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
GALE	2582	broad.mit.edu	37	1	24124241	24124241	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24124241C>G	uc009vqo.1	-	5	682	c.472G>C	c.(472-474)GGC>CGC	p.G158R	GALE_uc001bhv.1_Missense_Mutation_p.G158R|GALE_uc001bhw.1_Missense_Mutation_p.G158R|GALE_uc001bhx.1_Missense_Mutation_p.G158R|GALE_uc009vqp.1_Missense_Mutation_p.G158R|GALE_uc001bhy.1_Missense_Mutation_p.G158R|GALE_uc001bhz.1_Missense_Mutation_p.G84R|GALE_uc001bia.2_5'Flank	NM_001127621	NP_001121093	Q14376	GALE_HUMAN	UDP-galactose-4-epimerase	158					galactose catabolic process	cytosol	coenzyme binding|protein homodimerization activity|UDP-glucose 4-epimerase activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;1.79e-24)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;4.22e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0827)|LUSC - Lung squamous cell carcinoma(448;0.184)		TTGGACTTGCCGTAAGGGTTG	0.592													20	43	---	---	---	---	PASS
CLDN19	149461	broad.mit.edu	37	1	43200901	43200901	+	Intron	SNP	C	T	T	rs143708479	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43200901C>T	uc001cht.1	-						CLDN19_uc001chu.2_3'UTR|CLDN19_uc010ojv.1_3'UTR	NM_148960	NP_683763	Q8N6F1	CLD19_HUMAN	claudin 19 isoform a						calcium-independent cell-cell adhesion|response to stimulus|visual perception	basolateral plasma membrane|integral to membrane|tight junction	identical protein binding				0	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TACTGGCCAGCGTGGCCAGAC	0.657													31	45	---	---	---	---	PASS
IPO13	9670	broad.mit.edu	37	1	44422057	44422057	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44422057C>T	uc001ckx.2	+	3	1682	c.887C>T	c.(886-888)GCA>GTA	p.A296V		NM_014652	NP_055467	O94829	IPO13_HUMAN	importin 13	296	HEAT 4.				protein import into nucleus	cytoplasm|nucleus	protein binding|protein transporter activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				CTGCGGCAGGCAGTGCAGAAT	0.587													30	37	---	---	---	---	PASS
OSBPL9	114883	broad.mit.edu	37	1	52249639	52249639	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52249639T>A	uc001cst.2	+	18	1585	c.1566T>A	c.(1564-1566)CAT>CAA	p.H522Q	OSBPL9_uc001css.2_Missense_Mutation_p.H527Q|OSBPL9_uc001csx.2_RNA|OSBPL9_uc009vza.2_Missense_Mutation_p.H523Q|OSBPL9_uc001csu.2_Missense_Mutation_p.H532Q|OSBPL9_uc001csv.2_Missense_Mutation_p.H357Q|OSBPL9_uc001csw.2_Missense_Mutation_p.H509Q|OSBPL9_uc001csy.2_Missense_Mutation_p.H344Q|OSBPL9_uc001csz.2_Missense_Mutation_p.H344Q|OSBPL9_uc001cta.2_Missense_Mutation_p.H412Q|OSBPL9_uc001ctb.2_Missense_Mutation_p.H307Q	NM_024586	NP_078862	Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9 isoform e	522					lipid transport		lipid binding			central_nervous_system(1)	1						TCAATGCTCATATCTGGACCA	0.378													150	204	---	---	---	---	PASS
IFI44L	10964	broad.mit.edu	37	1	79107131	79107131	+	Silent	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79107131C>T	uc010oro.1	+	8	1340	c.1161C>T	c.(1159-1161)GTC>GTT	p.V387V	IFI44L_uc010orp.1_Silent_p.V124V|IFI44L_uc010orq.1_Silent_p.V124V	NM_006820	NP_006811	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	387						cytoplasm					0						TCATGAATGTCCATAAAATGC	0.313													15	323	---	---	---	---	PASS
GBP3	2635	broad.mit.edu	37	1	89473511	89473511	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89473511T>C	uc001dmt.2	-	11	1889	c.1684A>G	c.(1684-1686)AGA>GGA	p.R562G	GBP3_uc010oss.1_Missense_Mutation_p.R483G|GBP3_uc001dmu.2_Missense_Mutation_p.R428G|GBP3_uc001dmv.2_RNA	NM_018284	NP_060754	Q9H0R5	GBP3_HUMAN	guanylate binding protein 3	562	Potential.					integral to membrane	GTP binding|GTPase activity			ovary(1)|pancreas(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		CCTTGGCATCTCTCCTTTAGT	0.378													9	728	---	---	---	---	PASS
POLR3C	10623	broad.mit.edu	37	1	145597524	145597524	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145597524C>T	uc001eoh.2	-	10	1221	c.1060G>A	c.(1060-1062)GTA>ATA	p.V354I	NBPF10_uc001emp.3_Intron|POLR3C_uc001eog.2_Missense_Mutation_p.V367I|POLR3C_uc001eoi.2_Intron|POLR3C_uc009wix.2_Missense_Mutation_p.V354I	NM_006468	NP_006459	Q9BUI4	RPC3_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	354					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|regulation of transcription from RNA polymerase III promoter|response to virus	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity			ovary(1)	1	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		Epithelial(2;7.55e-13)			CTCTCCTGTACGACGGACTCC	0.448													46	85	---	---	---	---	PASS
PBXIP1	57326	broad.mit.edu	37	1	154920626	154920626	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154920626C>T	uc001ffr.2	-	6	685	c.626G>A	c.(625-627)GGG>GAG	p.G209E	PBXIP1_uc001ffs.2_Missense_Mutation_p.G180E|PBXIP1_uc010pep.1_Missense_Mutation_p.G54E	NM_020524	NP_065385	Q96AQ6	PBIP1_HUMAN	pre-B-cell leukemia homeobox interacting protein	209					cell differentiation|multicellular organismal development|negative regulation of transcription, DNA-dependent	cytosol|microtubule|nucleus	protein binding|transcription corepressor activity			large_intestine(1)	1	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GAGGAGGACCCCCAGGCCAAG	0.627													5	7	---	---	---	---	PASS
FCRL3	115352	broad.mit.edu	37	1	157666163	157666163	+	Intron	SNP	A	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157666163A>C	uc001frb.2	-						FCRL3_uc001fqx.3_Intron|FCRL3_uc001fqy.3_Intron|FCRL3_uc001fqz.3_Intron|FCRL3_uc009wsn.2_Intron|FCRL3_uc009wso.2_Intron|FCRL3_uc001fra.2_5'UTR|FCRL3_uc001frc.1_Intron	NM_052939	NP_443171	Q96P31	FCRL3_HUMAN	Fc receptor-like 3 precursor							integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(1)	4	all_hematologic(112;0.0378)					TGGCAGGGACATCAAGGTCAA	0.512													10	22	---	---	---	---	PASS
FCGR3B	2215	broad.mit.edu	37	1	161595993	161595993	+	Silent	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161595993C>T	uc009wul.2	-	4	793	c.519G>A	c.(517-519)AGG>AGA	p.R173R		NM_000570	NP_000561	O75015	FCG3B_HUMAN	low affinity immunoglobulin gamma Fc region	173	Ig-like C2-type 2.				immune response	anchored to membrane|extracellular region|plasma membrane	IgG binding|receptor activity				0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CAACAAGCCCCCTGCAGAAGT	0.463													164	249	---	---	---	---	PASS
F5	2153	broad.mit.edu	37	1	169510581	169510581	+	Silent	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169510581A>G	uc001ggg.1	-	13	3892	c.3747T>C	c.(3745-3747)CTT>CTC	p.L1249L		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	1249	2-8.|35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	GGTCTAAAGAAAGGGTTGTAT	0.517													10	528	---	---	---	---	PASS
SCYL3	57147	broad.mit.edu	37	1	169857865	169857865	+	Silent	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169857865A>G	uc001ggs.2	-	2	315	c.117T>C	c.(115-117)GTT>GTC	p.V39V	SCYL3_uc001ggt.2_Silent_p.V39V|SCYL3_uc001ggu.2_RNA	NM_181093	NP_851607	Q8IZE3	PACE1_HUMAN	SCY1-like 3 isoform 2	39	Protein kinase.				cell migration	Golgi apparatus|lamellipodium	ATP binding|protein binding|protein kinase activity			ovary(1)|skin(1)	2	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TATACACAAAAACTGAAGCAA	0.373													10	681	---	---	---	---	PASS
CEP350	9857	broad.mit.edu	37	1	179989116	179989116	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179989116C>T	uc001gnt.2	+	12	2590	c.2207C>T	c.(2206-2208)CCT>CTT	p.P736L	CEP350_uc009wxl.2_Missense_Mutation_p.P735L|CEP350_uc001gnu.2_Missense_Mutation_p.P570L	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	736						centrosome|nucleus|spindle				ovary(4)	4						TGGATGCAGCCTGAAAGATTG	0.368													4	215	---	---	---	---	PASS
EPHX1	2052	broad.mit.edu	37	1	226030115	226030115	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226030115A>G	uc001hpk.2	+	7	1060	c.980A>G	c.(979-981)GAG>GGG	p.E327G	EPHX1_uc001hpl.2_Missense_Mutation_p.E327G	NM_001136018	NP_001129490	P07099	HYEP_HUMAN	epoxide hydrolase 1	327					aromatic compound catabolic process|response to toxin	endoplasmic reticulum membrane|integral to membrane|microsome	cis-stilbene-oxide hydrolase activity|epoxide hydrolase activity			ovary(3)|lung(1)	4	Breast(184;0.197)					TATATTCTAGAGAAGTTTTCC	0.592													39	92	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21230217	21230217	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21230217C>T	uc002red.2	-	26	9651	c.9523G>A	c.(9523-9525)GCT>ACT	p.A3175T		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3175	Heparin-binding.|Basic (possible receptor binding region).				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	TTATACTGAGCTTTTACACTT	0.368													6	248	---	---	---	---	PASS
HADHB	3032	broad.mit.edu	37	2	26502013	26502013	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26502013T>C	uc002rgz.2	+	9	892	c.641T>C	c.(640-642)GTT>GCT	p.V214A	HADHB_uc010ykv.1_Missense_Mutation_p.V192A|HADHB_uc010ykw.1_Missense_Mutation_p.V199A|HADHB_uc002rha.2_Intron|HADHB_uc010ykx.1_Missense_Mutation_p.V140A	NM_000183	NP_000174	P55084	ECHB_HUMAN	mitochondrial trifunctional protein, beta	214					fatty acid beta-oxidation	mitochondrial nucleoid	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acyltransferase activity|enoyl-CoA hydratase activity|protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCCCTGCGGTTTCTGAGTTC	0.507													24	38	---	---	---	---	PASS
CAD	790	broad.mit.edu	37	2	27456649	27456649	+	Silent	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27456649C>T	uc002rji.2	+	21	3534	c.3372C>T	c.(3370-3372)GTC>GTT	p.V1124V	CAD_uc010eyw.2_Silent_p.V1061V	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	1124	CPSase B.|ATP-grasp 2.|CPSase (Carbamoyl-phosphate synthase).				'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|neuronal cell body|nuclear matrix|terminal button	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	ATCCCGTGGTCATCTCCAAGT	0.587													10	12	---	---	---	---	PASS
OR7E91P	79315	broad.mit.edu	37	2	71256242	71256242	+	RNA	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71256242T>C	uc002sho.2	+	3		c.412T>C			OR7E91P_uc010fdz.2_RNA	NR_002185				Homo sapiens olfactory receptor, family 7, subfamily E, member 91 pseudogene, mRNA (cDNA clone IMAGE:3996998).												0						AATGTGCTTCTTCCTCTCCAA	0.572													8	5	---	---	---	---	PASS
PTCD3	55037	broad.mit.edu	37	2	86360354	86360354	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86360354A>G	uc002sqw.2	+	18	1493	c.1427A>G	c.(1426-1428)AAG>AGG	p.K476R	PTCD3_uc002sqx.1_Missense_Mutation_p.K66R|SNORD94_uc010fgr.1_5'Flank	NM_017952	NP_060422	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3 precursor	476	PPR 8.					mitochondrion	protein binding			ovary(1)	1						GTTACCTTGAAGTGGTATGAG	0.338													9	613	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109367729	109367729	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109367729G>A	uc002tem.3	+	10	1409	c.1283G>A	c.(1282-1284)CGA>CAA	p.R428Q		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	428					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						GGTGCTATTCGAGCACATAAT	0.353													8	512	---	---	---	---	PASS
NCKAP5	344148	broad.mit.edu	37	2	133531448	133531448	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133531448T>A	uc002ttp.2	-	16	5443	c.5069A>T	c.(5068-5070)AAC>ATC	p.N1690I	NCKAP5_uc002ttq.2_Missense_Mutation_p.N371I	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	1690							protein binding				0						CTCTTGCAAGTTTTCATTTGC	0.338													6	548	---	---	---	---	PASS
BAZ2B	29994	broad.mit.edu	37	2	160243076	160243076	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160243076C>A	uc002uao.2	-	22	3611	c.3259G>T	c.(3259-3261)GGA>TGA	p.G1087*	BAZ2B_uc002uap.2_Nonsense_Mutation_p.G1051*	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1087	DDT.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						AATGTACTTCCAGAGAGAACA	0.348													4	143	---	---	---	---	PASS
TANK	10010	broad.mit.edu	37	2	162091890	162091890	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162091890C>T	uc002ubr.1	+	8	1297	c.1139C>T	c.(1138-1140)TCG>TTG	p.S380L	TANK_uc002ubs.2_Missense_Mutation_p.S380L	NM_004180	NP_004171	Q92844	TANK_HUMAN	TRAF interacting protein TANK isoform a	380						cytosol	metal ion binding|protein binding			ovary(1)	1						GACAGTGACTCGGTGGTACTA	0.418													136	202	---	---	---	---	PASS
NCKAP1	10787	broad.mit.edu	37	2	183822244	183822244	+	Silent	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183822244T>C	uc002upc.2	-	19	2364	c.1962A>G	c.(1960-1962)GAA>GAG	p.E654E	NCKAP1_uc002upb.2_Silent_p.E660E	NM_013436	NP_038464	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 1	654					apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			CCCTTTCAGGTTCCCCTTTCT	0.388													9	470	---	---	---	---	PASS
ERBB4	2066	broad.mit.edu	37	2	212495282	212495282	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212495282A>G	uc002veg.1	-	17	2082	c.1984T>C	c.(1984-1986)TTC>CTC	p.F662L	ERBB4_uc002veh.1_Missense_Mutation_p.F662L|ERBB4_uc010zji.1_Missense_Mutation_p.F652L|ERBB4_uc010zjj.1_Missense_Mutation_p.F652L|ERBB4_uc010fut.1_Missense_Mutation_p.F662L	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	662	Potential.				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)		ACCAGAATGAAGAGCCCACCA	0.403										TSP Lung(8;0.080)			9	295	---	---	---	---	PASS
RUFY4	285180	broad.mit.edu	37	2	218954615	218954615	+	Intron	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218954615C>T	uc002vgw.2	+						RUFY4_uc002vgy.1_RNA|RUFY4_uc010fvl.1_Intron	NM_198483	NP_940885	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4								metal ion binding			pancreas(1)	1		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		ACCTCAGCGCCCACTTGGGGA	0.592													3	10	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191524	10191524	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191524G>T	uc003bvc.2	+	3	730	c.517G>T	c.(517-519)GAG>TAG	p.E173*	VHL_uc003bvd.2_Nonsense_Mutation_p.E132*	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	173					anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.E173fs*26(1)|p.E173fs*>42(1)|p.P172fs*39(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		AGTCAAGCCTGAGAATTACAG	0.527		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				43	21	---	---	---	---	PASS
SLMAP	7871	broad.mit.edu	37	3	57913033	57913033	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57913033C>G	uc003dje.1	+	22	2610	c.2405C>G	c.(2404-2406)CCC>CGC	p.P802R	SLMAP_uc003djd.1_Missense_Mutation_p.P785R|SLMAP_uc003djf.1_Missense_Mutation_p.P764R|SLMAP_uc003djg.1_3'UTR|SLMAP_uc011bez.1_Missense_Mutation_p.P270R|SLMAP_uc011bfa.1_Missense_Mutation_p.P336R|SLMAP_uc003dji.1_3'UTR|SLMAP_uc011bfb.1_Missense_Mutation_p.P336R|SLMAP_uc011bfc.1_3'UTR	NM_007159	NP_009090	Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	802	Cytoplasmic (Potential).				muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		AAACCCTGGCCCTGGATGCCC	0.517													42	39	---	---	---	---	PASS
ROBO1	6091	broad.mit.edu	37	3	78656071	78656071	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78656071T>C	uc003dqe.2	-	29	4764	c.4556A>G	c.(4555-4557)GAC>GGC	p.D1519G	ROBO1_uc003dqb.2_Missense_Mutation_p.D1480G|ROBO1_uc003dqc.2_Missense_Mutation_p.D1419G|ROBO1_uc003dqd.2_Missense_Mutation_p.D1474G|ROBO1_uc010hoh.2_Missense_Mutation_p.D711G|ROBO1_uc011bgl.1_Missense_Mutation_p.D1091G	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	1519	Cytoplasmic (Potential).				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TGATGATCTGTCTGTTCTTGC	0.483													6	301	---	---	---	---	PASS
SLC9A10	285335	broad.mit.edu	37	3	111923204	111923204	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111923204A>C	uc003dyu.2	-	17	2255	c.2033T>G	c.(2032-2034)TTC>TGC	p.F678C	SLC9A10_uc011bhu.1_Intron|SLC9A10_uc010hqc.2_Missense_Mutation_p.F630C	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger	678	Ion transport-like.|Helical; (Potential).				cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5						TGCTAACTCGAATATGTTCCA	0.294													158	110	---	---	---	---	PASS
FRYL	285527	broad.mit.edu	37	4	48501346	48501346	+	3'UTR	SNP	A	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48501346A>T	uc003gyh.1	-	64					FRYL_uc003gye.1_3'UTR|FRYL_uc003gyf.1_3'UTR|FRYL_uc003gyg.1_3'UTR	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						GCTGCCAGAAAGTTATCAGTG	0.343													37	44	---	---	---	---	PASS
TMPRSS11F	389208	broad.mit.edu	37	4	68995527	68995527	+	Intron	SNP	C	T	T	rs148740696		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68995527C>T	uc003hdt.1	-							NM_207407	NP_997290	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F						proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1						TGAATACTTACGCGTACATCA	0.443													119	179	---	---	---	---	PASS
UGT2B28	54490	broad.mit.edu	37	4	70152481	70152481	+	Silent	SNP	A	G	G	rs141618560		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70152481A>G	uc003hej.2	+	3	884	c.882A>G	c.(880-882)GAA>GAG	p.E294E	UGT2B28_uc010ihr.2_Silent_p.E294E	NM_053039	NP_444267	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family,	294					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1					Flunitrazepam(DB01544)	AAATGGAGGAATTTGTACAGA	0.393													15	695	---	---	---	---	PASS
HTN3	3347	broad.mit.edu	37	4	70898954	70898954	+	3'UTR	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70898954G>A	uc003hew.2	+	5						NM_000200	NP_000191	P15516	HIS3_HUMAN	histatin 3						biomineral tissue development|defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular region	metal ion binding|protein binding			ovary(1)|skin(1)	2						CAGTAATCACGGGGCATGATT	0.343													5	382	---	---	---	---	PASS
C4orf26	152816	broad.mit.edu	37	4	76489543	76489543	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76489543A>G	uc003hip.1	+	2	322	c.287A>G	c.(286-288)AAC>AGC	p.N96S	C4orf26_uc011cbn.1_Intron|C4orf26_uc011cbo.1_Missense_Mutation_p.T111A	NM_178497	NP_848592	Q17RF5	CD026_HUMAN	hypothetical protein LOC152816 precursor	96						extracellular region					0			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TCAAGGTGTAACCACCGTTTT	0.463													7	177	---	---	---	---	PASS
TSPAN5	10098	broad.mit.edu	37	4	99407929	99407929	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99407929C>T	uc003hub.2	-	3	589	c.239G>A	c.(238-240)TGC>TAC	p.C80Y	TSPAN5_uc011cdz.1_Missense_Mutation_p.C9Y	NM_005723	NP_005714	P62079	TSN5_HUMAN	transmembrane 4 superfamily member 9	80	Helical; (Potential).					integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)		CGCTCCAATGCACCCTGCAAA	0.483													28	189	---	---	---	---	PASS
SLC7A11	23657	broad.mit.edu	37	4	139103536	139103536	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139103536A>G	uc011chb.1	-	9	1311	c.1031T>C	c.(1030-1032)GTT>GCT	p.V344A		NM_014331	NP_055146	Q9UPY5	XCT_HUMAN	solute carrier family 7, (cationic amino acid	344	Cytoplasmic (Potential).				blood coagulation|cellular nitrogen compound metabolic process|leukocyte migration|response to toxin	integral to membrane|plasma membrane	cystine:glutamate antiporter activity|protein binding			skin(1)	1	all_hematologic(180;0.166)				L-Cystine(DB00138)|L-Glutamic Acid(DB00142)|Sulfasalazine(DB00795)	TCGAGACGCAACATAGAATAA	0.423													6	251	---	---	---	---	PASS
SDHA	6389	broad.mit.edu	37	5	256624	256624	+	3'UTR	SNP	G	A	A	rs79810985	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:256624G>A	uc003jao.3	+	15					SDHA_uc011clw.1_3'UTR|SDHA_uc003jap.3_3'UTR|SDHA_uc003jaq.3_3'UTR|SDHA_uc003jar.3_3'UTR	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,						nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	GTCTTCATACGCTTCTGCACT	0.488									Familial_Paragangliomas				3	27	---	---	---	---	PASS
BRD9	65980	broad.mit.edu	37	5	891953	891953	+	Silent	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:891953G>A	uc003jbq.2	-	2	236	c.69C>T	c.(67-69)CCC>CCT	p.P23P	TRIP13_uc003jbr.2_5'Flank|BRD9_uc003jbl.2_5'Flank|BRD9_uc003jbm.2_RNA|BRD9_uc003jbn.2_RNA|BRD9_uc011cmb.1_5'UTR|BRD9_uc003jbo.2_5'UTR|BRD9_uc011cmc.1_RNA|TRIP13_uc010ite.1_5'Flank	NM_023924	NP_076413	Q9H8M2	BRD9_HUMAN	bromodomain containing 9 isoform 1	23							nucleic acid binding				0			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			GCTTCTCCAGGGGCTTGTCGG	0.557													5	96	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21751719	21751719	+	3'UTR	SNP	G	A	A	rs72173073		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21751719G>A	uc010iuc.2	-	12					CDH12_uc011cno.1_3'UTR|CDH12_uc003jgk.2_3'UTR|uc003jgj.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						TTGTCCCAGAgtgtgtgtgtg	0.244										HNSCC(59;0.17)			3	1	---	---	---	---	PASS
CDH12	1010	broad.mit.edu	37	5	21751722	21751722	+	3'UTR	SNP	T	A	A	rs77099217		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21751722T>A	uc010iuc.2	-	12					CDH12_uc011cno.1_3'UTR|CDH12_uc003jgk.2_3'UTR|uc003jgj.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						TCCCAGAgtgtgtgtgtgtgt	0.249										HNSCC(59;0.17)			3	1	---	---	---	---	PASS
NNT	23530	broad.mit.edu	37	5	43702815	43702815	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43702815C>A	uc003joe.2	+	21	3343	c.3088C>A	c.(3088-3090)CTT>ATT	p.L1030I	NNT_uc003jof.2_Missense_Mutation_p.L1030I	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	1030	Mitochondrial matrix.				tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)	CATGCCAGTCCTTGAGGTCTG	0.363													100	187	---	---	---	---	PASS
CMYA5	202333	broad.mit.edu	37	5	79027932	79027932	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79027932C>G	uc003kgc.2	+	2	3416	c.3344C>G	c.(3343-3345)ACT>AGT	p.T1115S		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1115						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AAGCAGAAAACTCAAGCATAT	0.408													8	127	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	90149227	90149227	+	Silent	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90149227A>G	uc003kju.2	+	80	17427	c.17331A>G	c.(17329-17331)CTA>CTG	p.L5777L	GPR98_uc003kjt.2_Silent_p.L3483L|GPR98_uc003kjw.2_Silent_p.L1438L	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	5777	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CAGAGAGGCTACTGGATGTCC	0.398													86	128	---	---	---	---	PASS
SLCO4C1	353189	broad.mit.edu	37	5	101592957	101592957	+	Nonsense_Mutation	SNP	G	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101592957G>C	uc003knm.2	-	8	1618	c.1331C>G	c.(1330-1332)TCA>TGA	p.S444*		NM_180991	NP_851322	Q6ZQN7	SO4C1_HUMAN	solute carrier organic anion transporter family,	444	Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|sodium-independent organic anion transport|spermatogenesis	basolateral plasma membrane|integral to membrane	sodium-independent organic anion transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		TCTGAATTTTGAAACAAGGAA	0.363													147	224	---	---	---	---	PASS
P4HA2	8974	broad.mit.edu	37	5	131533917	131533917	+	Silent	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131533917C>T	uc003kwh.2	-	12	1917	c.1353G>A	c.(1351-1353)GTG>GTA	p.V451V	P4HA2_uc003kwg.2_Intron|P4HA2_uc003kwi.2_Intron|P4HA2_uc003kwk.2_Intron|P4HA2_uc003kwl.2_Silent_p.V451V|P4HA2_uc003kwj.2_Intron	NM_004199	NP_004190	O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha II subunit isoform 1	451	Fe2OG dioxygenase.					endoplasmic reticulum lumen	electron carrier activity|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity|protein binding				0		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)	AGAAAGTAGCCACACGATTCC	0.498													5	295	---	---	---	---	PASS
REEP2	51308	broad.mit.edu	37	5	137776732	137776732	+	Silent	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137776732C>T	uc003lcz.2	+	2	182	c.60C>T	c.(58-60)GCC>GCT	p.A20A	REEP2_uc003lda.2_Silent_p.A20A|REEP2_uc011cyt.1_5'UTR	NM_016606	NP_057690	Q9BRK0	REEP2_HUMAN	receptor accessory protein 2	20	Helical; (Potential).					integral to membrane					0			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			TGTACCCAGCCTATTCTTCCT	0.577													37	58	---	---	---	---	PASS
STC2	8614	broad.mit.edu	37	5	172745139	172745139	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172745139A>G	uc003mco.1	-	4	1930	c.620T>C	c.(619-621)ATC>ACC	p.I207T	STC2_uc003mcn.1_Missense_Mutation_p.I122T	NM_003714	NP_003705	O76061	STC2_HUMAN	stanniocalcin 2 precursor	207					cell surface receptor linked signaling pathway|cell-cell signaling	extracellular region	hormone activity			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GAAGCTCAAGATGGAGCACAG	0.647													17	22	---	---	---	---	PASS
CPLX2	10814	broad.mit.edu	37	5	175306022	175306022	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175306022G>C	uc003mde.1	+	4	489	c.143G>C	c.(142-144)CGT>CCT	p.R48P	CPLX2_uc003mdf.1_Missense_Mutation_p.R48P	NM_006650	NP_006641	Q6PUV4	CPLX2_HUMAN	complexin 2	48	Potential.|Interaction with the SNARE complex (By similarity).				mast cell degranulation|positive regulation of synaptic plasticity|vesicle docking involved in exocytosis	cytosol				ovary(1)	1	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			gaggaggagCGTAAGGCCAAG	0.408													8	9	---	---	---	---	PASS
SERPINB6	5269	broad.mit.edu	37	6	2954917	2954917	+	Silent	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2954917G>A	uc003muk.2	-	3	2334	c.339C>T	c.(337-339)TTC>TTT	p.F113F	SERPINB6_uc003mui.2_5'UTR|SERPINB6_uc003muj.2_RNA|SERPINB6_uc003mul.2_Silent_p.F113F|SERPINB6_uc003mum.2_Silent_p.F113F|SERPINB6_uc003mun.2_Silent_p.F113F|SERPINB6_uc003muo.2_Silent_p.F113F	NM_004568	NP_004559	P35237	SPB6_HUMAN	serine (or cysteine) proteinase inhibitor, clade	113					regulation of proteolysis	centrosome|cytosol|protein complex	protease binding|serine-type endopeptidase inhibitor activity				0	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	CTGCTTGGTAGAATTTTTGGC	0.433													20	517	---	---	---	---	PASS
JARID2	3720	broad.mit.edu	37	6	15246614	15246614	+	5'UTR	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15246614G>A	uc003nbj.2	+	1					JARID2_uc011diu.1_Intron|JARID2_uc011div.1_5'Flank	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein						central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				ATTTCAAGGCGAATCTGGCTT	0.358													19	44	---	---	---	---	PASS
PHF1	5252	broad.mit.edu	37	6	33382102	33382102	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33382102C>T	uc003oeh.2	+	9	1071	c.835C>T	c.(835-837)CCC>TCC	p.P279S	PHF1_uc011drh.1_RNA|PHF1_uc003oei.2_Missense_Mutation_p.P279S|PHF1_uc010jux.2_Missense_Mutation_p.P79S	NM_024165	NP_077084	O43189	PHF1_HUMAN	PHD finger protein 1 isoform b	279					chromatin modification	nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Ovarian(999;0.0443)				TGAGATCCTCCCCTTCACTTC	0.488											OREG0017346	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	309	---	---	---	---	PASS
KIAA1009	22832	broad.mit.edu	37	6	84881403	84881403	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84881403A>G	uc010kbp.2	-	17	2298	c.2201T>C	c.(2200-2202)CTC>CCC	p.L734P	KIAA1009_uc003pkj.3_Missense_Mutation_p.L658P|KIAA1009_uc003pki.3_Missense_Mutation_p.L120P	NM_014895	NP_055710	Q5TB80	QN1_HUMAN	KIAA1009 protein	734	Potential.				cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TTGTTCTTGGAGATCTTTTAC	0.274													8	667	---	---	---	---	PASS
MAP3K5	4217	broad.mit.edu	37	6	136960707	136960707	+	Silent	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136960707A>G	uc003qhc.2	-	13	2269	c.1908T>C	c.(1906-1908)TAT>TAC	p.Y636Y	MAP3K5_uc011edj.1_5'UTR|MAP3K5_uc011edk.1_Silent_p.Y481Y	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase	636					activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		CTGTACAGAAATAGATTTGGA	0.299													6	282	---	---	---	---	PASS
SNX8	29886	broad.mit.edu	37	7	2314823	2314823	+	Silent	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2314823C>T	uc003slw.2	-	3	385	c.342G>A	c.(340-342)GTG>GTA	p.V114V		NM_013321	NP_037453	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	114	PX.				cell communication|early endosome to Golgi transport|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		CCTGGAAGACCACGAAGTCAT	0.562													49	44	---	---	---	---	PASS
USP42	84132	broad.mit.edu	37	7	6154957	6154957	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6154957T>C	uc011jwo.1	+	3	368	c.245T>C	c.(244-246)CTA>CCA	p.L82P	USP42_uc011jwn.1_5'UTR|USP42_uc010kth.1_Intron|USP42_uc011jwp.1_Missense_Mutation_p.L82P|USP42_uc011jwq.1_5'UTR|USP42_uc011jwr.1_5'Flank	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	82					cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		TTTCTAGCCCTAGGTGATGGC	0.363													193	150	---	---	---	---	PASS
DLX6	1750	broad.mit.edu	37	7	96639202	96639202	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96639202C>T	uc003uom.2	+	4	641	c.641C>T	c.(640-642)GCG>GTG	p.A214V	DLX6AS_uc003uol.2_Intron|DLX6AS_uc010lfo.1_Intron	NM_005222	NP_005213	P56179	DLX6_HUMAN	distal-less homeobox 6	124					nervous system development|skeletal system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					CAGGGCTCGGCGGCCCTGTCG	0.577													21	34	---	---	---	---	PASS
POT1	25913	broad.mit.edu	37	7	124503402	124503402	+	Splice_Site	SNP	A	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124503402A>T	uc003vlm.2	-	8	1147	c.546_splice	c.e8+1	p.K182_splice	POT1_uc011koe.1_Splice_Site|POT1_uc003vlk.2_Splice_Site|POT1_uc003vll.2_Splice_Site|POT1_uc003vlo.2_Splice_Site_p.K51_splice|POT1_uc003vln.2_Splice_Site	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1						DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						AAAAATATGTACCTTTAGAAG	0.368													38	81	---	---	---	---	PASS
AKR1B1	231	broad.mit.edu	37	7	134143812	134143812	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134143812C>T	uc003vrp.1	-	1	77	c.3G>A	c.(1-3)ATG>ATA	p.M1I	AKR1B1_uc003vrq.1_RNA	NM_001628	NP_001619	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1	1					C21-steroid hormone biosynthetic process|carbohydrate metabolic process|response to stress	cytosol|extracellular space|nucleus	alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding			ovary(3)	3					NADH(DB00157)|Sulindac(DB00605)	GACGGCTTGCCATGGCTGCTG	0.692											OREG0018334	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	6	---	---	---	---	PASS
TAS2R39	259285	broad.mit.edu	37	7	142880963	142880963	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142880963G>T	uc011ksw.1	+	1	452	c.452G>T	c.(451-453)AGG>ATG	p.R151M		NM_176881	NP_795362	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	151	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			skin(1)	1	Melanoma(164;0.059)					CTCAAACTGAGGTGGAGAATT	0.428													5	282	---	---	---	---	PASS
FASTK	10922	broad.mit.edu	37	7	150774944	150774944	+	Intron	SNP	G	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150774944G>T	uc003wix.1	-						uc011kvf.1_5'Flank|FASTK_uc003wiw.1_Intron|FASTK_uc003wiy.1_Intron|FASTK_uc003wiz.1_Intron|FASTK_uc003wja.1_3'UTR	NM_006712	NP_006703	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|regulation of RNA splicing		ATP binding|Fas-activated serine/threonine kinase activity|protein binding			lung(2)|stomach(2)	4			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)		CAGGGGCCCAGCCAGCCATCC	0.637													12	18	---	---	---	---	PASS
SNTG1	54212	broad.mit.edu	37	8	51705288	51705288	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51705288G>T	uc010lxy.1	+	20	1824	c.1453G>T	c.(1453-1455)GCC>TCC	p.A485S	SNTG1_uc003xqs.1_Missense_Mutation_p.A485S|SNTG1_uc010lxz.1_Missense_Mutation_p.A448S|SNTG1_uc011ldl.1_RNA	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	485					cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				CTTCTTTGCTGCCAAGGTAGC	0.393													8	495	---	---	---	---	PASS
C8orf76	84933	broad.mit.edu	37	8	124232341	124232341	+	3'UTR	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124232341C>T	uc003yqc.1	-	6						NM_032847	NP_116236	Q96K31	CH076_HUMAN	hypothetical protein LOC84933								binding			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			TTTTATAACCCACTAAGCCAA	0.328													5	431	---	---	---	---	PASS
EIF2C2	27161	broad.mit.edu	37	8	141545588	141545588	+	Silent	SNP	C	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141545588C>A	uc003yvn.2	-	17	2290	c.2250G>T	c.(2248-2250)CTG>CTT	p.L750L	EIF2C2_uc010men.2_Silent_p.L673L|EIF2C2_uc010meo.2_Intron	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1	750	Piwi.				mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)			CGTGACTACACAGGTAGAAGT	0.557													43	57	---	---	---	---	PASS
GNE	10020	broad.mit.edu	37	9	36229107	36229107	+	Splice_Site	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36229107T>C	uc010mlh.2	-	6	1198	c.983_splice	c.e6-1	p.G328_splice	CLTA_uc003zzf.1_Intron|GNE_uc010mlg.2_Splice_Site_p.G328_splice|GNE_uc011lpl.1_Splice_Site_p.G218_splice|GNE_uc010mli.2_Splice_Site_p.G359_splice|GNE_uc010mlj.2_Splice_Site_p.G323_splice	NM_005476	NP_005467	Q9Y223	GLCNE_HUMAN	UDP-N-acetylglucosamine-2-epimerase/N-						cell adhesion|lipopolysaccharide biosynthetic process|N-acetylneuraminate metabolic process|UDP-N-acetylglucosamine metabolic process		ATP binding|N-acylmannosamine kinase activity|UDP-N-acetylglucosamine 2-epimerase activity				0			STAD - Stomach adenocarcinoma(86;0.228)			CATTCTCCCCTAGGTAAAACC	0.393													6	291	---	---	---	---	PASS
MELK	9833	broad.mit.edu	37	9	36665415	36665415	+	Silent	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36665415A>G	uc003zzn.2	+	14	1383	c.1245A>G	c.(1243-1245)ACA>ACG	p.T415T	MELK_uc011lpm.1_Silent_p.T284T|MELK_uc011lpn.1_Silent_p.T374T|MELK_uc011lpo.1_Silent_p.T221T|MELK_uc010mll.2_Silent_p.T383T|MELK_uc011lpp.1_Silent_p.T367T|MELK_uc010mlm.2_Silent_p.T344T|MELK_uc011lpq.1_Silent_p.T221T|MELK_uc011lpr.1_Silent_p.T344T|MELK_uc011lps.1_Silent_p.T335T	NM_014791	NP_055606	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	415				T->A: No effect on interaction with PPP1R8.		cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			TATGCAGAACACCTGCAAATA	0.348													138	229	---	---	---	---	PASS
