation initiation factor 2B,	29					cellular response to stimulus|oligodendrocyte development|regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex|membrane fraction|plasma membrane	protein binding|translation initiation factor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.67e-05)|Epithelial(86;0.000353)|all cancers(50;0.00489)		CTCCAGCAACGTCCGGATGGC	0.368													42	67	---	---	---	---	PASS
EIF2B1	1967	broad.mit.edu	37	12	124116922	124116922	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124116922T>A	uc001ufm.2	-	2	228	c.85A>T	c.(85-87)ACG>TCG	p.T29S	GTF2H3_uc001ufo.1_5'Flank|GTF2H3_uc010tau.1_5'Flank|EIF2B1_uc001ufn.2_Missense_Mutation_p.T29S|EIF2B1_uc010tat.1_Missense_Mutation_p.T29S	NM_001414	NP_001405	Q14232	EI2BA_HUMAN	eukaryotic translation initiation factor 2B,	29					cellular response to stimulus|oligodendrocyte development|regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex|membrane fraction|plasma membrane	protein binding|translation initiation factor activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.67e-05)|Epithelial(86;0.000353)|all cancers(50;0.00489)		TCCAGCAACGTCCGGATGGCA	0.368													39	66	---	---	---	---	PASS
SLC38A6	145389	broad.mit.edu	37	14	61512080	61512080	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61512080C>T	uc001xfg.1	+	11	877	c.761C>T	c.(760-762)CCA>CTA	p.P254L	SLC38A6_uc001xfh.1_Missense_Mutation_p.P254L|SLC38A6_uc001xfi.2_RNA|SLC38A6_uc001xfj.1_RNA|SLC38A6_uc001xfk.2_RNA|SLC38A6_uc010trz.1_Missense_Mutation_p.P231L	NM_153811	NP_722518	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	254	Helical; (Potential).				amino acid transport|sodium ion transport	integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		TATGCCTTACCAACCATGGCT	0.318													6	501	---	---	---	---	PASS
FAM71D	161142	broad.mit.edu	37	14	67691958	67691958	+	3'UTR	SNP	G	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67691958G>C	uc001xja.1	+	8					FAM71D_uc010aqn.1_RNA	NM_173526	NP_775797	Q8N9W8	FA71D_HUMAN	hypothetical protein LOC161142											ovary(1)	1		all_hematologic(31;0.0116)		all cancers(60;0.00107)|BRCA - Breast invasive adenocarcinoma(234;0.00993)|OV - Ovarian serous cystadenocarcinoma(108;0.012)		AAAGTTGATGGAAAAACATGT	0.328													39	261	---	---	---	---	PASS
OCA2	4948	broad.mit.edu	37	15	28267703	28267703	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28267703T>G	uc001zbh.3	-	6	700	c.590A>C	c.(589-591)TAT>TCT	p.Y197S	OCA2_uc010ayv.2_Missense_Mutation_p.Y197S	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	197	Helical; (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		TTGATCCGGATATAGGCTGAA	0.448									Oculocutaneous_Albinism				59	46	---	---	---	---	PASS
AKAP13	11214	broad.mit.edu	37	15	86118435	86118435	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86118435C>T	uc002blv.1	+	6	906	c.736C>T	c.(736-738)CAT>TAT	p.H246Y	AKAP13_uc002blt.1_Missense_Mutation_p.H246Y|AKAP13_uc002blu.1_Missense_Mutation_p.H246Y	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	246					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						TTCTGTGAGGCATCATCGAGA	0.433													29	108	---	---	---	---	PASS
FLYWCH1	84256	broad.mit.edu	37	16	2983245	2983245	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2983245G>A	uc002csd.2	+	5	1274	c.911G>A	c.(910-912)TGC>TAC	p.C304Y	FLYWCH1_uc002csb.2_Missense_Mutation_p.C303Y|FLYWCH1_uc002csc.2_Missense_Mutation_p.C303Y|FLYWCH1_uc010bsv.2_5'UTR	NM_032296	NP_115672	Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1 isoform a	304	FLYWCH-type 2.					nucleus	DNA binding|metal ion binding				0						TATTGGACCTGCCGGGACCAC	0.657													9	7	---	---	---	---	PASS
OR2C1	4993	broad.mit.edu	37	16	3406081	3406081	+	Silent	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3406081G>A	uc002cuw.1	+	1	193	c.141G>A	c.(139-141)TTG>TTA	p.L47L		NM_012368	NP_036500	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C,	47	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						CCATCATCTTGCTTTCCCGCC	0.507													59	63	---	---	---	---	PASS
ERCC4	2072	broad.mit.edu	37	16	14020601	14020601	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14020601A>G	uc002dce.2	+	3	581	c.572A>G	c.(571-573)TAT>TGT	p.Y191C	ERCC4_uc010bva.2_Missense_Mutation_p.Y191C	NM_005236	NP_005227	Q92889	XPF_HUMAN	excision repair cross-complementing rodent	191					double-strand break repair via homologous recombination|meiotic mismatch repair|negative regulation of telomere maintenance|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|nucleotide-excision repair, DNA incision, 5'-to lesion|resolution of meiotic recombination intermediates|telomere maintenance via telomere shortening|transcription-coupled nucleotide-excision repair	nuclear chromosome, telomeric region|nucleoplasm|nucleotide-excision repair factor 1 complex	damaged DNA binding|protein C-terminus binding|protein N-terminus binding|single-stranded DNA binding|single-stranded DNA specific endodeoxyribonuclease activity			lung(4)|ovary(3)|skin(2)|pancreas(1)	10						AGGAAACTGTATCTGTGGCCA	0.348			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				5	221	---	---	---	---	PASS
SMG1	23049	broad.mit.edu	37	16	18869586	18869586	+	Silent	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18869586T>C	uc002dfm.2	-	29	4503	c.4140A>G	c.(4138-4140)GAA>GAG	p.E1380E	SMG1_uc010bwb.2_Silent_p.E1240E|SMG1_uc010bwa.2_Silent_p.E111E	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	1380	FAT.|Interaction with SMG8 and SMG9.				DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						AACGTAAAGCTTCACTGAAGA	0.378													6	250	---	---	---	---	PASS
SCNN1B	6338	broad.mit.edu	37	16	23360188	23360188	+	Missense_Mutation	SNP	A	G	G	rs150466803		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23360188A>G	uc002dln.2	+	2	444	c.268A>G	c.(268-270)ATG>GTG	p.M90V		NM_000336	NP_000327	P51168	SCNNB_HUMAN	sodium channel, nonvoltage-gated 1, beta	90	Extracellular (By similarity).				excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	CTTCAAGACCATGGACTTCCC	0.602													5	7	---	---	---	---	PASS
RBBP6	5930	broad.mit.edu	37	16	24583810	24583810	+	3'UTR	SNP	A	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24583810A>C	uc002dmh.2	+	18					RBBP6_uc002dmi.2_3'UTR|RBBP6_uc010bxr.2_3'UTR|RBBP6_uc002dmk.2_3'UTR	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN	retinoblastoma-binding protein 6 isoform 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0518)		AGTCATCTGTATTAAATTTTG	0.194													28	52	---	---	---	---	PASS
RUNDC2C	440352	broad.mit.edu	37	16	29376089	29376089	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29376089C>T	uc002dsj.1	+	5	828	c.431C>T	c.(430-432)TCT>TTT	p.S144F	uc010vct.1_Intron|RUNDC2C_uc010bys.1_RNA|RUNDC2C_uc010vdo.1_Missense_Mutation_p.S125F	NM_001012391	NP_001012391			RecName: Full=RUN domain-containing protein 2A;												0						GAGCAGAACTCTGGGGACATG	0.453													6	283	---	---	---	---	PASS
AMFR	267	broad.mit.edu	37	16	56403223	56403223	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56403223T>C	uc002eiy.2	-	11	1602	c.1397A>G	c.(1396-1398)GAG>GGG	p.E466G	AMFR_uc002eix.2_Missense_Mutation_p.E100G	NM_001144	NP_001135	Q9UKV5	AMFR2_HUMAN	autocrine motility factor receptor	466	CUE.				endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|protein oligomerization|protein polyubiquitination	integral to endoplasmic reticulum membrane|integral to membrane of membrane fraction	protein binding|protein binding|receptor activity|ubiquitin-protein ligase activity|zinc ion binding			breast(2)	2						GGGAAACATCTCTTGAATCTG	0.453													7	317	---	---	---	---	PASS
CNOT1	23019	broad.mit.edu	37	16	58589762	58589762	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58589762T>C	uc002env.2	-	20	2823	c.2530A>G	c.(2530-2532)ATA>GTA	p.I844V	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Missense_Mutation_p.I839V|CNOT1_uc002enx.2_Missense_Mutation_p.I844V|CNOT1_uc002enz.1_Missense_Mutation_p.I273V	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	844					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)		TCATCATCTATCTCTTTACTA	0.433													7	411	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													4	44	---	---	---	---	PASS
KIAA0513	9764	broad.mit.edu	37	16	85120766	85120766	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85120766G>C	uc002fiu.2	+	12	1400	c.1180G>C	c.(1180-1182)GAT>CAT	p.D394H	KIAA0513_uc010voj.1_Missense_Mutation_p.D384H	NM_014732	NP_055547	O60268	K0513_HUMAN	hypothetical protein LOC9764	394						cytoplasm				breast(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.234)		TGGCAACCTGGATGAAGGTGC	0.597											OREG0023994	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	35	60	---	---	---	---	PASS
SEZ6	124925	broad.mit.edu	37	17	27286442	27286442	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27286442G>A	uc002hdp.2	-	9	2014	c.1820C>T	c.(1819-1821)CCC>CTC	p.P607L	SEZ6_uc010crx.1_5'Flank|SEZ6_uc002hdm.2_RNA|SEZ6_uc010cry.1_Missense_Mutation_p.P607L|SEZ6_uc002hdq.1_Missense_Mutation_p.P482L	NM_178860	NP_849191	Q53EL9	SEZ6_HUMAN	seizure related 6 homolog isoform 1	607	Extracellular (Potential).|CUB 2.					integral to membrane|plasma membrane				large_intestine(1)|central_nervous_system(1)	2	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)			TGGCCAGTTGGGAGAGAGTAC	0.587													12	18	---	---	---	---	PASS
SLFN14	342618	broad.mit.edu	37	17	33884273	33884273	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33884273T>A	uc010ctu.1	-	1	838	c.809A>T	c.(808-810)GAA>GTA	p.E270V		NM_001129820	NP_001123292	P0C7P3	SLN14_HUMAN	schlafen family member 14	270							ATP binding			central_nervous_system(1)	1						GTTTTCGATTTCTTTTTTTAG	0.378													7	526	---	---	---	---	PASS
CASKIN2	57513	broad.mit.edu	37	17	73500959	73500959	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73500959C>T	uc002joc.2	-	11	1676	c.1126G>A	c.(1126-1128)GAA>AAA	p.E376K	CASKIN2_uc010wsc.1_Missense_Mutation_p.E294K	NM_020753	NP_065804	Q8WXE0	CSKI2_HUMAN	cask-interacting protein 2 isoform a	376						cytoplasm				pancreas(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGGGGTTCTTCGGCAGGAGGC	0.701													7	8	---	---	---	---	PASS
CCDC11	220136	broad.mit.edu	37	18	47777195	47777195	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47777195T>C	uc002lee.2	-	5	1020	c.929A>G	c.(928-930)AAC>AGC	p.N310S		NM_145020	NP_659457	Q96M91	CCD11_HUMAN	coiled-coil domain containing 11	310	Potential.									ovary(1)|pancreas(1)|skin(1)	3				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		GAGCTTCATGTTCAAGTCCTG	0.423													8	649	---	---	---	---	PASS
POLI	11201	broad.mit.edu	37	18	51809261	51809261	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51809261G>A	uc002lfj.3	+	6	919	c.851G>A	c.(850-852)CGT>CAT	p.R284H	POLI_uc010xds.1_Missense_Mutation_p.R205H|POLI_uc002lfk.3_Missense_Mutation_p.R181H|POLI_uc002lfl.1_Missense_Mutation_p.R216H|POLI_uc010dpg.2_Translation_Start_Site	NM_007195	NP_009126	Q9UNA4	POLI_HUMAN	DNA polymerase iota	284					DNA repair|DNA replication	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding|protein binding			ovary(2)|kidney(1)	3				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		AATAGTGTGCGTGATCTCCAA	0.358								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					34	270	---	---	---	---	PASS
ZNF443	10224	broad.mit.edu	37	19	12542271	12542271	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12542271A>G	uc002mtu.2	-	4	913	c.715T>C	c.(715-717)TCC>CCC	p.S239P		NM_005815	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	239	C2H2-type 4.				induction of apoptosis|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1						CTTAGATAGGAACTGTAAAAA	0.363													6	290	---	---	---	---	PASS
OR10H5	284433	broad.mit.edu	37	19	15905371	15905371	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15905371C>A	uc010xos.1	+	1	513	c.513C>A	c.(511-513)CAC>CAA	p.H171Q		NM_001004466	NP_001004466	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H,	171	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						TCTGTGGACACAAGGAGATCC	0.607													67	90	---	---	---	---	PASS
ZNF99	7652	broad.mit.edu	37	19	22951153	22951153	+	Silent	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22951153T>C	uc010xrh.1	-	3	243	c.243A>G	c.(241-243)AAA>AAG	p.K81K		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TCCAAGGCTCTTTCCCTTGCT	0.368													7	429	---	---	---	---	PASS
ZNF649	65251	broad.mit.edu	37	19	52394722	52394722	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52394722C>T	uc002pxy.2	-	5	935	c.667G>A	c.(667-669)GAA>AAA	p.E223K	ZNF577_uc010ydf.1_5'Flank	NM_023074	NP_075562	Q9BS31	ZN649_HUMAN	zinc finger protein 649	223	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00152)|OV - Ovarian serous cystadenocarcinoma(262;0.0185)		CTCTCGTGTTCAGTGAGCCTG	0.498													73	100	---	---	---	---	PASS
ZNF606	80095	broad.mit.edu	37	19	58491157	58491157	+	Silent	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58491157A>G	uc002qqw.2	-	7	1509	c.891T>C	c.(889-891)TCT>TCC	p.S297S	ZNF606_uc010yhp.1_Silent_p.S207S	NM_025027	NP_079303	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	297	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		TATGATTGAAAGATTTAACAG	0.318													8	517	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47244458	47244458	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47244458G>A	uc002xtw.1	-	38	4833	c.4810C>T	c.(4810-4812)CGG>TGG	p.R1604W	PREX1_uc002xtv.1_Missense_Mutation_p.R901W	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	1604					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CCGTGGCTCCGTGCCAAGATG	0.692													11	2	---	---	---	---	PASS
SAMSN1	64092	broad.mit.edu	37	21	15858235	15858235	+	Nonstop_Mutation	SNP	A	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15858235A>T	uc002yju.1	-	8	1202	c.1120T>A	c.(1120-1122)TGA>AGA	p.*374R	SAMSN1_uc010gky.1_Nonstop_Mutation_p.*206R|SAMSN1_uc002yjv.1_Nonstop_Mutation_p.*442R	NM_022136	NP_071419	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization	374					negative regulation of adaptive immune response|negative regulation of B cell activation|negative regulation of peptidyl-tyrosine phosphorylation	cytoplasm|nucleus|ruffle	phosphotyrosine binding			ovary(3)|pancreas(1)	4				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		ATGCGTGTTCAGTCACTTGGC	0.353													19	357	---	---	---	---	PASS
KRTAP15-1	254950	broad.mit.edu	37	21	31812784	31812784	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31812784C>A	uc002yod.2	+	1	139	c.139C>A	c.(139-141)CTC>ATC	p.L47I		NM_181623	NP_853654	Q3LI76	KR151_HUMAN	keratin associated protein 15-1	47						intermediate filament					0						GGGCTCCTCTCTCTACAATGG	0.483													41	73	---	---	---	---	PASS
HIRA	7290	broad.mit.edu	37	22	19375312	19375312	+	Silent	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19375312T>C	uc002zpf.1	-	11	1255	c.1035A>G	c.(1033-1035)GTA>GTG	p.V345V	HIRA_uc011agx.1_Silent_p.V211V|HIRA_uc010grn.1_Silent_p.V345V|HIRA_uc010gro.1_Silent_p.V301V|HIRA_uc010grp.2_RNA	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective	345	WD 7.				chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)					CCATAGAGCATACCAAGATGC	0.587													4	56	---	---	---	---	PASS
MED15	51586	broad.mit.edu	37	22	20929497	20929497	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20929497T>C	uc002zsp.2	+	9	1330	c.1250T>C	c.(1249-1251)TTG>TCG	p.L417S	MED15_uc002zsq.2_Intron|MED15_uc010gso.2_Intron|MED15_uc002zsr.2_Intron|MED15_uc011ahs.1_Intron|MED15_uc002zss.2_Intron|MED15_uc011ahu.1_Missense_Mutation_p.L143S|MED15_uc002zst.2_Missense_Mutation_p.L33S	NM_001003891	NP_001003891	Q96RN5	MED15_HUMAN	mediator complex subunit 15 isoform a	417	Pro-rich.				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding			skin(1)	1	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			TCCATCCCTTTGGGCAGACAG	0.627													8	13	---	---	---	---	PASS
LOC91316	91316	broad.mit.edu	37	22	24056489	24056489	+	Intron	SNP	A	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24056489A>G	uc010gub.1	-						LOC91316_uc011aiz.1_RNA					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0						TAGCTGAAGAAGTCAAAGTCT	0.552													5	11	---	---	---	---	PASS
C22orf31	25770	broad.mit.edu	37	22	29456493	29456493	+	Silent	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29456493T>C	uc003aej.1	-	2	469	c.342A>G	c.(340-342)AAA>AAG	p.K114K		NM_015370	NP_056185	O95567	CV031_HUMAN	hypothetical protein LOC25770	114											0						GCTGGGTGGCTTTCATCACTG	0.517													6	178	---	---	---	---	PASS
CENPM	79019	broad.mit.edu	37	22	42335169	42335169	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42335169C>A	uc003bbn.2	-	6	502	c.434G>T	c.(433-435)CGC>CTC	p.R145L	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|CENPM_uc003bbm.2_Missense_Mutation_p.R111L|CENPM_uc003bbo.2_3'UTR|CENPM_uc010gyq.2_Missense_Mutation_p.R23L	NM_024053	NP_076958	Q9NSP4	CENPM_HUMAN	centromere protein M isoform a	145					mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleus					0						GCGCACCAGGCGCTGCGCCAT	0.637													4	4	---	---	---	---	PASS
MED12	9968	broad.mit.edu	37	X	70360569	70360569	+	Silent	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70360569T>C	uc004dyy.2	+	42	6328	c.6129T>C	c.(6127-6129)CGT>CGC	p.R2043R	MED12_uc004dyz.2_Silent_p.R2042R|MED12_uc004dza.2_Silent_p.R1893R|MED12_uc010nla.2_Silent_p.R672R	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	2043	Gln-rich.|Interaction with CTNNB1 and GLI3.				androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)					CAGGCGTCCGTTCAACAGCCA	0.323													4	32	---	---	---	---	PASS
NHSL2	340527	broad.mit.edu	37	X	71358471	71358471	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71358471C>T	uc011mqa.1	+	6	1073	c.1073C>T	c.(1072-1074)GCA>GTA	p.A358V	NHSL2_uc004eak.1_5'UTR|NHSL2_uc010nli.2_Missense_Mutation_p.A127V	NM_001013627	NP_001013649	Q5HYW2	NHSL2_HUMAN	NHS-like 2	358											0	Renal(35;0.156)					CCTCACCAGGCACGGAGTGGC	0.552													37	4	---	---	---	---	PASS
KIAA2022	340533	broad.mit.edu	37	X	73963362	73963362	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73963362T>C	uc004eby.2	-	3	1647	c.1030A>G	c.(1030-1032)ACC>GCC	p.T344A		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	344					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15						TTGGGGCAGGTAGTAAAGACG	0.468													46	6	---	---	---	---	PASS
NKRF	55922	broad.mit.edu	37	X	118726468	118726468	+	5'UTR	SNP	G	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118726468G>A	uc004erq.2	-	1					NKRF_uc004err.2_5'UTR	NM_017544	NP_060014	O15226	NKRF_HUMAN	transcription factor NRF						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|double-stranded RNA binding			ovary(1)|central_nervous_system(1)	2						CATCAAGCGTGGGCTGTACCT	0.363													4	139	---	---	---	---	PASS
HAUS7	55559	broad.mit.edu	37	X	152720472	152720472	+	Intron	SNP	T	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152720472T>A	uc004fho.1	-						HAUS7_uc004fhl.2_Intron|HAUS7_uc004fhm.2_Intron|HAUS7_uc004fhn.1_Missense_Mutation_p.M334L|HAUS7_uc004fhp.1_RNA	NM_017518	NP_059988	Q99871	HAUS7_HUMAN	HAUS augmin-like complex subunit 7						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleolus|plasma membrane|spindle	thioesterase binding				0						ACTGTAGTCATCGTAACTAAA	0.502													64	8	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	324	324	+	RNA	SNP	C	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:324C>T	uc004coq.3	-	1		c.43G>A			uc004cor.1_5'Flank|uc004cos.3_5'Flank					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		CCCCGCTTCTGGCCACAGCAC	0.438													12	1	---	---	---	---	PASS
MTOR	2475	broad.mit.edu	37	1	11169052	11169052	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11169052delA	uc001asd.2	-						MTOR_uc001asc.2_Intron	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						tcaaacaaacaaaaaaaaGAC	0.144													4	2	---	---	---	---	