VPS13A	23230	broad.mit.edu	37	9	79936445	79936445	+	Silent	SNP	C	T	T	rs139782359		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79936445C>T	uc004akr.2	+	44	5873	c.5613C>T	c.(5611-5613)TTC>TTT	p.F1871F	VPS13A_uc004akp.3_Silent_p.F1871F|VPS13A_uc004akq.3_Silent_p.F1871F|VPS13A_uc004aks.2_Silent_p.F1832F|VPS13A_uc004akt.2_Silent_p.F211F	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A	1871					Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10						CAGCTGACTTCGTAAAGGATC	0.343													59	107	---	---	---	---	PASS
AUH	549	broad.mit.edu	37	9	94118164	94118164	+	Splice_Site	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94118164C>T	uc004arf.3	-	3	453	c.418_splice	c.e3+1	p.G140_splice	AUH_uc004arg.3_Splice_Site_p.A140_splice|AUH_uc011ltu.1_Splice_Site_p.G140_splice	NM_001698	NP_001689	Q13825	AUHM_HUMAN	AU RNA binding protein/enoyl-Coenzyme A						branched chain family amino acid catabolic process|mRNA catabolic process	mitochondrial matrix	enoyl-CoA hydratase activity|methylglutaconyl-CoA hydratase activity|mRNA 3'-UTR binding				0						TATTTACATACCAGCACAGAA	0.338													32	442	---	---	---	---	PASS
C9orf84	158401	broad.mit.edu	37	9	114486177	114486177	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114486177A>G	uc004bfr.2	-	12	1792	c.1657T>C	c.(1657-1659)TCT>CCT	p.S553P	C9orf84_uc011lwt.1_RNA|C9orf84_uc004bfq.2_Missense_Mutation_p.S514P|C9orf84_uc010mug.2_Missense_Mutation_p.S499P	NM_173521	NP_775792	Q5VXU9	CI084_HUMAN	hypothetical protein LOC158401 isoform 1	553										ovary(2)	2						AGTGTCAAAGAACATGCTTCT	0.274													7	480	---	---	---	---	PASS
CCAR1	55749	broad.mit.edu	37	10	70502139	70502139	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70502139G>T	uc001joo.2	+	6	450	c.331G>T	c.(331-333)GTT>TTT	p.V111F	CCAR1_uc001jol.1_RNA|CCAR1_uc001jom.1_5'UTR|CCAR1_uc009xpx.1_Missense_Mutation_p.V85F|CCAR1_uc001jon.1_Intron|CCAR1_uc010qiz.1_Missense_Mutation_p.V96F|CCAR1_uc010qja.1_Missense_Mutation_p.V96F|CCAR1_uc010qjb.1_RNA	NM_018237	NP_060707	Q8IX12	CCAR1_HUMAN	cell-cycle and apoptosis regulatory protein 1	111					apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7						ATAGCCAGCTGTTGCACTGCC	0.378													169	261	---	---	---	---	PASS
CAMK2G	818	broad.mit.edu	37	10	75574945	75574945	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75574945A>G	uc001jvm.1	-	20	1618	c.1499T>C	c.(1498-1500)ATT>ACT	p.I500T	CAMK2G_uc001jvo.1_Missense_Mutation_p.I471T|CAMK2G_uc001jvq.1_Missense_Mutation_p.I448T|CAMK2G_uc001jvr.1_Missense_Mutation_p.I439T|CAMK2G_uc001jvp.1_Missense_Mutation_p.I462T|CAMK2G_uc001jvs.1_Missense_Mutation_p.I483T|CAMK2G_uc001jvt.1_RNA|CAMK2G_uc001jvu.1_Missense_Mutation_p.I440T|CAMK2G_uc009xrp.1_Missense_Mutation_p.I89T	NM_172171	NP_751911	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II	502					insulin secretion|interferon-gamma-mediated signaling pathway|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding|calmodulin-dependent protein kinase activity			lung(1)|stomach(1)	2	Prostate(51;0.0112)					GTCCTCCCCAATCACGTGGAC	0.612													15	31	---	---	---	---	PASS
ATE1	11101	broad.mit.edu	37	10	123683801	123683801	+	Silent	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123683801G>A	uc001lfp.2	-	2	232	c.150C>T	c.(148-150)CTC>CTT	p.L50L	ATE1_uc001lfq.2_Silent_p.L50L|ATE1_uc010qtr.1_5'UTR|ATE1_uc010qts.1_Intron|ATE1_uc010qtt.1_Silent_p.L43L|ATE1_uc001lfr.2_5'UTR|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972	O95260	ATE1_HUMAN	arginyltransferase 1 isoform 2	50					protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				CTCGGTCTATGAGATCCTGAT	0.393													131	272	---	---	---	---	PASS
FAM24B	196792	broad.mit.edu	37	10	124610003	124610003	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124610003G>A	uc001lgt.2	-	3	363	c.29C>T	c.(28-30)GCG>GTG	p.A10V	CUZD1_uc001lgs.2_5'UTR|CUZD1_uc010qtz.1_Intron|LOC399815_uc001lgu.3_5'Flank	NM_152644	NP_689857	Q8N5W8	FA24B_HUMAN	hypothetical protein LOC196792 precursor	10						extracellular region					0		all_neural(114;0.0765)|Lung NSC(174;0.163)|all_lung(145;0.205)		Colorectal(40;0.136)|COAD - Colon adenocarcinoma(40;0.141)		GAGCAAGGCCGCCAGGATACC	0.458													4	225	---	---	---	---	PASS
GPR26	2849	broad.mit.edu	37	10	125447555	125447555	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125447555G>A	uc001lhh.2	+	3	946	c.893G>A	c.(892-894)CGA>CAA	p.R298Q		NM_153442	NP_703143	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	298	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)				TCCTTACTGCGACACCAGTAC	0.597													6	41	---	---	---	---	PASS
ZRANB1	54764	broad.mit.edu	37	10	126662823	126662823	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126662823T>C	uc001lic.2	+	5	1654	c.1283T>C	c.(1282-1284)TTG>TCG	p.L428S	ZRANB1_uc010qug.1_Missense_Mutation_p.L454S	NM_017580	NP_060050	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1	428	TRAF-binding.				positive regulation of Wnt receptor signaling pathway|protein K63-linked deubiquitination|Wnt receptor signaling pathway	aggresome|centrosome|intermediate filament cytoskeleton|nucleolus	cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|kidney(1)	2		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)		GCTACACGTTTGGACAGTCGA	0.423													77	139	---	---	---	---	PASS
LSP1	4046	broad.mit.edu	37	11	1908764	1908764	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1908764G>T	uc001lui.2	+	10	1166	c.991G>T	c.(991-993)GTG>TTG	p.V331L	LSP1_uc001luj.2_Missense_Mutation_p.V459L|LSP1_uc001luk.2_Missense_Mutation_p.V269L|LSP1_uc001lul.2_Missense_Mutation_p.V269L|LSP1_uc001lum.2_Missense_Mutation_p.V269L	NM_002339	NP_002330	P33241	LSP1_HUMAN	lymphocyte-specific protein 1 isoform 1	331					cellular component movement|cellular defense response	actin cytoskeleton|Golgi apparatus|plasma membrane	actin binding|signal transducer activity			large_intestine(1)	1		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		GTATGAGAAGGTGCTTGTGGA	0.587													30	90	---	---	---	---	PASS
LOC645332	645332	broad.mit.edu	37	11	67560590	67560590	+	3'UTR	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67560590C>T	uc001omt.3	-	4					LOC645332_uc001omu.3_3'UTR	NR_024249				SubName: Full=cDNA FLJ57700, weakly similar to Protein FAM86A;												0						AAGTTTTATCCGCTTTCCCAT	0.413													3	24	---	---	---	---	PASS
DLG2	1740	broad.mit.edu	37	11	83673941	83673941	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83673941C>T	uc001paj.2	-	9	1315	c.1012G>A	c.(1012-1014)GAC>AAC	p.D338N	DLG2_uc001pai.2_Missense_Mutation_p.D287N|DLG2_uc010rsy.1_Missense_Mutation_p.D305N|DLG2_uc010rsz.1_Missense_Mutation_p.D338N|DLG2_uc010rta.1_Missense_Mutation_p.D338N|DLG2_uc001pak.2_Missense_Mutation_p.D443N|DLG2_uc010rtb.1_Missense_Mutation_p.D305N|DLG2_uc001pal.1_Missense_Mutation_p.D338N|DLG2_uc001pam.1_Missense_Mutation_p.D377N	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2	338						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)				GTGTAGTCGTCGTCAACAAGC	0.423													10	362	---	---	---	---	PASS
TMEM133	83935	broad.mit.edu	37	11	100863191	100863191	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100863191A>G	uc001pgf.2	+	1	381	c.152A>G	c.(151-153)TAC>TGC	p.Y51C		NM_032021	NP_114410	Q9H2Q1	TM133_HUMAN	transmembrane protein 133	51	Helical; (Potential).					integral to membrane					0		Acute lymphoblastic leukemia(157;0.000869)|all_hematologic(158;0.014)		BRCA - Breast invasive adenocarcinoma(274;0.0675)		TTTGCCTCCTACCCTTTTTTG	0.398													81	110	---	---	---	---	PASS
ARHGAP20	57569	broad.mit.edu	37	11	110461416	110461416	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110461416G>T	uc001pkz.1	-	12	1546	c.1261C>A	c.(1261-1263)CAC>AAC	p.H421N	ARHGAP20_uc001pky.1_Missense_Mutation_p.H398N|ARHGAP20_uc009yyb.1_Missense_Mutation_p.H385N|ARHGAP20_uc001pla.1_Missense_Mutation_p.H385N|ARHGAP20_uc001plb.2_5'Flank	NM_020809	NP_065860	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	421	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		CAGTCTAGGTGTACTTCGACT	0.408													22	441	---	---	---	---	PASS
ANKK1	255239	broad.mit.edu	37	11	113270770	113270770	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113270770G>T	uc001pny.2	+	8	2173	c.2079G>T	c.(2077-2079)TGG>TGT	p.W693C		NM_178510	NP_848605	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	693	ANK 11.						ATP binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|ovary(1)|breast(1)	8		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		AGGTGGGCTGGACACCCGCCC	0.632													4	6	---	---	---	---	PASS
DRD2	1813	broad.mit.edu	37	11	113286211	113286211	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113286211G>A	uc001pnz.2	-	4	976	c.655C>T	c.(655-657)CGC>TGC	p.R219C	DRD2_uc010rwv.1_Missense_Mutation_p.R218C|DRD2_uc001poa.3_Missense_Mutation_p.R219C|DRD2_uc001pob.3_Missense_Mutation_p.R219C|DRD2_uc009yyr.1_Missense_Mutation_p.R219C	NM_000795	NP_000786	P14416	DRD2_HUMAN	dopamine receptor D2 isoform long	219	Cytoplasmic (By similarity).|Interaction with PPP1R9B (By similarity).				activation of phospholipase C activity by dopamine receptor signaling pathway|adenohypophysis development|adult walking behavior|arachidonic acid secretion|axonogenesis|behavioral response to cocaine|behavioral response to ethanol|branching morphogenesis of a nerve|cerebral cortex GABAergic interneuron migration|circadian regulation of gene expression|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|intracellular protein kinase cascade|negative regulation of blood pressure|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of dopamine receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|negative regulation of synaptic transmission, glutamatergic|neurological system process involved in regulation of systemic arterial blood pressure|peristalsis|phosphatidylinositol metabolic process|positive regulation of dopamine uptake|positive regulation of growth hormone secretion|positive regulation of neuroblast proliferation|prepulse inhibition|protein localization|regulation of heart rate|regulation of long-term neuronal synaptic plasticity|regulation of potassium ion transport|regulation of sodium ion transport|regulation of synaptic transmission, GABAergic|release of sequestered calcium ion into cytosol|response to amphetamine|response to drug|response to histamine|response to morphine|sensory perception of smell|synapse assembly|temperature homeostasis|visual learning	integral to plasma membrane	dopamine D2 receptor activity|dopamine receptor activity, coupled via Gi/Go|drug binding|potassium channel regulator activity|protein binding			pancreas(1)|skin(1)	2		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Carphenazine(DB01038)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Domperidone(DB01184)|Droperidol(DB00450)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Mesoridazine(DB00933)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Sulpiride(DB00391)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Ziprasidone(DB00246)|Zuclopenthixol(DB01624)	CGCTTGCGGCGTCTGCGGAGG	0.577													10	190	---	---	---	---	PASS
ARHGEF12	23365	broad.mit.edu	37	11	120350798	120350798	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120350798A>G	uc001pxl.1	+	38	3903	c.3896A>G	c.(3895-3897)AAC>AGC	p.N1299S	ARHGEF12_uc009zat.2_Missense_Mutation_p.N1280S|ARHGEF12_uc009zau.1_Missense_Mutation_p.N1196S	NM_015313	NP_056128	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	1299					apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|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	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		GTCATCCAGAACTCTGAAAAT	0.468			T	MLL	AML								8	163	---	---	---	---	PASS
VSIG2	23584	broad.mit.edu	37	11	124618329	124618329	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124618329T>C	uc001qas.2	-	6	884	c.808A>G	c.(808-810)AGG>GGG	p.R270G	VSIG2_uc001qat.2_Missense_Mutation_p.R270G	NM_014312	NP_055127	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2	270	Cytoplasmic (Potential).					integral to plasma membrane|membrane fraction				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.215)	Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0215)		TTCTTCCCCCTCTCTTTCTGG	0.607													5	98	---	---	---	---	PASS
PTPRO	5800	broad.mit.edu	37	12	15742466	15742466	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15742466A>G	uc001rcv.1	+	25	3662	c.3488A>G	c.(3487-3489)GAC>GGC	p.D1163G	PTPRO_uc001rcw.1_Missense_Mutation_p.D1135G|PTPRO_uc001rcx.1_Missense_Mutation_p.D352G|PTPRO_uc001rcy.1_Missense_Mutation_p.D352G|PTPRO_uc001rcz.1_Missense_Mutation_p.D324G|PTPRO_uc001rda.1_Missense_Mutation_p.D324G	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O	1163	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)				GAGTTTGTTGACATCTTAGGG	0.463													7	343	---	---	---	---	PASS
LOC100133893	100133893	broad.mit.edu	37	12	27916081	27916081	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27916081A>T	uc010sjs.1	-	3	613	c.613T>A	c.(613-615)TCC>ACC	p.S205T		NM_001146221	NP_001139693			MANSC domain-containing protein												0						TCATTCAGGGAAGTAAATCTT	0.378													168	299	---	---	---	---	PASS
OR6C6	283365	broad.mit.edu	37	12	55688388	55688388	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55688388A>G	uc010sph.1	-	1	629	c.629T>C	c.(628-630)GTA>GCA	p.V210A		NM_001005493	NP_001005493	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C,	210	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|skin(1)	2						AATCACTAATACCAGTGTGAC	0.413													5	190	---	---	---	---	PASS
GLIPR1	11010	broad.mit.edu	37	12	75884191	75884191	+	Silent	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75884191T>C	uc001sxs.2	+	3	574	c.426T>C	c.(424-426)GTT>GTC	p.V142V	GLIPR1_uc009zsb.1_Missense_Mutation_p.F166S	NM_006851	NP_006842	P48060	GLIP1_HUMAN	GLI pathogenesis-related 1 precursor	142					cellular lipid metabolic process	extracellular region|integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3						TTCAGGTTGTTTGGGCAGATA	0.378													7	366	---	---	---	---	PASS
KNTC1	9735	broad.mit.edu	37	12	123035903	123035903	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123035903A>G	uc001ucv.2	+	14	1287	c.1124A>G	c.(1123-1125)GAT>GGT	p.D375G	KNTC1_uc010taf.1_Missense_Mutation_p.D338G	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore	375					cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		TGCAAAAATGATCCAAAGTAG	0.239													8	669	---	---	---	---	PASS
SLC15A4	121260	broad.mit.edu	37	12	129293991	129293991	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129293991G>A	uc001uhu.2	-	4	1092	c.1039C>T	c.(1039-1041)CTT>TTT	p.L347F	SLC15A4_uc001uhv.2_RNA	NM_145648	NP_663623	Q8N697	S15A4_HUMAN	solute carrier family 15, member 4	347					oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		CTCAAATGAAGACTCTGTAAA	0.358													218	366	---	---	---	---	PASS
SLC15A4	121260	broad.mit.edu	37	12	129293993	129293993	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129293993C>A	uc001uhu.2	-	4	1090	c.1037G>T	c.(1036-1038)AGT>ATT	p.S346I	SLC15A4_uc001uhv.2_RNA	NM_145648	NP_663623	Q8N697	S15A4_HUMAN	solute carrier family 15, member 4	346					oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		CAAATGAAGACTCTGTAAAAC	0.368													216	365	---	---	---	---	PASS
ZMYM2	7750	broad.mit.edu	37	13	20638656	20638656	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20638656G>C	uc001umr.2	+	20	3401	c.3103G>C	c.(3103-3105)GAA>CAA	p.E1035Q	ZMYM2_uc001ums.2_Missense_Mutation_p.E1035Q|ZMYM2_uc001umt.2_Missense_Mutation_p.E1035Q|ZMYM2_uc001umv.2_Missense_Mutation_p.E415Q|ZMYM2_uc001umw.2_Missense_Mutation_p.E488Q	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	1035					regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		AGAATATGAGGAACAGCCCAG	0.338													87	599	---	---	---	---	PASS
SLC46A3	283537	broad.mit.edu	37	13	29275084	29275084	+	3'UTR	SNP	T	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29275084T>G	uc001usi.2	-	5					SLC46A3_uc001usg.2_3'UTR|SLC46A3_uc001usj.2_Nonstop_Mutation_p.*464Y|SLC46A3_uc001ush.2_3'UTR	NM_181785	NP_861450	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3 isoform a						transmembrane transport	integral to membrane				central_nervous_system(1)|skin(1)	2		Lung SC(185;0.0367)		all cancers(112;0.159)		CAATAGCAGCTTAACAGGCTC	0.318													82	140	---	---	---	---	PASS
SLITRK5	26050	broad.mit.edu	37	13	88329235	88329235	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88329235T>C	uc001vln.2	+	2	1811	c.1592T>C	c.(1591-1593)CTC>CCC	p.L531P	SLITRK5_uc010tic.1_Missense_Mutation_p.L290P	NM_015567	NP_056382	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5 precursor	531	Extracellular (Potential).|LRR 12.					integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5	all_neural(89;0.101)|Medulloblastoma(90;0.163)					TTGACCCTCCTCAGGCTAAAC	0.522													4	38	---	---	---	---	PASS
DNAJC3	5611	broad.mit.edu	37	13	96361504	96361504	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96361504G>A	uc001vmq.2	+	2	214	c.106G>A	c.(106-108)GAT>AAT	p.D36N	DNAJC3_uc001vmp.2_Missense_Mutation_p.D36N|DNAJC3_uc001vmr.2_Missense_Mutation_p.D36N	NM_006260	NP_006251	Q13217	DNJC3_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 3	36					protein folding|response to unfolded protein|response to virus		heat shock protein binding|protein kinase inhibitor activity|unfolded protein binding				0	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.126)			AGTAAATGCAGATGTTGAGAA	0.318													164	239	---	---	---	---	PASS
CLYBL	171425	broad.mit.edu	37	13	100517099	100517099	+	Missense_Mutation	SNP	G	A	A	rs145666717	byFrequency	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100517099G>A	uc001vok.2	+	5	582	c.568G>A	c.(568-570)GGG>AGG	p.G190R	CLYBL_uc010tix.1_Missense_Mutation_p.G190R|CLYBL_uc010tiy.1_Missense_Mutation_p.G156R	NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like precursor	190					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)					CCTGAAGGTCGGGCCTCAAGT	0.478													4	224	---	---	---	---	PASS
ATP11A	23250	broad.mit.edu	37	13	113464970	113464970	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113464970C>T	uc001vsi.3	+	5	459	c.371C>T	c.(370-372)GCC>GTC	p.A124V	ATP11A_uc001vsj.3_Missense_Mutation_p.A124V|ATP11A_uc001vsm.1_5'UTR	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a	124	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				GCAGACAATGCCATGAACCAG	0.323													26	63	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	19856672	19856672	+	RNA	SNP	C	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19856672C>A	uc001vvq.1	-	5		c.858G>T								Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																		TTTCTTCTTTCACTCTTCAGG	0.249													4	4	---	---	---	---	PASS
POLE2	5427	broad.mit.edu	37	14	50136257	50136257	+	Silent	SNP	G	A	A	rs139370609	byFrequency	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50136257G>A	uc001wwu.2	-	6	491	c.477C>T	c.(475-477)AGC>AGT	p.S159S	SDCCAG1_uc010anj.1_Intron|POLE2_uc001wwv.2_RNA	NM_002692	NP_002683	P56282	DPOE2_HUMAN	DNA-directed DNA polymerase epsilon 2	159					DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA binding|DNA-directed DNA polymerase activity			ovary(1)|skin(1)	2	all_epithelial(31;0.0021)|Breast(41;0.0124)					ATTTGCTTCCGCTTTCATCAG	0.348													132	217	---	---	---	---	PASS
ZBTB1	22890	broad.mit.edu	37	14	64990020	64990020	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64990020C>T	uc001xhh.3	+	4	2229	c.1798C>T	c.(1798-1800)CAT>TAT	p.H600Y	ZBTB1_uc010aqg.2_Missense_Mutation_p.H600Y|ZBTB1_uc001xhi.2_Missense_Mutation_p.H600Y	NM_001123329	NP_001116801	Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1 isoform	600	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		CTATACTGTTCATACTAAGGA	0.388													4	130	---	---	---	---	PASS
C14orf43	91748	broad.mit.edu	37	14	74205845	74205845	+	Silent	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74205845G>A	uc001xot.2	-	2	1650	c.867C>T	c.(865-867)GGC>GGT	p.G289G	C14orf43_uc001xou.2_Silent_p.G289G|C14orf43_uc010tud.1_Silent_p.G289G|C14orf43_uc010arw.2_RNA	NM_194278	NP_919254	Q6PJG2	CN043_HUMAN	hypothetical protein LOC91748	289	Pro-rich.|Gln-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00358)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)|OV - Ovarian serous cystadenocarcinoma(108;0.115)		CTGGCTGCAGGCCAAAGTCCT	0.537													3	21	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102500478	102500478	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102500478A>G	uc001yks.2	+	55	10743	c.10579A>G	c.(10579-10581)AAC>GAC	p.N3527D		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	3527					cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						GATGCGTCAGAACTTGTTCAC	0.507													8	169	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106331329	106331329	+	Splice_Site	SNP	C	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106331329C>A	uc010tyt.1	-	3491		c.53293_splice	c.e3491+1		uc001yrs.2_5'Flank|uc001yrt.2_5'Flank|uc001yrw.1_5'Flank|uc001yrx.1_5'Flank|uc001yrz.1_5'Flank|uc001yse.2_5'Flank|uc001ysf.2_Intron|uc001ysj.2_5'Flank|uc001ysk.1_5'Flank|uc001ysl.1_5'Flank|uc001ysm.1_5'Flank|uc001ysn.1_Intron|uc001yso.1_Intron					Parts of antibodies, mostly variable regions.												0						TCAGGCCAGACCCAGGCCGGC	0.677													3	32	---	---	---	---	PASS
FAM189A1	23359	broad.mit.edu	37	15	29544657	29544657	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29544657G>A	uc010azk.1	-	3	302	c.302C>T	c.(301-303)GCA>GTA	p.A101V		NM_015307	NP_056122	O60320	F1891_HUMAN	hypothetical protein LOC23359	101	Helical; (Potential).					integral to membrane					0						TACACACACTGCAGAAAGCAG	0.393													5	339	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	42987397	42987397	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42987397A>T	uc010udj.1	+	3	5006	c.4004A>T	c.(4003-4005)CAA>CTA	p.Q1335L	uc010bcw.2_RNA					Homo sapiens mRNA for KIAA1300 protein, partial cds.																		TTGATGCTGCAAGACTACCAG	0.577													4	91	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	42987398	42987398	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42987398A>T	uc010udj.1	+	3	5007	c.4005A>T	c.(4003-4005)CAA>CAT	p.Q1335H	uc010bcw.2_RNA					Homo sapiens mRNA for KIAA1300 protein, partial cds.																		TGATGCTGCAAGACTACCAGC	0.577													4	89	---	---	---	---	PASS
ZSCAN29	146050	broad.mit.edu	37	15	43661269	43661269	+	Silent	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43661269T>C	uc001zrk.1	-	2	522	c.375A>G	c.(373-375)AAA>AAG	p.K125K	ZSCAN29_uc001zrj.1_Silent_p.K5K|ZSCAN29_uc010bdf.1_Silent_p.K124K|ZSCAN29_uc001zrl.1_RNA|ZSCAN29_uc010bdg.1_Silent_p.K124K|ZSCAN29_uc001zrm.2_Silent_p.K124K|TUBGCP4_uc001zrn.2_5'Flank|TUBGCP4_uc001zro.2_5'Flank	NM_152455	NP_689668	Q8IWY8	ZSC29_HUMAN	zinc finger protein 690	125					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		CTTGTGATGATTTCGGGGGTG	0.522													41	70	---	---	---	---	PASS
MYO5C	55930	broad.mit.edu	37	15	52564877	52564877	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52564877C>T	uc010bff.2	-	6	787	c.650G>A	c.(649-651)CGG>CAG	p.R217Q	MYO5C_uc010uga.1_RNA|MYO5C_uc010ugb.1_RNA|MYO5C_uc010ugc.1_Missense_Mutation_p.R180Q	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC	217	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)		TTTCCCAAACCGACTACTATT	0.358													13	596	---	---	---	---	PASS
MYO5A	4644	broad.mit.edu	37	15	52615570	52615570	+	Silent	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52615570T>C	uc002aby.2	-	36	4951	c.4707A>G	c.(4705-4707)AAA>AAG	p.K1569K	MYO5A_uc002abx.3_Silent_p.K1542K|MYO5A_uc010ugd.1_Silent_p.K291K	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1	1569	Dilute.				actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		CACTGTACTGTTTCAAGCAGT	0.378													8	510	---	---	---	---	PASS
CORO2B	10391	broad.mit.edu	37	15	69003112	69003112	+	Silent	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69003112C>T	uc002arj.3	+	4	404	c.375C>T	c.(373-375)AAC>AAT	p.N125N	CORO2B_uc010bic.2_Silent_p.N120N|CORO2B_uc002ark.2_5'Flank	NM_006091	NP_006082	Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B	125	WD 1.				actin cytoskeleton organization	actin cytoskeleton|cytoplasm|membrane	actin filament binding			ovary(3)|skin(2)|large_intestine(1)	6						TGAAGCGGAACATGACGGAGG	0.657													4	8	---	---	---	---	PASS
KIAA1024	23251	broad.mit.edu	37	15	79748707	79748707	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79748707T>A	uc002bew.1	+	2	293	c.218T>A	c.(217-219)GTG>GAG	p.V73E	KIAA1024_uc010unk.1_Missense_Mutation_p.V73E	NM_015206	NP_056021	Q9UPX6	K1024_HUMAN	hypothetical protein LOC23251	73						integral to membrane				pancreas(2)|ovary(1)|central_nervous_system(1)	4						AAATGCACTGTGAATAACCAG	0.468													44	64	---	---	---	---	PASS
SLC28A1	9154	broad.mit.edu	37	15	85448772	85448772	+	Silent	SNP	G	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85448772G>T	uc002blg.2	+	8	808	c.606G>T	c.(604-606)GTG>GTT	p.V202V	SLC28A1_uc010upd.1_Silent_p.V124V|SLC28A1_uc010bnb.2_Silent_p.V202V|SLC28A1_uc010upe.1_Silent_p.V202V|SLC28A1_uc010upf.1_Silent_p.V202V|SLC28A1_uc010upg.1_Silent_p.V202V	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28, member 1 isoform 1	202					nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GGTGGTAGGTGTCCTGGAGGG	0.602													16	209	---	---	---	---	PASS
SEMA4B	10509	broad.mit.edu	37	15	90768565	90768565	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90768565T>A	uc002boy.2	+	12	1740	c.1457T>A	c.(1456-1458)ATT>AAT	p.I486N	SEMA4B_uc002boz.2_Missense_Mutation_p.I486N|SEMA4B_uc010uqd.1_Missense_Mutation_p.I324N|SEMA4B_uc002bpa.2_Missense_Mutation_p.I324N|SEMA4B_uc010bnv.1_Missense_Mutation_p.I124N	NM_020210	NP_064595			semaphorin 4B precursor											ovary(1)|breast(1)|kidney(1)	3	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			GTGCACATCATTGAGGAGCTG	0.637													9	18	---	---	---	---	PASS
SYNGR3	9143	broad.mit.edu	37	16	2043317	2043317	+	3'UTR	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2043317G>A	uc002cod.2	+	4						NM_004209	NP_004200	O43761	SNG3_HUMAN	synaptogyrin 3						positive regulation of transporter activity	cell junction|integral to plasma membrane|synaptic vesicle					0						TGCCCAGGACGTGTGTCCCTA	0.652													3	10	---	---	---	---	PASS
CREBBP	1387	broad.mit.edu	37	16	3786097	3786097	+	Silent	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3786097T>C	uc002cvv.2	-	28	4872	c.4668A>G	c.(4666-4668)CTA>CTG	p.L1556L	CREBBP_uc002cvw.2_Silent_p.L1518L	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	1556	Poly-Glu.|Interaction with TRERF1.				cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CTTCTTGTTCTAGTTCCTTAA	0.488			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				6	327	---	---	---	---	PASS
JMJD5	79831	broad.mit.edu	37	16	27232002	27232002	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27232002A>G	uc002doh.2	+	8	1384	c.1202A>G	c.(1201-1203)TAC>TGC	p.Y401C	JMJD5_uc010vcn.1_Missense_Mutation_p.Y439C|JMJD5_uc010bxw.2_Missense_Mutation_p.Y205C|JMJD5_uc010bxx.2_RNA	NM_024773	NP_079049	Q8N371	KDM8_HUMAN	jumonji domain containing 5 isoform 2	401	JmjC.				G2/M transition of mitotic cell cycle|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|histone demethylase activity (H3-K36 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(2)|upper_aerodigestive_tract(1)	3						TACTGGCATTACGTGCGGGCT	0.542													5	157	---	---	---	---	PASS
HIRIP3	8479	broad.mit.edu	37	16	30006455	30006455	+	Silent	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30006455C>T	uc002dve.2	-	3	731	c.270G>A	c.(268-270)GAG>GAA	p.E90E	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|INO80E_uc002dvg.1_5'Flank|INO80E_uc002dvh.1_5'Flank|INO80E_uc002dvi.1_5'Flank|INO80E_uc002dvj.1_5'Flank|INO80E_uc002dvk.1_5'Flank|HIRIP3_uc002dvf.2_Silent_p.E90E	NM_003609	NP_003600	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3	90					chromatin assembly or disassembly	nucleus	protein binding			central_nervous_system(1)	1						ACCTTTTTCTCTCCGGGTCGC	0.488													46	65	---	---	---	---	PASS
LOC146481	146481	broad.mit.edu	37	16	34713678	34713678	+	Intron	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34713678T>C	uc002edx.3	-						LOC146481_uc010vgd.1_RNA					Homo sapiens hypothetical protein LOC146481, mRNA (cDNA clone IMAGE:4639919), partial cds.												0						GAGGAGGGGGTCTCGGCTTTT	0.502													18	40	---	---	---	---	PASS
PAPD5	64282	broad.mit.edu	37	16	50261849	50261849	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50261849C>T	uc010vgo.1	+	12	1890	c.1855C>T	c.(1855-1857)CAG>TAG	p.Q619*	PAPD5_uc010cbi.2_RNA|PAPD5_uc002efz.2_Nonsense_Mutation_p.Q363*|PAPD5_uc002ega.2_Nonsense_Mutation_p.Q410*	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a	493	Ser-rich.				cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		GGAGTCCTCTCAGGCAGTTGG	0.488													100	129	---	---	---	---	PASS
SLC38A7	55238	broad.mit.edu	37	16	58705890	58705890	+	Intron	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58705890C>T	uc002eod.1	-						SLC38A7_uc002eob.1_Intron|SLC38A7_uc002eoc.1_Intron|SLC38A7_uc010vil.1_Intron|SLC38A7_uc002eoe.1_3'UTR	NM_018231	NP_060701	Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7						amino acid transport|sodium ion transport	integral to membrane				ovary(1)	1						CTCTTTTCTACAGGCTTCAGT	0.577													3	1	---	---	---	---	PASS
SLC7A6	9057	broad.mit.edu	37	16	68328656	68328656	+	Silent	SNP	C	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68328656C>A	uc002evt.1	+	9	1380	c.1071C>A	c.(1069-1071)TCC>TCA	p.S357S	SLC7A6_uc002evu.1_Silent_p.S357S|SLC7A6_uc002evv.1_RNA|SLC7A6_uc010cfc.1_RNA	NM_001076785	NP_001070253	Q92536	YLAT2_HUMAN	solute carrier family 7 (cationic amino acid	357	Cytoplasmic (Potential).				blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity|antiporter activity			central_nervous_system(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.0948)		ACCTTCTGTCCATGATCCACA	0.517													99	185	---	---	---	---	PASS
GGNBP2	79893	broad.mit.edu	37	17	34942076	34942076	+	Intron	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34942076A>G	uc002hnb.2	+						GGNBP2_uc002hna.2_3'UTR|GGNBP2_uc002hnc.1_Intron	NM_024835	NP_079111	Q9H3C7	GGNB2_HUMAN	zinc finger protein 403						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		CAAAAACGAAAAATGGTAAAT	0.214													4	30	---	---	---	---	PASS
MED13	9969	broad.mit.edu	37	17	60060140	60060140	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60060140A>G	uc002izo.2	-	16	3301	c.3224T>C	c.(3223-3225)CTC>CCC	p.L1075P		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1075					androgen 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|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						TGAAAGGATGAGGTTTACATA	0.413													6	261	---	---	---	---	PASS
AMZ2	51321	broad.mit.edu	37	17	66251944	66251944	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66251944C>A	uc002jgs.1	+	7	971	c.854C>A	c.(853-855)CCT>CAT	p.P285H	AMZ2_uc002jgr.1_Missense_Mutation_p.P285H|AMZ2_uc002jgt.1_Missense_Mutation_p.P285H|AMZ2_uc002jgu.1_Missense_Mutation_p.P285H|AMZ2_uc002jgv.1_Missense_Mutation_p.P285H|AMZ2_uc002jgw.1_Missense_Mutation_p.P227H|AMZ2_uc002jgy.1_Missense_Mutation_p.P285H	NM_001033572	NP_001028744	Q86W34	AMZ2_HUMAN	archaemetzincins-2 isoform 1	285							metallopeptidase activity|zinc ion binding				0	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			GACCGGCGCCCTCTAAACCTT	0.498													27	56	---	---	---	---	PASS
FN3K	64122	broad.mit.edu	37	17	80706748	80706748	+	Silent	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80706748T>C	uc010wvs.1	+	5	547	c.486T>C	c.(484-486)GAT>GAC	p.D162D	FN3K_uc002kfw.1_Silent_p.D117D	NM_022158	NP_071441	Q9H479	FN3K_HUMAN	fructosamine 3 kinase	162					fructoselysine metabolic process		fructosamine-3-kinase activity				0	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			AGTGGCAGGATGACTGGCCGA	0.507													13	21	---	---	---	---	PASS
MYL12A	10627	broad.mit.edu	37	18	3255814	3255814	+	Silent	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3255814G>A	uc002klr.2	+	4	809	c.414G>A	c.(412-414)GTG>GTA	p.V138V	MYL12A_uc002kls.2_Silent_p.V144V	NM_006471	NP_006462	P19105	ML12A_HUMAN	myosin, light chain 12A, regulatory,	138	EF-hand 3.					myosin complex	calcium ion binding|protein binding				0						ATGAGGAAGTGGATGAGCTGT	0.433													5	289	---	---	---	---	PASS
POTEC	388468	broad.mit.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14513764C>T	uc010dln.2	-	10	1884	c.1430G>A	c.(1429-1431)CGG>CAG	p.R477Q	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	477										skin(3)	3						AAGTTGTTTCCGGGTATCATT	0.358													8	499	---	---	---	---	PASS
LAMA3	3909	broad.mit.edu	37	18	21418771	21418771	+	Silent	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21418771A>G	uc002kuq.2	+	26	3206	c.3120A>G	c.(3118-3120)GAA>GAG	p.E1040E	LAMA3_uc002kur.2_Silent_p.E1040E	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	1040	Domain IV 1 (domain IV B).				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)	TACCTATTGAAGAATTCTCAG	0.428													7	387	---	---	---	---	PASS
C18orf10	25941	broad.mit.edu	37	18	34378398	34378398	+	Intron	SNP	T	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34378398T>G	uc002kzw.1	-						C18orf10_uc002kzv.1_Intron|C18orf10_uc010xci.1_Intron|C18orf10_uc002kzx.1_Intron|C18orf10_uc002kzy.3_Missense_Mutation_p.H224P	NM_015476	NP_056291	Q68CL5	TPGS2_HUMAN	tubulin polyglutamylase complex subunit 2							cytoplasm|microtubule				skin(1)	1						CAATGGCAGGTGTTCCTCCCT	0.388													8	53	---	---	---	---	PASS
PSTPIP2	9050	broad.mit.edu	37	18	43572169	43572169	+	Splice_Site	SNP	C	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43572169C>A	uc002lbp.3	-	11	838	c.742_splice	c.e11-1	p.M248_splice	PSTPIP2_uc002lbq.3_Intron	NM_024430	NP_077748	Q9H939	PPIP2_HUMAN	proline-serine-threonine phosphatase interacting							membrane				ovary(1)	1						GTTCGTACATCTAATAAAAAA	0.338													93	154	---	---	---	---	PASS
TCEB3C	162699	broad.mit.edu	37	18	44555070	44555070	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44555070T>A	uc010xdb.1	-	1	1380	c.1144A>T	c.(1144-1146)AAT>TAT	p.N382Y	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_145653	NP_663628	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide	382	Activation domain (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	DNA binding				0						AGTGCGGCATTGTCTTTCTCT	0.577													13	593	---	---	---	---	PASS
SERPINB4	6318	broad.mit.edu	37	18	61325784	61325784	+	Silent	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61325784T>C	uc002ljg.2	-	4	458	c.432A>G	c.(430-432)CGA>CGG	p.R144R	SERPINB3_uc002lji.2_Silent_p.R144R|SERPINB3_uc010dqa.2_Silent_p.R144R|SERPINB3_uc010dqb.2_3'UTR			P48594	SPB4_HUMAN	SubName: Full=Squamous cell carcinoma antigen 2;	144					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|lung(1)	3						TAATCTTCTTTCGACTTTCTT	0.408													9	697	---	---	---	---	PASS
ZNF236	7776	broad.mit.edu	37	18	74620408	74620408	+	Silent	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74620408G>A	uc002lmi.2	+	14	2622	c.2424G>A	c.(2422-2424)ACG>ACA	p.T808T	ZNF236_uc002lmj.2_RNA	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	808					cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		TGCCGCAGACGGCAGAGGTGG	0.632													5	8	---	---	---	---	PASS
MRPL54	116541	broad.mit.edu	37	19	3765311	3765311	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3765311A>T	uc002lyq.3	+	2	300	c.266A>T	c.(265-267)GAT>GTT	p.D89V		NM_172251	NP_758455	Q6P161	RM54_HUMAN	mitochondrial ribosomal protein L54 precursor	89						mitochondrion|ribosome					0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGAAACCGGATGCTGAGTAC	0.577													36	72	---	---	---	---	PASS
SMARCA4	6597	broad.mit.edu	37	19	11113809	11113809	+	Silent	SNP	G	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11113809G>T	uc002mqf.3	+	12	2201	c.1917G>T	c.(1915-1917)CTG>CTT	p.L639L	SMARCA4_uc010dxp.2_Silent_p.L639L|SMARCA4_uc010dxo.2_Silent_p.L639L|SMARCA4_uc002mqg.1_Silent_p.L639L|SMARCA4_uc010dxq.2_Silent_p.L639L|SMARCA4_uc010dxr.2_Silent_p.L639L|SMARCA4_uc002mqj.3_Silent_p.L639L|SMARCA4_uc010dxs.2_Silent_p.L639L	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	639					chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CCGGGCAGCTGGAGGCCTGGC	0.627			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				26	34	---	---	---	---	PASS
MIR181D	574457	broad.mit.edu	37	19	13985689	13985689	+	RNA	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13985689G>A	hsa-mir-181d|MI0003139	+			c.1G>A			uc010dzg.1_5'Flank|NANOS3_uc002mxj.3_5'Flank																	0						GCCTGGGCACGTCCCCTCCCC	0.612													10	18	---	---	---	---	PASS
TECR	9524	broad.mit.edu	37	19	14673981	14673981	+	Intron	SNP	C	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14673981C>A	uc002mza.2	+						TECR_uc002mzb.2_Intron|TECR_uc010xns.1_5'UTR|TECR_uc002mzc.2_Intron|TECR_uc002mzd.2_Intron|TECR_uc002mze.2_5'Flank|TECR_uc002mzf.1_5'Flank	NM_138501	NP_612510	Q9NZ01	TECR_HUMAN	glycoprotein, synaptic 2						fatty acid elongation|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	integral to endoplasmic reticulum membrane	trans-2-enoyl-CoA reductase (NADPH) activity|very long-chain-acyl-CoA dehydrogenase activity				0						CTGGGCTCCCCGCAGAGCTGA	0.627													9	24	---	---	---	---	PASS
OR10H3	26532	broad.mit.edu	37	19	15852604	15852604	+	Silent	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15852604C>T	uc010xoq.1	+	1	402	c.402C>T	c.(400-402)AAC>AAT	p.N134N		NM_013938	NP_039226	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H,	134	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TGCATTACAACATGCTAATGA	0.517													36	230	---	---	---	---	PASS
SIN3B	23309	broad.mit.edu	37	19	16976225	16976225	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16976225A>G	uc002ney.1	+	12	1498	c.1484A>G	c.(1483-1485)GAC>GGC	p.D495G	SIN3B_uc002nez.1_Missense_Mutation_p.D463G|SIN3B_uc010xpi.1_Missense_Mutation_p.D53G	NM_015260	NP_056075	O75182	SIN3B_HUMAN	SIN3 homolog B, transcription regulator	495	Interaction with SDS3 and HDAC1 (By similarity).|Interaction with NCOR1 (By similarity).				cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	protein binding			ovary(2)	2						CCATAGTTAGACGTTGTCCTG	0.562													4	54	---	---	---	---	PASS
OCEL1	79629	broad.mit.edu	37	19	17338790	17338790	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17338790C>G	uc002nfp.2	+	4	596	c.594C>G	c.(592-594)AGC>AGG	p.S198R		NM_024578	NP_078854	Q9H607	OCEL1_HUMAN	occludin/ELL domain containing 1	198										central_nervous_system(1)	1						CCCTGCTGAGCTCCCTGCCCC	0.647													6	16	---	---	---	---	PASS
PDCD2L	84306	broad.mit.edu	37	19	34904640	34904640	+	Splice_Site	SNP	A	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34904640A>C	uc002nvj.2	+	5	720	c.687_splice	c.e5-2	p.S229_splice		NM_032346	NP_115722	Q9BRP1	PDD2L_HUMAN	programmed cell death 2-like							cytoplasm				ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			TTCTGTTTTTAGCCTTCCTAA	0.303													117	205	---	---	---	---	PASS
NFKBID	84807	broad.mit.edu	37	19	36379420	36379420	+	3'UTR	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36379420G>A	uc002oci.1	-	12					NFKBID_uc002och.1_3'UTR|NFKBID_uc002ocj.1_3'UTR	NM_139239	NP_640332	Q8NI38	IKBD_HUMAN	nuclear factor of kappa light polypeptide gene						inflammatory response	nucleus					0						CCCGCAGGACGGTGGGGACTG	0.537													3	49	---	---	---	---	PASS
ZNF567	163081	broad.mit.edu	37	19	37210381	37210381	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37210381A>G	uc010xtl.1	+	6	977	c.755A>G	c.(754-756)AAA>AGA	p.K252R	ZNF567_uc002oeo.1_Missense_Mutation_p.K252R|ZNF567_uc010xtk.1_Missense_Mutation_p.K252R|ZNF567_uc002oep.3_Missense_Mutation_p.K221R|ZNF567_uc002oeq.1_Missense_Mutation_p.K221R	NM_152603	NP_689816	Q8N184	ZN567_HUMAN	zinc finger protein 567	252					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATTGAAAAAAAACATACATGC	0.353													5	93	---	---	---	---	PASS
CYP2A7	1549	broad.mit.edu	37	19	41448080	41448080	+	Intron	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41448080C>T	uc002opo.2	-						CYP2B7P1_uc002opq.2_RNA	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GCTACGGCTTCCTGCTCATGC	0.567													26	43	---	---	---	---	PASS
FOSB	2354	broad.mit.edu	37	19	45974531	45974531	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45974531G>A	uc002pbx.3	+	3	1119	c.527G>A	c.(526-528)CGG>CAG	p.R176Q	ERCC1_uc002pbu.1_Intron|FOSB_uc002pbw.2_3'UTR|FOSB_uc010eke.2_Intron|FOSB_uc002pby.3_Intron|FOSB_uc010eka.1_Missense_Mutation_p.R137Q|FOSB_uc010ekb.1_Missense_Mutation_p.R176Q|FOSB_uc010ekc.1_Intron|FOSB_uc010ekf.2_Missense_Mutation_p.R137Q|FOSB_uc010ekd.1_Intron|FOSB_uc010ekg.2_Intron|FOSB_uc002pca.3_Missense_Mutation_p.R127Q	NM_006732	NP_006723	P53539	FOSB_HUMAN	FBJ murine osteosarcoma viral oncogene homolog B	176	Basic motif.				behavior|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(2)|lung(1)	3		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00814)|Epithelial(262;0.18)|GBM - Glioblastoma multiforme(486;0.242)		AGGAACCGGCGGAGGGAGCTG	0.622													5	35	---	---	---	---	PASS
KIR3DL1	3811	broad.mit.edu	37	19	55377281	55377281	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55377281T>C	uc002qhl.3	+	7	1085	c.1022T>C	c.(1021-1023)GTT>GCT	p.V341A	KIR3DL2_uc010esh.2_Missense_Mutation_p.V324A|KIR3DL2_uc002qho.3_Missense_Mutation_p.V341A			P43629	KI3L1_HUMAN	SubName: Full=KIR3DS1;	341	Helical; (Potential).				immune response|regulation of immune response	integral to plasma membrane	HLA-B specific inhibitory MHC class I receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|skin(1)	5				GBM - Glioblastoma multiforme(193;0.0192)		CACCTGCATGTTCTGATTGGG	0.358													9	774	---	---	---	---	PASS
TNNT1	7138	broad.mit.edu	37	19	55645562	55645562	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55645562C>G	uc002qjb.3	-	12	711	c.622G>C	c.(622-624)GCC>CCC	p.A208P	TNNT1_uc002qiz.3_Intron|TNNT1_uc002qja.3_Intron|TNNT1_uc002qjc.3_Intron|TNNT1_uc002qje.3_Intron|TNNT1_uc002qjd.3_Intron	NM_003283	NP_003274	P13805	TNNT1_HUMAN	troponin T1, skeletal, slow isoform a	208					muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		GGCAGCCAGGCAGACCGGGCC	0.448													10	14	---	---	---	---	PASS
WFDC3	140686	broad.mit.edu	37	20	44402939	44402939	+	3'UTR	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44402939A>G	uc002xpf.1	-	7					WFDC3_uc002xpj.1_RNA|WFDC3_uc002xph.1_RNA|WFDC3_uc010ghh.1_RNA	NM_080614	NP_542181	Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3 precursor							extracellular region	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)				CAGCGGCAGGAGGAGAAGCAG	0.547													7	23	---	---	---	---	PASS
SFRS15	57466	broad.mit.edu	37	21	33066563	33066563	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33066563G>A	uc002ypd.2	-	11	1702	c.1276C>T	c.(1276-1278)CGA>TGA	p.R426*	SFRS15_uc002ype.2_Nonsense_Mutation_p.R426*|SFRS15_uc010glu.2_Nonsense_Mutation_p.R411*|SFRS15_uc002ypf.1_Nonsense_Mutation_p.R100*	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	426						nucleus	nucleotide binding|RNA binding				0						GACATATGTCGCTTAACCTCT	0.318													5	470	---	---	---	---	PASS
SLC5A4	6527	broad.mit.edu	37	22	32633231	32633231	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32633231C>G	uc003ami.2	-	7	666	c.664G>C	c.(664-666)GCA>CCA	p.A222P		NM_014227	NP_055042	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (low affinity glucose	222	Helical; (Potential).				carbohydrate transport|sodium ion transport	integral to membrane	symporter activity				0						CATCACTTACCAAACCCCATG	0.502													41	69	---	---	---	---	PASS
BRD1	23774	broad.mit.edu	37	22	50187904	50187904	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50187904C>T	uc003biv.2	-	6	2624	c.2137G>A	c.(2137-2139)GGC>AGC	p.G713S	BRD1_uc011arf.1_Missense_Mutation_p.G308S|BRD1_uc011arg.1_Missense_Mutation_p.G762S|BRD1_uc011arh.1_Missense_Mutation_p.G713S|BRD1_uc003biu.3_Missense_Mutation_p.G713S	NM_014577	NP_055392	O95696	BRD1_HUMAN	bromodomain containing protein 1	713					histone H3 acetylation	MOZ/MORF histone acetyltransferase complex	zinc ion binding			pancreas(1)	1		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TCCTCCAGGCCCAGGTGGGCT	0.597													9	19	---	---	---	---	PASS
FAM9C	171484	broad.mit.edu	37	X	13058025	13058025	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13058025C>G	uc004cvh.1	-	6	550	c.340G>C	c.(340-342)GAT>CAT	p.D114H	FAM9C_uc004cvg.2_Missense_Mutation_p.D114H	NM_174901	NP_777561	Q8IZT9	FAM9C_HUMAN	family with sequence similarity 9, member C	114						nucleus					0						ATTCTATAATCACGTTTCTGC	0.363													7	369	---	---	---	---	PASS
UXT	8409	broad.mit.edu	37	X	47516998	47516998	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47516998C>T	uc004din.2	-	4	277	c.221G>A	c.(220-222)GGC>GAC	p.G74D	UXT_uc004dim.2_Missense_Mutation_p.G86D|LOC100133957_uc011mls.1_5'Flank|LOC100133957_uc011mlt.1_5'Flank	NM_004182	NP_004173	Q9UBK9	UXT_HUMAN	ubiquitously-expressed transcript isoform 2	74					centrosome organization|mitochondrion transport along microtubule|protein folding	centrosome|nucleus|prefoldin complex	beta-tubulin binding|microtubule binding|unfolded protein binding				0						GAAGTTACAGCCCAAATCCAC	0.473													4	110	---	---	---	---	PASS
TEX13A	56157	broad.mit.edu	37	X	104465016	104465016	+	Silent	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104465016G>A	uc004ema.2	-	2	178	c.66C>T	c.(64-66)AAC>AAT	p.N22N	IL1RAPL2_uc004elz.1_Intron|TEX13A_uc004emb.2_Silent_p.N22N	NM_031274	NP_112564	Q9BXU3	TX13A_HUMAN	testis expressed sequence 13A	22						intracellular	zinc ion binding			ovary(2)	2						CCATTTTCTCGTTGATGAAGG	0.542													4	52	---	---	---	---	PASS
AGTR2	186	broad.mit.edu	37	X	115304083	115304083	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115304083G>A	uc004eqh.3	+	3	757	c.550G>A	c.(550-552)GTC>ATC	p.V184I		NM_000686	NP_000677	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	184	Extracellular (Potential).				behavior|blood vessel remodeling|brain development|G-protein signaling, coupled to cGMP nucleotide second messenger|intracellular protein kinase cascade|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of heart rate|negative regulation of nerve growth factor receptor signaling pathway|nitric oxide mediated signal transduction|positive regulation of apoptosis|positive regulation of nitric-oxide synthase activity|positive regulation of phosphoprotein phosphatase activity|positive regulation of vasodilation|regulation of systemic arterial blood pressure by circulatory renin-angiotensin		angiotensin type II receptor activity|receptor antagonist activity			ovary(2)|lung(1)	3						TTTTCGAGACGTCAGAACCAT	0.408													7	190	---	---	---	---	PASS
RENBP	5973	broad.mit.edu	37	X	153205589	153205589	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153205589A>G	uc004fjo.1	-	9	1213	c.1043T>C	c.(1042-1044)CTC>CCC	p.L348P		NM_002910	NP_002901	P51606	RENBP_HUMAN	renin binding protein	348					mannose metabolic process|regulation of blood pressure		endopeptidase inhibitor activity|mannose-6-phosphate isomerase activity|N-acylglucosamine 2-epimerase activity			ovary(1)|pancreas(1)	2	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				N-Acetyl-D-glucosamine(DB00141)	TTGGTAGAAGAGGCGCAGCAG	0.607													22	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	6477	6477	+	5'UTR	SNP	G	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:6477G>A	uc011mfh.1	+	1					uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		TCCTAATCACAGCAGTCCTAC	0.493													63	3	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	1316788	1316788	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1316788delG								AURKAIP1 (5970 upstream) : CCNL2 (4303 downstream)																							ATGAGCCTGTGGGGCCCTGCA	0.627													4	2	---	---	---	---	
PRDM16	63976	broad.mit.edu	37	1	3254345	3254345	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3254345delT	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		CTGACCGGCATTTCCACCCCT	0.493			T	EVI1	MDS|AML								4	2	---	---	---	---	
CA6	765	broad.mit.edu	37	1	9023265	9023265	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9023265delC	uc001apm.2	+						CA6_uc009vmn.2_Intron	NM_001215	NP_001206	P23280	CAH6_HUMAN	carbonic anhydrase VI precursor						one-carbon metabolic process	extracellular region	carbonate dehydratase activity|zinc ion binding			ovary(2)	2	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)		ggccacacctcccagcctccc	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	12986614	12986614	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12986614delT								PRAMEF8 (6048 upstream) : PRAMEF5 (11688 downstream)																							CAGCACAGCCTTTTTTTGTTA	0.448													6	5	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15247376	15247376	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15247376delG	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						AGGGTCTCCTGGTGGAGAACT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17053517	17053521	+	IGR	DEL	AAAAG	-	-	rs67944636		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17053517_17053521delAAAAG								ESPNP (6865 upstream) : CROCC (13247 downstream)																							AAGATTAGAAAAAAGAAACATGAAT	0.327													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18768881	18768881	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18768881delC								IGSF21 (63905 upstream) : KLHDC7A (38543 downstream)																							TCTCTCTTCTCCCCATGCCTC	0.478													4	2	---	---	---	---	
IFFO2	126917	broad.mit.edu	37	1	19237627	19237628	+	Intron	INS	-	ATC	ATC	rs140597067	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19237627_19237628insATC	uc001bbd.2	-							NM_001136265	NP_001129737	Q5TF58	IFFO2_HUMAN	intermediate filament family orphan 2												0						GTTATTATGGGatcatctcagc	0.163													4	3	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21324220	21324221	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21324220_21324221insA	uc001bec.2	-						EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beg.2_Intron|EIF4G3_uc010odk.1_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		TATGCCAAAAGAAAAAAAACCC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	22598813	22598813	+	IGR	DEL	A	-	-	rs67655358		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22598813delA								WNT4 (128428 upstream) : ZBTB40 (179531 downstream)																							AAGAATCAGCAAaaaaaaaaa	0.179													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25188041	25188041	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25188041delG								CLIC4 (17226 upstream) : RUNX3 (37962 downstream)																							GCTATTGTTAGGGGGCGTCCC	0.478													4	2	---	---	---	---	
RUNX3	864	broad.mit.edu	37	1	25229102	25229102	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25229102delG	uc001bjq.2	-	5	1170	c.759delC	c.(757-759)CCCfs	p.P253fs	RUNX3_uc010oen.1_Frame_Shift_Del_p.P200fs|RUNX3_uc009vrj.2_Frame_Shift_Del_p.P267fs|RUNX3_uc001bjr.2_Frame_Shift_Del_p.P267fs|RUNX3_uc001bjs.2_RNA	NM_004350	NP_004341	Q13761	RUNX3_HUMAN	runt-related transcription factor 3 isoform 2	253	Pro/Ser/Thr-rich.			P -> S (in Ref. 2; CAA56093).	cell proliferation|induction of apoptosis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|protein phosphorylation|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		TTGGCAGCGTGGGGAAGGAGC	0.647													4	2	---	---	---	---	
CATSPER4	378807	broad.mit.edu	37	1	26524015	26524016	+	Intron	INS	-	TT	TT	rs10902719	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26524015_26524016insTT	uc010oez.1	+						CATSPER4_uc010oey.1_Intron|CATSPER4_uc009vsf.2_Intron	NM_198137	NP_937770	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|voltage-gated ion channel activity			ovary(1)	1		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		TGTTTTGTGGCTTGTTTGGGGG	0.550													4	3	---	---	---	---	
AIM1L	55057	broad.mit.edu	37	1	26665582	26665583	+	Intron	INS	-	CT	CT			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26665582_26665583insCT	uc001bmd.3	-						AIM1L_uc001bmf.3_5'Flank	NM_001039775	NP_001034864	Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like								sugar binding			pancreas(1)	1		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		tgacttccacactctgcctctc	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	27312187	27312187	+	IGR	DEL	T	-	-	rs3010105	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27312187delT								C1orf172 (25290 upstream) : TRNP1 (8008 downstream)																							GAAAAAAAAATACTGTGATAA	0.318													4	2	---	---	---	---	
CSMD2	114784	broad.mit.edu	37	1	34403043	34403043	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34403043delG	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				gtaaaagagtggggtggcagt	0.194													4	2	---	---	---	---	
CLSPN	63967	broad.mit.edu	37	1	36214086	36214086	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36214086delT	uc001bzi.2	-	13	2472	c.2392delA	c.(2392-2394)AGTfs	p.S798fs	CLSPN_uc009vux.2_Frame_Shift_Del_p.S734fs	NM_022111	NP_071394	Q9HAW4	CLSPN_HUMAN	claspin	798					activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GGGAAAAAACTGGTCCCACGG	0.483													178	98	---	---	---	---	
MACF1	23499	broad.mit.edu	37	1	39945876	39945876	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39945876delT	uc010oiu.1	+						MACF1_uc010ois.1_Intron|MACF1_uc001cde.1_Intron|MACF1_uc001cdf.1_Intron|MACF1_uc001cdg.2_Intron|MACF1_uc001cdh.2_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ATATATGGCCTTTAAGATGAC	0.338													4	2	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42276688	42276688	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42276688delT	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TAGGATGCCCTTTTCCAGCCC	0.318													4	2	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42344729	42344730	+	Intron	INS	-	A	A	rs141296010	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42344729_42344730insA	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron|HIVEP3_uc001chb.1_Intron	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				TGCAGGCACCTAAGCACTTCTG	0.515													4	2	---	---	---	---	
KIAA0467	23334	broad.mit.edu	37	1	43880873	43880873	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43880873delC	uc009vws.1	+	5	703	c.619delC	c.(619-621)CCCfs	p.P207fs				Q5T011	SZT2_HUMAN	Homo sapiens mRNA for KIAA0467 protein, partial cds.	207						peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GCAGTACGATCCCCAGAGCCA	0.547											OREG0013431	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
KDM4A	9682	broad.mit.edu	37	1	44116980	44116980	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44116980delT	uc001cjx.2	+						KDM4A_uc010oki.1_Intron	NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A						interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1						ATGTAAGCAGTATAGAGCAGT	0.328													4	2	---	---	---	---	
NASP	4678	broad.mit.edu	37	1	46083510	46083510	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46083510delA	uc001coi.1	+						NASP_uc001coh.1_Intron|NASP_uc001coj.1_Intron|NASP_uc010olr.1_Intron|NASP_uc001col.1_Intron	NM_002482	NP_002473	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein isoform 2						blastocyst development|cell cycle|cell proliferation|DNA replication|histone exchange|protein transport	cytoplasm|nucleus	Hsp90 protein binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					CTTGATGGGCAAAACCATTAG	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	47792624	47792624	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47792624delT								TAL1 (12805 upstream) : CMPK1 (6845 downstream)																							ttgttgttgattttttttttt	0.154													6	3	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49173986	49173986	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49173986delG	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		AAGGAGAGCTGGGGCTGGAAG	0.552													4	2	---	---	---	---	
OSBPL9	114883	broad.mit.edu	37	1	52121112	52121112	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52121112delG	uc001cst.2	+						OSBPL9_uc001css.2_Intron|OSBPL9_uc001csx.2_Intron|OSBPL9_uc009vza.2_Intron|OSBPL9_uc001csu.2_Intron|OSBPL9_uc001csv.2_Intron|OSBPL9_uc001csw.2_Intron	NM_024586	NP_078862	Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9 isoform e						lipid transport		lipid binding			central_nervous_system(1)	1						gaatccttctggtgctctgaa	0.000													4	2	---	---	---	---	
SCP2	6342	broad.mit.edu	37	1	53419986	53419986	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53419986delA	uc001cur.1	+						SCP2_uc001cus.1_Intron|SCP2_uc010ono.1_Intron|SCP2_uc010onp.1_Intron|SCP2_uc009vzi.1_Intron|SCP2_uc001cuq.1_Intron	NM_002979	NP_002970	P22307	NLTP_HUMAN	sterol carrier protein 2 isoform 1 proprotein						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|lipid transport	mitochondrion|nucleus|peroxisomal matrix	propanoyl-CoA C-acyltransferase activity|propionyl-CoA C2-trimethyltridecanoyltransferase activity|protein binding|sterol binding			breast(1)	1						actttgtgtcaaaaaaaaaaa	0.075													4	2	---	---	---	---	
GLIS1	148979	broad.mit.edu	37	1	54004924	54004925	+	Intron	INS	-	AG	AG	rs150258290	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54004924_54004925insAG	uc001cvr.1	-							NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN	GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1						gattcacacacacacacacacc	0.193													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58760378	58760378	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58760378delG	uc001cyt.1	-							NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						agcacagagtggggaagcctt	0.000													4	2	---	---	---	---	
MYSM1	114803	broad.mit.edu	37	1	59154367	59154367	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59154367delC	uc009wab.1	-						MYSM1_uc001czc.2_Intron|MYSM1_uc001czd.2_3'UTR	NM_001085487	NP_001078956	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1						histone deubiquitination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin remodeling complex	DNA binding|histone binding|metal ion binding|metallopeptidase activity|transcription coactivator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(1)	1	all_cancers(7;9.36e-06)					TATTTTATTTCAAAAAAAAAA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59466321	59466321	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59466321delA								JUN (216536 upstream) : LOC729467 (131289 downstream)																							TTCAGATCTCAAAAAAAAgaa	0.199													4	3	---	---	---	---	
INADL	10207	broad.mit.edu	37	1	62390847	62390847	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62390847delG	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron|INADL_uc001dac.2_Intron	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						actccagcctgggtgacagag	0.020													4	2	---	---	---	---	
SGIP1	84251	broad.mit.edu	37	1	67108780	67108781	+	Intron	INS	-	CAACTGTGGAAATGGTGGGTACTGAGCTGTC	CAACTGTGGAAATGGTGGGTACTGAGCTGTC	rs144607167	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67108780_67108781insCAACTGTGGAAATGGTGGGTACTGAGCTGTC	uc001dcr.2	+							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						TGCTAAAAAAACGCTAATCCCT	0.411													4	2	---	---	---	---	
LRRC7	57554	broad.mit.edu	37	1	70581741	70581741	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70581741delA	uc001dep.2	+						LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.2_Intron	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						TATGTTTGATAAAAAGAAAAC	0.279													4	2	---	---	---	---	
USP33	23032	broad.mit.edu	37	1	78188044	78188044	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78188044delA	uc001dht.2	-						USP33_uc001dhs.2_Intron|USP33_uc001dhu.2_Intron|USP33_uc001dhv.2_Intron|USP33_uc001dhw.2_Intron	NM_015017	NP_055832	Q8TEY7	UBP33_HUMAN	ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3						TCATAATAGcaaaaaaaaaaa	0.279													5	5	---	---	---	---	
LPHN2	23266	broad.mit.edu	37	1	82051550	82051551	+	Intron	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82051550_82051551delAC	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)		AATGcacacaacacacacacac	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	83683600	83683604	+	IGR	DEL	TTAAG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83683600_83683604delTTAAG								None (None upstream) : TTLL7 (651455 downstream)																							TACTGTATATTTAAGTTGTTATTAC	0.312													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	84216927	84216928	+	Intron	DEL	TC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84216927_84216928delTC	uc001diz.3	-											Homo sapiens cDNA clone IMAGE:4815396.																		GGCTGACTGGTCTAGGCTTTGA	0.475													4	2	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	85904164	85904164	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85904164delT	uc001dlb.2	-						DDAH1_uc001dlc.2_Intron|DDAH1_uc009wco.2_Intron	NM_012137	NP_036269	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	GTTCTTCCACTTTTTGGAAGA	0.224													4	2	---	---	---	---	
TGFBR3	7049	broad.mit.edu	37	1	92165900	92165901	+	Intron	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92165900_92165901delTG	uc001doh.2	-						TGFBR3_uc009wde.2_Intron|TGFBR3_uc010osy.1_Intron|TGFBR3_uc001doi.2_Intron|TGFBR3_uc001doj.2_Intron	NM_003243	NP_003234	Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III						BMP signaling pathway|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cell growth|cell migration|definitive erythrocyte differentiation|heart trabecula formation|immune response|intracellular protein kinase cascade|liver development|negative regulation of cellular component movement|negative regulation of epithelial cell proliferation|palate development|pathway-restricted SMAD protein phosphorylation|response to follicle-stimulating hormone stimulus|response to luteinizing hormone stimulus|response to prostaglandin E stimulus|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis	external side of plasma membrane|extracellular space|inhibin-betaglycan-ActRII complex|integral to plasma membrane|intracellular membrane-bounded organelle	coreceptor activity|heparin binding|PDZ domain binding|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type III|type II transforming growth factor beta receptor binding			ovary(3)	3		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		CTTGGGAAAATGTGACCCAAAC	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98936934	98936935	+	IGR	DEL	CT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98936934_98936935delCT								MIR137 (425207 upstream) : SNX7 (190301 downstream)																							AAGAGACAGACTCtctctctct	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	102249529	102249529	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102249529delA								S1PR1 (542453 upstream) : OLFM3 (18598 downstream)																							AAATGGAAGCAACAGAAAATG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	104061698	104061698	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104061698delA								COL11A1 (487646 upstream) : RNPC3 (6880 downstream)																							TGCATACATTAAAAAAAATGT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116474721	116474721	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116474721delT								NHLH2 (90974 upstream) : SLC22A15 (44398 downstream)																							CTTCTTCAGATTTTGATGGGA	0.214													4	2	---	---	---	---	
MAN1A2	10905	broad.mit.edu	37	1	118061986	118061986	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118061986delA	uc001ehd.1	+							NM_006699	NP_006690	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity				0	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		aaattgaaacaaaaaaaatac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	118175426	118175429	+	IGR	DEL	CTCT	-	-	rs34292119		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118175426_118175429delCTCT								FAM46C (4416 upstream) : GDAP2 (230679 downstream)																							GAGGTGCTCCCTCTCTCTCTCTAG	0.490													4	2	---	---	---	---	
WARS2	10352	broad.mit.edu	37	1	119637504	119637505	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119637504_119637505insA	uc001ehn.2	-						WARS2_uc010oxf.1_Intron|WARS2_uc001ehm.2_Intron|WARS2_uc010oxg.1_Intron|WARS2_uc010oxh.1_Intron|WARS2_uc010oxi.1_Intron	NM_015836	NP_056651	Q9UGM6	SYWM_HUMAN	mitochondrial tryptophanyl tRNA synthetase 2						tryptophanyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|tryptophan-tRNA ligase activity				0	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	ATAACTTTAGGAAAAAAAAAGA	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143536419	143536420	+	IGR	INS	-	TT	TT	rs75386219	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143536419_143536420insTT								None (None upstream) : LOC100286793 (111219 downstream)																							GTGAATATAACTGTCATTTACA	0.257													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144028377	144028377	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144028377delA	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		AGAGAGAATGAAAAAAAAAGT	0.368													3	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145012913	145012914	+	Intron	INS	-	T	T	rs67707497		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145012913_145012914insT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron|uc001emj.2_5'Flank	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		ATCAAAGAGCCTTTTTTCTCTA	0.317			T	PDGFRB	MPD								5	4	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145029489	145029489	+	Intron	DEL	T	-	-	rs11291304		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145029489delT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AAACAGGTGATTTTTTTCCCC	0.289			T	PDGFRB	MPD								2	4	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145207564	145207564	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145207564delT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_5'Flank|NOTCH2NL_uc001emn.3_5'Flank|NOTCH2NL_uc001emm.3_5'Flank|NOTCH2NL_uc001emo.2_5'Flank|NOTCH2NL_uc010oyh.1_5'Flank			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						CACACCTCCATTTTTTTTTTC	0.373													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148920241	148920241	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148920241delC								NBPF16 (161930 upstream) : LOC645166 (8045 downstream)																							TTGTCCCTCTCCCCACCTCCA	0.219													4	2	---	---	---	---	
OTUD7B	56957	broad.mit.edu	37	1	149981891	149981892	+	Intron	DEL	CA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149981891_149981892delCA	uc001etn.2	-							NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne						negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CTCCCTCTCTcacacacacaca	0.356													4	2	---	---	---	---	