EFHD2	79180	broad.mit.edu	37	1	15739297	15739297	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15739297delT	uc001awh.2	+							NM_024329	NP_077305	Q96C19	EFHD2_HUMAN	EF-hand domain family, member D2							membrane raft					0		Renal(390;0.00145)|Breast(348;0.00173)|Colorectal(325;0.00215)|all_lung(284;0.00366)|Lung NSC(340;0.00395)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)|Hepatocellular(190;0.152)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.59e-07)|COAD - Colon adenocarcinoma(227;3.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000119)|KIRC - Kidney renal clear cell carcinoma(229;0.00251)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		gcaaactcacttttttttaca	0.000													4	2	---	---	---	---	
NIPAL3	57185	broad.mit.edu	37	1	24795816	24795816	+	3'UTR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24795816delG	uc001bjh.2	+	12					NIPAL3_uc009vrc.2_3'UTR	NM_020448	NP_065181	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3							integral to membrane					0						CTTTGTCTCTGGGAAAGGATG	0.433													4	2	---	---	---	---	
STMN1	3925	broad.mit.edu	37	1	26213774	26213774	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26213774delA	uc010oev.1	-						STMN1_uc001bky.2_Intron	NM_001145454	NP_001138926	P16949	STMN1_HUMAN	stathmin 1 isoform b						cell differentiation|intracellular signal transduction|microtubule depolymerization|mitotic spindle organization|nervous system development|response to virus	cytoplasm|microtubule	signal transducer activity|tubulin binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000163)|all_lung(284;0.000234)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.013)|READ - Rectum adenocarcinoma(331;0.0649)		GTGGTTTGTTAAACAATGACA	0.493													4	2	---	---	---	---	
ARID1A	8289	broad.mit.edu	37	1	27058857	27058857	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27058857delT	uc001bmv.1	+						ARID1A_uc001bmt.1_Intron|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Intron	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a						androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		tctagcatgatttttttgtgg	0.139			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								4	2	---	---	---	---	
PTP4A2	8073	broad.mit.edu	37	1	32384928	32384928	+	5'UTR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32384928delA	uc001bty.1	-	2					PTP4A2_uc010ogs.1_5'UTR|PTP4A2_uc001btz.1_5'UTR	NM_080391	NP_536316	Q12974	TP4A2_HUMAN	protein tyrosine phosphatase type IVA, member 2							early endosome|plasma membrane	prenylated protein tyrosine phosphatase activity|protein binding|protein tyrosine/serine/threonine phosphatase activity				0		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)				TTCGGACTCCAAAAAATCCAA	0.363													4	2	---	---	---	---	
KIAA0319L	79932	broad.mit.edu	37	1	35925632	35925632	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35925632delA	uc001byx.2	-						KIAA0319L_uc010ohv.1_Intron	NM_024874	NP_079150	Q8IZA0	K319L_HUMAN	dyslexia susceptibility 2-like							cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CAGAAATCCTAAAAAAAATTT	0.373													4	2	---	---	---	---	
EIF2C1	26523	broad.mit.edu	37	1	36353262	36353262	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36353262delT	uc001bzl.2	+						EIF2C1_uc001bzk.2_Intron	NM_012199	NP_036331	Q9UL18	AGO1_HUMAN	eukaryotic translation initiation factor 2C, 1						negative regulation of translation involved in gene silencing by miRNA|nuclear-transcribed mRNA catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|polysome	protein binding|RNA binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTATTCAAGCTTTTTTTTTTA	0.463													3	3	---	---	---	---	
BMP8B	656	broad.mit.edu	37	1	40229212	40229212	+	Intron	DEL	A	-	-	rs113575841		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40229212delA	uc001cdz.1	-						PPIE_uc001cdv.2_Intron|PPIE_uc001cdw.2_Intron	NM_001720	NP_001711	P34820	BMP8B_HUMAN	bone morphogenetic protein 8B preproprotein						cartilage development|cell differentiation|growth|ossification	extracellular space	cytokine activity|growth factor activity				0	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AAAACTGAACAAAAAAAAAAC	0.338													9	4	---	---	---	---	
FAF1	11124	broad.mit.edu	37	1	51237638	51237638	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51237638delA	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)		TTCTAAATGCAAAAAAAATTG	0.219													4	2	---	---	---	---	
C1orf168	199920	broad.mit.edu	37	1	57259106	57259106	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57259106delA	uc001cym.3	-						C1orf168_uc009vzu.1_Intron|C1orf168_uc009vzv.1_Intron	NM_001004303	NP_001004303	Q5VWT5	CA168_HUMAN	hypothetical protein LOC199920											ovary(3)|skin(2)	5						ttcaatatgcaaaaaaaatat	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	62656595	62656595	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62656595delT								INADL (12249 upstream) : L1TD1 (3901 downstream)																							CCTGGAATTCTTTTTCTAGGG	0.388													4	2	---	---	---	---	
KANK4	163782	broad.mit.edu	37	1	62726329	62726330	+	Intron	DEL	CA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62726329_62726330delCA	uc001dah.3	-						KANK4_uc001dai.3_Intron|KANK4_uc001daf.3_Intron|KANK4_uc001dag.3_Intron	NM_181712	NP_859063	Q5T7N3	KANK4_HUMAN	ankyrin repeat domain 38											ovary(3)|skin(2)|lung(1)	6						TCTCCAAAGTCACCAGTGGCAC	0.550													4	2	---	---	---	---	
SGIP1	84251	broad.mit.edu	37	1	67138714	67138714	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67138714delG	uc001dcr.2	+						SGIP1_uc010opd.1_Intron|SGIP1_uc001dcs.2_Intron|SGIP1_uc001dct.2_Intron|uc010ope.1_Intron|SGIP1_uc009wat.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						TATTTCTATTGGGTGAGCACC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	77704116	77704116	+	IGR	DEL	T	-	-	rs148093794		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77704116delT								PIGK (18984 upstream) : AK5 (43626 downstream)																							GCCAGTGTCATTTTTTTTTTT	0.055													5	4	---	---	---	---	
LPHN2	23266	broad.mit.edu	37	1	82096005	82096005	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82096005delG	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)		CCAGAGGAGTGGGCAGTGACA	0.189													4	2	---	---	---	---	
CCDC18	343099	broad.mit.edu	37	1	93667241	93667242	+	Intron	INS	-	TTATA	TTATA	rs138170855	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93667241_93667242insTTATA	uc001dpq.2	+							NM_206886	NP_996769	Q5T9S5	CCD18_HUMAN	sarcoma antigen NY-SAR-41											ovary(2)|breast(2)|pancreas(1)	5		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		ATTGTTTTGTGTTTTATTTTTC	0.257													9	6	---	---	---	---	
PTBP2	58155	broad.mit.edu	37	1	97279080	97279080	+	3'UTR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97279080delT	uc001drq.2	+	14					PTBP2_uc001drn.2_3'UTR|PTBP2_uc001dro.2_3'UTR|PTBP2_uc010otz.1_3'UTR|PTBP2_uc001drp.2_RNA|PTBP2_uc009wdw.2_3'UTR|PTBP2_uc001drr.2_3'UTR|PTBP2_uc010oua.1_3'UTR|PTBP2_uc001dru.2_RNA|PTBP2_uc001drs.1_3'UTR|PTBP2_uc001drt.2_3'UTR	NM_021190	NP_067013	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2								nucleotide binding				0		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)		TTGGGGTTTCTTTTTTTTTTC	0.338													9	6	---	---	---	---	
KCND3	3752	broad.mit.edu	37	1	112387381	112387382	+	Intron	DEL	TC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112387381_112387382delTC	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)		ctctcatccttctctctctccc	0.000													4	2	---	---	---	---	
PTPN22	26191	broad.mit.edu	37	1	114377352	114377352	+	Intron	DEL	A	-	-	rs79608028		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114377352delA	uc001eds.2	-						PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron|PTPN22_uc001edu.2_Intron	NM_015967	NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ctgctaaattaaaaaaaaaaa	0.000													8	5	---	---	---	---	
AMPD1	270	broad.mit.edu	37	1	115226614	115226614	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115226614delT	uc001efe.1	-						AMPD1_uc001eff.1_Intron	NM_000036	NP_000027	P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1 (isoform M)						purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|large_intestine(1)|skin(1)	4	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	tgaatgagggtttagggaatg	0.100													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145150817	145150817	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145150817delT	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						tttgtctatatttttgcttat	0.154													4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	146215510	146215511	+	Intron	INS	-	AC	AC			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146215510_146215511insAC	uc001emp.3	+							NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		gagaaagacagagagagagaga	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149032494	149032494	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149032494delA								LOC645166 (79440 upstream) : LOC388692 (246982 downstream)																							CAGAGAATTCATCACTGACTT	0.294													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	156148183	156148183	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156148183delC								SEMA4A (649 upstream) : SLC25A44 (15547 downstream)																							CCTCCAGCATCCCCACTCGCT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	160905990	160905990	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160905990delT								ITLN1 (51030 upstream) : ITLN2 (8827 downstream)																							ttttttattatttttttttta	0.075													4	3	---	---	---	---	
RABGAP1L	9910	broad.mit.edu	37	1	174339876	174339877	+	Intron	INS	-	TAGG	TAGG	rs148014630	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174339876_174339877insTAGG	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.2_Intron|RABGAP1L_uc001gjz.2_Intron	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						CTATTTATTTATATTTTCAATT	0.272													5	4	---	---	---	---	
FAM129A	116496	broad.mit.edu	37	1	184862649	184862649	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184862649delA	uc001gra.2	-						FAM129A_uc009wyh.1_Intron|FAM129A_uc009wyi.1_Intron	NM_052966	NP_443198	Q9BZQ8	NIBAN_HUMAN	niban protein isoform 2						negative regulation of protein phosphorylation|positive regulation of protein phosphorylation|positive regulation of translation|response to endoplasmic reticulum stress	cytoplasm|nucleus|plasma membrane				ovary(3)|skin(1)	4						AAGTTAAATGAAAAAAAAATA	0.363													4	2	---	---	---	---	
NFASC	23114	broad.mit.edu	37	1	204885312	204885312	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204885312delC	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)			CTTGCTGTGACCCAGAGCTGC	0.517													4	2	---	---	---	---	
IARS2	55699	broad.mit.edu	37	1	220276387	220276387	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220276387delT	uc001hmc.2	+							NM_018060	NP_060530	Q9NSE4	SYIM_HUMAN	mitochondrial isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	ttcttttttcttttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222625286	222625287	+	IGR	DEL	AC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222625286_222625287delAC								DUSP10 (709825 upstream) : HHIPL2 (70315 downstream)																							CCTTGAAGCTACAATCACTGAT	0.535													4	2	---	---	---	---	
CAPN9	10753	broad.mit.edu	37	1	230914561	230914562	+	Intron	DEL	AA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230914561_230914562delAA	uc001htz.1	+						CAPN9_uc009xfg.1_Intron|CAPN9_uc001hua.1_Intron	NM_006615	NP_006606	O14815	CAN9_HUMAN	calpain 9 isoform 1						digestion|proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				TTTTACTTTTAAAAAATTTTCC	0.168													4	2	---	---	---	---	
TSNAX-DISC1	100303453	broad.mit.edu	37	1	231677662	231677662	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231677662delT	uc010pwg.1	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|TSNAX_uc001huw.2_Intron	NM_001012959	NP_001012977			disrupted in schizophrenia 1 isoform S												0						ctcctcattgttactctgctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	247461159	247461161	+	IGR	DEL	AAG	-	-	rs143108701		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247461159_247461161delAAG								VN1R5 (40713 upstream) : ZNF496 (2462 downstream)																							GTGGGGACTCAAGAGACAGCCTC	0.493													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	904970	904970	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:904970delA	uc010ewg.2	-						uc010ewh.1_3'UTR					Homo sapiens cDNA FLJ46162 fis, clone TESTI4002520.																		TGCCTTGTTCAAAAAAATATT	0.264													4	2	---	---	---	---	
TTC15	51112	broad.mit.edu	37	2	3423958	3423958	+	Intron	DEL	A	-	-	rs112164644		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3423958delA	uc002qxm.1	+						TTC15_uc002qxn.1_Intron|TTC15_uc010ewm.1_Intron	NM_016030	NP_057114	Q8WVT3	TTC15_HUMAN	tetratricopeptide repeat domain 15								binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)		ttcagcatttaaaaaaaaaac	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	5631888	5631888	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5631888delT								None (None upstream) : SOX11 (200911 downstream)																							AGTCATGCAATTTTTTTGCCT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10640560	10640560	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10640560delC								ODC1 (52107 upstream) : NOL10 (70334 downstream)																							TGTTTAGGAACCACCATGGGG	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12098002	12098002	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12098002delT								LPIN1 (130471 upstream) : TRIB2 (758996 downstream)																							TCTTGGAGGCTTTTAGGATGC	0.468													4	2	---	---	---	---	
YIPF4	84272	broad.mit.edu	37	2	32523031	32523031	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32523031delT	uc002rok.2	+							NM_032312	NP_115688	Q9BSR8	YIPF4_HUMAN	Yip1 domain family, member 4							endoplasmic reticulum|integral to membrane	protein binding				0	Acute lymphoblastic leukemia(172;0.155)					TAGTAAACACTTTTTTTTTGC	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35742589	35742589	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35742589delA								None (None upstream) : CRIM1 (840808 downstream)																							aaataagtctagggacaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37960284	37960285	+	IGR	INS	-	T	T	rs142685273	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37960284_37960285insT								CDC42EP3 (60958 upstream) : FAM82A1 (192177 downstream)																							AAGGGAAGAAGTTTAATCTCAG	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38001167	38001168	+	IGR	DEL	AA	-	-	rs66903481		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38001167_38001168delAA								CDC42EP3 (101841 upstream) : FAM82A1 (151294 downstream)																							ATTTTGCAGCAAAAAAAGCCAT	0.426													4	3	---	---	---	---	
GEMIN6	79833	broad.mit.edu	37	2	38996689	38996690	+	Intron	DEL	TC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38996689_38996690delTC	uc002rrb.2	+									Q8WXD5	GEMI6_HUMAN	Homo sapiens GEMIN6 mRNA, complete cds.						ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding				0		all_hematologic(82;0.21)				ttttttcttttctttttttttt	0.188													4	2	---	---	---	---	
SLC8A1	6546	broad.mit.edu	37	2	40679680	40679680	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40679680delC	uc002rsd.3	-						SLC8A1_uc002rsa.2_5'Flank|SLC8A1_uc010fan.1_5'Flank|SLC8A1_uc002rsc.1_Intron	NM_001112802	NP_001106273	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium						cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	AGAACCCTGACCCCCAATTCG	0.512													4	2	---	---	---	---	
MTA3	57504	broad.mit.edu	37	2	42814333	42814333	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42814333delA	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						actctgtctcaaaaaaaaaag	0.000													4	2	---	---	---	---	
LRPPRC	10128	broad.mit.edu	37	2	44162166	44162166	+	Intron	DEL	A	-	-	rs11899538	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44162166delA	uc002rtr.2	-						LRPPRC_uc010yob.1_Intron	NM_133259	NP_573566	P42704	LPPRC_HUMAN	leucine-rich PPR motif-containing protein						mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				AAAATGGGGGAAAAAAAGAAA	0.299													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46220016	46220017	+	Intron	INS	-	CTG	CTG	rs138203937	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46220016_46220017insCTG	uc002rut.2	+							NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			CCCAGACAACACTGCTGCTGCT	0.396											OREG0014591	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	53703660	53703660	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53703660delA								None (None upstream) : ASB3 (193458 downstream)																							ggaaggagggaAAAAAAAAAG	0.169													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	56256654	56256654	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56256654delC	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																		TCTCCTTTTGCCATTAGAACA	0.393													4	2	---	---	---	---	
HK2	3099	broad.mit.edu	37	2	75073445	75073446	+	Intron	INS	-	T	T	rs145694749	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75073445_75073446insT	uc002snd.2	+							NM_000189	NP_000180	P52789	HXK2_HUMAN	hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2						TGCAACCTGCCTTTTTTTTCCA	0.297													6	3	---	---	---	---	
TACR1	6869	broad.mit.edu	37	2	75414546	75414546	+	Intron	DEL	T	-	-	rs140238921	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75414546delT	uc002sng.2	-						TACR1_uc002snh.2_Intron	NM_001058	NP_001049	P25103	NK1R_HUMAN	tachykinin receptor 1 isoform long						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|detection of abiotic stimulus|mechanosensory behavior	integral to plasma membrane	protein binding			ovary(1)	1					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)	CCTGGGACTATTTTTTGAAAG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	83802227	83802227	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83802227delT								None (None upstream) : FUNDC2P2 (715579 downstream)																							aatgctacactacatccacct	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89161689	89161689	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89161689delT	uc010ytr.1	-						uc002sti.1_5'Flank|uc002stj.1_Intron					Parts of antibodies, mostly variable regions.																		tatttatttattttttaGAAA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91798815	91798815	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91798815delA								None (None upstream) : LOC654342 (6377 downstream)																							aacaaaaaacaaaCCCCCCCC	0.114													4	2	---	---	---	---	
C2orf55	343990	broad.mit.edu	37	2	99443770	99443770	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99443770delT	uc002szf.1	-							NM_207362	NP_997245	Q6NV74	CB055_HUMAN	hypothetical protein LOC343990												0						AAATACtttctttttttttcc	0.234													3	3	---	---	---	---	
AFF3	3899	broad.mit.edu	37	2	100492613	100492613	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100492613delC	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						catgctcattccctaggacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	120044094	120044096	+	IGR	DEL	AGG	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120044094_120044096delAGG								STEAP3 (20869 upstream) : C2orf76 (15924 downstream)																							tgggggagacaggaggaggtgcc	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	123748450	123748450	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123748450delG								None (None upstream) : None (None downstream)																							AAGACAATGTGGTAGATGCTA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130164412	130164412	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130164412delA								None (None upstream) : LOC389033 (516023 downstream)																							tgcatcctctaaatttttgtg	0.000													4	2	---	---	---	---	