OTUD7B	56957	broad.mit.edu	37	1	149981906	149981907	+	Intron	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149981906_149981907delAC	uc001etn.2	-							NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne						negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			acacacacaaacacacacacac	0.342													4	2	---	---	---	---	
POGZ	23126	broad.mit.edu	37	1	151389070	151389071	+	Intron	DEL	GT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151389070_151389071delGT	uc001eyd.1	-						POGZ_uc001eye.1_Intron|POGZ_uc010pdb.1_Intron|POGZ_uc001eyf.1_Intron|POGZ_uc010pdc.1_Intron|POGZ_uc009wmv.1_Intron|POGZ_uc010pdd.1_Intron	NM_015100	NP_055915	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain						cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			TCTTAAACAAGTGTGAATAAAA	0.213													4	2	---	---	---	---	
SMG5	23381	broad.mit.edu	37	1	156242370	156242370	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156242370delT	uc001foc.3	-							NM_015327	NP_056142	Q9UPR3	SMG5_HUMAN	SMG5 homolog nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|nucleus	protein phosphatase 2A binding			ovary(2)|skin(2)|pancreas(1)	5	Hepatocellular(266;0.158)					TGACCTCttcttttttttttt	0.234													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159942299	159942299	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159942299delC	uc001fuu.2	+											Homo sapiens full length insert cDNA clone ZE01A04.																		attatcctagcccccagggct	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	160046209	160046209	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160046209delC								KCNJ10 (6248 upstream) : KCNJ9 (5151 downstream)																							GCATGGCTCACCACAGGATTC	0.463													4	2	---	---	---	---	
MAEL	84944	broad.mit.edu	37	1	166955596	166955596	+	5'Flank	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166955596delA	uc001gdy.1	+						MAEL_uc001gdz.1_5'Flank	NM_032858	NP_116247	Q96JY0	MAEL_HUMAN	maelstrom homolog						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|multicellular organismal development|piRNA metabolic process|spermatogenesis	piP-body	DNA binding			skin(1)	1						atgttgttataaaaaaaAGCA	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	170137113	170137113	+	IGR	DEL	A	-	-	rs11360504		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170137113delA								METTL11B (190 upstream) : LOC284688 (103434 downstream)																							GGATTTTCTGAAAAAAAAATG	0.338													3	6	---	---	---	---	
C1orf129	80133	broad.mit.edu	37	1	170983602	170983602	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170983602delT	uc010plz.1	+							NM_001163629	NP_001157101	Q5TGP6	CA129_HUMAN	hypothetical protein LOC80133 isoform 1								binding			pancreas(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					ATCGCCTTACTTTTTTTTTTT	0.303													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	173303019	173303019	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173303019delC	uc001gix.1	-											Homo sapiens cDNA FLJ45305 fis, clone BRHIP3004193.																		catcagctctcctggttttct	0.000													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175526396	175526396	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175526396delC	uc009wwu.1	-						TNR_uc010pmz.1_Intron|uc001gkr.1_RNA|uc001gks.2_RNA	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					agccagaggacccaacaaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	182262554	182262555	+	IGR	INS	-	CAGCCCT	CAGCCCT	rs148867357	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182262554_182262555insCAGCCCT								ZNF648 (231707 upstream) : GLUL (89114 downstream)																							CCAGCCCATCCCAGTGACCTCA	0.510													3	3	---	---	---	---	
EDEM3	80267	broad.mit.edu	37	1	184723562	184723563	+	Intron	DEL	AG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184723562_184723563delAG	uc010pok.1	-						EDEM3_uc010pol.1_Intron|EDEM3_uc010pom.1_Intron|EDEM3_uc001gqy.2_Intron	NM_025191	NP_079467	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			skin(1)	1						TCGCAATGACAGGCACCCCTCC	0.649													17	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	185574358	185574358	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185574358delA	uc001gro.2	-											Homo sapiens clone IMAGp998C217408Q2 mRNA sequence.																		ACATTCAACCAAAAAAAGGAa	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192484865	192484865	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192484865delT								RGS21 (148453 upstream) : RGS1 (59992 downstream)																							TTCTCCTTCCTTTTTCCCTAT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199406179	199406179	+	IGR	DEL	G	-	-	rs11306368		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199406179delG								MIR181A1 (577897 upstream) : NR5A2 (590591 downstream)																							GGCCATCACTGGGGTGAAGCC	0.463													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199481379	199481379	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199481379delG								MIR181A1 (653097 upstream) : NR5A2 (515391 downstream)																							TGGGCTGGATGGGCAGTTGCT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199661061	199661062	+	IGR	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199661061_199661062delAC								MIR181A1 (832779 upstream) : NR5A2 (335708 downstream)																							TCCCCCGCCAACACACACACTA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	201316083	201316084	+	IGR	INS	-	C	C	rs141491844	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201316083_201316084insC								PKP1 (13968 upstream) : TNNT2 (12059 downstream)																							TACCAGCCCTGCCCCCCCCAGA	0.505											OREG0014075	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	201317519	201317520	+	IGR	INS	-	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201317519_201317520insG								PKP1 (15404 upstream) : TNNT2 (10623 downstream)																							GGGCGGGAGGTGGGGGTGTCAT	0.584											OREG0014075	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
PPP1R12B	4660	broad.mit.edu	37	1	202380166	202380166	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202380166delG	uc001gya.1	+						PPP1R12B_uc001gxy.2_Intron|PPP1R12B_uc009xad.1_Intron|PPP1R12B_uc009xae.1_Intron|PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			GCTCTGTGTAGAGGTATGGTG	0.428													4	2	---	---	---	---	
C1orf186	440712	broad.mit.edu	37	1	206241189	206241190	+	Intron	INS	-	G	G	rs138368139	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206241189_206241190insG	uc001hdt.1	-							NM_001007544	NP_001007545	Q6ZWK4	CA186_HUMAN	hypothetical protein LOC440712							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.0754)			AGGCAGAGGCAGGTGAAATTTT	0.505													4	2	---	---	---	---	
SRGAP2	23380	broad.mit.edu	37	1	206597619	206597619	+	Intron	DEL	T	-	-	rs11119945	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206597619delT	uc001hdy.2	+						SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron|SRGAP2_uc010prv.1_Intron	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)					TACCAAAAAATAAAAAAGTGT	0.249													3	3	---	---	---	---	
TRAF5	7188	broad.mit.edu	37	1	211538512	211538512	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211538512delA	uc001hih.2	+						TRAF5_uc001hii.2_Intron|TRAF5_uc010psx.1_Intron|TRAF5_uc010psy.1_Intron|TRAF5_uc001hij.2_Intron	NM_004619	NP_004610	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis	CD40 receptor complex|centrosome|internal side of plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(2)|ovary(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		aggctgtctcaaaaaaaaaac	0.174													6	4	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	217038068	217038069	+	Intron	INS	-	TT	TT	rs141584307	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217038068_217038069insTT	uc001hky.1	-						ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain 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)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CGTGGAGTAACAGACCAACTTA	0.495													6	3	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	217221283	217221285	+	Intron	DEL	GAA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217221283_217221285delGAA	uc010puc.1	-						ESRRG_uc001hkz.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain 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)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CGGTATCGGGGAAGAAGAAGAAG	0.443													4	2	---	---	---	---	
SLC30A10	55532	broad.mit.edu	37	1	220057507	220057507	+	RNA	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220057507delC	uc001hlu.1	-	4		c.536delG						Q6XR72	ZNT10_HUMAN	Synthetic construct DNA, clone: pF1KB7405, Homo sapiens SLC30A10 gene for solute carrier family 30, member 10, without stop codon, in Flexi system.						zinc ion transport	integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)		gttggctcctcccccagctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	235028594	235028594	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235028594delC								IRF2BP2 (283323 upstream) : TOMM20 (244066 downstream)																							GAAGGGACATCCCATGGCCCA	0.537													4	2	---	---	---	---	
ARID4B	51742	broad.mit.edu	37	1	235332554	235332555	+	Intron	DEL	TG	-	-	rs6681842	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235332554_235332555delTG	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hwp.2_Intron	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			cgtttttttttgtttgtttgtt	0.163													4	2	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245861178	245861178	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245861178delA	uc001ibf.1	+							NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			gtcgtctctcaaaaaaaaaca	0.000													4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246445203	246445203	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246445203delC	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		AAAAAGGACTCCTAAATCAGA	0.373													4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246528926	246528927	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246528926_246528927insA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		ACTCTCCCCATAAAAAAAAAGT	0.371													4	2	---	---	---	---	
MYT1L	23040	broad.mit.edu	37	2	2171772	2171773	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2171772_2171773insA	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc002qxf.1_Intron	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		Cattttattttaaaaaaaaata	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6015982	6015982	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6015982delA								SOX11 (174466 upstream) : LOC150622 (56837 downstream)																							gcattatcataaaaaaactaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19571081	19571081	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19571081delC								OSR1 (12709 upstream) : TTC32 (525437 downstream)																							accttatcctcccatctgctg	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	25585580	25585580	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25585580delG								DNMT3A (20121 upstream) : DTNB (14534 downstream)																							TCAAGAGTGAGGAAAAAAAGA	0.527													4	2	---	---	---	---	
CENPA	1058	broad.mit.edu	37	2	27012696	27012697	+	Intron	INS	-	AA	AA	rs147063119	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27012696_27012697insAA	uc002rhr.2	+						CENPA_uc002rht.2_Intron|CENPA_uc002rhs.2_Intron	NM_001809	NP_001800	P49450	CENPA_HUMAN	centromere protein A isoform a						CenH3-containing nucleosome assembly at centromere|establishment of mitotic spindle orientation|interspecies interaction between organisms|kinetochore assembly|mitotic prometaphase|protein localization to chromosome, centromeric region	condensed nuclear chromosome kinetochore|cytosol|nucleoplasm|nucleosome	chromatin binding|DNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					cagcagctctcgagcaactgtg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	27760904	27760904	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27760904delA								GCKR (14356 upstream) : C2orf16 (38485 downstream)																							AAGATGTGGGAAAGGGAAGCG	0.423													4	2	---	---	---	---	
PPP1CB	5500	broad.mit.edu	37	2	28990226	28990227	+	Intron	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28990226_28990227insT	uc002rmg.2	+						PPP1CB_uc010ymj.1_Intron|PPP1CB_uc010ymk.1_Intron|PPP1CB_uc010yml.1_Intron|PPP1CB_uc002rmh.2_Intron	NM_206876	NP_996759	P62140	PP1B_HUMAN	protein phosphatase 1, catalytic subunit, beta						cell cycle|cell division|glycogen metabolic process|triglyceride catabolic process	MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|myosin phosphatase activity|myosin-light-chain-phosphatase activity|protein binding			skin(1)	1	Acute lymphoblastic leukemia(172;0.155)					atatgttgtggtttttttttta	0.000													4	4	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29550751	29550752	+	Intron	DEL	GA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29550751_29550752delGA	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GATGTGACTCGAGAAAGGAAAG	0.545			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	33967899	33967899	+	IGR	DEL	T	-	-	rs61707548		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33967899delT								MYADML (14615 upstream) : None (None downstream)																							tatttagagctcctttttttt	0.000													4	3	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46343888	46343888	+	Intron	DEL	A	-	-	rs67450130		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46343888delA	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)			CTGTTCGGAGAAAAAAAAAGC	0.473													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49172376	49172376	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49172376delG								LHCGR (189496 upstream) : FSHR (17277 downstream)																							TGACTGCCCTGGGAACTGATT	0.443													4	2	---	---	---	---	
NRXN1	9378	broad.mit.edu	37	2	51017600	51017600	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51017600delA	uc010fbq.2	-						NRXN1_uc002rxe.3_Intron	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			AATCAAAaccaaaaataaaag	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60195111	60195111	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60195111delG								None (None upstream) : BCL11A (483192 downstream)																							GGGAAATGTTGGTAAGGCTTT	0.423													4	2	---	---	---	---	
C2orf86	51057	broad.mit.edu	37	2	63476620	63476621	+	Intron	INS	-	T	T	rs148811544	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63476620_63476621insT	uc002sch.2	-						C2orf86_uc002sce.2_Intron|C2orf86_uc002scf.2_Intron|C2orf86_uc010ypu.1_Intron|C2orf86_uc002scg.2_Intron	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0						TAATAAAGATGTTTATCTAGCC	0.381													4	2	---	---	---	---	
ACTR2	10097	broad.mit.edu	37	2	65473289	65473289	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65473289delC	uc002sdq.2	+						ACTR2_uc010yqf.1_Intron|ACTR2_uc002sdp.2_Intron|ACTR2_uc010yqg.1_Intron	NM_005722	NP_005713	P61160	ARP2_HUMAN	actin-related protein 2 isoform b						cellular component movement	Arp2/3 protein complex|cell projection|cytoplasm	actin binding|ATP binding				0						AAGTTTTTTTCCCCCTGATGT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67010412	67010412	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67010412delT								MEIS1 (210522 upstream) : ETAA1 (614030 downstream)																							CAATAGGAGATTTTTTTTGTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	68123990	68123990	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68123990delT								ETAA1 (486457 upstream) : C1D (145343 downstream)																							gccacagcccttgaaaatcaa	0.204													4	2	---	---	---	---	
AAK1	22848	broad.mit.edu	37	2	69817315	69817315	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69817315delT	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron|AAK1_uc010fdm.1_Intron	NM_014911	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0						CTCTACAGTCTCCACAAACTA	0.458													4	2	---	---	---	---	
TGFA	7039	broad.mit.edu	37	2	70720449	70720449	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70720449delG	uc002sgs.3	-						TGFA_uc010fdq.2_Intron|TGFA_uc010fdr.2_Intron|TGFA_uc002sgt.3_Intron|TGFA_uc002sgu.2_Intron|TGFA_uc002sgv.2_Intron|TGFA_uc002sgw.2_Intron	NM_003236	NP_003227	P01135	TGFA_HUMAN	transforming growth factor, alpha isoform 1						activation of MAPK activity|cell proliferation|positive regulation of cell division|positive regulation of epidermal growth factor receptor activity|positive regulation of epithelial cell proliferation|positive regulation of mitosis	cell surface|extracellular space|integral to membrane|plasma membrane	epidermal growth factor receptor binding|growth factor activity|MAP kinase kinase activity|signal transducer activity			prostate(1)	1						GGGGGAACCTGGGCTGTTCCA	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	71939877	71939878	+	IGR	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71939877_71939878delAC								DYSF (25985 upstream) : CYP26B1 (416489 downstream)																							TAAAacacatacacacacaccc	0.248													4	2	---	---	---	---	
SEMA4F	10505	broad.mit.edu	37	2	74889572	74889572	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74889572delG	uc002sna.1	+						SEMA4F_uc010ysb.1_Intron|SEMA4F_uc010ffq.1_Intron|SEMA4F_uc010ffr.1_Intron|SEMA4F_uc002snb.1_Intron|SEMA4F_uc002snc.1_Intron	NM_004263	NP_004254	O95754	SEM4F_HUMAN	semaphorin W precursor						cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)|skin(1)	4						GGTGCTTCTTGGGCTGTCCTA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	77761297	77761297	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77761297delG								LRRTM4 (11795 upstream) : SNAR-H (420736 downstream)																							TCCAATTAGAGGGGAGGCAAA	0.403													4	2	---	---	---	---	
IMMT	10989	broad.mit.edu	37	2	86385440	86385440	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86385440delT	uc002sqz.3	-						IMMT_uc002sqy.3_Intron|IMMT_uc002srb.3_Intron|IMMT_uc002sra.3_Intron|IMMT_uc010ytd.1_Intron|IMMT_uc010yte.1_Intron|IMMT_uc002src.1_Intron	NM_006839	NP_006830	Q16891	IMMT_HUMAN	inner membrane protein, mitochondrial isoform 1							integral to mitochondrial inner membrane	protein binding			skin(1)	1						AATTCCAAACTTTTTTTTTTT	0.294													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89109794	89109794	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89109794delA								FLJ40330 (3669 upstream) : None (None downstream)																							ATCAGGTTGCAAAAAAAAAGT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	95636225	95636225	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95636225delG								TEKT4 (93657 upstream) : MAL (55254 downstream)																							CCTAAATGGTGGTCAAAGGCT	0.498													4	2	---	---	---	---	
ACTR1B	10120	broad.mit.edu	37	2	98281700	98281700	+	5'Flank	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98281700delC	uc002syb.2	-							NM_005735	NP_005726	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B,							centrosome|dynactin complex	ATP binding|protein binding			skin(1)	1						ATATACCTCTCCCAATGGGtt	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	104623500	104623500	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104623500delT								None (None upstream) : LOC150568 (427305 downstream)																							tttcttttacttttttttctt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107372817	107372817	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107372817delT								RGPD3 (288016 upstream) : ST6GAL2 (45241 downstream)																							CACCTGGCCATTTACAGGATG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107935357	107935357	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107935357delT								ST6GAL2 (431794 upstream) : LOC729121 (504163 downstream)																							TAGAAGAACATTACGGTCGTT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	112404302	112404302	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112404302delA								LOC541471 (151610 upstream) : ANAPC1 (122339 downstream)																							ttttcaaaacaaaaaaaaagg	0.000													3	3	---	---	---	---	
FBLN7	129804	broad.mit.edu	37	2	112907960	112907960	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112907960delA	uc002tho.1	+						FBLN7_uc002thn.2_Intron|FBLN7_uc010fki.1_Intron|FBLN7_uc010fkj.1_Intron	NM_153214	NP_694946	Q53RD9	FBLN7_HUMAN	fibulin 7 isoform 1						cell adhesion	proteinaceous extracellular matrix	calcium ion binding|heparin binding			ovary(1)|central_nervous_system(1)	2						GTACCAGAAGAAAAAAAAAAT	0.478													4	2	---	---	---	---	
ACTR3	10096	broad.mit.edu	37	2	114688657	114688657	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114688657delT	uc002tkx.1	+						ACTR3_uc010yyc.1_Intron|ACTR3_uc010yyd.1_Intron	NM_005721	NP_005712	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog						cellular component movement|cilium morphogenesis	Arp2/3 protein complex	actin binding|ATP binding			skin(1)	1						ATTCAGGGTATTTTTTTTTTA	0.303													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122089613	122089613	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122089613delC								TFCP2L1 (46835 upstream) : CLASP1 (5741 downstream)																							GAGACCACATCCTAGTTGGGG	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	124124577	124124577	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124124577delC								None (None upstream) : CNTNAP5 (658287 downstream)																							CCTACCGTTTCCCATTACCAC	0.378													4	2	---	---	---	---	
WDR33	55339	broad.mit.edu	37	2	128471022	128471022	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128471022delA	uc002tpg.1	-							NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1						postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		GTCCAAATGCAAACTCTACAG	0.323													4	2	---	---	---	---	
SAP130	79595	broad.mit.edu	37	2	128716845	128716845	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128716845delA	uc002tpp.2	-						SAP130_uc002tpn.2_Intron|SAP130_uc002tpo.2_Intron|SAP130_uc010fmd.2_Intron|SAP130_uc002tpq.1_Intron	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		gagcagagacaaaaaaaagtc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129981924	129981925	+	IGR	INS	-	A	A	rs145443128	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129981924_129981925insA								HS6ST1 (905753 upstream) : LOC389033 (698510 downstream)																							AAGACGGATGTAAAAAAAAAGG	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131375380	131375381	+	IGR	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131375380_131375381delTG								LOC150527 (67909 upstream) : C2orf14 (62242 downstream)																							ATGAAGAGGTTGTGTGTGTGTG	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132896717	132896717	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132896717delT								C2orf27B (337483 upstream) : NCRNA00164 (8447 downstream)																							TTTGTAGCTGTTTTTTTTATA	0.358													3	5	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	133677711	133677712	+	Intron	INS	-	T	T	rs147058918	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133677711_133677712insT	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|uc002ttr.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						CCTTTTCATGATTTTTTTTCTT	0.396													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134569436	134569437	+	IGR	INS	-	G	G	rs145428635	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134569436_134569437insG								NCKAP5 (243405 upstream) : MGAT5 (442393 downstream)																							tagggaagtaaaatgggaagga	0.000													3	3	---	---	---	---	
MGAT5	4249	broad.mit.edu	37	2	135079832	135079832	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135079832delT	uc002ttv.1	+							NM_002410	NP_002401	Q09328	MGT5A_HUMAN	N-acetylglucosaminyltransferase V						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0964)		CATTGTTCCATTTTAGAATTA	0.348													4	2	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	137872510	137872510	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137872510delT	uc002tva.1	+						THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		CTGCTGGATGTTTTTTTTTTC	0.393													9	4	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142138001	142138001	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142138001delC	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		gataaaatctccccagctcac	0.000										TSP Lung(27;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	145741899	145741900	+	Intron	DEL	CA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145741899_145741900delCA	uc002twc.2	+											Homo sapiens hypothetical gene supported by BC043549; BX648102, mRNA (cDNA clone IMAGE:5172341).																		ttttcttcttcatttctctcta	0.000													4	2	---	---	---	---	
MBD5	55777	broad.mit.edu	37	2	148905350	148905351	+	Intron	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148905350_148905351delTG	uc002twm.3	+							NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)		gtgaagggcctgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	150336177	150336177	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150336177delT								LYPD6 (6040 upstream) : MMADHC (89973 downstream)																							atcctgtcaattttttctctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	154002148	154002148	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154002148delT								ARL6IP6 (384381 upstream) : RPRM (331704 downstream)																							CAGAGATGGATTAGGTCCAAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	158550621	158550621	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158550621delA								ACVR1C (65222 upstream) : ACVR1 (42337 downstream)																							AACACATTTTAAAAAATAATG	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162135166	162135166	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162135166delG								TANK (42484 upstream) : PSMD14 (29620 downstream)																							tcctcattctgtctcaaaccc	0.040													9	4	---	---	---	---	
LRP2	4036	broad.mit.edu	37	2	170117551	170117551	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170117551delG	uc002ues.2	-						LRP2_uc010zdf.1_Intron	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	tcagccacctggtgggcagat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173399860	173399860	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173399860delT								ITGA6 (28679 upstream) : PDK1 (20241 downstream)																							acttaatctgttttttttttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174678098	174678098	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174678098delA								CDCA7 (444380 upstream) : SP3 (95161 downstream)																							GGAAAAGGGGAAAAAAAGGAA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	176171631	176171631	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176171631delA								ATP5G3 (125141 upstream) : KIAA1715 (618779 downstream)																							TCATTGATCTAGGAAACTCAT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	184846814	184846814	+	IGR	DEL	T	-	-	rs11311556		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184846814delT								NUP35 (820407 upstream) : ZNF804A (616279 downstream)																							CTCTTCTCCATCTCTGAAATG	0.413													1	5	---	---	---	---	
FAM171B	165215	broad.mit.edu	37	2	187577884	187577884	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187577884delG	uc002ups.2	+						FAM171B_uc002upr.1_Intron	NM_177454	NP_803237	Q6P995	F171B_HUMAN	KIAA1946							integral to membrane	DNA binding			ovary(6)|breast(3)|central_nervous_system(1)	10						AGCATGAAGTGAGAGGGTGGT	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	187841452	187841452	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187841452delG								ZSWIM2 (127555 upstream) : CALCRL (366399 downstream)																							TAATGTTCTTGTTCTGTGGCC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	204985885	204985885	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204985885delA								ICOS (159589 upstream) : PARD3B (424631 downstream)																							atcacctgtcaaaaacattta	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	206518328	206518328	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206518328delC								PARD3B (37791 upstream) : NRP2 (28896 downstream)																							GAGAGCCATACCCCAGATGGA	0.378													4	2	---	---	---	---	
NDUFS1	4719	broad.mit.edu	37	2	207009169	207009169	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207009169delA	uc002vbe.2	-						NDUFS1_uc010ziq.1_Intron|NDUFS1_uc010zir.1_Intron|NDUFS1_uc010zis.1_Intron|NDUFS1_uc010zit.1_Intron|NDUFS1_uc010ziu.1_Intron	NM_005006	NP_004997	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)	TCTGACAGCTAAAAAAGTCAA	0.234													4	2	---	---	---	---	
IDH1	3417	broad.mit.edu	37	2	209115979	209115979	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209115979delT	uc002vcs.2	-						IDH1_uc002vct.2_Intron|IDH1_uc002vcu.2_Intron	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble						2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity			central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TTTTttttcctttttttttta	0.119			Mis		gliobastoma 								5	4	---	---	---	---	
MAP2	4133	broad.mit.edu	37	2	210574397	210574397	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210574397delA	uc002vde.1	+						MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Intron	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	AACAAATCAGAAAAAAAAAAT	0.209													4	3	---	---	---	---	
UNC80	285175	broad.mit.edu	37	2	210787259	210787260	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210787259_210787260insA	uc010zjc.1	+						UNC80_uc002vdk.2_Intron	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1							integral to membrane					0						TGGCATCCTTTAAAAAAAAATT	0.287													4	2	---	---	---	---	
TNS1	7145	broad.mit.edu	37	2	218674305	218674307	+	Intron	DEL	TGC	-	-	rs148777884	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218674305_218674307delTGC	uc002vgt.2	-						TNS1_uc002vgr.2_Intron|TNS1_uc002vgs.2_Intron|TNS1_uc002vgq.2_Intron	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		gatggataggtgcatggatggat	0.020													4	3	---	---	---	---	
COL6A3	1293	broad.mit.edu	37	2	238305660	238305661	+	Intron	INS	-	GATAGATA	GATAGATA	rs150558878	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238305660_238305661insGATAGATA	uc002vwl.2	-						COL6A3_uc002vwo.2_Intron|COL6A3_uc010znj.1_Intron|COL6A3_uc002vwq.2_Intron|COL6A3_uc002vwr.2_Intron|COL6A3_uc010znk.1_Intron	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		gttagatagatgatagatagat	0.203													11	6	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10129212	10129212	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10129212delA	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_Intron|C3orf24_uc003buz.2_Intron	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CTTCCTTTTCAAAAAAAAAAA	0.308			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	3	---	---	---	---	
GRIP2	80852	broad.mit.edu	37	3	14535494	14535495	+	Intron	DEL	CT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14535494_14535495delCT	uc011avi.1	-						GRIP2_uc010heh.2_Intron|GRIP2_uc011avh.1_Intron	NM_001080423	NP_001073892	Q9C0E4	GRIP2_HUMAN	glutamate receptor interacting protein 2						synaptic transmission	cytosol|plasma membrane	protein binding			pancreas(1)	1						cttcctctaactctctctcagt	0.198													4	2	---	---	---	---	
STAC	6769	broad.mit.edu	37	3	36547497	36547515	+	Intron	DEL	AGAGTTTTTGATTCATCAG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36547497_36547515delAGAGTTTTTGATTCATCAG	uc003cgh.1	+						STAC_uc011aya.1_Intron	NM_003149	NP_003140	Q99469	STAC_HUMAN	SH3 and cysteine rich domain						intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			skin(2)|ovary(1)|pancreas(1)	4						ccctgtccccagagtttttgattcatcagatctgaggca	0.091													5	8	---	---	---	---	
SCN5A	6331	broad.mit.edu	37	3	38598922	38598923	+	Intron	INS	-	TGT	TGT			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38598922_38598923insTGT	uc003cio.2	-						SCN5A_uc003cin.2_Intron|SCN5A_uc003cil.3_Intron|SCN5A_uc010hhi.2_Intron|SCN5A_uc010hhk.2_Intron|SCN5A_uc011ayr.1_Intron|SCN5A_uc010hhj.1_Intron	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha						blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)	CAGCATCTAAATGCCTGGGTGG	0.535													4	2	---	---	---	---	
LARS2	23395	broad.mit.edu	37	3	45527821	45527821	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45527821delT	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155	Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	TGAAGGCATATTTAGAACTGT	0.418													4	2	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52677265	52677265	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52677265delG	uc003des.2	-	9	1006	c.994delC	c.(994-996)CGTfs	p.R332fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.R332fs|PBRM1_uc003der.2_Intron|PBRM1_uc003det.2_Frame_Shift_Del_p.R332fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.R332fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.R332fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.R332fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.R332fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.R332fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.R230fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	332					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTTTCTCACCGGTAATACTTG	0.443			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								123	209	---	---	---	---	