TMEM163	81615	broad.mit.edu	37	2	135368526	135368526	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135368526delG	uc002ttx.2	-						TMEM163_uc002tty.2_Intron	NM_030923	NP_112185	Q8TC26	TM163_HUMAN	transmembrane protein 163							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)		actgtcttttgaagagacggg	0.149													4	2	---	---	---	---	
LYPD6B	130576	broad.mit.edu	37	2	149990652	149990653	+	Intron	DEL	GA	-	-	rs11689777		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149990652_149990653delGA	uc002twv.1	+						LYPD6B_uc002tww.1_Intron|LYPD6B_uc002twx.1_Intron	NM_177964	NP_808879	Q8NI32	LPD6B_HUMAN	LY6/PLAUR domain containing 6B							anchored to membrane|plasma membrane					0						ctgaagaaaggagagagagaga	0.124													4	2	---	---	---	---	
GALNT13	114805	broad.mit.edu	37	2	155055634	155055635	+	Intron	INS	-	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155055634_155055635insT	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron|GALNT13_uc010foc.1_Intron	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						AATTTCTTCTGTTTTTTTTTAA	0.347													4	2	---	---	---	---	
METTL5	29081	broad.mit.edu	37	2	170678827	170678828	+	Intron	DEL	TC	-	-	rs145553288		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170678827_170678828delTC	uc002ufn.2	-						METTL5_uc002ufo.2_Intron|METTL5_uc002ufp.2_Intron|METTL5_uc002ufq.1_Intron	NM_014168	NP_054887	Q9NRN9	METL5_HUMAN	methyltransferase like 5								methyltransferase activity|nucleic acid binding			central_nervous_system(1)	1						CTGTGCCCAGTCTCTGAGGTAA	0.337													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	172373370	172373370	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172373370delG								DCAF17 (31810 upstream) : CYBRD1 (5496 downstream)																							ccacagctgtggagaagggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	175593521	175593522	+	Intron	DEL	CA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175593521_175593522delCA	uc002uiw.2	+											Homo sapiens cDNA FLJ11228 fis, clone PLACE1008329.																		TTCCCAGCTTCACTGGCCTCCC	0.540													4	2	---	---	---	---	
ATF2	1386	broad.mit.edu	37	2	175979807	175979807	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175979807delT	uc002ujl.2	-						ATF2_uc010fqv.2_Intron|ATF2_uc002ujv.2_Intron|ATF2_uc002ujm.2_Intron|ATF2_uc002ujn.2_Intron|ATF2_uc002ujo.2_Intron|ATF2_uc002ujp.2_Intron|ATF2_uc002ujq.2_Intron|ATF2_uc002ujr.2_Intron|ATF2_uc010fqu.2_Intron|ATF2_uc002ujs.2_Intron|ATF2_uc002ujt.2_Intron|ATF2_uc002uju.2_Intron|ATF2_uc002ujw.1_Intron|ATF2_uc002ujx.1_Intron|ATF2_uc002ujy.1_Intron	NM_001880	NP_001871	P15336	ATF2_HUMAN	activating transcription factor 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|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	nucleoplasm	protein dimerization activity|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(1)|breast(1)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.125)			aaaaGACTCGTTTTTTTTTTT	0.249													4	4	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179586107	179586107	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179586107delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTCATAACATTTTTTTTTTA	0.139													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	200702822	200702822	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200702822delC	uc002uvg.2	-											Homo sapiens hypothetical protein LOC348751, mRNA (cDNA clone IMAGE:5311172).																		GGTCATGTTACAGAGACACTG	0.458													4	2	---	---	---	---	
AOX1	316	broad.mit.edu	37	2	201477727	201477728	+	Intron	DEL	GT	-	-	rs75169215	byFrequency	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201477727_201477728delGT	uc002uvx.2	+						AOX1_uc010zhf.1_Intron|AOX1_uc010fsu.2_Intron	NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1						inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	CTCtgtgtgcgtgtgtgtgtgt	0.223													4	2	---	---	---	---	
CASP8	841	broad.mit.edu	37	2	202131059	202131060	+	Intron	INS	-	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202131059_202131060insT	uc002uxr.1	+						CASP8_uc010ftc.1_Intron|CASP8_uc002uxo.1_Intron|CASP8_uc002uxp.1_Intron|CASP8_uc002uxq.1_Intron|CASP8_uc002uxs.1_Intron|CASP8_uc002uxt.1_Intron|CASP8_uc002uxu.1_Intron|CASP8_uc010ftd.1_Intron|CASP8_uc002uxv.1_Intron|CASP8_uc002uxw.1_Intron|CASP8_uc002uxy.1_5'Flank|CASP8_uc002uxx.1_5'Flank|CASP8_uc010ftf.2_5'Flank	NM_033355	NP_203519	Q14790	CASP8_HUMAN	caspase 8 isoform B precursor						activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor	centrosome|cytosol|mitochondrial outer membrane	cysteine-type endopeptidase activity|protein binding|protein binding			upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1)	5						GTCTGGTGTTCTTTTTTTCTCT	0.332										HNSCC(4;0.00038)			4	2	---	---	---	---	
NBEAL1	65065	broad.mit.edu	37	2	204056042	204056043	+	Intron	INS	-	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204056042_204056043insA	uc002uzt.3	+						NBEAL1_uc002uzs.3_Intron	NM_001114132	NP_001107604	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1 isoform 3								binding			ovary(1)|skin(1)	2						TTTGACAACTGaaaaaaaaaaa	0.257													4	5	---	---	---	---	
MAP2	4133	broad.mit.edu	37	2	210451932	210451932	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210451932delA	uc002vde.1	+						MAP2_uc002vdc.1_Intron|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	CTGAGCTGCTAAATTCTCTGT	0.463													4	2	---	---	---	---	
ERBB4	2066	broad.mit.edu	37	2	212243221	212243222	+	3'UTR	DEL	AA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212243221_212243222delAA	uc002veg.1	-	28					ERBB4_uc002veh.1_3'UTR|ERBB4_uc010zji.1_3'UTR|ERBB4_uc010zjj.1_3'UTR	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		TCACACTGCTAAAAGATATTTG	0.421										TSP Lung(8;0.080)			4	2	---	---	---	---	
DIRC3	729582	broad.mit.edu	37	2	218174739	218174739	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218174739delC	uc002vgn.1	-						DIRC3_uc002vgo.2_Intron					Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0						GGTTAAGAGTCCCCTGCATGA	0.418													4	2	---	---	---	---	
SPHKAP	80309	broad.mit.edu	37	2	228987006	228987006	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228987006delT	uc002vpq.2	-						SPHKAP_uc002vpp.2_Intron|SPHKAP_uc010zlx.1_Intron	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein							cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		CCCCTTTTGATTTTTTTTTAA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	233280282	233280282	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233280282delT								ALPPL2 (4860 upstream) : ALPI (40551 downstream)																							AGCTTCCCCCTTTGCTACCAG	0.557													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	236720812	236720812	+	Intron	DEL	T	-	-	rs10715633		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236720812delT	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						TCAAAAAAACTTTTTTTTTTT	0.517													3	3	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	240148689	240148690	+	Intron	DEL	AC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240148689_240148690delAC	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010zoa.1_Intron|HDAC4_uc010fza.2_Intron|HDAC4_uc002vyl.1_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)		caccaacacaacacacacacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	11979853	11979853	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11979853delT								C3orf31 (91501 upstream) : SYN2 (66009 downstream)																							TCTTGTAAAGTTTTTTTTTTC	0.274													4	2	---	---	---	---	
FGD5	152273	broad.mit.edu	37	3	14965853	14965853	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14965853delC	uc003bzc.2	+						FGD5_uc011avk.1_Intron|FGD5_uc003bzd.2_Intron	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5						ctctacctctcccctcctcct	0.358													4	2	---	---	---	---	
RARB	5915	broad.mit.edu	37	3	25612436	25612436	+	Intron	DEL	A	-	-	rs111980473		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25612436delA	uc011awl.1	+						RARB_uc003cdi.1_Intron|RARB_uc003cdh.2_Intron	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)	TACCAGAAAGAAAAAAAAAAA	0.428													5	3	---	---	---	---	
LZTFL1	54585	broad.mit.edu	37	3	45881332	45881332	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45881332delC	uc003cox.1	-						LZTFL1_uc003coy.1_Intron|LZTFL1_uc011bak.1_Intron	NM_020347	NP_065080	Q9NQ48	LZTL1_HUMAN	leucine zipper transcription factor-like 1												0				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		tgaattcctacccacccttca	0.000													4	2	---	---	---	---	
CCDC36	339834	broad.mit.edu	37	3	49282622	49282622	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49282622delT	uc003cwk.2	+						CCDC36_uc003cwl.3_3'UTR|CCDC36_uc011bck.1_Intron	NM_178173	NP_835467	Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36											ovary(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		TCATTCTCAAttttttttttt	0.229													4	2	---	---	---	---	
HEMK1	51409	broad.mit.edu	37	3	50615441	50615442	+	Intron	DEL	GT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50615441_50615442delGT	uc003dau.2	+						HEMK1_uc003dav.2_Intron|HEMK1_uc003daw.2_Intron	NM_016173	NP_057257	Q9Y5R4	HEMK1_HUMAN	HemK methyltransferase family member 1						DNA methylation		DNA binding|N-methyltransferase activity|protein methyltransferase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000283)|KIRC - Kidney renal clear cell carcinoma(197;0.0179)|Kidney(197;0.0212)		ACACATACACGTGTGTGTGTGC	0.569													6	3	---	---	---	---	
PRKCD	5580	broad.mit.edu	37	3	53197105	53197108	+	Intron	DEL	GTGT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53197105_53197108delGTGT	uc003dgl.2	+						PRKCD_uc003dgm.2_Intron	NM_006254	NP_006245	Q05655	KPCD_HUMAN	protein kinase C, delta						activation of phospholipase C activity|cellular component disassembly involved in apoptosis|cellular senescence|interferon-gamma-mediated signaling pathway|intracellular signal transduction|mRNA metabolic process|negative regulation of insulin receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein binding|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of ceramide biosynthetic process|positive regulation of glucosylceramide catabolic process|positive regulation of protein dephosphorylation|positive regulation of sphingomyelin catabolic process|protein stabilization|regulation of receptor activity|termination of signal transduction	cytosol|endoplasmic reticulum|nucleoplasm	ATP binding|calcium-independent protein kinase C activity|enzyme activator activity|enzyme binding|insulin receptor substrate binding|metal ion binding|protein C-terminus binding			central_nervous_system(4)|lung(3)|stomach(1)|skin(1)	9		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)		gtgtgtgtgcgtgtgtgtgtgACA	0.480													4	2	---	---	---	---	
PRICKLE2	166336	broad.mit.edu	37	3	64129270	64129270	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64129270delC	uc003dmf.2	-							NM_198859	NP_942559	Q7Z3G6	PRIC2_HUMAN	prickle-like 2							cytoplasm|nuclear membrane	zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		TCAGAGCAGACAAACCCAGGC	0.303													4	2	---	---	---	---	
CNTN3	5067	broad.mit.edu	37	3	74385951	74385951	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74385951delA	uc003dpm.1	-							NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor						cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		TTGGGAATACAAAAAAAAAAA	0.323													4	2	---	---	---	---	
GBE1	2632	broad.mit.edu	37	3	81698381	81698381	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81698381delT	uc003dqg.2	-						GBE1_uc011bgm.1_Intron	NM_000158	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		ATTGAGTAAATTTTTTTTTAA	0.284									Glycogen_Storage_Disease_type_IV				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	81988602	81988603	+	IGR	DEL	CT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81988602_81988603delCT								GBE1 (177652 upstream) : None (None downstream)																							TTGCTGCTCGCTCTCTCTCTCC	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	86420202	86420203	+	IGR	INS	-	AC	AC	rs140290395	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86420202_86420203insAC								CADM2 (302254 upstream) : VGLL3 (566922 downstream)																							aaaactcagcaacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	87134304	87134305	+	IGR	DEL	GA	-	-	rs148583943		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87134304_87134305delGA								VGLL3 (94047 upstream) : CHMP2B (142108 downstream)																							cagaaactgtgagagagaaggg	0.000													2	6	---	---	---	---	
ABI3BP	25890	broad.mit.edu	37	3	100567966	100567967	+	Intron	INS	-	AGCA	AGCA	rs139291889	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100567966_100567967insAGCA	uc003dun.2	-						ABI3BP_uc003duo.2_Intron|ABI3BP_uc011bhd.1_5'Flank|ABI3BP_uc003dum.2_5'Flank	NM_015429	NP_056244	Q7Z7G0	TARSH_HUMAN	ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4						TATCAGAAGTGAGCACCCTTGA	0.317													4	3	---	---	---	---	
IMPG2	50939	broad.mit.edu	37	3	101005514	101005514	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101005514delC	uc003duq.1	-						IMPG2_uc011bhe.1_Intron	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2						visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3						ATGGCATGTGCTGCATTATAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	103291232	103291232	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103291232delG								None (None upstream) : None (None downstream)																							AATGTTGCCTGGGATTTGGTG	0.388													4	2	---	---	---	---	
ALCAM	214	broad.mit.edu	37	3	105268802	105268803	+	Intron	DEL	TT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105268802_105268803delTT	uc003dvx.2	+						ALCAM_uc003dvw.1_Intron|ALCAM_uc003dvy.2_Intron|ALCAM_uc010hpp.2_Intron|ALCAM_uc003dvz.2_Intron	NM_001627	NP_001618	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3						TTTACTAATCTTTGTAGATATT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	129049672	129049672	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129049672delA								C3orf47 (6260 upstream) : RPL32P3 (52006 downstream)																							GTGCAGAGGGAAATGCTCTCT	0.463													4	2	---	---	---	---	
NPHP3	27031	broad.mit.edu	37	3	132416370	132416371	+	Intron	INS	-	ACTC	ACTC	rs145715450	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132416370_132416371insACTC	uc003epe.1	-						NPHP3_uc003epd.1_Intron	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3						maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1						TAATATATCTTATTCTAATATG	0.238													15	9	---	---	---	---	
EPHB1	2047	broad.mit.edu	37	3	134734089	134734089	+	Intron	DEL	T	-	-	rs67152221		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134734089delT	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						CAGTGCCTGGttttttttttt	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137099906	137099909	+	IGR	DEL	CAAA	-	-	rs113766551		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137099906_137099909delCAAA								IL20RB (369986 upstream) : SOX14 (383670 downstream)																							tacaaaaaagcaaacaaacaaaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139405839	139405839	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139405839delA								NMNAT3 (8999 upstream) : CLSTN2 (248188 downstream)																							CTTCAGCAACAAAGCAACCAG	0.284													4	2	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	139772234	139772234	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139772234delG	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						GATTGTGTCTGAGGATAAACT	0.433										HNSCC(16;0.037)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	155806144	155806144	+	IGR	DEL	C	-	-	rs72235815		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155806144delC								GMPS (150626 upstream) : KCNAB1 (32193 downstream)																							GATTTAAAATCCTGTGCCCCA	0.398													3	3	---	---	---	---	
LEKR1	389170	broad.mit.edu	37	3	156754040	156754040	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156754040delC	uc003fba.1	+							NM_001004316	NP_001004316	Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1												0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			acataaacagccagctatgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	158478077	158478078	+	IGR	DEL	TT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158478077_158478078delTT								RARRES1 (27802 upstream) : MFSD1 (41834 downstream)																							taTTCACATATTTAAAAATTAA	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	168242268	168242268	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168242268delA								GOLIM4 (428851 upstream) : MIR551B (27374 downstream)																							gtctgactccaaatcttcact	0.010													4	2	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	169245668	169245669	+	Intron	DEL	CT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169245668_169245669delCT	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						GTGATACGGGCTCTCTCTCTTC	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	170669196	170669196	+	IGR	DEL	G	-	-	rs74369722		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170669196delG								EIF5A2 (42770 upstream) : SLC2A2 (44941 downstream)																							AGCaaaaaaagaaaaaaaaaa	0.393													8	4	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	170826163	170826164	+	Intron	INS	-	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170826163_170826164insA	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|MIR569_hsa-mir-569|MI0003576_5'Flank	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			TAGTAACAATTAAAAAAAAAAG	0.238													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	178830943	178830944	+	Intron	INS	-	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178830943_178830944insG	uc003fjj.2	-											Homo sapiens cDNA clone IMAGE:4821793.																		ccagcttttttgaagcctcatt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184115474	184115475	+	IGR	INS	-	T	T	rs141215226	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184115474_184115475insT								CHRD (7855 upstream) : EPHB3 (164112 downstream)																							CAGAGTGAGCATAAAACAATAG	0.287													1	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184372619	184372619	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184372619delA								EPHB3 (72424 upstream) : MAGEF1 (55537 downstream)																							AGCAGAGGCCAAAAAAAGCTT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193741516	193741516	+	IGR	DEL	A	-	-	rs112169354		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193741516delA								LOC100128023 (29489 upstream) : HES1 (112418 downstream)																							AGTTCTTCATAAAAAAAAGAA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195293658	195293659	+	IGR	INS	-	G	G	rs72298612		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195293658_195293659insG								PPP1R2 (23434 upstream) : APOD (1914 downstream)																							TCATTCACATAAAAAAAAATGA	0.356													4	2	---	---	---	---	