MAGI1	9223	broad.mit.edu	37	3	65376001	65376001	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65376001delA	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hnx.1_Intron	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		CCAAAAAGAGAAAATGAGGTA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	70751550	70751550	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70751550delA								MITF (734064 upstream) : FOXP1 (253187 downstream)																							TGATGCACTCAAAAACATCTT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	74628213	74628213	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74628213delA								CNTN3 (57870 upstream) : FAM86D (842492 downstream)																							aaagaggttgaaaaaatttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	106551779	106551780	+	IGR	INS	-	TTAA	TTAA			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106551779_106551780insTTAA								CBLB (963513 upstream) : LOC100302640 (3880 downstream)																							aattaaatagtttaatttttgg	0.000													4	2	---	---	---	---	
PVRL3	25945	broad.mit.edu	37	3	110901502	110901502	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110901502delT	uc003dxu.1	+							NM_015480	NP_056295	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3 precursor						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane	cell adhesion molecule binding|protein homodimerization activity			upper_aerodigestive_tract(2)	2						gttttcaaactttttttttta	0.000													4	2	---	---	---	---	
ZBTB20	26137	broad.mit.edu	37	3	114626063	114626064	+	Intron	INS	-	AG	AG	rs138373593	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114626063_114626064insAG	uc003ebm.2	-						ZBTB20_uc003ebn.2_Intron|ZBTB20_uc003ebp.2_Intron	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		CAGCAGAATGTAGTTAGGCTAA	0.356													1	5	---	---	---	---	
SEMA5B	54437	broad.mit.edu	37	3	122718642	122718642	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122718642delG	uc003efz.1	-						SEMA5B_uc011bju.1_Intron|SEMA5B_uc003ega.1_Intron|SEMA5B_uc010hro.1_Intron|SEMA5B_uc010hrp.1_Intron	NM_001031702	NP_001026872	Q9P283	SEM5B_HUMAN	semaphorin 5B isoform 1						cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)		TCTCTGGAGTGGGGCCTAAGA	0.443													3	4	---	---	---	---	
ATP2C1	27032	broad.mit.edu	37	3	130716086	130716086	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130716086delC	uc003enl.2	+						ATP2C1_uc011blg.1_Intron|ATP2C1_uc011blh.1_Intron|ATP2C1_uc011bli.1_Intron|ATP2C1_uc003enk.2_Intron|ATP2C1_uc003enm.2_Intron|ATP2C1_uc003enn.2_Intron|ATP2C1_uc003eno.2_Intron|ATP2C1_uc003enp.2_Intron|ATP2C1_uc003enq.2_Intron|ATP2C1_uc003enr.2_Intron|ATP2C1_uc003ens.2_Intron|ATP2C1_uc003ent.2_Intron|ATP2C1_uc003enu.2_Intron	NM_014382	NP_055197	P98194	AT2C1_HUMAN	calcium-transporting ATPase 2C1 isoform 1a						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)	TGTCATTTGGCCACTCCAGCA	0.328									Hailey-Hailey_disease				4	2	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131761895	131761895	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131761895delT	uc003eom.2	-						CPNE4_uc003eol.2_5'Flank	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						TCCAAACTGCTTAAAGGTGAA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	133940981	133940981	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133940981delC								RYK (-28605 upstream) : RYK (-65003 downstream)																							GTACCCTTTTCAAGCTAGGTC	0.423													4	2	---	---	---	---	
DZIP1L	199221	broad.mit.edu	37	3	137820359	137820359	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137820359delC	uc003erq.2	-						DZIP1L_uc003err.1_Intron	NM_173543	NP_775814	Q8IYY4	DZI1L_HUMAN	DAZ interacting protein 1-like							intracellular	zinc ion binding			ovary(1)|pancreas(1)	2						ACACCAGCTTCCCATCGCAAG	0.657													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139432702	139432703	+	IGR	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139432702_139432703delTG								NMNAT3 (35862 upstream) : CLSTN2 (221324 downstream)																							AGGACCTAATTGTGTTTTGGAA	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139620224	139620225	+	IGR	INS	-	AG	AG	rs148905988	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139620224_139620225insAG								NMNAT3 (223384 upstream) : CLSTN2 (33802 downstream)																							TAAGAGAGTGcagagagagaga	0.213													4	2	---	---	---	---	
GRK7	131890	broad.mit.edu	37	3	141514620	141514621	+	Intron	INS	-	A	A	rs111715389		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141514620_141514621insA	uc011bnd.1	+							NM_139209	NP_631948	Q8WTQ7	GRK7_HUMAN	G-protein-coupled receptor kinase 7 precursor						visual perception	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5						tgctctatgttaaaaaaaaaaa	0.218													3	3	---	---	---	---	
TRPC1	7220	broad.mit.edu	37	3	142499494	142499495	+	Intron	DEL	CC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142499494_142499495delCC	uc003evc.2	+						TRPC1_uc003evb.2_Intron	NM_003304	NP_003295	P48995	TRPC1_HUMAN	transient receptor potential cation channel,						axon guidance|cytosolic calcium ion homeostasis|positive regulation of release of sequestered calcium ion into cytosol|response to calcium ion	cytosol|integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2						TTATGGTTTTCCCCAAAGCTGT	0.322													11	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144872270	144872270	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144872270delT								None (None upstream) : PLOD2 (914958 downstream)																							ttgggtggcctaactcaaagg	0.000													4	2	---	---	---	---	
PLOD2	5352	broad.mit.edu	37	3	145858816	145858816	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145858816delT	uc003evs.1	-						PLOD2_uc011bnm.1_Intron|PLOD2_uc003evr.1_Intron	NM_000935	NP_000926	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase						protein modification process|response to hypoxia	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein binding			ovary(1)|skin(1)	2					Vitamin C(DB00126)	ATAAGTTTTATTATGAGGTTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147024472	147024472	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147024472delG								PLSCR5 (700469 upstream) : ZIC4 (79365 downstream)																							GCAAAAAGGAGGAAGCATGTA	0.368													4	2	---	---	---	---	
WWTR1	25937	broad.mit.edu	37	3	149393339	149393339	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149393339delC	uc003exh.2	-							NM_015472	NP_056287	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1						hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity			breast(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			AATAATGGTACCGAAGAAATT	0.308													4	2	---	---	---	---	
PLCH1	23007	broad.mit.edu	37	3	155222685	155222686	+	Intron	DEL	CT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155222685_155222686delCT	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			AGGTCAAGGGCTCTCAGCAGTG	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157553332	157553332	+	IGR	DEL	T	-	-	rs71626431		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157553332delT								C3orf55 (234313 upstream) : SHOX2 (260469 downstream)																							agcttaagtctgacaccgccc	0.000													0	6	---	---	---	---	
RSRC1	51319	broad.mit.edu	37	3	158096839	158096839	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158096839delC	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			ctaccacttacctagaccaag	0.000													4	2	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	158969410	158969411	+	Intron	INS	-	AT	AT	rs149413911	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158969410_158969411insAT	uc003fcq.1	+						SCHIP1_uc003fcr.1_Intron|IQCJ_uc003fco.2_Intron|IQCJ_uc010hvy.1_Intron|IQCJ_uc003fcp.1_Intron	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			atttttattgcaCACACACACA	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161122644	161122645	+	IGR	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161122644_161122645insT								C3orf57 (32773 upstream) : OTOL1 (91951 downstream)																							CATATTTCTGATTTTTTTTTTC	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166123959	166123959	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166123959delT								BCHE (568706 upstream) : ZBBX (834122 downstream)																							agcttcaaacttttttttttt	0.000													4	3	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	171156272	171156272	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171156272delG	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|TNIK_uc003fhq.2_Intron	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)			GACACGTCCTGGTGAATTACG	0.413													4	2	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173971041	173971042	+	Intron	DEL	TT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173971041_173971042delTT	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			CAATATGCTCTTTTTATTCTGA	0.347													4	2	---	---	---	---	
KCNMB2	10242	broad.mit.edu	37	3	178288472	178288472	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178288472delA	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron|KCNMB2_uc003fje.2_Intron|KCNMB2_uc003fjf.2_Intron	NM_181361	NP_852006	Q9Y691	KCMB2_HUMAN	calcium-activated potassium channel beta 2						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of vasoconstriction	voltage-gated potassium channel complex	calcium-activated potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(1)	1	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)			AGAACAAGTGAAAAAAGGAGC	0.353													4	2	---	---	---	---	
EIF4G1	1981	broad.mit.edu	37	3	184046178	184046178	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184046178delA	uc003fnp.2	+						EIF4G1_uc003fnt.2_Intron|EIF4G1_uc003fnq.2_Intron|EIF4G1_uc003fnr.2_Intron|EIF4G1_uc010hxx.2_Intron|EIF4G1_uc003fns.2_Intron|EIF4G1_uc010hxy.2_Intron|EIF4G1_uc003fnv.3_Intron|EIF4G1_uc003fnu.3_Intron|EIF4G1_uc003fnw.2_Intron|EIF4G1_uc003fnx.2_Intron|EIF4G1_uc003fny.3_Intron|EIF4G1_uc003foa.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4						insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			aaactgtctcaaaaaaaaaac	0.209													5	4	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	187891356	187891356	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187891356delA	uc011bsg.1	+							NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		actccatctcaaaaaaaaagt	0.189			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189652058	189652058	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189652058delA								TP63 (36990 upstream) : LEPREL1 (22461 downstream)																							CATAGTAAGCAATGAAATGGA	0.348													4	2	---	---	---	---	
FGF12	2257	broad.mit.edu	37	3	192392019	192392019	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192392019delC	uc003fsy.2	-							NM_004113	NP_004104	P61328	FGF12_HUMAN	fibroblast growth factor 12 isoform 2						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		AATCAAAACACCATGAATGTT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	192860418	192860419	+	IGR	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192860418_192860419insT								C3orf59 (224468 upstream) : HRASLS (98499 downstream)																							AAGTAAAATGATTTTTTTTCTA	0.292													4	2	---	---	---	---	
C3orf43	255798	broad.mit.edu	37	3	196241917	196241918	+	Intron	INS	-	AG	AG			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196241917_196241918insAG	uc003fws.2	-						C3orf43_uc003fwr.2_Intron	NM_001077657	NP_001071125	Q147U7	CC043_HUMAN	hypothetical protein LOC255798							integral to membrane				ovary(1)	1	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;2.13e-23)|all cancers(36;2e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00298)		gccACAGAGACAGAATTCTAAT	0.223													86	60	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	409829	409835	+	IGR	DEL	TGTACAT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:409829_409835delTGTACAT								ZNF141 (32070 upstream) : ABCA11P (9389 downstream)																							GGTGTGAGGATGTACATCACACGACAG	0.449													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4911691	4911691	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4911691delA								MSX1 (46033 upstream) : CYTL1 (104625 downstream)																							agctgcagagaaaaaagtcac	0.000													4	2	---	---	---	---	
WFS1	7466	broad.mit.edu	37	4	6295731	6295732	+	Intron	INS	-	TC	TC	rs141974389	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6295731_6295732insTC	uc003giy.2	+						WFS1_uc003gix.2_Intron|WFS1_uc003giz.2_Intron	NM_001145853	NP_001139325	O76024	WFS1_HUMAN	wolframin						endoplasmic reticulum calcium ion homeostasis|endoplasmic reticulum unfolded protein response|ER overload response|ER-associated protein catabolic process|glucose homeostasis|kidney development|negative regulation of neuron apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|polyubiquitinated misfolded protein transport|positive regulation of calcium ion transport|positive regulation of growth|positive regulation of protein ubiquitination|positive regulation of proteolysis|protein stabilization|renal water homeostasis|sensory perception of sound|visual perception	dendrite|integral to endoplasmic reticulum membrane	activating transcription factor binding|ATPase binding|transporter activity|ubiquitin protein ligase binding			central_nervous_system(2)	2				Colorectal(103;0.0512)		aggctgcctcatctctttgctg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	11496579	11496579	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11496579delC								HS3ST1 (66042 upstream) : None (None downstream)																							TCTCAGAGGTCCAGAAGTTCC	0.318													4	2	---	---	---	---	
BOD1L	259282	broad.mit.edu	37	4	13601273	13601274	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13601273_13601274delAG	uc003gmz.1	-	10	7367_7368	c.7250_7251delCT	c.(7249-7251)TCTfs	p.S2417fs	BOD1L_uc010idr.1_Frame_Shift_Del_p.S1754fs	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	2417							DNA binding			ovary(5)|breast(1)	6						CTTGCCCTGCAGAGGGCTTGTG	0.584													101	48	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	17083981	17083981	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17083981delC								LDB2 (183557 upstream) : QDPR (404039 downstream)																							TCCTCCCTCACCCCATCCCCA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	17257995	17257995	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17257995delT								LDB2 (357571 upstream) : QDPR (230025 downstream)																							ccctcTTGACttttttttttt	0.010													3	3	---	---	---	---	
LAP3	51056	broad.mit.edu	37	4	17605951	17605951	+	Intron	DEL	T	-	-	rs112969379		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17605951delT	uc003gph.1	+							NM_015907	NP_056991	P28838	AMPL_HUMAN	leucine aminopeptidase 3						proteolysis	nucleus	aminopeptidase activity|magnesium ion binding|manganese ion binding|metalloexopeptidase activity|zinc ion binding				0						CAAAAATAGGTTAACAGTTAT	0.199													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18647430	18647430	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18647430delA								LCORL (624045 upstream) : None (None downstream)																							TGAAAAGGGGAAAAAAAGTTT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24063147	24063148	+	IGR	INS	-	AATA	AATA	rs147540311	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24063147_24063148insAATA								PPARGC1A (171447 upstream) : MIR573 (458667 downstream)																							GTTCTCAATGCAATATCTGTGG	0.475													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	34651461	34651462	+	IGR	INS	-	GGA	GGA	rs140859102	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34651461_34651462insGGA								None (None upstream) : None (None downstream)																							tcattgtctggggagatttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	40318885	40318885	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40318885delA								RHOH (72604 upstream) : CHRNA9 (18584 downstream)																							AGAATCAAGCAAAAACCCCCA	0.413													4	2	---	---	---	---	
APBB2	323	broad.mit.edu	37	4	41127223	41127223	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41127223delA	uc003gvl.2	-						APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						TTCATAACTTAAAGCACAAGA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	41875228	41875229	+	IGR	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41875228_41875229insA								PHOX2B (124241 upstream) : TMEM33 (61908 downstream)																							CCTGAAGGAATAAAAAAAAAGA	0.351													4	2	---	---	---	---	
BEND4	389206	broad.mit.edu	37	4	42119952	42119952	+	Intron	DEL	A	-	-	rs35028663		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42119952delA	uc003gwn.2	-						BEND4_uc003gwm.2_Intron	NM_207406	NP_997289	Q6ZU67	BEND4_HUMAN	BEN domain containing 4 isoform a												0						GTGCAAAAGTAAAAAAAAAAA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	43197883	43197883	+	IGR	DEL	T	-	-	rs35304137		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43197883delT								GRXCR1 (165210 upstream) : KCTD8 (978039 downstream)																							TACTAGTACATTTTTTTTTGA	0.363													1	5	---	---	---	---	
FRYL	285527	broad.mit.edu	37	4	48569480	48569481	+	Intron	INS	-	TG	TG			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48569480_48569481insTG	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gyi.1_5'Flank	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						AAATGGGACTTTATGATTTAAA	0.277													187	122	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58880996	58880996	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58880996delT								IGFBP7 (904457 upstream) : None (None downstream)																							TCAGTTTTTATTTACCATCTT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	65311691	65311691	+	IGR	DEL	G	-	-	rs35654485		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65311691delG								TECRL (36513 upstream) : EPHA5 (873591 downstream)																							gaacaaaggtggaaggggatt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	66710125	66710125	+	IGR	DEL	C	-	-	rs11289604		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66710125delC								EPHA5 (174472 upstream) : MIR1269 (432417 downstream)																							ATATTAATTGCCATTTGTTGT	0.313													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	78930632	78930632	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78930632delT								MRPL1 (56688 upstream) : FRAS1 (48092 downstream)																							tattatttccttttctcatca	0.100													4	2	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81838143	81838143	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81838143delA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						TATGAAGAGCAAAAAAAGGGT	0.348													4	2	---	---	---	---	
SCD5	79966	broad.mit.edu	37	4	83552279	83552279	+	3'UTR	DEL	A	-	-	rs72177305		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83552279delA	uc003hna.2	-	5						NM_001037582	NP_001032671	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5 isoform a						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity			ovary(1)	1		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				caaaacaaacaaaaaaaaaaa	0.144													3	3	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	92030641	92030641	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92030641delA	uc003hsv.3	+						FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						GTCCTAAGTTAAAAAAAAAAA	0.313													1	5	---	---	---	---	
UNC5C	8633	broad.mit.edu	37	4	96166485	96166485	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96166485delA	uc003htp.1	-						UNC5C_uc010ilc.1_Intron|UNC5C_uc003htq.2_Intron	NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor						apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		atagacagagaaaAAAAAAAG	0.194													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	97690175	97690175	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97690175delA								PDHA2 (927551 upstream) : C4orf37 (789859 downstream)																							AGTGAACAAGAAGAAAGAGAG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	99171463	99171463	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99171463delC								C4orf37 (107072 upstream) : RAP1GDS1 (11064 downstream)																							gcaacagcctcctggaagctc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	104896160	104896161	+	IGR	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104896160_104896161insA								TACR3 (255187 upstream) : CXXC4 (497184 downstream)																							TTCGTCCCTTGAAAAAAAAATG	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111313933	111313934	+	IGR	INS	-	A	A	rs112181942		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111313933_111313934insA								ELOVL6 (194113 upstream) : ENPEP (83295 downstream)																							CGGCAGAAGCTGTTTTTTTTTT	0.381													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	118526454	118526458	+	IGR	DEL	TGTGC	-	-	rs147293565		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118526454_118526458delTGTGC								TRAM1L1 (519718 upstream) : NDST3 (428315 downstream)																							TGTTCTGTGATGTGCTGTGCTGCCA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	120228083	120228084	+	IGR	DEL	AT	-	-	rs71595362		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120228083_120228084delAT								C4orf3 (6115 upstream) : FABP2 (10322 downstream)																							attcacaaacatgtggaaattt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	120403787	120403788	+	IGR	DEL	AG	-	-	rs71595392		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120403787_120403788delAG								FABP2 (160471 upstream) : PDE5A (11764 downstream)																							acggggggatagagagagagag	0.000													4	2	---	---	---	---	
MFSD8	256471	broad.mit.edu	37	4	128842168	128842168	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128842168delA	uc003ifp.2	-						MFSD8_uc011cgu.1_Intron	NM_152778	NP_689991	Q8NHS3	MFSD8_HUMAN	major facilitator superfamily domain containing						cell death|transmembrane transport	integral to membrane|lysosomal membrane				ovary(1)|liver(1)	2						AAGTCAGATTAAAAAAAATAA	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	135480803	135480804	+	IGR	INS	-	AG	AG			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135480803_135480804insAG								PABPC4L (357900 upstream) : None (None downstream)																							acccttcacacagtctccagtt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	136148442	136148442	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136148442delT								None (None upstream) : None (None downstream)																							AGAGGAACAATTTTTTCCAAG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	141767812	141767812	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141767812delT								TBC1D9 (90341 upstream) : RNF150 (18913 downstream)																							taagtatttatttttttgtta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	145499548	145499549	+	IGR	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145499548_145499549insT								GYPA (437644 upstream) : HHIP (67624 downstream)																							GCTGGTCTGCAGGgctctggag	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	155861789	155861789	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155861789delT								RBM46 (111825 upstream) : NPY2R (267992 downstream)																							TATTTGTAAGTTTTTAGCATC	0.388													4	2	---	---	---	---	
ACCN5	51802	broad.mit.edu	37	4	156756908	156756908	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156756908delT	uc003ipe.1	-							NM_017419	NP_059115	Q9NY37	ACCN5_HUMAN	amiloride-sensitive cation channel 5,							integral to membrane|plasma membrane				ovary(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0464)|Kidney(143;0.058)|COAD - Colon adenocarcinoma(41;0.141)		AATCACTCCATTAGCCCTGTT	0.313													4	2	---	---	---	---	
GRIA2	2891	broad.mit.edu	37	4	158190734	158190734	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158190734delC	uc003ipm.3	+						GRIA2_uc011cit.1_Intron|GRIA2_uc003ipl.3_Intron|GRIA2_uc003ipk.3_Intron|GRIA2_uc010iqh.1_Intron	NM_001083619	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2 isoform 2						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|endoplasmic reticulum membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)	ATCATCATCACCACTGCAGCT	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	163335021	163335022	+	IGR	INS	-	AAAG	AAAG	rs140964962	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163335021_163335022insAAAG								FSTL5 (249835 upstream) : NAF1 (712838 downstream)																							tatagagagaaagagagggaga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	170644634	170644634	+	IGR	DEL	T	-	-	rs72084175		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170644634delT								CLCN3 (2478 upstream) : C4orf27 (5986 downstream)																							TCAAAAGTGATTTTTTTTTTT	0.348													4	2	---	---	---	---	
C4orf27	54969	broad.mit.edu	37	4	170669783	170669783	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170669783delA	uc003isl.3	-							NM_017867	NP_060337	Q9NWY4	CD027_HUMAN	hypothetical protein LOC54969							nucleus				ovary(1)|pancreas(1)	2		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.018)|LUSC - Lung squamous cell carcinoma(193;0.116)		tcggcctcccaaagtgctgga	0.085													19	18	---	---	---	---	
SORBS2	8470	broad.mit.edu	37	4	186575632	186575632	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186575632delT	uc003iyl.2	-						SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Intron|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cky.1_Intron|SORBS2_uc003iyp.2_Intron|SORBS2_uc011cku.1_Intron|SORBS2_uc011ckv.1_Intron|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Intron|SORBS2_uc003iyf.2_Intron|SORBS2_uc003iyo.1_Intron	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)		GACAGACAGGTTTTTTTTTCT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190627455	190627455	+	IGR	DEL	A	-	-	rs68065627		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190627455delA								None (None upstream) : FRG1 (234519 downstream)																							TTCAAAGCCTAAAAGCTTTGA	0.234													3	6	---	---	---	---	
CLPTM1L	81037	broad.mit.edu	37	5	1321591	1321591	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1321591delT	uc003jch.2	-						CLPTM1L_uc003jcg.2_Intron	NM_030782	NP_110409	Q96KA5	CLP1L_HUMAN	CLPTM1-like						apoptosis	integral to membrane				breast(1)|central_nervous_system(1)	2	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		AGCTCTTCGCTTTTTTTTTTA	0.423													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3030558	3030558	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3030558delA								C5orf38 (275046 upstream) : IRX1 (565610 downstream)																							actcagcactaaaaagaaacg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4007134	4007134	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4007134delC								IRX1 (405618 upstream) : None (None downstream)																							TATTGGAAATCCCAGGGTAGC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4317458	4317458	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4317458delC								IRX1 (715942 upstream) : LOC340094 (717014 downstream)																							tattgagctgcccctacgtac	0.124													4	2	---	---	---	---	
ADAMTS16	170690	broad.mit.edu	37	5	5314806	5314806	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5314806delT	uc003jdl.2	+							NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						TCCCCATGGATTTTTTTCACG	0.219													4	2	---	---	---	---	
NSUN2	54888	broad.mit.edu	37	5	6600492	6600493	+	Intron	INS	-	T	T	rs72527888		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6600492_6600493insT	uc003jdu.2	-						NSUN2_uc003jds.2_Intron|NSUN2_uc003jdt.2_Intron|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1						CATTTCATCTGGATCCGAGGGG	0.426													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	16939479	16939479	+	IGR	DEL	T	-	-	rs78783027		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16939479delT								MYO10 (3094 upstream) : LOC285696 (190658 downstream)																							TTCCATTATCTTTTTTTTTTA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	18716247	18716247	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18716247delT								None (None upstream) : CDH18 (756910 downstream)																							GAATCTTCTGTTTTGTGGCCA	0.418													4	2	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21492253	21492254	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21492253_21492254insA	uc010iub.2	+						GUSBP1_uc011cnn.1_Intron|GUSBP1_uc003jgh.3_Intron	NR_027028				SubName: Full=Putative uncharacterized protein GUSBL2;												0						gagactgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	21824317	21824317	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21824317delT	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						AAATTTTTAATTTTTTTTTCA	0.463										HNSCC(59;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28493920	28493920	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28493920delA								None (None upstream) : None (None downstream)																							gttccaggtgaaattctatag	0.015													4	2	---	---	---	---	
RAI14	26064	broad.mit.edu	37	5	34815049	34815050	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34815049_34815050insA	uc003jir.2	+						RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Intron|RAI14_uc010ius.1_Intron|RAI14_uc003jis.2_Intron|RAI14_uc003jit.2_Intron|RAI14_uc011cok.1_Intron	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)					TTTCTTCATTTAAAAAAAAAAG	0.119													5	3	---	---	---	---	
RAD1	5810	broad.mit.edu	37	5	34913363	34913363	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34913363delA	uc003jix.2	-						RAD1_uc003jiw.2_Intron|RAD1_uc003jiy.2_Intron|BRIX1_uc003jiz.2_5'Flank|BRIX1_uc011col.1_5'Flank|BRIX1_uc003jja.2_5'Flank	NM_002853	NP_002844	O60671	RAD1_HUMAN	RAD1 homolog						DNA damage checkpoint|DNA repair|DNA replication|meiotic prophase I	nucleoplasm	3'-5' exonuclease activity|damaged DNA binding|exodeoxyribonuclease III activity|protein binding				0	all_lung(31;0.000107)	Lung NSC(810;5.19e-05)|Ovarian(839;0.0448)|Breast(839;0.198)	COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			CTTGTAAATTAAAAAAAAAAT	0.289								Other_conserved_DNA_damage_response_genes					4	2	---	---	---	---	
SPEF2	79925	broad.mit.edu	37	5	35706090	35706090	+	Intron	DEL	T	-	-	rs33975419		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35706090delT	uc003jjo.2	+						SPEF2_uc003jjq.3_Intron|SPEF2_uc003jjp.1_Intron	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GAATAAAAGATTTTTTCTCTC	0.289													3	3	---	---	---	---	
C5orf33	133686	broad.mit.edu	37	5	36217543	36217543	+	Intron	DEL	T	-	-	rs74940541		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36217543delT	uc003jkf.3	-						C5orf33_uc010iux.2_Intron|C5orf33_uc003jkg.3_Intron|C5orf33_uc011cov.1_Intron	NM_001085411	NP_001078880	Q4G0N4	NAKD1_HUMAN	hypothetical protein LOC133686 isoform 1								NAD+ kinase activity				0	all_lung(31;5.63e-05)		Epithelial(62;0.0254)|all cancers(62;0.0805)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TCTCTACTGCTTTTTTTTTTG	0.294													6	3	---	---	---	---	
NUP155	9631	broad.mit.edu	37	5	37337631	37337631	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37337631delA	uc003jku.1	-						NUP155_uc003jkt.1_Intron|NUP155_uc010iuz.1_Intron	NM_153485	NP_705618	O75694	NU155_HUMAN	nucleoporin 155kDa isoform 1						carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATGTTTTCAGAAAAAAAAAGA	0.279													4	3	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38432202	38432203	+	Intron	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38432202_38432203delAC	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron|EGFLAM_uc003jle.1_Intron|EGFLAM_uc003jlf.1_Intron	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					GATTCTGCGAACACACACACAA	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	39557090	39557093	+	IGR	DEL	TCTT	-	-	rs145528782		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39557090_39557093delTCTT								DAB2 (131755 upstream) : None (None downstream)																							AAACGGTCTCTCTTTCTCTGCCCT	0.431													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40578771	40578772	+	IGR	DEL	CC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40578771_40578772delCC								None (None upstream) : PTGER4 (101260 downstream)																							cacagcacagccccatccaagc	0.119													4	2	---	---	---	---	
ELOVL7	79993	broad.mit.edu	37	5	60118184	60118184	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60118184delC	uc003jsi.3	-						ELOVL7_uc010iwk.2_Intron|ELOVL7_uc003jsj.3_Intron	NM_024930	NP_079206	A1L3X0	ELOV7_HUMAN	elongation of very long chain fatty acids-like						fatty acid elongation, polyunsaturated fatty acid|fatty acid elongation, saturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)				CCACTGAAAACCCCAAGCCTG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	65867586	65867587	+	IGR	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65867586_65867587delAC								SFRS12 (390874 upstream) : MAST4 (24589 downstream)																							AACTTAAAATACACACACACAC	0.243													6	3	---	---	---	---	