CPLX1	10815	broad.mit.edu	37	4	807651	807652	+	Intron	DEL	CA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:807651_807652delCA	uc003gbi.2	-						CPLX1_uc003gbj.2_Intron	NM_006651	NP_006642	O14810	CPLX1_HUMAN	complexin 1						glutamate secretion	cytosol					0				Colorectal(103;0.187)		ccagaattcccacacacacaca	0.114													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6672393	6672393	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6672393delT								MRFAP1 (27944 upstream) : LOC93622 (3425 downstream)																							cctttgacactttgaactgtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	8649300	8649300	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8649300delT								CPZ (27814 upstream) : HMX1 (219473 downstream)																							taaataattattttttttaaa	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	11956474	11956475	+	IGR	INS	-	A	A	rs149187146	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11956474_11956475insA								HS3ST1 (525937 upstream) : None (None downstream)																							gcaaaGAAGAGAAAAAAAACAA	0.188													3	4	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21121005	21121005	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21121005delG	uc003gqf.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_147183	NP_671712	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 4							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				CTCAGTGGGTGGGTGGATGCT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	28907815	28907816	+	IGR	INS	-	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28907815_28907816insT								None (None upstream) : None (None downstream)																							taacaacttcattttttttttt	0.035													4	2	---	---	---	---	
N4BP2	55728	broad.mit.edu	37	4	40105583	40105583	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40105583delT	uc003guy.3	+						N4BP2_uc010ifq.2_Intron|N4BP2_uc010ifr.2_Intron	NM_018177	NP_060647	Q86UW6	N4BP2_HUMAN	Nedd4 binding protein 2							cytoplasm	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding			lung(3)|breast(2)|kidney(2)|ovary(1)	8						ATGCTAGttcttttttttttg	0.174													6	3	---	---	---	---	
FRYL	285527	broad.mit.edu	37	4	48588927	48588928	+	Intron	INS	-	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48588927_48588928insC	uc003gyh.1	-						FRYL_uc003gyk.2_Intron	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						AAAGAATACAGAAATAATTCAA	0.257													6	3	---	---	---	---	
USP46	64854	broad.mit.edu	37	4	53518151	53518151	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53518151delG	uc003gzn.2	-						USP46_uc003gzm.3_Intron|USP46_uc011bzr.1_Intron|USP46_uc011bzs.1_Intron	NM_022832	NP_073743	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46 isoform 1						behavior|protein deubiquitination|regulation of synaptic transmission, GABAergic|ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0295)			CATGACTTTTGCTTTGGTCTC	0.388													4	2	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79404376	79404376	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79404376delT	uc003hlb.2	+							NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						AGTGATGTGCTTTTTTATTTT	0.363													4	2	---	---	---	---	
COPS4	51138	broad.mit.edu	37	4	83984562	83984563	+	Intron	INS	-	T	T	rs5859856		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83984562_83984563insT	uc003hoa.2	+						COPS4_uc003hob.2_Intron|COPS4_uc010ijw.2_Intron|COPS4_uc010ijx.2_Intron	NM_016129	NP_057213	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4						cullin deneddylation	cytoplasm|signalosome	protein binding			kidney(1)	1		Hepatocellular(203;0.114)				aatttataaaattttttttgag	0.074													4	2	---	---	---	---	
C4orf37	285555	broad.mit.edu	37	4	99055730	99055731	+	Intron	INS	-	TAA	TAA	rs143595982	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99055730_99055731insTAA	uc003htt.1	-							NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)		ATTTTCAGAACTGTCTAGTCAG	0.262													4	3	---	---	---	---	
COL25A1	84570	broad.mit.edu	37	4	110169731	110169735	+	Intron	DEL	ATGGC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110169731_110169735delATGGC	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)		ATTTTCATAAATGGCATGAAAATAA	0.463													4	2	---	---	---	---	
PRSS12	8492	broad.mit.edu	37	4	119273079	119273080	+	Intron	DEL	CA	-	-	rs111877944		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119273079_119273080delCA	uc003ica.1	-							NM_003619	NP_003610	P56730	NETR_HUMAN	neurotrypsin precursor							membrane	scavenger receptor activity			skin(1)	1						TACACGAGCGCACACACACACA	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	121003243	121003244	+	IGR	DEL	TG	-	-	rs112400167		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121003243_121003244delTG								MAD2L1 (15230 upstream) : PRDM5 (612686 downstream)																							AGGCCAGATTtgtgtgtgtgtg	0.327													2	4	---	---	---	---	
SLC10A7	84068	broad.mit.edu	37	4	147193328	147193329	+	Intron	INS	-	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147193328_147193329insA	uc010ioz.2	-						SLC10A7_uc003ikr.2_Intron|SLC10A7_uc010ipa.2_Intron|SLC10A7_uc003iks.2_Intron	NM_001029998	NP_001025169	Q0GE19	NTCP7_HUMAN	solute carrier family 10 (sodium/bile acid							integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)					GTAGATTATGTTTTAAAAGCAT	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	148038479	148038480	+	IGR	INS	-	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148038479_148038480insC								TTC29 (171445 upstream) : MIR548G (227301 downstream)																							TTGGAAATTTTCCCCAGACTCC	0.426													4	2	---	---	---	---	
PET112L	5188	broad.mit.edu	37	4	152631662	152631662	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152631662delC	uc003iml.2	-						PET112L_uc003imm.3_Intron	NM_004564	NP_004555	O75879	GATB_HUMAN	PET112-like precursor							mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding				0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)			L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	tattccttaacccacgtcagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	158863104	158863104	+	IGR	DEL	A	-	-	rs72279831		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158863104delA								LOC340017 (365809 upstream) : FAM198B (182629 downstream)																							attaatgaagaaaaacagaca	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	170687499	170687500	+	IGR	DEL	AA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170687499_170687500delAA								C4orf27 (8406 upstream) : MFAP3L (220250 downstream)																							TTATACAGCTAAATGGTGGTGA	0.416													4	2	---	---	---	---	
GALNTL6	442117	broad.mit.edu	37	4	173939675	173939675	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173939675delG	uc003isv.2	+							NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4						tcactgtctagggagggatag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	184001697	184001698	+	IGR	DEL	TG	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184001697_184001698delTG								FAM92A3 (40426 upstream) : C4orf38 (16476 downstream)																							TTTGCAGCTTTGTAAGAAGAGT	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8152000	8152000	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8152000delG								MTRR (250767 upstream) : SEMA5A (883138 downstream)																							GCAACAGAAAGGAGATGTGCT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	9551163	9551164	+	IGR	INS	-	CAT	CAT			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9551163_9551164insCAT								SNORD123 (2137 upstream) : TAS2R1 (77945 downstream)																							CCTCACACATACATCATCATCA	0.371													4	2	---	---	---	---	
MARCH6	10299	broad.mit.edu	37	5	10352155	10352156	+	5'Flank	DEL	AC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10352155_10352156delAC	uc003jet.1	+						MARCH6_uc011cmu.1_5'Flank|MARCH6_uc003jeu.1_5'Flank|MARCH6_uc011cmv.1_5'Flank	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						CGCCCCCCATACACACACATTC	0.495													4	2	---	---	---	---	
FBXL7	23194	broad.mit.edu	37	5	15692848	15692848	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15692848delA	uc003jfn.1	+							NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3						ACATAGGGCTAAAAATGTTCT	0.463													4	2	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21539615	21539616	+	Intron	INS	-	TA	TA	rs143282782	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21539615_21539616insTA	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						aacagaaagacatactgcctga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23311348	23311348	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23311348delT								CDH12 (457617 upstream) : PRDM9 (196376 downstream)																							gaagatatacttgagactgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27755780	27755780	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27755780delG								CDH9 (717091 upstream) : None (None downstream)																							acaaaaaaaagctcatccacc	0.000													4	2	---	---	---	---	
ZFR	51663	broad.mit.edu	37	5	32399914	32399914	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32399914delA	uc003jhr.1	-							NM_016107	NP_057191	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein						multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding				0				STAD - Stomach adenocarcinoma(35;0.19)		AAAAGTTAGCAAAAAAAAAAT	0.299													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	44936205	44936205	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44936205delT								MRPS30 (120591 upstream) : HCN1 (323148 downstream)																							aactttcaggttcattgccat	0.129													4	2	---	---	---	---	
CENPK	64105	broad.mit.edu	37	5	64826132	64826132	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64826132delA	uc003jts.2	-						CENPK_uc003jtt.2_Intron|CENPK_uc003jtu.2_Intron	NM_022145	NP_071428	Q9BS16	CENPK_HUMAN	SoxLZ/Sox6 leucine zipper binding protein						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00466)		tgtcataaagaaaaaaaaaat	0.184													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	67430422	67430422	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67430422delT								CD180 (937805 upstream) : PIK3R1 (81182 downstream)																							CTCAGGGTGCTTTTTCCCCAA	0.453													4	2	---	---	---	---	
EDIL3	10085	broad.mit.edu	37	5	83402821	83402821	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83402821delC	uc003kio.1	-						EDIL3_uc003kip.1_Intron	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like						cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		GGAAATAATTCTTGCTTCTCA	0.353													1	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87404837	87404838	+	IGR	INS	-	TG	TG	rs142841971	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87404837_87404838insTG								CCNH (696001 upstream) : TMEM161B (86186 downstream)																							GGAAAAAGGGCTGTGTGGGATG	0.401													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	99683400	99683401	+	IGR	DEL	AC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99683400_99683401delAC								None (None upstream) : LOC100133050 (31808 downstream)																							GAACTCTGTTACCACAGTATCT	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	121598426	121598426	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121598426delT								ZNF474 (109169 upstream) : SNCAIP (48960 downstream)																							ctgacacttcttttgtcatag	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	127022273	127022273	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127022273delG								CTXN3 (27952 upstream) : FLJ33630 (253862 downstream)																							GTGGGTCTTTGTTGAGTCTAG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	127563476	127563476	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127563476delT								SLC12A2 (38097 upstream) : FBN2 (30126 downstream)																							gagacaatacttttattgtac	0.055													4	2	---	---	---	---	
LARS	51520	broad.mit.edu	37	5	145540213	145540214	+	Intron	INS	-	ATTT	ATTT	rs140796536	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145540213_145540214insATTT	uc003lnx.1	-						LARS_uc011dbq.1_Intron|LARS_uc011dbr.1_Intron|LARS_uc011dbs.1_Intron	NM_020117	NP_064502	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase						leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	CAATTACTTTAATTTACTTAAA	0.208													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148191839	148191840	+	Intron	INS	-	A	A	rs77130335	byFrequency	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148191839_148191840insA	uc003lpp.1	-							NM_024577		Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tgaagataaccaaaaaaagaag	0.000													4	2	---	---	---	---	
CAMK2A	815	broad.mit.edu	37	5	149632187	149632187	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149632187delC	uc003lru.2	-						CAMK2A_uc003lrt.2_Intron|CAMK2A_uc010jhe.2_Intron|CAMK2A_uc010jhf.1_Intron	NM_171825	NP_741960	Q9UQM7	KCC2A_HUMAN	calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission	cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ttaagtgcctcccagggttgt	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154061098	154061099	+	IGR	DEL	CA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154061098_154061099delCA								HAND1 (203274 upstream) : MIR1303 (4237 downstream)																							CATACACATGCACACACACAAA	0.416													4	2	---	---	---	---	
C5orf4	10826	broad.mit.edu	37	5	154230846	154230846	+	5'Flank	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154230846delT	uc003lvs.3	-						C5orf4_uc011dde.1_5'Flank	NM_032385	NP_115761	Q96IV6	CE004_HUMAN	hypothetical protein LOC10826						fatty acid biosynthetic process	integral to membrane	iron ion binding|oxidoreductase activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTCAGTCCCCTTTTTTTCCTC	0.154													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	156052226	156052226	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156052226delT	uc003lwd.3	+						SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			gtttcttcactttttttttct	0.214													4	2	---	---	---	---	
PWWP2A	114825	broad.mit.edu	37	5	159505455	159505455	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159505455delT	uc003lxv.3	-						PWWP2A_uc011dec.1_Intron	NM_052927	NP_443159	Q96N64	PWP2A_HUMAN	PWWP domain containing 2A isoform a												0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CACTTGAGTGTTTTTTTAAAA	0.348													4	2	---	---	---	---	
FABP6	2172	broad.mit.edu	37	5	159627849	159627849	+	Intron	DEL	T	-	-	rs5872633		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159627849delT	uc003lxx.1	+						FABP6_uc003lxz.1_Intron|uc003lxy.1_Intron	NM_001130958	NP_001124430	P51161	FABP6_HUMAN	gastrotropin isoform 1						bile acid and bile salt transport|bile acid metabolic process|negative regulation of cell proliferation	cytosol	transporter activity				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCTTCAAACCTAGCCCTTGGG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	160508894	160508894	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160508894delG								LOC285629 (143261 upstream) : GABRB2 (206542 downstream)																							gtcatgtaatgcttgtaaact	0.075													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165833996	165833996	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165833996delA								None (None upstream) : ODZ2 (877847 downstream)																							AGCTAGGGGGAAAAAGGTACT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165936461	165936462	+	IGR	DEL	AA	-	-	rs34820519		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165936461_165936462delAA								None (None upstream) : ODZ2 (775381 downstream)																							ACAAATGTGTAAAAAAAAAAAA	0.322													1	6	---	---	---	---	
ERGIC1	57222	broad.mit.edu	37	5	172286492	172286493	+	Intron	INS	-	A	A	rs140388993	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172286492_172286493insA	uc003mbw.3	+							NM_001031711	NP_001026881	Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate						ER to Golgi vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGAAGGGTGGGAAAAAAAAATG	0.347													4	5	---	---	---	---	
CLTB	1212	broad.mit.edu	37	5	175820172	175820173	+	Intron	DEL	AG	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175820172_175820173delAG	uc003meh.2	-						CLTB_uc003mei.2_Intron|CLTB_uc011dfn.1_Intron	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)		cgcttctcccagacctgttcct	0.144													4	2	---	---	---	---	
LMAN2	10960	broad.mit.edu	37	5	176761175	176761176	+	Intron	INS	-	ACCACAACC	ACCACAACC			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176761175_176761176insACCACAACC	uc003mge.2	-						LMAN2_uc003mgd.2_Intron	NM_006816	NP_006807	Q12907	LMAN2_HUMAN	lectin, mannose-binding 2 precursor						protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	metal ion binding|sugar binding				0	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAAGAGCCCAGACCACAACCAC	0.644													6	5	---	---	---	---	
LOC202181	202181	broad.mit.edu	37	5	177061544	177061545	+	Intron	DEL	CT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177061544_177061545delCT	uc011dgc.1	-						LOC202181_uc011dgb.1_Intron	NM_198567	NP_940969			hypothetical protein LOC375484												0						CTATGCAAACCTCTCTCTCTAT	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	179868685	179868686	+	IGR	DEL	GC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179868685_179868686delGC								GFPT2 (88370 upstream) : CNOT6 (52731 downstream)																							ACCACTCAGGGCAAGGGTGTGG	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8400782	8400782	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8400782delA								EEF1E1 (297954 upstream) : SLC35B3 (10951 downstream)																							TAGAATTATGAAAAAAAAAAT	0.244													4	3	---	---	---	---	
HIVEP1	3096	broad.mit.edu	37	6	12014279	12014279	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12014279delT	uc003nac.2	+							NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TAGttcagcgtttttgtgtga	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	23784276	23784276	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23784276delA								None (None upstream) : NRSN1 (342138 downstream)																							CGCCACTGCCAAAGAAAATCT	0.423													4	2	---	---	---	---	
ACOT13	55856	broad.mit.edu	37	6	24703636	24703636	+	3'UTR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24703636delA	uc003nek.2	+	3					ACOT13_uc010jpv.2_3'UTR	NM_018473	NP_060943	Q9NPJ3	ACO13_HUMAN	acyl-CoA thioesterase 13 isoform 1						protein homotetramerization	mitochondrion	acyl-CoA thioesterase activity				0						atttcccactaaaaggaagct	0.015													4	2	---	---	---	---	
MTCH1	23787	broad.mit.edu	37	6	36953604	36953604	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36953604delC	uc003ond.1	-						MTCH1_uc003onc.1_Intron|MTCH1_uc010jwo.1_Intron|MTCH1_uc003one.3_Intron|MTCH1_uc011dtt.1_Intron	NM_014341	NP_055156	Q9NZJ7	MTCH1_HUMAN	mitochondrial carrier homolog 1						activation of caspase activity|neuronal ion channel clustering|positive regulation of apoptosis|regulation of signal transduction|transport	integral to membrane|mitochondrial inner membrane	protein binding				0						CCTCCCATCTCCCTACGGCGC	0.652													4	2	---	---	---	---	
CDC5L	988	broad.mit.edu	37	6	44394653	44394654	+	Intron	DEL	GT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44394653_44394654delGT	uc003oxl.2	+							NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like						cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)|skin(1)	6	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCCGTGTTCAGTGTGATAGACC	0.381													4	2	---	---	---	---	