AGGF1	55109	broad.mit.edu	37	5	76345770	76345770	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76345770delT	uc003ket.2	+							NM_018046	NP_060516	Q8N302	AGGF1_HUMAN	angiogenic factor VG5Q						angiogenesis|cell adhesion|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|RNA processing|vasculogenesis	extracellular region|perinuclear region of cytoplasm	eukaryotic cell surface binding|nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		TGCTTTTCTCTTTTTTTGACC	0.313													4	2	---	---	---	---	
ZFYVE16	9765	broad.mit.edu	37	5	79769032	79769032	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79769032delT	uc003kgr.3	+						ZFYVE16_uc003kgq.3_Intron|ZFYVE16_uc003kgs.3_Intron|ZFYVE16_uc003kgt.3_Intron|ZFYVE16_uc003kgu.3_Intron	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16						BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		GGCAAGACACTTTTTCTTTCA	0.393													4	2	---	---	---	---	
HAPLN1	1404	broad.mit.edu	37	5	83006366	83006366	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83006366delA	uc003kin.2	-							NM_001884	NP_001875	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1						cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding			large_intestine(3)|ovary(1)|skin(1)	5		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)		gtagttcaggaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	96199716	96199716	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96199716delT	uc003kmo.1	-											Homo sapiens cDNA FLJ37666 fis, clone BRHIP2011576.																		AAATTCTTGATTTTTTTTTAC	0.323													4	2	---	---	---	---	
PPIP5K2	23262	broad.mit.edu	37	5	102513852	102513853	+	Intron	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102513852_102513853insT	uc003kod.3	+						PPIP5K2_uc011cva.1_Intron|PPIP5K2_uc003koe.2_Intron|PPIP5K2_uc003kof.2_Intron	NM_015216	NP_056031	O43314	VIP2_HUMAN	Histidine acid phosphatase domain containing 1						inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity			ovary(1)|skin(1)	2						TTTTATGCATATTGCAATACCT	0.213													5	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	103379637	103379637	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103379637delT								NUDT12 (481147 upstream) : None (None downstream)																							ATGCCTTCCCTTTTTGTTTTT	0.169													4	2	---	---	---	---	
MAN2A1	4124	broad.mit.edu	37	5	109051575	109051575	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109051575delT	uc003kou.1	+							NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		TAGAATGAACTTTTTTTTTTA	0.289													6	3	---	---	---	---	
DCP2	167227	broad.mit.edu	37	5	112317888	112317889	+	Intron	INS	-	TA	TA	rs141928564	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112317888_112317889insTA	uc003kqh.2	+						DCP2_uc011cwa.1_Intron|DCP2_uc003kqg.2_Intron	NM_152624	NP_689837	Q8IU60	DCP2_HUMAN	DCP2 decapping enzyme						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus|RNA-induced silencing complex	exoribonuclease activity, producing 5'-phosphomonoesters|manganese ion binding|protein binding|protein binding|RNA binding				0		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		TCCTCTCTAATATGTCCAAAGT	0.386													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	130301151	130301151	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130301151delG								CHSY3 (778825 upstream) : HINT1 (193724 downstream)																							aaggaaaggaggcagtttctt	0.000													4	2	---	---	---	---	
ACSL6	23305	broad.mit.edu	37	5	131284631	131284631	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131284631delT	uc003kvv.1	-							NM_015256		Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6						fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane|plasma membrane	ATP binding|long-chain fatty acid-CoA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACCAAGGGGATTTTCCTTAAC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133259736	133259736	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133259736delA								FSTL4 (311513 upstream) : C5orf15 (31463 downstream)																							cttttaaAACAAAAAAAATCC	0.219													4	2	---	---	---	---	
VDAC1	7416	broad.mit.edu	37	5	133330325	133330326	+	Intron	DEL	CT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133330325_133330326delCT	uc003kyp.1	-						VDAC1_uc003kyq.1_Intron|VDAC1_uc003kyr.1_Intron	NM_003374	NP_003365	P21796	VDAC1_HUMAN	voltage-dependent anion channel 1						apoptosis|interspecies interaction between organisms	mitochondrial nucleoid|mitochondrial outer membrane|plasma membrane|pore complex	porin activity|protein binding|voltage-gated anion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)	CCACCAGAACCTCAAGAAATAC	0.535													4	2	---	---	---	---	
DDX46	9879	broad.mit.edu	37	5	134099965	134099966	+	Intron	INS	-	T	T	rs113290220		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134099965_134099966insT	uc003kzw.2	+						DDX46_uc003kzv.1_Intron	NM_014829	NP_055644	Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ATCAAACAGTGttttttttttt	0.228													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134922215	134922216	+	IGR	INS	-	AC	AC	rs139708460	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134922215_134922216insAC								CXCL14 (7246 upstream) : LOC340074 (62158 downstream)																							AGTGATCTCAGACACAGACATG	0.441													0	6	---	---	---	---	
SPOCK1	6695	broad.mit.edu	37	5	136558742	136558743	+	Intron	DEL	AC	-	-	rs147996127	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136558742_136558743delAC	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ccctactcttacggagctaata	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	138744329	138744332	+	IGR	DEL	GGTG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138744329_138744332delGGTG								SPATA24 (4553 upstream) : DNAJC18 (3049 downstream)																							agcaggacttggtggggcagcaca	0.113													4	2	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142494508	142494508	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142494508delT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATGTTGTTGGTGTCATGAAGG	0.498													3	3	---	---	---	---	
SPINK5	11005	broad.mit.edu	37	5	147476284	147476285	+	Intron	DEL	TC	-	-	rs79956492	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147476284_147476285delTC	uc003lox.2	+						SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tttctttctttctttttttctt	0.198													4	2	---	---	---	---	
HTR4	3360	broad.mit.edu	37	5	147834206	147834206	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147834206delT	uc003lpj.1	-						HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron	NM_001040169	NP_001035259	Q13639	5HT4R_HUMAN	serotonin 5-HT4 receptor isoform a						G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)	CAAAGCCCTCTTTTGGCAAAT	0.303													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148375835	148375836	+	3'UTR	DEL	AG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148375835_148375836delAG	uc003lpu.2	-	17					SH3TC2_uc003lpp.1_Intron|SH3TC2_uc010jgw.2_3'UTR|SH3TC2_uc003lps.2_RNA|SH3TC2_uc003lpt.2_3'UTR|SH3TC2_uc010jgx.2_3'UTR	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			taagagagaaaGAGAGAGAGAG	0.188													4	3	---	---	---	---	
PPARGC1B	133522	broad.mit.edu	37	5	149188147	149188147	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149188147delC	uc003lrc.2	+						PPARGC1B_uc003lrb.1_Intron|PPARGC1B_uc003lrd.2_Intron	NM_133263	NP_573570	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor						estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			AGCGTTTTTGCCCCCCACAGA	0.468													4	2	---	---	---	---	
LARP1	23367	broad.mit.edu	37	5	154181675	154181676	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154181675_154181676delTT	uc003lvp.2	+	11	2254_2255	c.1825_1826delTT	c.(1825-1827)TTTfs	p.F609fs	LARP1_uc003lvo.2_Frame_Shift_Del_p.F532fs|LARP1_uc010jie.1_Frame_Shift_Del_p.F404fs	NM_033551	NP_291029	Q6PKG0	LARP1_HUMAN	la related protein isoform 2	609							protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GGATTTTCTGTTTGACGAGGAG	0.515													179	89	---	---	---	---	
TIMD4	91937	broad.mit.edu	37	5	156381896	156381896	+	Intron	DEL	T	-	-	rs71922795		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156381896delT	uc003lwh.2	-						TIMD4_uc010jii.2_Intron	NM_138379	NP_612388	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain							integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ttttctttccttttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157793155	157793156	+	IGR	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157793155_157793156delTG								CLINT1 (506987 upstream) : EBF1 (329768 downstream)																							GGTTAAGGCATGTGTGTGTGTT	0.421													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167416422	167416422	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167416422delA	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		GACAGAGAAGAAAAAGCCATT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173214714	173214716	+	IGR	DEL	GGA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173214714_173214716delGGA								BOD1 (171048 upstream) : CPEB4 (100615 downstream)																							TCTTGTTGTGGGAGGATCTTGAT	0.360													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174065220	174065220	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174065220delT								HMP19 (529039 upstream) : MSX2 (86355 downstream)																							TGCTACTCTGTTTTCTATAAA	0.204													4	2	---	---	---	---	
COL23A1	91522	broad.mit.edu	37	5	177859733	177859733	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177859733delG	uc003mje.2	-							NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	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)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		CCAATGTTCTGGGGCTGGTAA	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	179367688	179367689	+	IGR	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179367688_179367689insT								TBC1D9B (32832 upstream) : RNF130 (14785 downstream)																							tcttggtgtggtttttttttca	0.020													4	2	---	---	---	---	
FLT4	2324	broad.mit.edu	37	5	180074312	180074312	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180074312delC	uc003mma.3	-						FLT4_uc003mlz.3_Intron|FLT4_uc011dgy.1_Intron|FLT4_uc011dgz.1_Intron|FLT4_uc011dha.1_Intron	NM_002020	NP_002011	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 2						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)	GCACACACAACCCACACAACC	0.507									Congenital_Hereditary_Lymphedema				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3612818	3612818	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3612818delG								SLC22A23 (156025 upstream) : C6orf145 (110018 downstream)																							CTGAGCCAAAGGGAGATTAAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3868007	3868007	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3868007delC								FAM50B (16457 upstream) : PRPF4B (153562 downstream)																							cattttatatcccagccaagt	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	11165124	11165126	+	IGR	DEL	AAG	-	-	rs146573606		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11165124_11165126delAAG								LOC221710 (26160 upstream) : NEDD9 (18405 downstream)																							ctgagagaccaagaagatgcccc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18998079	18998079	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18998079delG								MIR548A1 (425968 upstream) : ID4 (839538 downstream)																							ttcttgcacagggggagcagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	20014421	20014421	+	IGR	DEL	T	-	-	rs67065332		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20014421delT								ID4 (173507 upstream) : MBOAT1 (86514 downstream)																							CTACTCGCTATTTTTTTTTTT	0.388													4	3	---	---	---	---	
MRS2	57380	broad.mit.edu	37	6	24412226	24412226	+	Intron	DEL	A	-	-	rs67011833		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24412226delA	uc003neb.2	+						MRS2_uc003nea.2_Intron|MRS2_uc011djl.1_Intron|MRS2_uc011djm.1_Intron|MRS2_uc011djn.1_Intron|MRS2_uc003nec.2_Intron	NM_020662	NP_065713	Q9HD23	MRS2_HUMAN	MRS2-like, magnesium homeostasis factor						ion transport	integral to membrane|mitochondrial inner membrane					0						TTTTCTTTTGAAAAAAAAAAC	0.229													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28774404	28774404	+	IGR	DEL	A	-	-	rs67727203		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28774404delA								SCAND3 (219292 upstream) : TRIM27 (96376 downstream)																							AAAAGGAGGGAAAAAAAAGAC	0.388													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	29655322	29655324	+	IGR	DEL	GTT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29655322_29655324delGTT								ZFP57 (6435 upstream) : HLA-F (35793 downstream)																							TCTTCTGAGGGTTGTTGTTGTTG	0.227													4	2	---	---	---	---	
HLA-G	3135	broad.mit.edu	37	6	29798581	29798582	+	3'UTR	INS	-	ATTTGTTCATGCCT	ATTTGTTCATGCCT	rs1704		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29798581_29798582insATTTGTTCATGCCT	uc003nnw.2	+	8					HLA-G_uc011dmb.1_Intron|HLA-G_uc003raj.3_3'UTR|HLA-G_uc003nnz.3_3'UTR|HLA-G_uc010jrn.2_3'UTR|HLA-G_uc003nny.3_RNA|HLA-G_uc003ran.1_Intron	NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						TGAGTGGCAAGTCCCTTTGTGA	0.490													5	3	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32553909	32553910	+	Intron	INS	-	T	T	rs146253470	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32553909_32553910insT	uc003obk.3	-						HLA-DRB1_uc011dqa.1_5'Flank|HLA-DRB6_uc003obo.1_5'Flank|HLA-DRB1_uc003obp.3_Intron|HLA-DRB1_uc011dqc.1_5'Flank	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						CAGGGGCTCTCCGTATTTCCTC	0.401													3	3	---	---	---	---	
TBC1D22B	55633	broad.mit.edu	37	6	37277582	37277582	+	Intron	DEL	C	-	-	rs111767988		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37277582delC	uc003onn.2	+						TBC1D22B_uc010jwt.2_Intron|TBC1D22B_uc003ono.1_Intron|TBC1D22B_uc003onp.2_Intron	NM_017772	NP_060242	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B							intracellular	Rab GTPase activator activity				0			OV - Ovarian serous cystadenocarcinoma(102;0.241)			gtgatggaggcgcaccatgca	0.020													4	2	---	---	---	---	
BTBD9	114781	broad.mit.edu	37	6	38289599	38289600	+	Intron	DEL	AC	-	-	rs10535916		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38289599_38289600delAC	uc003ooa.3	-						BTBD9_uc003ony.3_Intron|BTBD9_uc010jwv.2_Intron|BTBD9_uc010jww.2_Intron|BTBD9_uc010jwx.2_Intron	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a						cell adhesion						0						CTTGTTTTATacacacacacac	0.302													4	2	---	---	---	---	
TNFRSF21	27242	broad.mit.edu	37	6	47235377	47235377	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47235377delA	uc003oyv.2	-							NM_014452	NP_055267	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily,						cellular lipid metabolic process	cytoplasm|integral to membrane	protein binding|receptor activity				0			Lung(136;0.189)			TGTGGGAAAGAAAAAGGGGCA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	51995302	51995303	+	IGR	DEL	GT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51995302_51995303delGT								PKHD1 (42879 upstream) : MIR206 (13844 downstream)																							agcaactctggtgtgtgtgttt	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57441568	57441568	+	Intron	DEL	T	-	-	rs11301075		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57441568delT	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)		AAGATCCATCTTTTTCTCTCT	0.318													4	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57503445	57503445	+	Intron	DEL	C	-	-	rs11343070		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57503445delC	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)		aagagcttcacaaaatgagtt	0.080													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57527818	57527818	+	IGR	DEL	G	-	-	rs67858073		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57527818delG								PRIM2 (14443 upstream) : GUSBL2 (718341 downstream)																							AACCAGAACTGGGGGCTGACA	0.348													3	3	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	66112224	66112224	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66112224delA	uc011dxu.1	-						EYS_uc003peq.2_Intron|EYS_uc003per.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						CAAAACATGCAAAAAAAATTT	0.214													10	9	---	---	---	---	
HMGN3	9324	broad.mit.edu	37	6	79911705	79911705	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79911705delA	uc003pit.2	-						HMGN3_uc003pis.2_Intron|HMGN3_uc003piu.1_3'UTR	NM_004242	NP_004233	Q15651	HMGN3_HUMAN	high mobility group nucleosomal binding domain 3						chromatin modification	chromatin|cytoplasm|nucleus	DNA binding|thyroid hormone receptor binding				0		all_cancers(76;0.000116)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0393)		BRCA - Breast invasive adenocarcinoma(397;0.125)		CATAATGATTAAAAAAAAAAA	0.368													6	3	---	---	---	---	
MRAP2	112609	broad.mit.edu	37	6	84759702	84759703	+	Intron	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84759702_84759703delTG	uc003pkg.3	+						MRAP2_uc010kbo.2_Intron	NM_138409	NP_612418	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2						positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding			skin(2)	2						CGTGCATTCATGTGTGTGTGTG	0.426													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85563014	85563014	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85563014delT								TBX18 (89115 upstream) : NT5E (596288 downstream)																							CTTACCACCATTTTTTTTCTC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	106459835	106459836	+	IGR	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106459835_106459836delAC								PREP (608866 upstream) : PRDM1 (74359 downstream)																							acaccacactacacacacacac	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112647042	112647042	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112647042delT								LAMA4 (71214 upstream) : RFPL4B (21490 downstream)																							GCTTTGCAGCTTTTTTTTTTC	0.453													4	2	---	---	---	---	
HS3ST5	222537	broad.mit.edu	37	6	114626959	114626959	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114626959delT	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840	Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		tcaccactgatttttgcacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	126925796	126925796	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126925796delT	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																		tttctatTGCTTTTTTTTTTC	0.129													4	2	---	---	---	---	
PTPRK	5796	broad.mit.edu	37	6	128436304	128436304	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128436304delC	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		CAGCACCATACCCCAAAATCA	0.473													4	2	---	---	---	---	
AKAP7	9465	broad.mit.edu	37	6	131520263	131520263	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131520263delT	uc003qck.2	+						AKAP7_uc011ebz.1_Intron|AKAP7_uc003qcl.1_Intron	NM_016377	NP_057461	O43687	AKA7A_HUMAN	A-kinase anchor protein 7 isoform gamma						intracellular signal transduction|ion transport	apical plasma membrane|intracellular|lateral plasma membrane	protein kinase A binding			ovary(2)	2	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		AAGCTAGTCCTTTTTTATACT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138084178	138084179	+	IGR	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138084178_138084179insT								OLIG3 (268647 upstream) : TNFAIP3 (104402 downstream)																							agcaaagaccctttttcctcat	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	141267606	141267607	+	IGR	DEL	AC	-	-	rs71787391		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141267606_141267607delAC								None (None upstream) : None (None downstream)																							ATATGTATAGacacacacacac	0.168													3	3	---	---	---	---	
AIG1	51390	broad.mit.edu	37	6	143608248	143608249	+	Intron	INS	-	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143608248_143608249insC	uc003qjh.2	+						AIG1_uc003qjf.2_Intron|AIG1_uc003qji.2_Intron	NM_016108	NP_057192	Q9NVV5	AIG1_HUMAN	androgen-induced 1							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(155;2.34e-05)|GBM - Glioblastoma multiforme(68;0.0246)		TTTCCTGGACACCCCCCTCCAT	0.505													4	2	---	---	---	---	
GRM1	2911	broad.mit.edu	37	6	146747328	146747329	+	Intron	INS	-	AAG	AAG	rs145800679	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146747328_146747329insAAG	uc010khw.1	+						GRM1_uc010khv.1_Intron|GRM1_uc003qll.2_Intron|GRM1_uc011edz.1_Intron|GRM1_uc011eea.1_Intron	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)	GCACTTCCTTTAGGAGTAGAGG	0.411													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	147974155	147974155	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147974155delG								SAMD5 (82998 upstream) : SASH1 (689574 downstream)																							TCCCACTTAAGTACATACTCT	0.363													4	3	---	---	---	---	
CNKSR3	154043	broad.mit.edu	37	6	154751360	154751360	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154751360delA	uc003qpy.2	-							NM_173515	NP_775786	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3						negative regulation of ERK1 and ERK2 cascade|negative regulation of peptidyl-serine phosphorylation|positive regulation of sodium ion transport	cytoplasm|membrane				ovary(2)|breast(1)|skin(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		GCTAAGTCCTAAAAATAAAGT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160266950	160266950	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160266950delT								PNLDC1 (25215 upstream) : MAS1 (61024 downstream)																							TAATCCTTTCTTTTTTTTTTT	0.308													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	161716189	161716189	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161716189delT								AGPAT4 (21082 upstream) : PARK2 (52402 downstream)																							ttacctaacatttttttttct	0.000													4	3	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162851190	162851191	+	Intron	INS	-	GAC	GAC	rs145121165	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162851190_162851191insGAC	uc003qtx.3	-						PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		atgatgacgatgacgacgacga	0.134													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164263458	164263458	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164263458delC								QKI (268566 upstream) : None (None downstream)																							TTGTTTCTAACCAAACATTAA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164830661	164830662	+	IGR	INS	-	A	A	rs151044326	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164830661_164830662insA								QKI (835769 upstream) : C6orf118 (862493 downstream)																							GCCCAGAAAAGAAAAAAAAAAT	0.381													4	3	---	---	---	---	
WDR27	253769	broad.mit.edu	37	6	169902893	169902893	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169902893delA	uc003qwx.2	-						WDR27_uc003qwv.1_Intron|WDR27_uc010kkw.1_Intron|WDR27_uc003qwy.2_Intron			A2RRH5	WDR27_HUMAN	RecName: Full=WD repeat-containing protein 27;											pancreas(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		CCCACGTTCCAGGGGTTAGGA	0.567													4	2	---	---	---	---	
FAM120B	84498	broad.mit.edu	37	6	170615212	170615213	+	5'Flank	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170615212_170615213insA	uc003qxp.2	+						FAM120B_uc003qxo.1_5'Flank|FAM120B_uc011ehd.1_5'Flank	NM_032448	NP_115824	Q96EK7	F120B_HUMAN	family with sequence similarity 120B						cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		CAACTTTCAGCTGAAGAGTAGT	0.584													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1184632	1184632	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1184632delA								C7orf50 (6739 upstream) : ZFAND2A (7912 downstream)																							tccatctcagaaaaaaaaaaG	0.313													4	2	---	---	---	---	
GNA12	2768	broad.mit.edu	37	7	2769130	2769131	+	3'UTR	INS	-	GA	GA	rs115457120	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2769130_2769131insGA	uc003smu.2	-	4					GNA12_uc011jwb.1_3'UTR|GNA12_uc003smt.2_3'UTR	NM_007353	NP_031379	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein)						G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|Rho protein signal transduction	brush border membrane|heterotrimeric G-protein complex	D5 dopamine receptor binding|G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		TCGAGCACTGCGAGAGAGAGTT	0.540													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	8326933	8326935	+	Intron	DEL	GCT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8326933_8326935delGCT	uc003srt.1	+											full-length cDNA clone CS0DC002YA18 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																		agtgaagtgagctgctgctgaca	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	8453449	8453450	+	IGR	INS	-	G	G	rs143893713	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8453449_8453450insG								ICA1 (151264 upstream) : NXPH1 (20135 downstream)																							GATACTAGGTTGTGCAAAAGTA	0.366													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	12534821	12534821	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12534821delT								VWDE (90969 upstream) : SCIN (61366 downstream)																							AACACACTCATTTTTTTTCCT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	18090004	18090007	+	IGR	DEL	AACC	-	-	rs72302849		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18090004_18090007delAACC								PRPS1L1 (22518 upstream) : HDAC9 (36565 downstream)																							CCACTCCCAGAACCTCTACACTGC	0.412													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	21041827	21041827	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21041827delA								RPL23P8 (174388 upstream) : SP4 (425862 downstream)																							TGATAAGACCAAATGCCACTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24169281	24169281	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24169281delT								STK31 (224916 upstream) : NPY (154528 downstream)																							TACTTATGAGTTTTAGGGCTG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	26019515	26019516	+	IGR	DEL	AG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26019515_26019516delAG								MIR148A (29909 upstream) : NFE2L3 (172331 downstream)																							atcattggaaagagagagagag	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	26555145	26555146	+	IGR	DEL	CT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26555145_26555146delCT								LOC441204 (16551 upstream) : KIAA0087 (17594 downstream)																							GGAGGAAGGGCTCTCTCTCTCA	0.495													4	2	---	---	---	---	
HIBADH	11112	broad.mit.edu	37	7	27658001	27658001	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27658001delG	uc003szf.2	-						HIBADH_uc003szg.2_Intron|HIBADH_uc003szh.2_Intron|HIBADH_uc003szi.2_Intron|uc003szj.2_Intron	NM_152740	NP_689953	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase precursor						branched chain family amino acid catabolic process|pentose-phosphate shunt|valine metabolic process	mitochondrial matrix	3-hydroxyisobutyrate dehydrogenase activity|NAD binding|phosphogluconate dehydrogenase (decarboxylating) activity			ovary(2)	2			GBM - Glioblastoma multiforme(3;0.0368)		NADH(DB00157)	CAACATGTCTGGGGCTGTTGG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	30249818	30249819	+	IGR	DEL	GA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30249818_30249819delGA								C7orf41 (47437 upstream) : ZNRF2 (74104 downstream)																							GTTGGCCAGGGAGAGAGAGAGA	0.554													4	2	---	---	---	---	
NOD1	10392	broad.mit.edu	37	7	30468287	30468288	+	Intron	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30468287_30468288insT	uc003tav.2	-							NM_006092	NP_006083	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain						activation of MAPK activity|detection of bacterium|induction of apoptosis|inflammatory response|innate immune response|interleukin-8 biosynthetic process|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of dendritic cell antigen processing and presentation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|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	basolateral plasma membrane|cytosol	ATP binding|CARD domain binding|caspase activator activity|peptidoglycan binding|protein homodimerization activity			ovary(1)|skin(1)	2						GCTGTTTTTTGTTTTTTTTTAA	0.327													4	2	---	---	---	---	
FAM188B	84182	broad.mit.edu	37	7	30816631	30816631	+	Intron	DEL	T	-	-	rs72270789		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30816631delT	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182												0						tttctttttcttttttttttt	0.154													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	33989214	33989214	+	Intron	DEL	T	-	-	rs112376084		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33989214delT	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						TGCCACTGTGTTTTTTTTTTT	0.368													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	34149443	34149444	+	Intron	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34149443_34149444insT	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						GAAAATTTGACTTTCTTGAGTA	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	34375859	34375859	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34375859delA								BMPER (181748 upstream) : AAA1 (14176 downstream)																							acagcaaaagaaaaaaaaagc	0.000													4	2	---	---	---	---	
AAA1	404744	broad.mit.edu	37	7	34402661	34402661	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34402661delT	uc010kwo.1	-						AAA1_uc010kwp.1_Intron|AAA1_uc003tdz.2_Intron|AAA1_uc010kwq.1_Intron					Homo sapiens AAA1 variant IA mRNA, complete cds; alternatively spliced.												0						agagatgtaattttttttttg	0.085													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35388599	35388599	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35388599delT								TBX20 (95357 upstream) : HERPUD2 (283673 downstream)																							TCTCCAGTGATTTTTTTTTTT	0.433													3	3	---	---	---	---	
TARP	445347	broad.mit.edu	37	7	38343711	38343712	+	Intron	INS	-	T	T	rs147524450	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38343711_38343712insT	uc003tge.1	-						uc003tfz.1_Intron|TARP_uc003tgf.1_Intron|TARP_uc003tgj.1_Intron|TARP_uc003tgh.1_Intron|TARP_uc003tgi.1_Intron|TARP_uc003tgg.1_Intron|uc003tgm.1_RNA			A2JGV3	A2JGV3_HUMAN	Homo sapiens TCRgamma alternate reading frame protein (TCRg) mRNA, complete cds.												0						GTGCGAATGACTTTTTTTCATG	0.173													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	38711080	38711080	+	IGR	DEL	T	-	-	rs35491808		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38711080delT								AMPH (40060 upstream) : FAM183B (13867 downstream)																							CCCAGCGTTGTTTTTTTTTGT	0.507													4	4	---	---	---	---	
C7orf10	79783	broad.mit.edu	37	7	40490012	40490012	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40490012delT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13								transferase activity			ovary(2)	2						GATTTTTTTCTTTTTTTTTTT	0.214													4	2	---	---	---	---	
C7orf10	79783	broad.mit.edu	37	7	40548308	40548309	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40548308_40548309insA	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13								transferase activity			ovary(2)	2						aatttcagtttaaaaaaaaaat	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41093833	41093836	+	IGR	DEL	TCAA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41093833_41093836delTCAA								C7orf10 (193476 upstream) : INHBA (634767 downstream)																							GGGGTCTTTTTCAATCTGTTCCAA	0.397													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	42796131	42796131	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42796131delA								GLI3 (519513 upstream) : C7orf25 (152743 downstream)																							CTTTGGAGAGAAAAAAAAAAG	0.353													2	6	---	---	---	---	
BLVRA	644	broad.mit.edu	37	7	43807445	43807445	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43807445delA	uc003tir.2	+						BLVRA_uc010kxv.2_Intron	NM_000712	NP_000703	P53004	BIEA_HUMAN	biliverdin reductase A precursor						heme catabolic process	cytosol	biliverdin reductase activity|zinc ion binding			ovary(1)	1					NADH(DB00157)	TGTTAATTACAAAAAAAAAAG	0.318													4	5	---	---	---	---	
H2AFV	94239	broad.mit.edu	37	7	44874383	44874384	+	Intron	INS	-	T	T	rs138727400		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44874383_44874384insT	uc003tma.2	-						H2AFV_uc003tlz.2_Intron|H2AFV_uc011kca.1_5'Flank|H2AFV_uc003tmb.2_Intron|H2AFV_uc003tmc.2_Intron|H2AFV_uc003tmd.2_Intron	NM_012412	NP_036544	Q71UI9	H2AV_HUMAN	H2A histone family, member V isoform 1						nucleosome assembly	nucleosome|nucleus	DNA binding				0						gtaaccatagcttttttttttt	0.054													4	2	---	---	---	---	
ABCA13	154664	broad.mit.edu	37	7	48280850	48280857	+	Intron	DEL	CTGGATGC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48280850_48280857delCTGGATGC	uc003toq.2	+						ABCA13_uc010kyr.2_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						TGGCAGCACTCTGGATGCCTATTCAGAG	0.394													9	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	50332888	50332889	+	IGR	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50332888_50332889delTG								C7orf72 (133530 upstream) : IKZF1 (11489 downstream)																							gaaggtgaactgaatgacctgc	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	55025857	55025858	+	IGR	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55025857_55025858delAC								SEC61G (198918 upstream) : EGFR (60867 downstream)																							AGTGAGGAGGACAAGGTTGATA	0.282													4	2	---	---	---	---	
LANCL2	55915	broad.mit.edu	37	7	55454330	55454330	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55454330delT	uc003tqp.2	+							NM_018697	NP_061167	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2						negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)|skin(1)	2	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			cttatccggcttttttttgct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61870487	61870487	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61870487delT								None (None upstream) : LOC643955 (881185 downstream)																							ggatattccctttttactgtt	0.000													4	2	---	---	---	---	
ZNF273	10793	broad.mit.edu	37	7	64352576	64352576	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64352576delA	uc003ttl.2	+							NM_021148	NP_066971	Q14593	ZN273_HUMAN	zinc finger protein 273						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(55;0.0295)|all_lung(88;0.0691)				TTTCATAGACAAAAAAAACAG	0.348													5	3	---	---	---	---	
VKORC1L1	154807	broad.mit.edu	37	7	65400962	65400962	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65400962delT	uc003tul.2	+						VKORC1L1_uc011kds.1_Intron	NM_173517	NP_775788	Q8N0U8	VKORL_HUMAN	vitamin K epoxide reductase complex, subunit							integral to membrane					0		Lung NSC(55;0.197)			Menadione(DB00170)|Warfarin(DB00682)	gtctctattctttttttttta	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67051237	67051238	+	IGR	DEL	AG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67051237_67051238delAG								STAG3L4 (264725 upstream) : None (None downstream)																							tagagtgagaagagagagaggt	0.203													4	2	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69755304	69755305	+	Intron	INS	-	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69755304_69755305insC	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		ATATCAGAGGGCATTTAACATT	0.312													163	188	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71261957	71261961	+	Intron	DEL	TTATT	-	-	rs72335478		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71261957_71261961delTTATT	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				TTTCCCTCTCTTATTTTAACAGCCA	0.454													5	3	---	---	---	---	
SPDYE7P	441251	broad.mit.edu	37	7	72339826	72339826	+	5'Flank	DEL	G	-	-	rs237936	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72339826delG	uc010lal.1	-							NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0						TCTTTTTTttgttgttgttgt	0.254													6	3	---	---	---	---	
NSUN5P2	260294	broad.mit.edu	37	7	72436916	72436917	+	Intron	DEL	GT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72436916_72436917delGT	uc010lao.2	-						uc003tws.1_Intron	NM_198853	NP_942150			tripartite motif-containing 74												0						ttGAAGATACgtgtgtgtgtgt	0.213													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	76448609	76448609	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76448609delA								POMZP3 (191989 upstream) : PMS2L11 (161530 downstream)																							cttttaactgaaaaaaaaagt	0.080													4	2	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76626816	76626817	+	Intron	INS	-	GAGGTGT	GAGGTGT			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76626816_76626817insGAGGTGT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						tgtgaggtgtggaggtgtgtgg	0.000													4	3	---	---	---	---	
STEAP2	261729	broad.mit.edu	37	7	89859613	89859613	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89859613delA	uc003ujz.2	+						STEAP2_uc010len.2_Intron|STEAP2_uc003uka.2_Intron|STEAP2_uc003ukb.2_Intron|STEAP2_uc003ukc.2_Intron|STEAP2_uc003ukd.2_Intron	NM_152999	NP_694544	Q8NFT2	STEA2_HUMAN	six transmembrane epithelial antigen of the						electron transport chain|endocytosis|Golgi to plasma membrane transport|ion transport|iron ion homeostasis|regulated secretory pathway|response to hormone stimulus	cytosol|early endosome|endosome membrane|integral to Golgi membrane|plasma membrane|trans-Golgi network transport vesicle|vesicular fraction	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity|transporter activity			ovary(2)	2	all_hematologic(106;0.112)					CTTAAAAGAGAAAAAAAAAAT	0.289													5	4	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	92020810	92020810	+	Intron	DEL	T	-	-	rs11311575		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92020810delT	uc003ulw.2	+						ANKIB1_uc010lew.1_Intron	NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTTTTGGTGATTTTTTTTTTC	0.279													9	4	---	---	---	---	
SGCE	8910	broad.mit.edu	37	7	94258955	94258956	+	Intron	DEL	AT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94258955_94258956delAT	uc003unl.2	-						SGCE_uc003unm.2_Intron|SGCE_uc003unn.2_Intron|SGCE_uc011kic.1_Intron|SGCE_uc011kid.1_Intron	NM_003919	NP_003910	O43556	SGCE_HUMAN	sarcoglycan, epsilon isoform 2						cell-matrix adhesion|muscle organ development	cytoplasm|cytoskeleton|integral to plasma membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(1)	1	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			ATATTTTATCATATATGTCTAT	0.252													57	28	---	---	---	---	
TMEM130	222865	broad.mit.edu	37	7	98453976	98453976	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98453976delC	uc003upo.2	-						TMEM130_uc011kiq.1_Intron|TMEM130_uc011kir.1_Intron|TMEM130_uc003upn.2_Intron	NM_001134450	NP_001127922	Q8N3G9	TM130_HUMAN	transmembrane protein 130 isoform a							Golgi membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AGCCAGGGCtccaggtcagct	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109336873	109336873	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109336873delA								C7orf66 (812236 upstream) : EIF3IP1 (262411 downstream)																							ctgactctataaaaaagagat	0.000													4	2	---	---	---	---	
DOCK4	9732	broad.mit.edu	37	7	111701671	111701671	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111701671delA	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Intron	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)				GCCACATTATAAAAAAAAACT	0.343													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	113314675	113314675	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113314675delC								LOC401397 (556038 upstream) : PPP1R3A (202207 downstream)																							aagacaGAGaccatcctttaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	115444567	115444567	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115444567delA								MDFIC (785304 upstream) : TFEC (130635 downstream)																							TCATCATTTGAAAGTACCTTC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	139924160	139924160	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139924160delA								LOC100134229 (44721 upstream) : SLC37A3 (109394 downstream)																							CCACCTAGGGAAAAAAAAATA	0.473													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141061162	141061162	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141061162delA								MRPS33 (346381 upstream) : AGK (189916 downstream)																							AACCAGTACTAAAAAAAAAAT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141221952	141221952	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141221952delC								MRPS33 (507171 upstream) : AGK (29126 downstream)																							CATAAAGAAACCATCTCTTAG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153503923	153503928	+	IGR	DEL	GGCAGG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153503923_153503928delGGCAGG								ACTR3B (951460 upstream) : DPP6 (80491 downstream)																							GGTGAGGAAAGGCAGGGGCAAAAAGA	0.393													3	4	---	---	---	---	
LOC100132707	100132707	broad.mit.edu	37	7	154731000	154731001	+	Intron	INS	-	C	C	rs11974501	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154731000_154731001insC	uc003wln.2	+						LOC100132707_uc011kvr.1_Intron|LOC100132707_uc003wlo.2_Intron					Homo sapiens cDNA FLJ32047 fis, clone NTONG2001137.												0						atctaaggtcaccatttttcat	0.089													392	250	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	154971006	154971006	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154971006delA								HTR5A (93547 upstream) : INSIG1 (118480 downstream)																							ccaaaacaggaaaaaaaaaat	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	22537562	22537563	+	IGR	DEL	GA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22537562_22537563delGA								BIN3 (10901 upstream) : EGR3 (7611 downstream)																							TGGATGGGCTGAGAGAGGGGAA	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	26522840	26522840	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26522840delT								DPYSL2 (7147 upstream) : ADRA1A (82827 downstream)																							tcctggctaattttatcaaca	0.000													4	2	---	---	---	---	
KCNU1	157855	broad.mit.edu	37	8	36776117	36776118	+	Intron	DEL	CA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36776117_36776118delCA	uc010lvw.2	+						KCNU1_uc003xjw.2_Intron	NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1							voltage-gated potassium channel complex	binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		ACCCCCCCACCACACACACACA	0.257													4	2	---	---	---	---	
ADAM18	8749	broad.mit.edu	37	8	39537956	39537956	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39537956delA	uc003xni.2	+						ADAM18_uc010lww.2_Intron|ADAM18_uc010lwx.2_Intron	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18						cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TCCTTATGTTAAAAAAAGTAC	0.259													4	2	---	---	---	---	
SNTG1	54212	broad.mit.edu	37	8	51366075	51366076	+	Intron	DEL	CT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51366075_51366076delCT	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				ggcttcaatgctcagaaacaac	0.168													4	2	---	---	---	---	
GGH	8836	broad.mit.edu	37	8	63929777	63929777	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63929777delA	uc003xuw.2	-							NM_003878	NP_003869	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase precursor						glutamine metabolic process	extracellular space|lysosome|melanosome	gamma-glutamyl-peptidase activity				0	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|L-Glutamic Acid(DB00142)	aaaAGAAACCAAAAAAAAAAC	0.179													4	2	---	---	---	---	
RIMS2	9699	broad.mit.edu	37	8	104922219	104922220	+	Intron	DEL	TA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104922219_104922220delTA	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron|RIMS2_uc003ylt.2_5'Flank	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TAGCACTCACTATATATATATA	0.282										HNSCC(12;0.0054)			10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	111283525	111283525	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111283525delT								KCNV1 (295449 upstream) : None (None downstream)																							GCTCTATGCATTTTTAACACA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	112916486	112916486	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112916486delC								None (None upstream) : CSMD3 (318675 downstream)																							aagagcccatccagagattct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	114542235	114542236	+	IGR	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114542235_114542236insT								CSMD3 (92993 upstream) : None (None downstream)																							GTTTTTGAGAGTTTTTTTTTCA	0.257													4	2	---	---	---	---	
ZHX2	22882	broad.mit.edu	37	8	123969537	123969537	+	Intron	DEL	A	-	-	rs67547249		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123969537delA	uc003ypk.1	+							NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2							cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CTGTGTTCACAAAAAAAAAAA	0.403													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130390288	130390289	+	IGR	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130390288_130390289delAC								None (None upstream) : GSDMC (370154 downstream)																							GCCCTGCAAAACACACACACAC	0.500													4	2	---	---	---	---	
FAM49B	51571	broad.mit.edu	37	8	130942822	130942823	+	Intron	DEL	AT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130942822_130942823delAT	uc003yss.2	-						FAM49B_uc003yst.2_Intron|FAM49B_uc003ysu.2_Intron|FAM49B_uc003ysv.2_Intron|FAM49B_uc003ysw.2_Intron|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)			TCAGTGCCACATACCAAAGACT	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134458998	134458998	+	IGR	DEL	A	-	-	rs34551206		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134458998delA								NDRG1 (149451 upstream) : ST3GAL1 (8093 downstream)																							CTGGCATACCAGGGGGGTCAG	0.567													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	135244660	135244660	+	IGR	DEL	A	-	-	rs112859771		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135244660delA								ST3GAL1 (660477 upstream) : ZFAT (245373 downstream)																							aggcaaaaagaaaaaaaaaag	0.000													7	5	---	---	---	---	
EIF2C2	27161	broad.mit.edu	37	8	141634105	141634106	+	Intron	INS	-	AGG	AGG	rs143064735	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141634105_141634106insAGG	uc003yvn.2	-						EIF2C2_uc010men.2_Intron|EIF2C2_uc010meo.2_Intron	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1						mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)			GTGATGGAGACAGGACAGGAGA	0.574													4	2	---	---	---	---	
SMARCA2	6595	broad.mit.edu	37	9	2039234	2039234	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2039234delT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		ctttacctgcttttttttttt	0.050													4	3	---	---	---	---	
SMARCA2	6595	broad.mit.edu	37	9	2088880	2088880	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2088880delT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		taattttagattttttttttt	0.333													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	2738092	2738092	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2738092delA								KCNV2 (8335 upstream) : KIAA0020 (66063 downstream)																							AGTAAGAGGTAAAAAAATGAG	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	15017688	15017689	+	Intron	INS	-	T	T	rs150778914	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15017688_15017689insT	uc003zln.1	-						LOC389705_uc010mid.1_Intron					Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																		TTTTGAAGTGATTTTTTTTAAA	0.332													6	6	---	---	---	---	
C9orf93	203238	broad.mit.edu	37	9	15578632	15578632	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15578632delT	uc003zmd.2	+						C9orf93_uc010mih.1_Intron|C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron|C9orf93_uc003zmc.2_Intron	NM_173550	NP_775821	Q6TFL3	CI093_HUMAN	hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)		TCTTATAAGATTTTTTTTTTC	0.199													2	5	---	---	---	---	
CNTLN	54875	broad.mit.edu	37	9	17308889	17308890	+	Intron	INS	-	T	T	rs144083775	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17308889_17308890insT	uc003zmz.2	+						CNTLN_uc003zmy.2_Intron|CNTLN_uc010mio.2_Intron	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)		taaattagttattttttGTGTT	0.178													13	6	---	---	---	---	
HAUS6	54801	broad.mit.edu	37	9	19076352	19076352	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19076352delA	uc003znk.2	-						HAUS6_uc011lmz.1_Intron|HAUS6_uc003znl.1_Intron|HAUS6_uc003znm.1_Intron	NM_017645	NP_060115	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2						accctgtctcaaaaaaaaata	0.000													4	2	---	---	---	---	
MTAP	4507	broad.mit.edu	37	9	21869899	21869900	+	Intron	INS	-	AT	AT	rs150809560	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21869899_21869900insAT	uc003zpi.1	+							NM_002451	NP_002442	Q13126	MTAP_HUMAN	5'-methylthioadenosine phosphorylase						nucleoside metabolic process	cytoplasm	phosphorylase activity|S-methyl-5-thioadenosine phosphorylase activity			central_nervous_system(1)	1		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)	Adenine(DB00173)	taaaatcccacatttatgatag	0.000													1	5	---	---	---	---	
FRMPD1	22844	broad.mit.edu	37	9	37676601	37676601	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37676601delG	uc004aag.1	+						FRMPD1_uc004aah.1_Intron	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1							cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		CAGCCCTACAGGAGGGAGAAG	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	38643838	38643838	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38643838delA								C9orf122 (20563 upstream) : CNTNAP3 (428928 downstream)																							TTGTGTGATTAAAAAAAAAAA	0.443													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67324302	67324302	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67324302delG								AQP7P1 (34810 upstream) : FAM27B (468628 downstream)																							ttcatctcatggggaaagtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68431239	68431242	+	IGR	DEL	GTAA	-	-	rs145348306		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68431239_68431242delGTAA								FAM27B (637050 upstream) : MIR1299 (570997 downstream)																							CAATCTTTGTGTAAGTATCTTTGT	0.309													11	5	---	---	---	---	
PIP5K1B	8395	broad.mit.edu	37	9	71487002	71487002	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71487002delA	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron|PIP5K1B_uc004agv.2_Intron	NM_003558	NP_003549	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)		TTCAGGAGGCAAACGTTGATT	0.468													4	2	---	---	---	---	
TRPM3	80036	broad.mit.edu	37	9	73569734	73569734	+	Intron	DEL	C	-	-	rs78164953		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73569734delC	uc004aid.2	-						TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron|TRPM3_uc004aii.2_Intron	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9						ccctacgcttcctggggtccc	0.174													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	76936512	76936512	+	IGR	DEL	C	-	-	rs3925038	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76936512delC								None (None upstream) : RORB (175740 downstream)																							ACAGCACATACGGTAAATTTC	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	78282842	78282842	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78282842delA								OSTF1 (520729 upstream) : PCSK5 (222718 downstream)																							ACCAAGACAGAAAAAAAAAGA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82517617	82517617	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82517617delA								TLE4 (175960 upstream) : None (None downstream)																							GTCTTGGTTTAAAAAAAAAAT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82835057	82835058	+	IGR	INS	-	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82835057_82835058insC								TLE4 (493400 upstream) : None (None downstream)																							gccccttttttccatataaggt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	88110830	88110830	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88110830delA								NTRK2 (472325 upstream) : AGTPBP1 (50625 downstream)																							atcaccaagcaaaacccctgc	0.189													4	2	---	---	---	---	
GOLM1	51280	broad.mit.edu	37	9	88708548	88708549	+	Intron	INS	-	TTAA	TTAA	rs150932544	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88708548_88708549insTTAA	uc004aol.2	-						GOLM1_uc010mqd.1_Intron|GOLM1_uc004aom.2_Intron	NM_016548	NP_057632	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1							Golgi apparatus|integral to plasma membrane					0						TACCTACTGGCTTAATTTAAAA	0.173													2	4	---	---	---	---	
FBP1	2203	broad.mit.edu	37	9	97372516	97372516	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97372516delC	uc004auw.3	-						FBP1_uc010mrl.2_Intron	NM_000507	NP_000498	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1						gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)	ATCACGGCAGCCTTCCCACCA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98770105	98770105	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98770105delG	uc010msa.1	+						uc011lun.1_Intron					RecName: Full=Uncharacterized protein C9orf102;																		gaacagggatgggaggcatgg	0.154													4	2	---	---	---	---	
CDC14B	8555	broad.mit.edu	37	9	99275128	99275130	+	Intron	DEL	TTT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99275128_99275130delTTT	uc004awj.2	-						CDC14B_uc004awk.2_Intron|CDC14B_uc004awl.2_Intron|CDC14B_uc004awi.2_Intron	NM_033331	NP_201588	O60729	CC14B_HUMAN	CDC14 homolog B isoform 2						activation of anaphase-promoting complex activity|DNA repair|G2/M transition DNA damage checkpoint	nucleolus|nucleoplasm	protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)				TCCTGTTGGCTTTTTTTTTTTAA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107250623	107250623	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107250623delT								SMC2 (346930 upstream) : OR13F1 (15921 downstream)																							TGAGGCCATGTTTTGGACATT	0.343													4	2	---	---	---	---	
NIPSNAP3B	55335	broad.mit.edu	37	9	107541733	107541734	+	Intron	DEL	AG	-	-	rs72048032		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107541733_107541734delAG	uc004bcj.1	+									Q9BS92	NPS3B_HUMAN	Homo sapiens cDNA FLJ11275 fis, clone PLACE1009375.											pancreas(1)|skin(1)	2						TTCAACAAAAAGAACCctctgc	0.099													3	4	---	---	---	---	
ABCA1	19	broad.mit.edu	37	9	107559855	107559856	+	Intron	INS	-	G	G	rs142547055	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107559855_107559856insG	uc004bcl.2	-							NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	cttttgaaaacggacattcaca	0.099													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111295377	111295377	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111295377delA								None (None upstream) : ACTL7B (321494 downstream)																							CAACAACAACAAAAAATACCT	0.413													4	2	---	---	---	---	
MUSK	4593	broad.mit.edu	37	9	113489860	113489861	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113489860_113489861insA	uc004bey.2	+						MUSK_uc004bex.2_Intron	NM_005592	NP_005583	O15146	MUSK_HUMAN	skeletal muscle receptor tyrosine kinase						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|ovary(2)|central_nervous_system(1)	6						ATAACCTTGTCAACCTTGGCTA	0.470													3	3	---	---	---	---	
HSDL2	84263	broad.mit.edu	37	9	115195223	115195223	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115195223delT	uc004bga.1	+						HSDL2_uc011lwv.1_Intron|HSDL2_uc004bgb.1_Intron|HSDL2_uc004bgc.1_Intron|HSDL2_uc011lww.1_Intron	NM_032303	NP_115679	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2							peroxisome	oxidoreductase activity|sterol binding				0						aatttttgtattttttttttt	0.000													5	3	---	---	---	---	
SNX30	401548	broad.mit.edu	37	9	115632553	115632553	+	3'UTR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115632553delT	uc004bgj.3	+	9					SNX30_uc004bgi.3_3'UTR	NM_001012994	NP_001013012	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30						cell communication|protein transport	cytoplasm	phosphatidylinositol binding				0						TAAGCAGTAGTTTTTTTGTTG	0.403													4	2	---	---	---	---	
DEC1	50514	broad.mit.edu	37	9	118106171	118106171	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118106171delA	uc004bjk.1	+						DEC1_uc004bjl.1_Intron	NM_017418	NP_059114	Q9P2X7	DEC1_HUMAN	deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1						atgaaaaaggaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120521832	120521835	+	IGR	DEL	TGTG	-	-	rs72113530		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120521832_120521835delTGTG								TLR4 (42068 upstream) : None (None downstream)																							GGCCAGAAGTtgtgtgtgtgtgtg	0.304													4	5	---	---	---	---	
MRRF	92399	broad.mit.edu	37	9	125047235	125047235	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125047235delA	uc004bmb.2	+						MRRF_uc004bmc.2_Intron|MRRF_uc011lyq.1_Intron|MRRF_uc010mvz.1_Intron|MRRF_uc010mwa.2_Intron|MRRF_uc011lyr.1_Intron|MRRF_uc004bmd.2_Intron|MRRF_uc004bme.2_Intron	NM_138777	NP_620132	Q96E11	RRFM_HUMAN	mitochondrial ribosome recycling factor isoform						ribosome disassembly|translation	mitochondrion	sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3						cctgctaattaaaaaaaaatg	0.000													4	2	---	---	---	---	
PTGS1	5742	broad.mit.edu	37	9	125152239	125152240	+	Intron	INS	-	A	A	rs112568439	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125152239_125152240insA	uc004bmg.1	+						PTGS1_uc011lys.1_Intron|PTGS1_uc010mwb.1_Intron|PTGS1_uc004bmf.1_Intron|PTGS1_uc004bmh.1_Intron|PTGS1_uc011lyt.1_Intron	NM_000962	NP_000953	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 isoform 1						cyclooxygenase pathway|hormone biosynthetic process|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process	endoplasmic reticulum membrane|Golgi apparatus|microsome|plasma membrane	heme binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peroxidase activity|prostaglandin-endoperoxide synthase activity			ovary(1)|skin(1)	2					Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dipyrone(DB04817)|Etodolac(DB00749)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Mesalazine(DB00244)|Minoxidil(DB00350)|Nabumetone(DB00461)|Naproxen(DB00788)|Phenacetin(DB03783)|Piroxicam(DB00554)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Tolmetin(DB00500)	agacagtgtctaaaaaaaaacc	0.233													4	3	---	---	---	---	
RC3H2	54542	broad.mit.edu	37	9	125667728	125667728	+	5'Flank	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125667728delC	uc010mwc.1	-						RC3H2_uc004bnc.2_5'Flank|RC3H2_uc004bne.3_5'Flank|RC3H2_uc011lzg.1_5'Flank	NM_001100588	NP_001094058	Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type zinc finger domains 2							cell surface|endomembrane system|membrane|membrane fraction|perinuclear region of cytoplasm	DNA binding|zinc ion binding			ovary(2)|lung(2)	4						AGCGTAGTAGCCCCAGCCACC	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	128138492	128138492	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128138492delT								GAPVD1 (11203 upstream) : MAPKAP1 (61182 downstream)																							aaatctgtacttttagctact	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	128198171	128198171	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128198171delT								GAPVD1 (70882 upstream) : MAPKAP1 (1503 downstream)																							CCTCCCAGCCTCTTAATCCAC	0.582													4	2	---	---	---	---	
RALGPS1	9649	broad.mit.edu	37	9	129816044	129816044	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129816044delA	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron	NM_014636	NP_055451	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1						AAGGGCTTTTAAAATACTCAG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137745540	137745540	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137745540delT	uc004cff.2	-											Homo sapiens cDNA clone IMAGE:5468304, partial cds.																		AACATCTTGCTTTTTTTCTTT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137791283	137791283	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137791283delA								FCN2 (11917 upstream) : FCN1 (10153 downstream)																							tttagaactgaaaaatgtaac	0.000													4	2	---	---	---	---	
DIP2C	22982	broad.mit.edu	37	10	505480	505480	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:505480delG	uc001ifp.2	-						DIP2C_uc009xhk.1_Intron	NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		TGCTGCACATGGGTTCTAGTA	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	772825	772825	+	IGR	DEL	C	-	-	rs111690924		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:772825delC								DIP2C (37217 upstream) : LARP4B (82659 downstream)																							catccactcaccaagcaccgt	0.159													2	4	---	---	---	---	
GTPBP4	23560	broad.mit.edu	37	10	1041446	1041447	+	Intron	DEL	AG	-	-	rs140435045		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1041446_1041447delAG	uc001ift.2	+						GTPBP4_uc010qac.1_Intron|GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		ttgggagcaaagagagggaatt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2833502	2833502	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2833502delA								None (None upstream) : PFKP (276250 downstream)																							GGTCGGATTTAAAAAAAAAGA	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	7020365	7020368	+	IGR	DEL	GAAT	-	-	rs138007072		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7020365_7020368delGAAT								PRKCQ (398127 upstream) : SFMBT2 (183881 downstream)																							atacacaaacgaatgaatgaacga	0.348													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	7149353	7149353	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7149353delG								PRKCQ (527115 upstream) : SFMBT2 (54896 downstream)																							GCTCAGGCTTGGGAGGCCTGG	0.493													4	2	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12501503	12501503	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12501503delA	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		CAGAAAATTGAAAAAAAAACC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	13452526	13452526	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13452526delG								SEPHS1 (62246 upstream) : BEND7 (27958 downstream)																							TTTGGGATCTGGTCTCTGGCA	0.507													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	13856090	13856090	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13856090delT	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						atggatttgattttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	19518628	19518628	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19518628delA								ARL5B (551688 upstream) : PLXDC2 (586744 downstream)																							AACAAACTATAACAACAACAG	0.393													0	7	---	---	---	---	
ARHGAP21	57584	broad.mit.edu	37	10	24885172	24885175	+	Intron	DEL	GAAA	-	-	rs144588497		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24885172_24885175delGAAA	uc001isb.2	-						ARHGAP21_uc010qdb.1_Intron	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21						signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8						CAAAGAGACTGAAAGAAAGAGAGG	0.358													3	3	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	57348441	57348441	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57348441delA	uc001jjv.1	-							NM_001142770	NP_001136242	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ATCATTTCTGAAAAAAAAAAT	0.284										HNSCC(58;0.16)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	60677700	60677701	+	IGR	DEL	CT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60677700_60677701delCT								BICC1 (88855 upstream) : PHYHIPL (258647 downstream)																							CTGTCAGGCACTCTCTCTCTCT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	62587743	62587743	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62587743delA								CDK1 (33139 upstream) : RHOBTB1 (41457 downstream)																							AATTAGTGGGAAAGCTGCGTG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	73135480	73135480	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73135480delC								SLC29A3 (12335 upstream) : CDH23 (21224 downstream)																							AGGCAGGAATCCCCAAACCCC	0.338													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	84078463	84078464	+	Intron	DEL	TT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84078463_84078464delTT	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		GTCACCACTCTTCTCACTGTTG	0.391													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	84730584	84730584	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84730584delA	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron|NRG3_uc001kcr.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		atagttttataaaggttttTG	0.060													4	2	---	---	---	---	
FAM190B	54462	broad.mit.edu	37	10	86140277	86140278	+	Intron	INS	-	T	T	rs138543680	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86140277_86140278insT	uc001kdh.1	+						FAM190B_uc010qmd.1_Intron	NM_018999	NP_061872	Q9H7U1	F190B_HUMAN	granule cell antiserum positive 14											ovary(3)|skin(1)	4						atgctcatatatggcgtgtgtg	0.030													4	3	---	---	---	---	
FAM190B	54462	broad.mit.edu	37	10	86217822	86217822	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86217822delT	uc001kdh.1	+						FAM190B_uc010qmd.1_Intron|FAM190B_uc001kdi.1_Intron|FAM190B_uc010qme.1_Intron	NM_018999	NP_061872	Q9H7U1	F190B_HUMAN	granule cell antiserum positive 14											ovary(3)|skin(1)	4						aaatttatcatttttttgcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	89813887	89813887	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89813887delG								PTEN (85356 upstream) : RNLS (78170 downstream)																							GTGGGCGTGTGGAGCTTGGGT	0.244													4	2	---	---	---	---	
RNLS	55328	broad.mit.edu	37	10	89966577	89966577	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89966577delT	uc010qms.1	-									Q5VYX0	RNLS_HUMAN	SubName: Full=cDNA FLJ55083, highly similar to Renalase (EC 1.4.-.-);							extracellular region	oxidoreductase activity			ovary(1)	1						AAAGAAGGCCTTTTTTTTGTA	0.393													6	3	---	---	---	---	
TM9SF3	56889	broad.mit.edu	37	10	98340022	98340023	+	Intron	DEL	TG	-	-	rs71486801		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98340022_98340023delTG	uc001kmm.3	-						TM9SF3_uc010qot.1_Intron	NM_020123	NP_064508	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3 precursor							integral to membrane	binding				0		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		GCTTCATCTTtgtgtgtgtgtg	0.218													4	2	---	---	---	---	