SUPT3H	8464	broad.mit.edu	37	6	44900722	44900722	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44900722delC	uc003oxo.2	-						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron|SUPT3H_uc011dvw.1_Intron	NM_181356	NP_852001	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog isoform 2						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3						AATTTTTATGCCCACAATATT	0.383													4	2	---	---	---	---	
RUNX2	860	broad.mit.edu	37	6	45485688	45485688	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45485688delA	uc011dvx.1	+						RUNX2_uc011dvy.1_Intron|RUNX2_uc003oxt.2_Intron	NM_001024630	NP_001019801	Q13950	RUNX2_HUMAN	runt-related transcription factor 2 isoform a						negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3						GCAGCTTCGTAATGTGCCAAT	0.398													4	2	---	---	---	---	
DST	667	broad.mit.edu	37	6	56574631	56574631	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56574631delC	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc011dxl.1_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CTGAGGTCTTCCCAGCAAAGA	0.090													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57432462	57432463	+	Intron	INS	-	GTTTATTT	GTTTATTT	rs10654142		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57432462_57432463insGTTTATTT	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)		tcacattttgggtttgcttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82804718	82804718	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82804718delA								FAM46A (342290 upstream) : IBTK (75238 downstream)																							accagttcagaaaaaaatact	0.025													4	2	---	---	---	---	
GPR63	81491	broad.mit.edu	37	6	97246106	97246106	+	3'UTR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97246106delA	uc010kcl.2	-	3					GPR63_uc003pou.2_3'UTR	NM_001143957	NP_001137429	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63							integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		CCCCAAAACCAAAAAAAAGTC	0.343													4	2	---	---	---	---	
C6orf167	253714	broad.mit.edu	37	6	97716066	97716066	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97716066delC	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron|C6orf167_uc010kcn.1_Intron|C6orf167_uc010kco.1_Intron|C6orf167_uc003ppc.2_Intron	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)		TCAAAAGtttctttttttttt	0.119													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	102798357	102798357	+	IGR	DEL	T	-	-	rs112551438		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102798357delT								GRIK2 (280400 upstream) : None (None downstream)																							tagtagagcatttttttttcc	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	104469160	104469161	+	IGR	DEL	GA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104469160_104469161delGA								None (None upstream) : HACE1 (706807 downstream)																							AATATTAAAGGAGAAAAATTTG	0.282													4	2	---	---	---	---	
HACE1	57531	broad.mit.edu	37	6	105216910	105216910	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105216910delT	uc003pqu.1	-						HACE1_uc010kcy.1_Intron|HACE1_uc010kcz.1_Intron|HACE1_uc010kcx.1_Intron|HACE1_uc003pqt.1_Intron	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		CTCATACACAtttttttttct	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	106252890	106252890	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106252890delC								PREP (401921 upstream) : PRDM1 (281305 downstream)																							GTTGGTCTCTCTTCCCAACTT	0.478													4	2	---	---	---	---	
RTN4IP1	84816	broad.mit.edu	37	6	107077059	107077060	+	5'UTR	INS	-	A	A	rs144527909	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107077059_107077060insA	uc003prj.2	-	1					QRSL1_uc003prl.2_5'Flank|QRSL1_uc003prm.2_5'Flank|RTN4IP1_uc010kdd.2_5'UTR|RTN4IP1_uc003prk.2_Intron	NM_032730	NP_116119	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1 precursor							mitochondrion	oxidoreductase activity|zinc ion binding				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		TGGAGAAACTGAAAGAAGAATA	0.421													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	113273390	113273390	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113273390delA								RFPL4B (600892 upstream) : MARCKS (905137 downstream)																							GGTGAGGAGGAAAAAAAAAGA	0.343													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	114050833	114050833	+	IGR	DEL	A	-	-	rs67055837		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114050833delA								None (None upstream) : MARCKS (127694 downstream)																							tcccaggcacacatctccctc	0.000													3	4	---	---	---	---	
PLEKHG1	57480	broad.mit.edu	37	6	151144487	151144487	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151144487delG	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron|PLEKHG1_uc011eem.1_Intron|PLEKHG1_uc003qnz.2_Intron	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		TTCTTTTTCAGGAAACAACAC	0.338													3	3	---	---	---	---	
SYNE1	23345	broad.mit.edu	37	6	152528207	152528207	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152528207delG	uc010kiw.2	-						SYNE1_uc010kiv.2_Intron|SYNE1_uc003qos.3_Intron|SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc003qor.3_Intron	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ttgtctatctgggcaagaaat	0.100										HNSCC(10;0.0054)			4	2	---	---	---	---	
ARID1B	57492	broad.mit.edu	37	6	157503048	157503048	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157503048delC	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron|ARID1B_uc010kjl.2_Intron	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		ACATGAGTCACCAGCCCCAAA	0.323													4	2	---	---	---	---	
PLG	5340	broad.mit.edu	37	6	161137479	161137479	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161137479delA	uc003qtm.3	+							NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen						extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	aaaaacaaacaaaaaaAAGAA	0.169													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166194842	166194842	+	RNA	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166194842delG	uc003qup.1	-	2		c.959delC								Homo sapiens cDNA FLJ33369 fis, clone BRACE2005904.																		ctaagacaCTGGGGATCAGGT	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170494463	170494464	+	IGR	DEL	AT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170494463_170494464delAT								C6orf208 (291494 upstream) : LOC154449 (68958 downstream)																							CGCTTCCCACATGTGTCTTGCT	0.495													4	2	---	---	---	---	
C7orf27	221927	broad.mit.edu	37	7	2584700	2584700	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2584700delA	uc003smi.2	-						C7orf27_uc003smh.3_5'Flank|C7orf27_uc003smj.1_Intron	NM_152743	NP_689956	Q6PJG6	BRAT1_HUMAN	hypothetical protein LOC221927 precursor						response to ionizing radiation	nucleus	protein binding				0		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;2.91e-14)		GCTGGGAAGCAAAAAAAGAAG	0.378													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3861423	3861423	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3861423delG	uc003smx.2	+							NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GAATCTCAGTGGTACTTCTGA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4403246	4403247	+	IGR	INS	-	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4403246_4403247insT								SDK1 (94617 upstream) : FOXK1 (280141 downstream)																							GAACAGCAGCATTTTTCTTTCT	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	15776403	15776403	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15776403delA								MEOX2 (50095 upstream) : ISPD (350749 downstream)																							gcctgcaatgaaaaagggaat	0.000													4	2	---	---	---	---	
ITGB8	3696	broad.mit.edu	37	7	20390501	20390501	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20390501delT	uc003suu.2	+						ITGB8_uc011jyh.1_Intron|ITGB8_uc003sut.2_Intron	NM_002214	NP_002205	P26012	ITB8_HUMAN	integrin, beta 8 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(3)	3						AGAAACATGGTTGTAAAAGGA	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	37861358	37861359	+	Intron	INS	-	A	A	rs151118719	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37861358_37861359insA	uc003tfl.2	+											Homo sapiens, clone IMAGE:3881224, mRNA.																		CTTTATTGGGGAAAAAAAATAG	0.252													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41229928	41229928	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41229928delA								C7orf10 (329571 upstream) : INHBA (498675 downstream)																							ataaagaaataaaaaagagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46319350	46319350	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46319350delT								IGFBP3 (358479 upstream) : TNS3 (995403 downstream)																							gttcaaagtatttttttttaa	0.000													4	2	---	---	---	---	
COBL	23242	broad.mit.edu	37	7	51177194	51177194	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51177194delA	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron|COBL_uc003tpp.3_Intron|COBL_uc003tpq.3_Intron	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)					TGACAGTCCTAAAATCCCATC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57698975	57698976	+	IGR	INS	-	AGTG	AGTG	rs145904451	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57698975_57698976insAGTG								ZNF716 (165710 upstream) : None (None downstream)																							AAAAAATGTACAGTGAGGGAAT	0.277													5	3	---	---	---	---	
ZNF92	168374	broad.mit.edu	37	7	64854208	64854208	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64854208delA	uc003ttz.2	+						ZNF92_uc003tua.2_Intron|ZNF92_uc010kzu.2_Intron|ZNF92_uc003tub.2_Intron	NM_152626	NP_689839	Q03936	ZNF92_HUMAN	zinc finger protein 92 isoform 2							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Lung NSC(55;0.159)				AGCTGTTTCCAAAAAAAATAG	0.224													4	2	---	---	---	---	
WBSCR22	114049	broad.mit.edu	37	7	73111776	73111776	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73111776delA	uc003tyt.2	+						WBSCR22_uc003tyu.2_Intron|WBSCR22_uc003tyv.2_Intron|WBSCR22_uc003tyw.1_Intron	NM_017528	NP_059998	O43709	WBS22_HUMAN	Williams Beuren syndrome chromosome region 22							nucleus	methyltransferase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)				GGGTGTCCAGAGCGGGGAATT	0.582													5	3	---	---	---	---	
PMS2L3	5387	broad.mit.edu	37	7	75142142	75142142	+	Intron	DEL	A	-	-	rs71519365		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75142142delA	uc003udp.2	-						PMS2L3_uc003udn.2_Intron|PMS2L3_uc003udq.2_Intron	NM_005395	NP_005386			SubName: Full=Postmeiotic segregation increased 2-like 3; SubName: Full=Postmeiotic segregation increased 2-like 3, isoform CRA_b;												0						tctcaaaaagaaaaaaaaaaa	0.129								Direct_reversal_of_damage|MMR					9	5	---	---	---	---	
ABCB1	5243	broad.mit.edu	37	7	87225384	87225384	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87225384delC	uc003uiz.1	-						ABCB1_uc011khc.1_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1						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)	CTTCCTTGTGCCTTTGATATT	0.284													4	2	---	---	---	---	
AKAP9	10142	broad.mit.edu	37	7	91732281	91732281	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91732281delT	uc003ulg.2	+						AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron|AKAP9_uc003ulj.2_Intron|AKAP9_uc003ull.2_Intron	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GCATGTCTGCTTTTTTTTTCT	0.388			T	BRAF	papillary thyroid								4	2	---	---	---	---	
ASB15	142685	broad.mit.edu	37	7	123254294	123254294	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123254294delA	uc003vku.1	+						ASB15_uc003vkv.1_Intron|ASB15_uc003vkw.1_Intron	NM_080928	NP_563616	Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box-containing 15						intracellular signal transduction					skin(2)|lung(1)	3						GTCATTACTGAAAAAAAAAAA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	136400166	136400166	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136400166delC								LUZP6 (737962 upstream) : CHRM2 (153233 downstream)																							caaaacaaaacaaaacaaaac	0.363													4	2	---	---	---	---	
KEL	3792	broad.mit.edu	37	7	142650083	142650084	+	Intron	DEL	TG	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142650083_142650084delTG	uc003wcb.2	-							NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase						proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)					AGCTGGTCTCTGTGACTGCTCT	0.495													4	2	---	---	---	---	
OR2A9P	441295	broad.mit.edu	37	7	144024376	144024377	+	Intron	INS	-	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144024376_144024377insT	uc003wec.1	-											SubName: Full=Seven transmembrane helix receptor;												0						CCTCCATAGAATTTTTTTTCAA	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	145088426	145088426	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145088426delC								TPK1 (555280 upstream) : CNTNAP2 (725027 downstream)																							AGGAGATGATCCCAAATCTGA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148347109	148347109	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148347109delA								C7orf33 (34158 upstream) : CUL1 (47897 downstream)																							accctgtctcaaaaaaaaaaa	0.204													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149745031	149745031	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149745031delA								ATP6V0E2 (167245 upstream) : ACTR3C (199271 downstream)																							GCTCCAGATTAAAAAAAAGGC	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152429179	152429179	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152429179delA								XRCC2 (55929 upstream) : ACTR3B (27672 downstream)																							ACTCTGTCTCAAAAAAAAAGA	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153020361	153020362	+	IGR	INS	-	C	C	rs114447776	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153020361_153020362insC								ACTR3B (467898 upstream) : DPP6 (564057 downstream)																							CGTTGAGGGTTCCTGCCATAGT	0.495													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158147097	158147098	+	Intron	DEL	CT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158147097_158147098delCT	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)		gatttgtgagctctcatcaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	10733403	10733403	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10733403delA								SOX7 (36104 upstream) : XKR6 (20254 downstream)																							TTCAGGATGCAAAGACAAGGT	0.488													4	2	---	---	---	---	
LPL	4023	broad.mit.edu	37	8	19817098	19817098	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19817098delT	uc003wzk.3	+							NM_000237	NP_000228	P06858	LIPL_HUMAN	lipoprotein lipase precursor						fatty acid biosynthetic process|lipoprotein metabolic process|phospholipid metabolic process|positive regulation of cholesterol storage|positive regulation of sequestering of triglyceride|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	anchored to membrane|chylomicron|plasma membrane|very-low-density lipoprotein particle	heparin binding|lipoprotein lipase activity|phospholipase activity|receptor binding|triglyceride lipase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	Clofibrate(DB00636)|Gemfibrozil(DB01241)|Orlistat(DB01083)	ACTAGTTATATTTTTTTATTT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21112214	21112214	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21112214delT								LZTS1 (999411 upstream) : GFRA2 (437316 downstream)																							gcaatctacatttttttttcc	0.000													6	3	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32542812	32542813	+	Intron	INS	-	G	G	rs73675404	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32542812_32542813insG	uc003xiv.2	+						NRG1_uc003xip.2_Intron|NRG1_uc003xir.2_Intron|NRG1_uc010lvl.2_Intron|NRG1_uc010lvm.2_Intron|NRG1_uc010lvn.2_Intron|NRG1_uc003xis.2_Intron|NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc003xix.2_Intron|NRG1_uc003xiy.2_Intron|NRG1_uc010lvt.2_Intron	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		taattacatttggggagtcaca	0.114													4	2	---	---	---	---	
DDHD2	23259	broad.mit.edu	37	8	38092660	38092660	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38092660delT	uc003xlb.2	+						DDHD2_uc003xla.2_Intron|DDHD2_uc003xlc.2_Intron|DDHD2_uc011lbl.1_Intron	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1						lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			ATTTAGAATATAACTCAGAAT	0.303													4	2	---	---	---	---	
EFCAB1	79645	broad.mit.edu	37	8	49642082	49642082	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49642082delA	uc003xqo.2	-						EFCAB1_uc003xqn.3_Intron|EFCAB1_uc011ldj.1_Intron|EFCAB1_uc010lxx.2_Intron|EFCAB1_uc011ldk.1_Intron	NM_024593	NP_078869	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1 isoform a								calcium ion binding				0		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				accctgtctcaaaaaaaaaaa	0.129													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	50214664	50214665	+	IGR	INS	-	GTG	GTG			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50214664_50214665insGTG								C8orf22 (226023 upstream) : SNTG1 (607684 downstream)																							gagttccaggcgtggtatcagc	0.000													3	3	---	---	---	---	
CHD7	55636	broad.mit.edu	37	8	61607475	61607475	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61607475delT	uc003xue.2	+							NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GAAAGGTTAGTTTGGCAGCAT	0.453													4	2	---	---	---	---	
CPA6	57094	broad.mit.edu	37	8	68482335	68482335	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68482335delT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			AAACAAGAACTTTTTTTTTTC	0.313													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94398912	94398912	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94398912delT								C8orf83 (369011 upstream) : FAM92A1 (313861 downstream)																							ATTACCAGCATTACCAGTTCA	0.473													4	2	---	---	---	---	
SNTB1	6641	broad.mit.edu	37	8	121613202	121613202	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121613202delA	uc010mdg.2	-						SNTB1_uc003ype.2_Intron	NM_021021	NP_066301	Q13884	SNTB1_HUMAN	basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			CTCTGATGGGAAGGAAAAGCA	0.522													4	2	---	---	---	---	
ANXA13	312	broad.mit.edu	37	8	124715977	124715977	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124715977delT	uc003yqu.2	-						ANXA13_uc003yqt.2_Intron	NM_004306	NP_004297	P27216	ANX13_HUMAN	annexin A13 isoform a						cell differentiation	plasma membrane	calcium ion binding|calcium-dependent phospholipid binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			TTTTAGAAGCTTTTTTACCCC	0.358													4	2	---	---	---	---	
FAM49B	51571	broad.mit.edu	37	8	130969717	130969718	+	Intron	INS	-	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130969717_130969718insA	uc003ysw.2	-						FAM49B_uc003ysx.2_Intron|FAM49B_uc003ysy.1_Intron	NM_016623	NP_057707	Q9NUQ9	FA49B_HUMAN	hypothetical protein LOC51571												0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			cacaagaactcaaaaagcacag	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138935239	138935256	+	IGR	DEL	ATTGACTGCTGCCCACAC	-	-	rs112262567		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138935239_138935256delATTGACTGCTGCCCACAC								None (None upstream) : FAM135B (207012 downstream)																							ccctcaacatattgactgctgcccacacattgactgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139102313	139102313	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139102313delT								None (None upstream) : FAM135B (39955 downstream)																							cagaacagagttttttataaa	0.000													4	2	---	---	---	---	
MPDZ	8777	broad.mit.edu	37	9	13135931	13135934	+	Intron	DEL	TGAG	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13135931_13135934delTGAG	uc010mia.1	-						MPDZ_uc003zky.3_Intron|MPDZ_uc010mib.2_Intron|MPDZ_uc010mhx.2_Intron|MPDZ_uc011lmm.1_Intron|MPDZ_uc003zkz.3_Intron|MPDZ_uc010mhy.2_Intron|MPDZ_uc010mhz.2_Intron|MPDZ_uc011lmn.1_Intron|MPDZ_uc003zlb.3_Intron	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein						interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)		cttatttccatgagtgtcttctta	0.039													5	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66460617	66460617	+	5'Flank	DEL	C	-	-	rs112623405		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66460617delC	uc004aeb.2	-						uc004aec.2_Intron					Homo sapiens cDNA clone IMAGE:3941306, partial cds.																		aatattttttcctcattctat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66461548	66461549	+	Intron	INS	-	T	T	rs149299153		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66461548_66461549insT	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		agcttaaggagttttgggtcac	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66515952	66515952	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66515952delT	uc010mnh.1	-											Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																		TTTCCACACATTTTTTTTACT	0.189													3	3	---	---	---	---	
PCSK5	5125	broad.mit.edu	37	9	78803334	78803334	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78803334delA	uc004ajz.2	+						PCSK5_uc004aka.2_Intron|PCSK5_uc004akb.2_Intron	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						TTGAGAGGAGAAAAAAAAGGG	0.458													4	2	---	---	---	---	
GAPVD1	26130	broad.mit.edu	37	9	128097667	128097667	+	Intron	DEL	A	-	-	rs13288223	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128097667delA	uc010mwx.2	+						GAPVD1_uc011lzs.1_Intron|GAPVD1_uc004bpp.2_Intron|GAPVD1_uc004bpq.2_Intron|GAPVD1_uc004bpr.2_Intron|GAPVD1_uc004bps.2_Intron|GAPVD1_uc010mwy.1_Intron	NM_015635	NP_056450	Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1						endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4						ttttttttttaaaaatggggc	0.000													6	3	---	---	---	---	
LRSAM1	90678	broad.mit.edu	37	9	130244908	130244908	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130244908delT	uc004brb.1	+						LRSAM1_uc010mxk.1_Intron|LRSAM1_uc004brc.1_Intron|LRSAM1_uc004brd.1_Intron|LRSAM1_uc004bre.1_Intron	NM_001005373	NP_001005373	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif						negative regulation of endocytosis|non-lytic virus budding|protein autoubiquitination|protein catabolic process|protein polyubiquitination|protein transport|ubiquitin-dependent endocytosis	cytoplasm|extracellular region|membrane part	hormone activity|ubiquitin-protein ligase activity|zinc ion binding				0						ggtgaaaagattttactttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	14539339	14539339	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14539339delA								FRMD4A (35196 upstream) : FAM107B (21220 downstream)																							AGAACTTTTCAAAGGATCTGC	0.333													4	2	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	67756569	67756569	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67756569delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						tacttccctgttttttttctt	0.000													4	2	---	---	---	---	
ADK	132	broad.mit.edu	37	10	76288058	76288058	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76288058delA	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_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)	TTTAAAACTTAAAAAAAAAGC	0.269													5	3	---	---	---	---	
KIF20B	9585	broad.mit.edu	37	10	91532223	91532223	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91532223delT	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron|KIF20B_uc001kgt.1_Intron|KIF20B_uc009xtw.1_Intron	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						Ctttatttgctttttttttgc	0.139													4	2	---	---	---	---	
ENTPD7	57089	broad.mit.edu	37	10	101456576	101456576	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101456576delT	uc001kqa.3	+						ENTPD7_uc009xwl.2_Intron	NM_020354	NP_065087	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase							cytoplasmic vesicle membrane|integral to membrane	hydrolase activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		TTACACAAAATTTTGGAATGA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	112247518	112247518	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112247518delA								SMNDC1 (182811 upstream) : DUSP5 (10107 downstream)																							AGGGAAACATAAATAATCAAA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	124109040	124109040	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124109040delG								BTBD16 (11364 upstream) : PLEKHA1 (25180 downstream)																							GGGGCAGAATGGGGACAtgtg	0.109													4	2	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127580879	127580879	+	Intron	DEL	A	-	-	rs112972524		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127580879delA	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)				caacatctccaatttttttgt	0.000													7	4	---	---	---	---	
TCERG1L	256536	broad.mit.edu	37	10	132945155	132945157	+	Intron	DEL	AGA	-	-	rs150973795	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132945155_132945157delAGA	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		TAGACCAGGGAGAACAACAACAT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15652350	15652351	+	IGR	DEL	AC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15652350_15652351delAC								INSC (383598 upstream) : SOX6 (335645 downstream)																							GTGCACATATACACACACACTT	0.327													4	2	---	---	---	---	
KCNJ11	3767	broad.mit.edu	37	11	17409650	17409650	+	5'UTR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17409650delC	uc001mna.2	-	1					KCNJ11_uc001mnb.3_Intron	NM_000525	NP_000516	B4DWI4	B4DWI4_HUMAN	potassium inwardly-rectifying channel J11							integral to membrane	ATP-activated inward rectifier potassium channel activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0276)|Colorectal(2;0.0633)		GCTCCGGTGACCCCCAGGGAG	0.687													4	2	---	---	---	---	
C11orf41	25758	broad.mit.edu	37	11	33581051	33581051	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33581051delG	uc001mup.3	+						C11orf41_uc001mun.1_Intron	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758							integral to membrane				ovary(2)	2						cgtcatcactggatacatctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49054171	49054171	+	IGR	DEL	T	-	-	rs34088774		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49054171delT								OR4A47 (542899 upstream) : FOLH1 (114017 downstream)																							CATACAAACCTATAGTTATAC	0.383													3	3	---	---	---	---	
LRRC55	219527	broad.mit.edu	37	11	56958045	56958045	+	RNA	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56958045delG	uc001njm.1	+	1		c.1585delG						Q6ZSA7	LRC55_HUMAN	Homo sapiens cDNA FLJ13339 fis, clone OVARC1001928.							integral to membrane					0						TGTATGTGATGGGGTATCTCT	0.438													4	2	---	---	---	---	
MYO7A	4647	broad.mit.edu	37	11	76903036	76903037	+	Intron	DEL	GA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76903036_76903037delGA	uc001oyb.2	+						MYO7A_uc010rsm.1_Intron|MYO7A_uc001oyc.2_Intron|MYO7A_uc009yus.1_Intron|MYO7A_uc009yut.1_Intron	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1						actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4						TGGCCCCGTTGAGGCTCCTCAT	0.653											OREG0021258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ANKRD42	338699	broad.mit.edu	37	11	82924235	82924235	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82924235delA	uc001ozz.1	+						ANKRD42_uc009yvi.1_3'UTR|ANKRD42_uc010rsv.1_Intron|ANKRD42_uc001paa.2_Intron|ANKRD42_uc001pab.1_Intron	NM_182603	NP_872409	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42											skin(1)	1						TGGGAGCGACAAAAAAAACAA	0.458													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83178070	83178070	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83178070delA	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)				agccccttacaaagtgtctgc	0.209													4	2	---	---	---	---	
FAT3	120114	broad.mit.edu	37	11	92433803	92433807	+	Intron	DEL	AAACC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92433803_92433807delAAACC	uc001pdj.3	+							NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GAAGATTTTTAAACCACAGGTAATC	0.395										TCGA Ovarian(4;0.039)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	102166571	102166571	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102166571delA								YAP1 (62417 upstream) : BIRC3 (21623 downstream)																							AAGACAGACTAAAAAAAATGC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	121142103	121142103	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121142103delA								TECTA (80590 upstream) : SC5DL (21285 downstream)																							tggagttcctaaaatgaggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127169687	127169687	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127169687delT	uc001qeh.2	+											Homo sapiens cDNA clone IMAGE:4794631.																		CTCAATAGCATTTTTTTTAAT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128255375	128255376	+	IGR	INS	-	TA	TA	rs149053687	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128255375_128255376insTA								None (None upstream) : ETS1 (73280 downstream)																							caATACACACGTATATATATAT	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	6510362	6510362	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6510362delC								LTBR (9630 upstream) : LOC678655 (37805 downstream)																							CATATGACATCCCAGAGATAT	0.189													4	2	---	---	---	---	
KLRG1	10219	broad.mit.edu	37	12	9159531	9159531	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9159531delG	uc001qvh.2	+						KLRG1_uc001qvg.2_Intron	NM_005810	NP_005801	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G,						cell surface receptor linked signaling pathway|cellular defense response|inflammatory response|regulation of immune response	integral to membrane	receptor activity|sugar binding			central_nervous_system(1)	1						aaatgatactgggaatgaacg	0.085													4	2	---	---	---	---	
PZP	5858	broad.mit.edu	37	12	9351361	9351361	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9351361delA	uc001qvl.2	-						PZP_uc009zgl.2_Intron	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5						ATAAAAAGATAGAATCAAAGC	0.343													4	2	---	---	---	---	
PRR4	11272	broad.mit.edu	37	12	11000107	11000107	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11000107delT	uc001qyz.3	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRR4_uc001qza.3_Intron	NM_007244	NP_009175	Q16378	PROL4_HUMAN	proline rich 4 (lacrimal) isoform 2						visual perception	extracellular space					0						GTGCCCACTGTTTTTTTTTTC	0.388													11	6	---	---	---	---	
LOC144438	144438	broad.mit.edu	37	12	49082927	49082927	+	RNA	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49082927delT	uc001rsd.3	-	1		c.3303delA				NR_024266				Homo sapiens cDNA FLJ11223 fis, clone PLACE1008209.												0						AGTCCTTCTCTTTTTTTCATT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	60826119	60826119	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60826119delT								SLC16A7 (650712 upstream) : None (None downstream)																							cacctcccccttagctctctt	0.000													4	2	---	---	---	---	
PTPRB	5787	broad.mit.edu	37	12	70990300	70990300	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70990300delA	uc001swb.3	-						PTPRB_uc010sto.1_Intron|PTPRB_uc010stp.1_Intron|PTPRB_uc001swc.3_Intron|PTPRB_uc001swa.3_Intron|PTPRB_uc001swd.3_Intron|PTPRB_uc009zrr.1_Intron|PTPRB_uc001swe.2_Intron	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B						angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TCACTTTCTTAAAAAAAAAAA	0.308													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	78986587	78986587	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78986587delC								NAV3 (379799 upstream) : SYT1 (271186 downstream)																							ttaaaaatgacaatccagctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89405717	89405717	+	RNA	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89405717delA	uc001tax.1	-	3		c.1695delT								Homo sapiens cDNA FLJ30500 fis, clone BRAWH2000471.																		ttgtgaagataaaatgaaaaa	0.159													4	2	---	---	---	---	
BTG1	694	broad.mit.edu	37	12	92495230	92495230	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92495230delG	uc001tbv.1	-						BTG1_uc001tbw.1_Intron|BTG1_uc001tbx.1_Intron|BTG1_uc009zss.1_Intron			P62324	BTG1_HUMAN	Homo sapiens full length insert cDNA clone YW25A12.						cell migration|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of endothelial cell differentiation|positive regulation of myoblast differentiation|regulation of apoptosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|transcription cofactor activity				0		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				aagaaagaaaggaaagaaaga	0.080			T	MYC	BCLL								4	2	---	---	---	---	
C12orf34	84915	broad.mit.edu	37	12	110181933	110181933	+	5'UTR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110181933delG	uc001tpd.1	+	2					MGC14436_uc010sxs.1_Intron|MGC14436_uc001tpe.2_Intron|C12orf34_uc001tpf.1_5'UTR	NM_032829	NP_116218	Q5U5X8	CL034_HUMAN	hypothetical protein LOC84915											ovary(1)	1						GCACCCCACTGGGGACCCCCA	0.682													4	2	---	---	---	---	
C12orf34	84915	broad.mit.edu	37	12	110202436	110202437	+	Intron	INS	-	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110202436_110202437insT	uc001tpd.1	+						MGC14436_uc010sxs.1_Intron|MGC14436_uc001tpe.2_Intron|C12orf34_uc001tpf.1_Intron	NM_032829	NP_116218	Q5U5X8	CL034_HUMAN	hypothetical protein LOC84915											ovary(1)	1						TACAGATATAATTTTTTTTTCC	0.356													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	117871273	117871274	+	IGR	DEL	CA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117871273_117871274delCA								NOS1 (71691 upstream) : KSR2 (19543 downstream)																							ACGGAACCCTcacacacacaca	0.094													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119199304	119199304	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119199304delC								SUDS3 (343465 upstream) : SRRM4 (220092 downstream)																							tttgaaagtgccatataaccg	0.154													4	2	---	---	---	---	
CCDC60	160777	broad.mit.edu	37	12	119927427	119927427	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119927427delC	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)		TAAGAAGGGTCAGGTTGTTTG	0.398													4	2	---	---	---	---	
WDR66	144406	broad.mit.edu	37	12	122362024	122362024	+	Intron	DEL	G	-	-	rs57342224	byFrequency	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122362024delG	uc009zxk.2	+							NM_144668	NP_653269	Q8TBY9	WDR66_HUMAN	WD repeat domain 66								calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		ATAGACTTGTGtttttttttt	0.189													4	2	---	---	---	---	
TMEM132B	114795	broad.mit.edu	37	12	125846828	125846828	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125846828delT	uc001uhe.1	+							NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CAAGGCTCTATCACACCCTGA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126857546	126857547	+	IGR	INS	-	AG	AG			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126857546_126857547insAG								TMEM132B (713957 upstream) : LOC100128554 (69480 downstream)																							GACTGAGCAGCAGAGAGAAAAA	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130456157	130456158	+	IGR	INS	-	A	A	rs148440703	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130456157_130456158insA								TMEM132D (67945 upstream) : LOC100190940 (61841 downstream)																							gtgttatgtagaaaaatatatt	0.025													4	2	---	---	---	---	
DKFZp686A1627	266695	broad.mit.edu	37	13	19651281	19651282	+	Intron	INS	-	T	T	rs138485383	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19651281_19651282insT	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0						AGATGAAAATGTATCTGTCTGA	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22837556	22837556	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22837556delA	uc001uoi.2	+						uc001uoj.2_Intron					Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																		TCGTCAAATGAATGTGATGAA	0.383													4	2	---	---	---	---	
MIPEP	4285	broad.mit.edu	37	13	24456118	24456118	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24456118delA	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)		TTATTCCTTGAAACCAAGTTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27549704	27549704	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27549704delA								GPR12 (214782 upstream) : USP12 (92734 downstream)																							TCAGAGAATGAAATACCCCGC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30612452	30612452	+	IGR	DEL	C	-	-	rs34935332		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30612452delC								UBL3 (187632 upstream) : KATNAL1 (164316 downstream)																							TTAGCCCATTCCCTCCTTTCA	0.418													6	3	---	---	---	---	
NBEA	26960	broad.mit.edu	37	13	36090400	36090400	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36090400delG	uc001uvb.2	+						NBEA_uc010abi.2_Intron|NBEA_uc010tee.1_Intron|NBEA_uc010tef.1_Intron|NBEA_uc010teg.1_Intron	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TTAAGATTCAGGAGTCAGTCA	0.373													4	2	---	---	---	---	
ALG5	29880	broad.mit.edu	37	13	37545924	37545924	+	Intron	DEL	A	-	-	rs113451324		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37545924delA	uc001uvy.2	-						ALG5_uc010teq.1_Intron|ALG5_uc010ter.1_Intron	NM_013338	NP_037470	Q9Y673	ALG5_HUMAN	dolichyl-phosphate beta-glucosyltransferase						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate beta-glucosyltransferase activity|oligosaccharyl transferase activity				0		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;5.79e-07)|Epithelial(112;1.81e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00785)|BRCA - Breast invasive adenocarcinoma(63;0.0127)|GBM - Glioblastoma multiforme(144;0.0472)		GTATATGCTTAAAAAAAAATC	0.289													5	3	---	---	---	---	
DIAPH3	81624	broad.mit.edu	37	13	60498658	60498658	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60498658delT	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron|DIAPH3_uc001vhv.2_Intron	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		AGAGTAGCTGTTTTTTTTTTT	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63621302	63621303	+	IGR	INS	-	C	C	rs112606463		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63621302_63621303insC								None (None upstream) : OR7E156P (690265 downstream)																							AGAATTTATTGCTTTTTTATGA	0.342													7	4	---	---	---	---	
LMO7	4008	broad.mit.edu	37	13	76301438	76301439	+	Intron	INS	-	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76301438_76301439insC	uc010thv.1	+						LMO7_uc001vjt.1_Intron	NM_005358	NP_005349	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 1							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)		ttatttatttatttatttattt	0.292													8	4	---	---	---	---	
LMO7	4008	broad.mit.edu	37	13	76301441	76301442	+	Intron	INS	-	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76301441_76301442insC	uc010thv.1	+						LMO7_uc001vjt.1_Intron	NM_005358	NP_005349	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 1							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)		tttatttatttatttatttaAT	0.302													8	4	---	---	---	---	
LMO7	4008	broad.mit.edu	37	13	76301442	76301443	+	Intron	INS	-	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76301442_76301443insG	uc010thv.1	+						LMO7_uc001vjt.1_Intron	NM_005358	NP_005349	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 1							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)		ttatttatttatttatttaATA	0.297													7	4	---	---	---	---	
CLYBL	171425	broad.mit.edu	37	13	100300170	100300170	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100300170delA	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron	NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GTTGTGAGAGAAAACTTCAGT	0.229													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102542692	102542693	+	Intron	INS	-	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102542692_102542693insA	uc001vpe.2	-						FGF14_uc001vpf.2_Intron	NM_004115	NP_004106	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1A						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGTCTTACCTGAAAAAAAAAAC	0.416													4	3	---	---	---	---	
TPP2	7174	broad.mit.edu	37	13	103251027	103251027	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103251027delG	uc001vpi.3	+							NM_003291	NP_003282	P29144	TPP2_HUMAN	tripeptidyl peptidase II						proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GAAAACAGCTGGGATAAGTGG	0.393													4	2	---	---	---	---	
TEP1	7011	broad.mit.edu	37	14	20869019	20869020	+	Intron	INS	-	AATCGTTTTCAGT	AATCGTTTTCAGT	rs147276664	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20869019_20869020insAATCGTTTTCAGT	uc001vxe.2	-						TEP1_uc010tlf.1_Intron|TEP1_uc010tlg.1_Intron	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1						telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CTTATAAATCAAATACAACAAC	0.381													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26704606	26704607	+	IGR	DEL	CA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26704606_26704607delCA								None (None upstream) : NOVA1 (210483 downstream)																							TTGTATTTGTCACACCATGAGC	0.401													4	2	---	---	---	---	
MPP5	64398	broad.mit.edu	37	14	67779676	67779676	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67779676delT	uc001xjc.2	+						MPP5_uc001xjd.2_Intron|ATP6V1D_uc001xje.2_Intron	NM_022474	NP_071919	Q8N3R9	MPP5_HUMAN	membrane protein, palmitoylated 5						tight junction assembly	cytoplasm|endomembrane system|tight junction	protein domain specific binding			ovary(1)	1				all cancers(60;0.000388)|OV - Ovarian serous cystadenocarcinoma(108;0.00762)|BRCA - Breast invasive adenocarcinoma(234;0.0106)		ATTTCCTGTATACATATTAAG	0.308													4	2	---	---	---	---	
FAM164C	79696	broad.mit.edu	37	14	75543423	75543423	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75543423delA	uc001xri.2	+						FAM164C_uc001xrh.2_Intron	NM_001042430	NP_001035895	Q53FD0	F164C_HUMAN	chromosome 14 open reading frame 140 isoform b											ovary(1)	1						gtctcatgttaaaaaaaagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	87928226	87928227	+	IGR	DEL	GC	-	-	rs77681061	byFrequency	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87928226_87928227delGC								None (None upstream) : GALC (375937 downstream)																							CTGGATTCTTGCTGACACAATA	0.520													4	2	---	---	---	---	
BTBD7	55727	broad.mit.edu	37	14	93762561	93762561	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93762561delT	uc001ybo.2	-						BTBD7_uc010aur.2_5'Flank|BTBD7_uc010two.1_5'Flank|BTBD7_uc001ybp.2_Intron|BTBD7_uc001ybq.3_5'Flank|BTBD7_uc001ybr.2_Intron	NM_001002860	NP_001002860	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7 isoform 1											pancreas(1)	1		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		CAGATCACAGTTTTTTTTAAA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21907782	21907782	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21907782delG								NF1P1 (773157 upstream) : LOC646214 (24732 downstream)																							tgagggtgatggaaatagtct	0.065													2	4	---	---	---	---	
POTEB	339010	broad.mit.edu	37	15	22070888	22070889	+	Intron	INS	-	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22070888_22070889insT	uc010tzr.1	-						POTEB_uc010tzq.1_Intron	NM_207355	NP_997238	Q6S5H4	POTEB_HUMAN	protein expressed in prostate, ovary, testis,												0						CCAACTCTGCATAagtcctagc	0.193													4	2	---	---	---	---	
EIF2AK4	440275	broad.mit.edu	37	15	40241088	40241089	+	Intron	INS	-	ATGT	ATGT	rs4270150		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40241088_40241089insATGT	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)		TTTTTATTTACCTAGGTAATGA	0.287													9	4	---	---	---	---	
BAHD1	22893	broad.mit.edu	37	15	40757341	40757341	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40757341delG	uc001zlu.2	+						BAHD1_uc001zlt.2_Intron|BAHD1_uc010bbp.1_Intron|BAHD1_uc001zlv.2_Intron	NM_014952	NP_055767	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1						heterochromatin formation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin silencing complex|chromosome	chromatin binding|DNA binding|protein binding				0		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		TTCTGGAGAAGGGGGGGACCT	0.547													4	2	---	---	---	---	
SLC30A4	7782	broad.mit.edu	37	15	45803690	45803690	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45803690delT	uc001zvj.2	-						C15orf21_uc001zvk.2_Intron|C15orf21_uc010beg.1_Intron|C15orf21_uc010beh.1_Intron|C15orf21_uc010bei.1_Intron|C15orf21_uc010bej.1_Intron|C15orf21_uc001zvm.1_Intron|C15orf21_uc001zvn.1_Intron	NM_013309	NP_037441	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter),						regulation of sequestering of zinc ion|response to toxin	endosome membrane|integral to membrane|late endosome	zinc ion transmembrane transporter activity				0		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		tctttttttcttttttttttg	0.040													4	2	---	---	---	---	
NEO1	4756	broad.mit.edu	37	15	73478927	73478928	+	Intron	INS	-	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73478927_73478928insT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron|NEO1_uc002avn.3_Intron	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor						axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1						TTTTTTTCTTCTTTTTTTTTCA	0.282													4	2	---	---	---	---	
HCN4	10021	broad.mit.edu	37	15	73647120	73647122	+	Intron	DEL	CAT	-	-	rs146021866	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73647120_73647122delCAT	uc002avp.2	-							NM_005477	NP_005468	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic						blood circulation|muscle contraction	integral to membrane	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity			ovary(5)|liver(1)	6				COAD - Colon adenocarcinoma(1;0.142)		tcatcatccccatcatcatcatc	0.207													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94713278	94713278	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94713278delT								None (None upstream) : MCTP2 (61523 downstream)																							CCTTATTCTATTCCTTTCCTT	0.303													4	2	---	---	---	---	
MAPK8IP3	23162	broad.mit.edu	37	16	1777453	1777457	+	Intron	DEL	TTGTG	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1777453_1777457delTTGTG	uc002cmk.2	+						MAPK8IP3_uc002cmi.1_Intron|MAPK8IP3_uc002cmj.1_Intron|MAPK8IP3_uc002cml.2_Intron|MAPK8IP3_uc010uvl.1_Intron	NM_015133	NP_055948	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting						vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding			breast(2)|central_nervous_system(1)	3						TCTGTAAGTCTTGTGTTGTGTGCGG	0.488													4	2	---	---	---	---	
TCEB2	6923	broad.mit.edu	37	16	2828025	2828025	+	5'Flank	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2828025delC	uc002crn.2	-						TCEB2_uc002crm.2_5'Flank	NM_007108	NP_009039	Q15370	ELOB_HUMAN	elongin B isoform a						positive regulation of viral transcription|protein complex assembly|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|nucleoplasm	protein binding				0						TGCAGAGACACCCCAGGCTGG	0.627													4	2	---	---	---	---	
ZNF500	26048	broad.mit.edu	37	16	4811010	4811010	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4811010delA	uc002cxp.1	-						ZNF500_uc002cxo.1_Intron|ZNF500_uc010uxt.1_Intron	NM_021646	NP_067678	O60304	ZN500_HUMAN	zinc finger protein 500						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3						AAGCATGATTAAAAAAACAAG	0.333													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7233944	7233944	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7233944delA	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		aagagaggctaaaatttcaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11729884	11729884	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11729884delA								LITAF (48562 upstream) : SNN (32417 downstream)																							gctcatctgtaaaagggggtg	0.294													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12451199	12451199	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12451199delA	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						ctaaaaatacaaaaaaaaata	0.000													2	4	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14577465	14577466	+	Intron	DEL	AT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14577465_14577466delAT	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						gtacacccacatgtcatccatc	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22703584	22703584	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22703584delC								LOC653786 (115398 upstream) : HS3ST2 (122276 downstream)																							CAGCTACACTCAACCACAAAT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26169219	26169219	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26169219delG								HS3ST4 (20211 upstream) : C16orf82 (909000 downstream)																							gccttctgctgggaggtcaaa	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32118178	32118178	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32118178delG								ZNF267 (189552 upstream) : HERC2P4 (44432 downstream)																							tgctctatttggactcttata	0.179													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32540003	32540004	+	IGR	INS	-	T	T	rs148326244		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32540003_32540004insT								HERC2P4 (376129 upstream) : TP53TG3B (144837 downstream)																							taaaaagaaaattaactgtgtc	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46434843	46434844	+	IGR	INS	-	A	A	rs147666366	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46434843_46434844insA								None (None upstream) : ANKRD26P1 (68405 downstream)																							ggaatcgagtggaagcattgaa	0.000													8	6	---	---	---	---	
PHKB	5257	broad.mit.edu	37	16	47598870	47598870	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47598870delT	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)				tctgtgtgtctttttttTTTT	0.194													12	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51459389	51459389	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51459389delT								SALL1 (274206 upstream) : None (None downstream)																							CCTTTGCCAGtttttttttgt	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54499324	54499324	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54499324delT								IRX3 (178946 upstream) : IRX5 (465787 downstream)																							cttttgttacttaggcatgga	0.005													4	2	---	---	---	---	
GFOD2	81577	broad.mit.edu	37	16	67719767	67719767	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67719767delT	uc002eub.2	-						GFOD2_uc002euc.2_Intron|GFOD2_uc010cen.2_Intron	NM_030819	NP_110446	Q3B7J2	GFOD2_HUMAN	glucose-fructose oxidoreductase domain							proteinaceous extracellular matrix	binding|oxidoreductase activity			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0151)|Epithelial(162;0.0505)|all cancers(182;0.242)		GGCTACtttcttttttttttg	0.299													3	3	---	---	---	---	
CFDP1	10428	broad.mit.edu	37	16	75446836	75446836	+	Intron	DEL	A	-	-	rs76178972		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75446836delA	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron|CFDP1_uc002fea.1_Intron	NM_006324	NP_006315	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1						AAAAGAATTGAAAAAAAAAAA	0.308													3	5	---	---	---	---	
ADAMTS18	170692	broad.mit.edu	37	16	77395786	77395787	+	Intron	INS	-	AAAA	AAAA	rs151022467	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77395786_77395787insAAAA	uc002ffc.3	-						ADAMTS18_uc010chc.1_Intron|ADAMTS18_uc002ffe.1_Intron|ADAMTS18_uc010vni.1_Intron	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						catctcaaattaaaaaaaatac	0.158													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79590179	79590179	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79590179delG								WWOX (343616 upstream) : MAF (37567 downstream)																							CATCTTTTTTGAAATGTCTTC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	3173097	3173097	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3173097delT								OR1A1 (53255 upstream) : OR3A2 (8088 downstream)																							ttggtagctcttttttgtctc	0.114													4	2	---	---	---	---	
P2RX1	5023	broad.mit.edu	37	17	3810094	3810094	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3810094delC	uc002fww.2	-						P2RX1_uc010ckm.1_Intron	NM_002558	NP_002549	P51575	P2RX1_HUMAN	purinergic receptor P2X1						platelet activation	integral to plasma membrane	calcium channel activity|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity			ovary(1)|skin(1)	2				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		gggcagataaccaaggcttgc	0.085													4	2	---	---	---	---	
ANKFY1	51479	broad.mit.edu	37	17	4103956	4103956	+	Intron	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4103956delG	uc002fxq.1	-						ANKFY1_uc002fxn.2_Intron|ANKFY1_uc002fxo.2_Intron|ANKFY1_uc002fxp.2_Intron|ANKFY1_uc010ckp.2_Intron|ANKFY1_uc002fxr.2_Intron	NM_016376	NP_057460	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1							endosome membrane	metal ion binding|protein binding			ovary(2)|skin(1)	3						GGGTGACCTTGCGATGAATGC	0.443													4	2	---	---	---	---	
MYH8	4626	broad.mit.edu	37	17	10302566	10302567	+	Intron	INS	-	TGTG	TGTG	rs141203224	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10302566_10302567insTGTG	uc002gmm.2	-						uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						gatactcaacctgtgtgtgtgt	0.099									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				5	3	---	---	---	---	
TRIM16	10626	broad.mit.edu	37	17	15519362	15519363	+	Intron	DEL	AG	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15519362_15519363delAG	uc002gor.1	-						CDRT1_uc002gov.3_Intron			O95361	TRI16_HUMAN	SubName: Full=Putative uncharacterized protein; Flags: Fragment;						histone H3 acetylation|histone H4 acetylation|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|positive regulation of transcription, DNA-dependent|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		TTATACAAGCAGAGAGAGAGAG	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25318507	25318507	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25318507delC								None (None upstream) : WSB1 (302599 downstream)																							CTCAATGAAACCCATGTAAGA	0.353													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	32756849	32756849	+	IGR	DEL	A	-	-	rs75550327		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32756849delA								CCL1 (66597 upstream) : C17orf102 (144293 downstream)																							catgcgtgagaaaaaaaaaag	0.000													6	3	---	---	---	---	
SLFN12L	342615	broad.mit.edu	37	17	33840240	33840241	+	Intron	DEL	GA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33840240_33840241delGA	uc002hjn.2	-							NM_001145027	NP_001138499			schlafen family member 12-like											ovary(1)	1						CAAGGTATCTGAGAAAATCCTC	0.322													4	2	---	---	---	---	
RUNDC3A	10900	broad.mit.edu	37	17	42386154	42386155	+	5'UTR	INS	-	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42386154_42386155insG	uc002igl.3	+	1					uc002igh.2_5'Flank|RUNDC3A_uc002igi.2_5'UTR|RUNDC3A_uc002igj.2_5'UTR|RUNDC3A_uc002igk.2_5'UTR	NM_001144825	NP_001138297	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A isoform 1						small GTPase mediated signal transduction		small GTPase regulator activity				0		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GGGCTCCGGGAGGGGTGGGGGG	0.693													4	2	---	---	---	---	
ITGA2B	3674	broad.mit.edu	37	17	42453970	42453970	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42453970delT	uc002igt.1	-						ITGA2B_uc002igu.1_Intron	NM_000419	NP_000410	P08514	ITA2B_HUMAN	integrin alpha 2b preproprotein						axon guidance|integrin-mediated signaling pathway|platelet activation|platelet degranulation	integrin complex|platelet alpha granule membrane	identical protein binding|receptor activity			ovary(2)|lung(1)	3		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Tirofiban(DB00775)	TTCAAAGACCttttttttttt	0.239													3	4	---	---	---	---	
TEX2	55852	broad.mit.edu	37	17	62254596	62254597	+	Intron	INS	-	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62254596_62254597insT	uc002jec.2	-						TEX2_uc002jed.2_Intron|TEX2_uc002jee.2_Intron	NM_018469	NP_060939	Q8IWB9	TEX2_HUMAN	testis expressed sequence 2						signal transduction|sphingolipid metabolic process	integral to membrane				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TTTAAACCAAATTATTTTTCAC	0.361													145	80	---	---	---	---	
ABCA5	23461	broad.mit.edu	37	17	67310249	67310251	+	Intron	DEL	ATT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67310249_67310251delATT	uc002jif.2	-						ABCA5_uc002jig.2_Intron|ABCA5_uc002jih.2_Intron|ABCA5_uc010dfe.2_Intron	NM_018672	NP_061142	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5						cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)					AAATGTAGaaattattattaaaa	0.261													4	2	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77333329	77333329	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77333329delT	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			AACATTGTGCTTACCTGACAA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14225639	14225639	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14225639delA								ZNF519 (93210 upstream) : LOC284233 (111783 downstream)																							aataaacattaaaaaaaaaaG	0.144													4	2	---	---	---	---	
LAMA3	3909	broad.mit.edu	37	18	21357216	21357217	+	Intron	INS	-	A	A	rs112665468		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21357216_21357217insA	uc002kuq.2	+						LAMA3_uc010dlv.1_Intron|LAMA3_uc002kur.2_Intron	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1						cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GATTTTATGTTAAAAAAAAAAA	0.317													2	6	---	---	---	---	
MEP1B	4225	broad.mit.edu	37	18	29769747	29769748	+	5'Flank	INS	-	T	T	rs140196454	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29769747_29769748insT	uc002kxj.3	+							NM_005925	NP_005916	Q16820	MEP1B_HUMAN	meprin A beta precursor						digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2						GTTTACTAGTCTAAGGACCAGT	0.317													3	5	---	---	---	---	
ST8SIA5	29906	broad.mit.edu	37	18	44272373	44272373	+	Intron	DEL	T	-	-	rs77603253		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44272373delT	uc002lcj.1	-						ST8SIA5_uc002lci.1_Intron|ST8SIA5_uc010xcy.1_Intron|ST8SIA5_uc010xcz.1_Intron|ST8SIA5_uc010dno.1_Intron	NM_013305	NP_037437	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3						tctttgtttcttttttttttt	0.224													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	51114606	51114606	+	IGR	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51114606delC								DCC (56824 upstream) : MBD2 (565969 downstream)																							atacaacactccactgcccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	51134434	51134435	+	IGR	DEL	GA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51134434_51134435delGA								DCC (76652 upstream) : MBD2 (546140 downstream)																							GTGCCTCTGGGAGAGAGAGAGA	0.248													4	2	---	---	---	---	
TXNL1	9352	broad.mit.edu	37	18	54270576	54270577	+	Intron	INS	-	A	A	rs146204123	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54270576_54270577insA	uc002lgg.2	-						TXNL1_uc010xdz.1_Intron|TXNL1_uc002lgh.2_Intron|TXNL1_uc002lgi.2_Intron	NM_004786	NP_004777	O43396	TXNL1_HUMAN	thioredoxin-like 1						cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	cytoplasm	electron carrier activity|protein disulfide oxidoreductase activity				0				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)		GAAGTTAATTTAAAAAATGATG	0.248													2	4	---	---	---	---	
CCDC102B	79839	broad.mit.edu	37	18	66677931	66677932	+	Intron	INS	-	A	A	rs147549639	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66677931_66677932insA	uc002lkk.2	+						CCDC102B_uc002lki.2_Intron	NM_001093729	NP_001087198	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				GTGTAAGGTGCAAAATACATCA	0.272													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71056551	71056551	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71056551delG								NETO1 (521741 upstream) : FBXO15 (684037 downstream)																							CTAATgtgctggaagcactgg	0.154													4	2	---	---	---	---	
CACNA1A	773	broad.mit.edu	37	19	13577023	13577023	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13577023delT	uc010dze.2	-						CACNA1A_uc002mwy.3_Intron	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	TTGGTTTTGCTTTTTTTTTTT	0.159													3	3	---	---	---	---	
BRD4	23476	broad.mit.edu	37	19	15361875	15361875	+	Intron	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15361875delA	uc002nar.2	-						BRD4_uc002nas.2_Intron	NM_058243	NP_490597	O60885	BRD4_HUMAN	bromodomain-containing protein 4 isoform long						interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			AGGAAGTGGTAGGGCTGGCCC	0.577			T	NUT|C15orf55	lethal midline carcinoma of young people						OREG0025318	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
WIZ	58525	broad.mit.edu	37	19	15541563	15541564	+	Intron	INS	-	T	T	rs147128691	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15541563_15541564insT	uc002nbc.2	-						WIZ_uc002nba.3_Intron|WIZ_uc002nbb.3_Intron	NM_021241	NP_067064	O95785	WIZ_HUMAN	widely-interspaced zinc finger motifs							nucleus	zinc ion binding				0						CTGGGTCTGAGTATGAGCTCTG	0.535													4	2	---	---	---	---	
USHBP1	83878	broad.mit.edu	37	19	17374674	17374674	+	Intron	DEL	A	-	-	rs77430153		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17374674delA	uc002nfs.1	-						USHBP1_uc002nft.1_Intron|USHBP1_uc010xpk.1_Intron|USHBP1_uc010eam.1_5'UTR	NM_031941	NP_114147	Q8N6Y0	USBP1_HUMAN	Usher syndrome 1C binding protein 1								PDZ domain binding			ovary(1)	1						agcaagactcaaaaaaaaaag	0.234													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	28529804	28529805	+	IGR	DEL	TG	-	-	rs140543160		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28529804_28529805delTG								LOC148189 (244956 upstream) : LOC148145 (926235 downstream)																							TCACTTATTCtgtgtgtgtgtg	0.297													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	33777204	33777204	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33777204delT								SLC7A10 (60448 upstream) : CEBPA (13638 downstream)																							GTGTTTGTCATTTGGCTCTGG	0.542													4	2	---	---	---	---	
MAG	4099	broad.mit.edu	37	19	35819635	35819635	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35819635delT	uc002nyz.1	+						CD22_uc010edt.2_5'Flank|CD22_uc010xst.1_5'Flank|CD22_uc010edu.2_5'Flank|CD22_uc010edv.2_5'Flank	NM_002361	NP_002352	P20916	MAG_HUMAN	myelin associated glycoprotein isoform a						blood coagulation|cell adhesion|leukocyte migration|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane	sugar binding			breast(3)|lung(2)|central_nervous_system(1)|skin(1)	7	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			TATGTGCTCCTCCCTCAACCC	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	37772004	37772005	+	IGR	DEL	GA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37772004_37772005delGA								ZNF383 (37430 upstream) : HKR1 (31734 downstream)																							agcgagaagggagagagagaga	0.223													4	2	---	---	---	---	
AXL	558	broad.mit.edu	37	19	41730694	41730695	+	Intron	DEL	TG	-	-	rs10547106		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41730694_41730695delTG	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						GTCACAGACCtgtgtgtgtgtg	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42971191	42971192	+	Intron	INS	-	C	C			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42971191_42971192insC	uc010eif.1	+						uc002ott.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron					Homo sapiens cDNA FLJ39530 fis, clone PUAEN2004400.																		GTTTCATATTTCCCCTTTTCCA	0.431													4	2	---	---	---	---	
DHX34	9704	broad.mit.edu	37	19	47854245	47854245	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47854245delC	uc010xyn.1	+						DHX34_uc010elc.1_5'Flank	NM_014681	NP_055496	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34							intracellular	ATP binding|ATP-dependent helicase activity|RNA binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		AGGCCATGAGCCCAGGGCAAA	0.468													4	2	---	---	---	---	
SNAR-B2	100170217	broad.mit.edu	37	19	50639642	50639642	+	5'Flank	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50639642delT	uc010yby.1	-							NR_024231				Homo sapiens small ILF3/NF90-associated RNA B2 (SNAR-B2), non-coding RNA.												0						gattttggtgtttttttttct	0.000													5	3	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50733855	50733855	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50733855delG	uc002prr.1	+	8	971	c.924delG	c.(922-924)CTGfs	p.L308fs	MYH14_uc010enu.1_Frame_Shift_Del_p.L316fs|MYH14_uc002prq.1_Frame_Shift_Del_p.L316fs	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2	308	Myosin head-like.				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)		ACCAGCTGCTGGGGGGCGCTG	0.657													4	2	---	---	---	---	
KLK12	43849	broad.mit.edu	37	19	51534417	51534417	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51534417delT	uc002pvg.1	-						KLK12_uc010ycp.1_Intron|KLK12_uc010ycq.1_Intron|KLK12_uc010ycr.1_Intron|KLK12_uc010ycs.1_Intron|KLK12_uc002pvh.1_Intron|KLK12_uc002pvi.1_Intron|KLK12_uc002pvj.1_Intron	NM_145894	NP_665901	Q9UKR0	KLK12_HUMAN	kallikrein 12 isoform 2						proteolysis	extracellular region|soluble fraction	serine-type endopeptidase activity			ovary(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)		ACTCAAGAACTTTCTTGTCTC	0.398													4	2	---	---	---	---	
IGLON5	402665	broad.mit.edu	37	19	51823139	51823140	+	Intron	DEL	TG	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51823139_51823140delTG	uc002pwc.2	+							NM_001101372	NP_001094842	A6NGN9	IGLO5_HUMAN	IgLON family member 5 precursor							extracellular region					0						tgtatgtgtttgtgtgtgtgtg	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	52350068	52350068	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52350068delG								FPR3 (20734 upstream) : ZNF577 (8988 downstream)																							atcccacactggcactgtgat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54533595	54533596	+	IGR	INS	-	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54533595_54533596insA								CACNG6 (17677 upstream) : VSTM1 (10489 downstream)																							gtatttttttcttgtatgtgac	0.188											OREG0025669	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	19	57274382	57274383	+	Intron	DEL	TC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57274382_57274383delTC	uc010ygp.1	+						uc002qnp.1_5'Flank					Homo sapiens cDNA clone IMAGE:4793694.																		CAGAGGCATTTCTCAGAAGTTT	0.342													4	2	---	---	---	---	
DEFB129	140881	broad.mit.edu	37	20	207700	207701	+	5'Flank	DEL	TA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:207700_207701delTA	uc002wda.2	+							NM_080831	NP_543021	Q9H1M3	DB129_HUMAN	beta defensin 129 precursor						defense response to bacterium	extracellular region				ovary(1)	1		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)			TCATCTTACCTATCTTATGTTT	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	3058938	3058939	+	IGR	INS	-	TT	TT	rs145801419	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3058938_3058939insTT								OXT (5776 upstream) : AVP (4264 downstream)																							ACTGGATACTCTGAACTCCTAG	0.248													3	4	---	---	---	---	
DDRGK1	65992	broad.mit.edu	37	20	3181263	3181264	+	Intron	DEL	GT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3181263_3181264delGT	uc002wic.2	-						DDRGK1_uc010gaw.2_Intron|DDRGK1_uc010gax.1_Intron	NM_023935	NP_076424	Q96HY6	DDRGK_HUMAN	DDRGK domain containing 1 precursor							endoplasmic reticulum	protein binding				0						CCATGAGTGCGTGTGTGTGTGT	0.505													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	4541935	4541936	+	IGR	INS	-	GAG	GAG	rs141351445	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4541935_4541936insGAG								ADRA1D (312276 upstream) : PRNP (124861 downstream)																							GTGGCAGATTAGAGGAGACATC	0.401													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	8875619	8875619	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8875619delA								PLCB1 (10074 upstream) : PLCB4 (174082 downstream)																							agcgctgtgtaagcctcttgg	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31472945	31472945	+	Intron	DEL	C	-	-	rs72263649		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31472945delC	uc010zub.1	+							NM_001143967	NP_001137439			EF-hand calcium binding domain 8																		CTCACCCTCTCCTGGGCAGTT	0.547													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	32281004	32281004	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32281004delA								E2F1 (6794 upstream) : PXMP4 (9547 downstream)																							CACAAGGAGGAAAAAAAAAAA	0.264													3	3	---	---	---	---	
EPB41L1	2036	broad.mit.edu	37	20	34720126	34720127	+	Intron	DEL	AG	-	-	rs147881549	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34720126_34720127delAG	uc002xev.2	+						EPB41L1_uc002xeu.2_Intron|EPB41L1_uc010zvo.1_Intron|EPB41L1_uc002xew.2_Intron|EPB41L1_uc002xex.2_Intron|EPB41L1_uc002xey.2_Intron|EPB41L1_uc002xez.2_Intron	NM_012156	NP_036288	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1						cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)					ctagacttctagaggtcaaaat	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48863364	48863365	+	IGR	DEL	CT	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48863364_48863365delCT								CEBPB (54152 upstream) : PTPN1 (263526 downstream)																							ATCAACCTCCCTCTCTCTCTCT	0.525													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49835094	49835095	+	IGR	DEL	TC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49835094_49835095delTC								KCNG1 (195419 upstream) : NFATC2 (172671 downstream)																							ACTTTTCTTTTCTACTCCCAAG	0.421													4	2	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51691477	51691477	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51691477delT	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)			caggtcagtgtttttcccact	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9854128	9854129	+	IGR	INS	-	G	G			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9854128_9854129insG								None (None upstream) : None (None downstream)																							tcaacctcctcacactgaattt	0.025													5	6	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11054219	11054220	+	Intron	INS	-	A	A			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11054219_11054220insA	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CTAAATGAAGTAAAGGGAGCAA	0.361													1	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11059163	11059163	+	Intron	DEL	G	-	-	rs141258961		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11059163delG	uc002yit.1	-						BAGE_uc002yiw.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)		ATCTCTCTGTGGGAAATGACT	0.368													6	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11069012	11069013	+	Intron	INS	-	C	C	rs150046862		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11069012_11069013insC	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)		tttttcaacttcaaaaaattaa	0.000													3	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11079770	11079771	+	Intron	DEL	TG	-	-	rs148543332		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11079770_11079771delTG	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)		TCCAAAACACTGTGCAGATGTA	0.168													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14367406	14367407	+	IGR	INS	-	C	C	rs140142693	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14367406_14367407insC								None (None upstream) : C21orf99 (43080 downstream)																							ttccttttacaccataggcctc	0.000													5	4	---	---	---	---	
BTG3	10950	broad.mit.edu	37	21	18971380	18971383	+	Intron	DEL	TTTT	-	-	rs144326749		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18971380_18971383delTTTT	uc002ykk.2	-						BTG3_uc002ykl.2_Intron	NM_006806	NP_006797	Q14201	BTG3_HUMAN	B-cell translocation gene 3 isoform b						negative regulation of cell proliferation|negative regulation of mitotic cell cycle	cytoplasm					0				Epithelial(23;0.000283)|all cancers(11;0.0012)|Lung(58;0.0191)|OV - Ovarian serous cystadenocarcinoma(11;0.0206)|COAD - Colon adenocarcinoma(22;0.0315)|LUSC - Lung squamous cell carcinoma(23;0.0703)|Colorectal(24;0.0971)		CTTTCCCTTATTTTCTTTCTACTA	0.279													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	24883040	24883041	+	IGR	DEL	TG	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24883040_24883041delTG								None (None upstream) : None (None downstream)																							tgtatgtatttgtgtgtgtgtg	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	28093898	28093898	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28093898delT								CYYR1 (148317 upstream) : ADAMTS1 (114710 downstream)																							ATGGCATTTATTTTTTAATCG	0.254													4	2	---	---	---	---	
HLCS	3141	broad.mit.edu	37	21	38348693	38348694	+	Intron	DEL	CA	-	-	rs73389853	by1000genomes	TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38348693_38348694delCA	uc002yvs.2	-							NM_000411	NP_000402	P50747	BPL1_HUMAN	holocarboxylase synthetase						cell proliferation|histone biotinylation|response to biotin	chromatin|cytosol|mitochondrion|nuclear lamina|nuclear matrix	ATP binding|biotin binding|biotin-[acetyl-CoA-carboxylase] ligase activity|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity|enzyme binding			ovary(2)|breast(1)|kidney(1)|liver(1)	5		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	GGAAGTCAGTcacacacacaca	0.188													4	2	---	---	---	---	
C21orf129	150135	broad.mit.edu	37	21	43137710	43137710	+	5'Flank	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43137710delG	uc010got.1	-						C21orf129_uc011aet.1_5'Flank|NCRNA00112_uc002yzm.2_RNA					RecName: Full=Uncharacterized protein C21orf129;												0						AGCCGGGCCTGGAGTCAGCCC	0.552													4	2	---	---	---	---	
HSF2BP	11077	broad.mit.edu	37	21	44988680	44988680	+	Intron	DEL	C	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44988680delC	uc002zdi.2	-						HSF2BP_uc011aey.1_Intron	NM_007031	NP_008962	O75031	HSF2B_HUMAN	heat shock transcription factor 2 binding						spermatogenesis|transcription from RNA polymerase II promoter	cytosol	binding			skin(1)	1				STAD - Stomach adenocarcinoma(101;0.18)		aaaatgctggccccacagctt	0.000													4	2	---	---	---	---	
PCNT	5116	broad.mit.edu	37	21	47787225	47787226	+	Intron	INS	-	T	T			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47787225_47787226insT	uc002zji.3	+						PCNT_uc002zjj.2_Intron	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					GTGAACTGGGCttttttttttt	0.292													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	38809318	38809318	+	IGR	DEL	G	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38809318delG								LOC400927 (14387 upstream) : KCNJ4 (13015 downstream)																							CGGCTGCAAAGGGGCGTTGCC	0.587											OREG0026560	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	22	44722403	44722403	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44722403delT								KIAA1644 (13672 upstream) : LDOC1L (166047 downstream)																							CAAAAAAAAATTTTTTTTCCC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	12043519	12043519	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12043519delA								MSL3 (249649 upstream) : FRMPD4 (113066 downstream)																							gacatctaagaaaaaaaaaag	0.000													4	2	---	---	---	---	
ATP7A	538	broad.mit.edu	37	X	77264922	77264922	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77264922delT	uc004ecx.3	+						ATP7A_uc004ecw.2_3'UTR	NM_000052	NP_000043	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide						ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0						CGTGTCTGCATTTTTTTTTTT	0.303													9	4	---	---	---	---	
DACH2	117154	broad.mit.edu	37	X	85559546	85559549	+	Intron	DEL	TCCC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85559546_85559549delTCCC	uc004eew.2	+						DACH2_uc004eex.2_Intron|DACH2_uc010nmq.2_Intron|DACH2_uc011mra.1_Intron|DACH2_uc010nmr.2_Intron	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5						CTGCAGTTCTTCCCTGAAGAGCTT	0.485													4	2	---	---	---	---	
NKAP	79576	broad.mit.edu	37	X	119059524	119059524	+	Intron	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119059524delT	uc004esh.2	-						NKAP_uc004esg.2_Intron	NM_024528	NP_078804	Q8N5F7	NKAP_HUMAN	NFKB activating protein						negative regulation of transcription, DNA-dependent|Notch signaling pathway|positive regulation of alpha-beta T cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	chromatin binding|protein binding			ovary(2)	2						TGACACGTCCtttttttttgt	0.169													4	2	---	---	---	---	
IL9R	3581	broad.mit.edu	37	X	155238775	155238776	+	Intron	DEL	TA	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155238775_155238776delTA	uc004fnv.1	+						IL9R_uc004fnu.1_Intron	NM_002186	NP_002177	Q01113	IL9R_HUMAN	interleukin 9 receptor precursor						cell proliferation	extracellular space|integral to plasma membrane	interleukin-9 receptor activity				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					tgtgtgtgtttatgtgtctgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9992109	9992109	+	IGR	DEL	T	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9992109delT								TTTY22 (341255 upstream) : None (None downstream)																							gggtttacagtttttctcaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13484201	13484201	+	IGR	DEL	A	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13484201delA								None (None upstream) : None (None downstream)																							cactgtaggcaaagcctagac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58977799	58977800	+	IGR	INS	-	CTCCATTCCG	CTCCATTCCG	rs9803593		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58977799_58977800insCTCCATTCCG								None (None upstream) : None (None downstream)																							actccattccactccagtcgac	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58983907	58983908	+	IGR	DEL	TC	-	-			TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58983907_58983908delTC								None (None upstream) : None (None downstream)																							tcttctctagtctctgcctaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59032844	59032844	+	IGR	DEL	C	-	-	rs76127193		TCGA-CZ-5469-01A-01D-1501-10	TCGA-CZ-5469-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59032844delC								None (None upstream) : None (None downstream)																							acataacaggcactataaatg	0.199													4	2	---	---	---	---	