C10orf12	26148	broad.mit.edu	37	10	98672818	98672818	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98672818delT	uc009xvg.1	+						LCOR_uc001kmr.2_Intron|LCOR_uc001kms.1_Intron|LCOR_uc001kmt.1_Intron|LCOR_uc001kmu.1_Intron	NM_015652	NP_056467	Q8N655	CJ012_HUMAN	hypothetical protein LOC26148											skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		tttaaagcacttttttttttt	0.000													3	3	---	---	---	---	
C10orf28	27291	broad.mit.edu	37	10	99994585	99994585	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99994585delT	uc001kow.3	+						C10orf28_uc001kox.3_Intron|C10orf28_uc001koy.3_Intron|C10orf28_uc009xvx.2_Intron|C10orf28_uc009xvy.2_Intron|C10orf28_uc001koz.3_Intron	NM_014472	NP_055287	Q4KMY3	Q4KMY3_HUMAN	growth inhibition and differentiation related								nucleotide binding			large_intestine(1)|skin(1)	2		Colorectal(252;0.234)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)		ATATTGGTGATTTTTTTTTTC	0.333													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102597000	102597000	+	IGR	DEL	T	-	-	rs113959996		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102597000delT								PAX2 (7303 upstream) : FAM178A (75326 downstream)																							GCTAATGTTATTTTTTTTTTA	0.308													4	3	---	---	---	---	
ACTR1A	10121	broad.mit.edu	37	10	104242538	104242538	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104242538delA	uc001kvv.2	-						ACTR1A_uc010qqn.1_Intron|ACTR1A_uc010qqo.1_Intron	NM_005736	NP_005727	P61163	ACTZ_HUMAN	ARP1 actin-related protein 1 homolog A,						G2/M transition of mitotic cell cycle|vesicle-mediated transport	centrosome|cytosol|dynactin complex	ATP binding			central_nervous_system(1)	1		Colorectal(252;0.122)		Epithelial(162;5.34e-09)|all cancers(201;1.43e-07)|BRCA - Breast invasive adenocarcinoma(275;0.222)		ctgctgagctaaaaaaaaaaa	0.005													4	4	---	---	---	---	
GSTO1	9446	broad.mit.edu	37	10	106026599	106026600	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106026599_106026600insA	uc001kya.2	+						GSTO2_uc001kyb.2_5'Flank	NM_004832	NP_004823	P78417	GSTO1_HUMAN	glutathione-S-transferase omega 1						xenobiotic metabolic process	cytosol	glutathione transferase activity|monodehydroascorbate reductase (NADH) activity				0		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)	ACATTATTTTCCAAATTCTGTT	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	106375807	106375807	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106375807delT								CCDC147 (160968 upstream) : SORCS3 (25052 downstream)																							CCTGAGTTCCTTTTTTTTCTC	0.463													4	2	---	---	---	---	
SORCS1	114815	broad.mit.edu	37	10	108582396	108582396	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108582396delA	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		AGCGGTACCCAAAAAAAGATC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	120307174	120307174	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120307174delT								C10orf84 (205335 upstream) : PRLHR (45742 downstream)																							CTTTCACTGCTTTTCGGAATC	0.527													4	2	---	---	---	---	
FGFR2	2263	broad.mit.edu	37	10	123353106	123353106	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123353106delG	uc010qtk.1	-						FGFR2_uc010qtg.1_Intron|FGFR2_uc010qth.1_Intron|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Intron|FGFR2_uc010qtl.1_Intron|FGFR2_uc010qtm.1_Intron|FGFR2_uc001lfl.3_Intron|FGFR2_uc001lfm.2_Intron|FGFR2_uc001lfn.3_Intron|FGFR2_uc010qtn.1_Intron|FGFR2_uc010qto.1_Intron|FGFR2_uc001lfo.1_Intron|FGFR2_uc010qtp.1_Intron|FGFR2_uc010qtq.1_Intron	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1						angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)	ACCACGATCTGGTGCTCTTAG	0.498		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				7	6	---	---	---	---	
HTRA1	5654	broad.mit.edu	37	10	124261629	124261630	+	Intron	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124261629_124261630delTG	uc001lgj.2	+							NM_002775	NP_002766	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1 precursor						proteolysis|regulation of cell growth	extracellular space	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				AGGTGGACTTTGTGTTTTctta	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125961023	125961023	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125961023delG								CHST15 (107817 upstream) : OAT (124849 downstream)																							AAGAAAAGAAGGGAGCAACAA	0.468													4	2	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127575513	127575516	+	Intron	DEL	TCTT	-	-	rs143617895		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127575513_127575516delTCTT	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)				TTTCCCCATGTCTTTCTGTCTCTT	0.412													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130776111	130776111	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130776111delC								MKI67 (851643 upstream) : MGMT (489343 downstream)																							AGCACAGAGTCCCCAGGCCCC	0.607													4	2	---	---	---	---	
TRIM21	6737	broad.mit.edu	37	11	4406233	4406233	+	3'UTR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4406233delA	uc001lyy.1	-	7						NM_003141	NP_003132	P19474	RO52_HUMAN	tripartite motif protein 21						cell cycle|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein deubiquitination|positive regulation of cell cycle|protein autoubiquitination|protein destabilization|protein monoubiquitination|protein polyubiquitination|protein trimerization	cytoplasmic mRNA processing body|nucleus	DNA binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|lung(1)	4		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		TGGAGAGGAGAAAAAAAAAAC	0.348													3	4	---	---	---	---	
OR51B5	282763	broad.mit.edu	37	11	5459254	5459254	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5459254delT	uc001maq.1	-						HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron	NM_001005567	NP_001005567	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTCATTATTGTTATAGGATTG	0.378													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	6892631	6892632	+	IGR	INS	-	AT	AT	rs147909070	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6892631_6892632insAT								OR10A2 (734 upstream) : OR10A4 (5247 downstream)																							ACATTCATGACAGAAAATCTCA	0.391													3	4	---	---	---	---	
SBF2	81846	broad.mit.edu	37	11	10133501	10133501	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10133501delA	uc001mib.2	-						SBF2_uc001mif.3_Intron	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		TATCAAGGGCAAAATCTCCTA	0.234													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21372815	21372815	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21372815delT	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						tgagtgaatattttttttgtt	0.085													2	5	---	---	---	---	
LUZP2	338645	broad.mit.edu	37	11	24619146	24619146	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24619146delA	uc001mqs.2	+						LUZP2_uc009yif.2_Intron|LUZP2_uc009yig.2_Intron	NM_001009909	NP_001009909	Q86TE4	LUZP2_HUMAN	leucine zipper protein 2 precursor							extracellular region				ovary(1)|skin(1)	2						AAAATTAGCTAAGCATCAGAC	0.313													4	2	---	---	---	---	
CAT	847	broad.mit.edu	37	11	34482536	34482536	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34482536delA	uc001mvm.2	+						CAT_uc009ykc.1_Intron|CAT_uc001mvn.2_5'Flank	NM_001752	NP_001743	P04040	CATA_HUMAN	catalase						hydrogen peroxide catabolic process|negative regulation of apoptosis|positive regulation of cell division|protein tetramerization|purine base metabolic process|purine nucleotide catabolic process|UV protection	peroxisomal matrix|peroxisomal membrane	catalase activity|heme binding|NADP binding|protein homodimerization activity			ovary(2)|pancreas(1)	3		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	ATGCAGAAGGAAAAAAAAAAG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	34839282	34839282	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34839282delA								EHF (156201 upstream) : APIP (57432 downstream)																							tttattacctacatagacagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	40025193	40025193	+	IGR	DEL	T	-	-	rs66811275		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40025193delT								None (None upstream) : LRRC4C (110560 downstream)																							ATGACTGATATTTAATGAGTC	0.308													3	3	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	40962684	40962685	+	Intron	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40962684_40962685insT	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)				AAAAAATTCAATTAGAAATGAG	0.277													4	2	---	---	---	---	
GPR137	56834	broad.mit.edu	37	11	64049205	64049205	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64049205delT	uc009ypj.1	+						BAD_uc001nzd.2_Intron|BAD_uc001nzc.2_Intron|BAD_uc009ypk.2_Intron|GPR137_uc010rni.1_5'Flank	NM_020155	NP_064540	Q96N19	G137A_HUMAN	G protein-coupled receptor 137							integral to membrane				central_nervous_system(1)	1						ctcttaactcttttttttgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	64179106	64179107	+	IGR	DEL	TG	-	-	rs34513839		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64179106_64179107delTG								RPS6KA4 (39420 upstream) : SLC22A11 (143991 downstream)																							agtgacaaattgtgtgtgtgtg	0.005													4	2	---	---	---	---	
CDC42BPG	55561	broad.mit.edu	37	11	64592215	64592215	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64592215delT	uc001obs.3	-							NM_017525	NP_059995	Q6DT37	MRCKG_HUMAN	CDC42 binding protein kinase gamma (DMPK-like)						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|centrosome	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(3)|central_nervous_system(1)	4						CTCAAAGTCCttttttttttc	0.249													6	3	---	---	---	---	
MRPL11	65003	broad.mit.edu	37	11	66203963	66203963	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66203963delA	uc001ohz.3	-						MRPL11_uc001ohy.3_Intron|MRPL11_uc001oia.3_Intron	NM_016050	NP_057134	Q9Y3B7	RM11_HUMAN	mitochondrial ribosomal protein L11 isoform a						translation		structural constituent of ribosome				0						TGCTCCCAGTAAAAAAAAAAA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69713252	69713255	+	IGR	DEL	CACA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69713252_69713255delCACA								FGF3 (79060 upstream) : ANO1 (211153 downstream)																							cacacacactcacacacacacaca	0.338													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79449738	79449738	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79449738delG								ODZ4 (298043 upstream) : None (None downstream)																							ggagttcctagggaaactgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	82116207	82116207	+	5'Flank	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82116207delA	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																		AAATCATGAGAAAAAAAAAAT	0.204													3	4	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83183022	83183023	+	Intron	INS	-	GGA	GGA	rs145240151	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83183022_83183023insGGA	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)				AAGAAACATTTGGAGGAGTTTT	0.401													1	5	---	---	---	---	
SYTL2	54843	broad.mit.edu	37	11	85461018	85461018	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85461018delA	uc010rth.1	-						SYTL2_uc010rtg.1_Intron|SYTL2_uc010rti.1_Intron|SYTL2_uc010rtj.1_Intron|SYTL2_uc001pbf.3_Intron	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g						intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CTGACCACCTAAAAAGGCTTC	0.443													4	2	---	---	---	---	
CCDC83	220047	broad.mit.edu	37	11	85611141	85611141	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85611141delA	uc001pbh.1	+						CCDC83_uc001pbg.1_Intron|CCDC83_uc001pbi.1_Intron|CCDC83_uc001pbj.1_Intron	NM_173556	NP_775827	Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83											skin(1)	1		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				GAGGATGTGCAAAACTCAATG	0.433													4	2	---	---	---	---	
CCDC81	60494	broad.mit.edu	37	11	86112755	86112755	+	Intron	DEL	A	-	-	rs74633923		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86112755delA	uc001pbx.1	+						CCDC81_uc001pbw.1_Intron|CCDC81_uc010rtq.1_Intron|CCDC81_uc001pby.1_Intron	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81 isoform 1											skin(1)	1		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				gactgaaattaaaaaaaaaat	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	94818906	94818906	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94818906delA								SFRS2B (14519 upstream) : ENDOD1 (4111 downstream)																							GACTATTGGGAAAAAAAAAAA	0.303													6	4	---	---	---	---	
MTMR2	8898	broad.mit.edu	37	11	95580632	95580632	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95580632delG	uc001pfu.2	-						MTMR2_uc001pfv.2_Intron|MTMR2_uc001pfs.2_Intron|MTMR2_uc001pft.2_Intron|MTMR2_uc010ruj.1_Intron	NM_016156	NP_057240	Q13614	MTMR2_HUMAN	myotubularin-related protein 2 isoform 1							nucleus	inositol or phosphatidylinositol phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ggaatctgaaggatggttcga	0.075													4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	95854251	95854252	+	Intron	INS	-	A	A	rs75486776		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95854251_95854252insA	uc001pfw.1	-							NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				AGAGTCAGGGGGGAGTGAAGGA	0.480			T	MECT1|CRTC3	salivary gland mucoepidermoid								4	2	---	---	---	---	
DYNC2H1	79659	broad.mit.edu	37	11	103082953	103082954	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103082953_103082954insA	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TCTTTCACATGAAAACATTTTT	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107627601	107627601	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107627601delA								SLN (44814 upstream) : SLC35F2 (34119 downstream)																							GACAATATACAAAAAAAAACA	0.423													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	108519708	108519708	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108519708delA								EXPH5 (55334 upstream) : DDX10 (16108 downstream)																							catagaggagaaaaaaaataa	0.000													4	2	---	---	---	---	
C11orf93	120376	broad.mit.edu	37	11	111175504	111175504	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111175504delA	uc010rwf.1	+						C11orf92_uc001ple.2_Intron	NM_001136105	NP_001129577	A8K830	CK093_HUMAN	hypothetical protein LOC120376												0						TCAAACATTGAAAAAAAAAAA	0.299													5	4	---	---	---	---	
ZBTB16	7704	broad.mit.edu	37	11	113971165	113971165	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113971165delC	uc001pop.2	+						ZBTB16_uc001poo.1_Intron|ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		ACCCTCTATGCCCCCTACTCC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114817558	114817559	+	IGR	DEL	TA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114817558_114817559delTA								FAM55B (239906 upstream) : CADM1 (222394 downstream)																							CATGTTTGTCTATATTCTTATt	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115019022	115019023	+	IGR	DEL	GT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115019022_115019023delGT								FAM55B (441370 upstream) : CADM1 (20930 downstream)																							tgggagggtggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
TRAPPC4	51399	broad.mit.edu	37	11	118891140	118891140	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118891140delT	uc010ryo.1	+						RPS25_uc001pun.2_5'Flank|TRAPPC4_uc010ryn.1_3'UTR|TRAPPC4_uc010ryp.1_Intron|TRAPPC4_uc001pup.2_Intron|TRAPPC4_uc010ryq.1_Intron	NM_016146	NP_057230	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4						dendrite development|ER to Golgi vesicle-mediated transport	cis-Golgi network|dendrite|endoplasmic reticulum|Golgi stack|synaptic vesicle	protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		GGCACAAttcttttttttttt	0.274													4	2	---	---	---	---	
PVRL1	5818	broad.mit.edu	37	11	119552953	119552953	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119552953delG	uc001pwv.2	-						PVRL1_uc001pwu.1_Intron|PVRL1_uc001pww.2_Intron	NM_002855	NP_002846	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 isoform 1						adherens junction organization|cell junction assembly|entry of virus into host cell|heterophilic cell-cell adhesion|homophilic cell adhesion|immune response	cell-cell adherens junction|extracellular region|integral to membrane	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity				0		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		CAGAGGAGCAGGGATCACCAC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	121223078	121223078	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121223078delC								SC5DL (38961 upstream) : SORL1 (99883 downstream)																							GGCAGATGCTCCCAGTCTCAG	0.537													4	2	---	---	---	---	
ARHGAP32	9743	broad.mit.edu	37	11	128936406	128936407	+	Intron	INS	-	A	A			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128936406_128936407insA	uc009zcp.2	-						ARHGAP32_uc009zcq.1_Intron|ARHGAP32_uc001qfb.2_Intron	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1						cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5						CTTGTTGATATATTGTTATGAG	0.302													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	130403426	130403426	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130403426delC								ADAMTS15 (59711 upstream) : SNX19 (342341 downstream)																							TTCAAACCGTCCCAGACTGTG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	130440169	130440170	+	IGR	DEL	GT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130440169_130440170delGT								ADAMTS15 (96454 upstream) : SNX19 (305597 downstream)																							ACgtgtgtgcgtgtgtgtgtgt	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	130516590	130516591	+	IGR	DEL	GC	-	-	rs143677873	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130516590_130516591delGC								ADAMTS15 (172875 upstream) : SNX19 (229176 downstream)																							GTTCAGGAAAGCgtgtgtgtgt	0.386													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133179108	133179108	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133179108delG	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		gaagaattctggcagatactg	0.000													4	2	---	---	---	---	
WNK1	65125	broad.mit.edu	37	12	936687	936689	+	Intron	DEL	TTG	-	-	rs80189368		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:936687_936689delTTG	uc001qio.3	+						WNK1_uc001qip.3_Intron	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			ATAGCCTTTTttgttgttgttgt	0.143													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	1779776	1779776	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1779776delT								WNT5B (23399 upstream) : ADIPOR2 (20471 downstream)																							AAATTACACCTTTTTTTCATA	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8180725	8180725	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8180725delC								SLC2A3 (91833 upstream) : FOXJ2 (4634 downstream)																							aataacatttccccacctcgt	0.184													4	2	---	---	---	---	
RPL13AP20	387841	broad.mit.edu	37	12	13026142	13026142	+	5'Flank	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13026142delT	uc010sho.1	+							NR_003932				SubName: Full=Ribosomal protein L13a variant; Flags: Fragment;												0						CTCTGAGGGCttttttttttc	0.249													4	3	---	---	---	---	
GRIN2B	2904	broad.mit.edu	37	12	14040349	14040349	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14040349delA	uc001rbt.2	-							NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TCTTCACAGGAAAAAAAAGTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	17387780	17387780	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17387780delA								LMO3 (625022 upstream) : RERGL (846024 downstream)																							ACTCCTGAGGAGCATCCAAAT	0.303													4	2	---	---	---	---	
PIK3C2G	5288	broad.mit.edu	37	12	18588317	18588317	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18588317delC	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561	O75747	P3C2G_HUMAN	phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)				TCTTACCTATCCCCAGTCCAT	0.438													4	2	---	---	---	---	
GYS2	2998	broad.mit.edu	37	12	21715578	21715585	+	Intron	DEL	GGGAGAAT	-	-	rs72575038		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21715578_21715585delGGGAGAAT	uc001rfb.2	-							NM_021957	NP_068776	P54840	GYS2_HUMAN	glycogen synthase 2						glucose metabolic process|glycogen biosynthetic process|response to glucose stimulus	cortical actin cytoskeleton|cytosol|ectoplasm|insoluble fraction|soluble fraction	glycogen (starch) synthase activity|protein homodimerization activity			lung(1)|skin(1)	2						AACATAGAAGGGGAGAATGGGATAAGCT	0.173													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	25937421	25937421	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25937421delA								IFLTD1 (135933 upstream) : RASSF8 (174548 downstream)																							AATACACATTAAAAAATCACT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	29068531	29068532	+	IGR	DEL	CC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29068531_29068532delCC								CCDC91 (365433 upstream) : FAR2 (233700 downstream)																							acagggatgtcccacaaagccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31400395	31400397	+	IGR	DEL	CCA	-	-	rs150244902		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31400395_31400397delCCA								DDX11 (142670 upstream) : FAM60A (33130 downstream)																							CAACCACCACCCACCAACACCCA	0.389													3	4	---	---	---	---	
ALG10	84920	broad.mit.edu	37	12	34175313	34175314	+	5'UTR	INS	-	A	A	rs145516165	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34175313_34175314insA	uc001rlm.2	+	1						NM_032834	NP_116223	Q5BKT4	AG10A_HUMAN	asparagine-linked glycosylation 10 homolog						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			skin(1)	1	Lung NSC(5;3.82e-05)|Acute lymphoblastic leukemia(23;0.0142)|all_hematologic(23;0.0429)	Lung NSC(34;0.204)|all_lung(34;0.235)				ATGCGATTGAGAGGGTAATCAT	0.584											OREG0021730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	41996653	41996653	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41996653delA								PDZRN4 (28269 upstream) : GXYLT1 (478997 downstream)																							taaaatatgtaaaaaatagta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	43374452	43374452	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43374452delC								PRICKLE1 (390880 upstream) : ADAMTS20 (373561 downstream)																							GGGAAGGGAGCCAGTTATACA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	45396983	45396984	+	IGR	INS	-	A	A	rs138818519	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45396983_45396984insA								NELL2 (89272 upstream) : DBX2 (11555 downstream)																							cctgcagtcacactgcctcctt	0.000													3	4	---	---	---	---	
SLC38A1	81539	broad.mit.edu	37	12	46617047	46617047	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46617047delA	uc001rpa.2	-						SLC38A1_uc001rpb.2_Intron|SLC38A1_uc001rpc.2_Intron|SLC38A1_uc001rpd.2_Intron|SLC38A1_uc001rpe.2_Intron|SLC38A1_uc010slh.1_Intron|SLC38A1_uc009zkj.1_Intron	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1						cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			aaatggggctaatacctacct	0.085													4	2	---	---	---	---	
ATF1	466	broad.mit.edu	37	12	51203602	51203603	+	Intron	INS	-	TGTTT	TGTTT	rs71443204		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51203602_51203603insTGTTT	uc001rww.3	+						ATF1_uc010smu.1_Intron	NM_005171	NP_005162	P18846	ATF1_HUMAN	activating transcription factor 1						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|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				EWSR1/ATF1(323)|FUS/ATF1(4)	soft_tissue(321)|ovary(2)|NS(2)|bone(2)|skin(2)	329						ACATTAGATACtgttttgtttt	0.025			T	EWSR1|FUS	malignant melanoma of soft parts |angiomatoid fibrous histiocytoma 								5	5	---	---	---	---	
CALCOCO1	57658	broad.mit.edu	37	12	54105694	54105695	+	3'UTR	DEL	GA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54105694_54105695delGA	uc001sef.2	-	15					CALCOCO1_uc001see.2_3'UTR|CALCOCO1_uc010som.1_3'UTR|CALCOCO1_uc010son.1_3'UTR|CALCOCO1_uc001seh.2_3'UTR|CALCOCO1_uc009znd.2_3'UTR|CALCOCO1_uc001seg.2_3'UTR	NM_020898	NP_065949	Q9P1Z2	CACO1_HUMAN	coiled-coil transcriptional coactivator isoform						steroid hormone receptor signaling pathway|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm	armadillo repeat domain binding|beta-catenin binding|ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|sequence-specific DNA binding|transcription regulatory region DNA binding			ovary(1)	1						gtgtgtgcatgagtgtgtattt	0.356													119	59	---	---	---	---	
MSRB3	253827	broad.mit.edu	37	12	65801707	65801708	+	Intron	DEL	GC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65801707_65801708delGC	uc001ssn.2	+						MSRB3_uc001ssm.2_Intron|MSRB3_uc009zqp.2_Intron	NM_198080	NP_932346	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		ccattgctttgcttacattatc	0.000													4	2	---	---	---	---	
CNOT2	4848	broad.mit.edu	37	12	70732857	70732858	+	Intron	DEL	TA	-	-	rs112904988	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70732857_70732858delTA	uc001svv.2	+						CNOT2_uc009zro.2_Intron|CNOT2_uc009zrp.2_Intron|CNOT2_uc009zrq.2_Intron|CNOT2_uc001svw.1_Intron	NM_014515	NP_055330	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	protein binding|RNA polymerase II transcription cofactor activity				0	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			tgtgtgtgtgtatatatatata	0.000													4	2	---	---	---	---	
PTPRB	5787	broad.mit.edu	37	12	71030067	71030067	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71030067delT	uc001swc.3	-						PTPRB_uc001swa.3_Intron|PTPRB_uc001swd.3_Intron|PTPRB_uc009zrr.1_Intron|PTPRB_uc001swe.2_Intron	NM_001109754	NP_001103224	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)			ACTCCCCATCTTTTTTTTTTT	0.299													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	78113692	78113692	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78113692delT								E2F7 (654332 upstream) : NAV3 (111377 downstream)																							tgaagccatcttgttctcggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80829464	80829464	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80829464delT								PPP1R12A (500229 upstream) : PTPRQ (8662 downstream)																							TGCTAAAAGCTTTGATGTAAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	88643313	88643314	+	IGR	INS	-	CA	CA	rs61942776		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88643313_88643314insCA								TMTC3 (49650 upstream) : KITLG (243255 downstream)																							tttatgagacccacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89121908	89121908	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89121908delA								KITLG (147670 upstream) : DUSP6 (619931 downstream)																							aaaagatcagaaagattggta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89720763	89720763	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89720763delA								KITLG (746525 upstream) : DUSP6 (21076 downstream)																							AAGGTTACAGAAAAAAAAATG	0.388													4	2	---	---	---	---	
DCN	1634	broad.mit.edu	37	12	91558156	91558156	+	Intron	DEL	A	-	-	rs11106023		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91558156delA	uc001tbs.2	-						DCN_uc001tbo.2_Intron|DCN_uc001tbp.2_Intron|DCN_uc001tbq.2_Intron|DCN_uc001tbr.2_Intron|DCN_uc001tbt.2_Intron|DCN_uc001tbu.2_Intron	NM_133503	NP_598010	P07585	PGS2_HUMAN	decorin isoform a preproprotein						organ morphogenesis	extracellular space				central_nervous_system(2)|ovary(1)|lung(1)	4						aaaaaaaaTTAAAAAAAAAAG	0.070													6	3	---	---	---	---	
TMCC3	57458	broad.mit.edu	37	12	94971958	94971958	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94971958delA	uc001tdj.2	-						TMCC3_uc001tdi.2_Intron	NM_020698	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3							integral to membrane				ovary(1)|skin(1)	2						aaagaaaaagaaaaaaaaaaG	0.139													4	2	---	---	---	---	
AMDHD1	144193	broad.mit.edu	37	12	96360515	96360516	+	Intron	INS	-	TT	TT			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96360515_96360516insTT	uc001tel.1	+						AMDHD1_uc009zth.1_Intron	NM_152435	NP_689648	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1						histidine catabolic process to glutamate and formamide	cytosol	imidazolonepropionase activity|metal ion binding			central_nervous_system(1)	1						TTTTTCGTAGATTTCCAGATTT	0.441													4	2	---	---	---	---	
ELK3	2004	broad.mit.edu	37	12	96606821	96606821	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96606821delG	uc001teo.1	+							NM_005230	NP_005221	P41970	ELK3_HUMAN	ELK3 protein						negative regulation of transcription, DNA-dependent|signal transduction	mitochondrion	protein binding|purine-rich negative regulatory element binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	all_cancers(2;0.00173)					tggaagtgctgggtaatgcaa	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97347912	97347912	+	IGR	DEL	A	-	-	rs11108743	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97347912delA								NEDD1 (451 upstream) : RMST (510887 downstream)																							gaaatgatttaaaaaaatgcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102464133	102464133	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102464133delT								CCDC53 (8234 upstream) : NUP37 (3842 downstream)																							AGGGCAACAATTTTTTTTTAT	0.328													4	2	---	---	---	---	
HCFC2	29915	broad.mit.edu	37	12	104487554	104487555	+	Intron	INS	-	T	T	rs11411208		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104487554_104487555insT	uc001tkj.3	+						HCFC2_uc009zul.2_Intron	NM_013320	NP_037452	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2						regulation of transcription from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleus	transcription coactivator activity			ovary(2)|central_nervous_system(1)	3						AAATGAGGCAATTTTTTTTTTT	0.322													4	4	---	---	---	---	
BRAP	8315	broad.mit.edu	37	12	112103180	112103180	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112103180delT	uc001tsn.3	-						BRAP_uc010syh.1_Intron|BRAP_uc009zvv.2_Intron	NM_006768	NP_006759	Q7Z569	BRAP_HUMAN	BRCA1 associated protein						MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1						TAAGCTTTGCTTTTTTTTTTC	0.443													3	3	---	---	---	---	
RASAL1	8437	broad.mit.edu	37	12	113569408	113569408	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113569408delT	uc001tum.1	-						RASAL1_uc010syp.1_Intron|RASAL1_uc001tul.2_Intron|RASAL1_uc001tun.1_Intron|RASAL1_uc010syq.1_Intron|RASAL1_uc001tuo.3_Intron|RASAL1_uc010syr.1_Intron	NM_004658	NP_004649	O95294	RASL1_HUMAN	RAS protein activator like 1						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	metal ion binding|phospholipid binding|Ras GTPase activator activity			ovary(2)|skin(2)	4						TCGAAATCTCTTAAGATGTGC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115212467	115212467	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115212467delT								TBX3 (90498 upstream) : None (None downstream)																							TGTTTTATTATTTTTTTAATT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116379126	116379127	+	IGR	INS	-	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116379126_116379127insC								None (None upstream) : MED13L (17256 downstream)																							tctatttataaccccttttggt	0.094													4	2	---	---	---	---	
TAOK3	51347	broad.mit.edu	37	12	118607978	118607979	+	Intron	INS	-	T	T	rs139594445	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118607978_118607979insT	uc001twx.2	-						TAOK3_uc001twv.2_Intron|TAOK3_uc001tww.2_Intron|TAOK3_uc001twy.3_Intron	NM_016281	NP_057365	Q9H2K8	TAOK3_HUMAN	TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ttctcaagcagttttttttttc	0.188													2	4	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119453149	119453149	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119453149delC	uc001txa.1	+							NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						ctttcataaaccccactgcta	0.000													4	2	---	---	---	---	
PSMD9	5715	broad.mit.edu	37	12	122350375	122350376	+	Intron	INS	-	GG	GG			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122350375_122350376insGG	uc001ubl.2	+						PSMD9_uc009zxj.2_Intron|PSMD9_uc001ubm.2_Intron	NM_002813	NP_002804	O00233	PSMD9_HUMAN	proteasome 26S non-ATPase subunit 9						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of insulin secretion|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of insulin secretion|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|proteasome regulatory particle assembly|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	nucleus|proteasome regulatory particle	bHLH transcription factor binding|transcription coactivator activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000117)|Epithelial(86;0.000415)|BRCA - Breast invasive adenocarcinoma(302;0.231)		aatcagtgtgtggtagaatctc	0.000													4	2	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124923762	124923763	+	Intron	INS	-	A	A	rs148634946	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124923762_124923763insA	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		cagagggagacagagacccaga	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127511624	127511624	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127511624delG	uc001uho.2	-											Homo sapiens cDNA clone IMAGE:4829480.																		TTGGAAGACTGATGCCTTTAG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128761521	128761524	+	IGR	DEL	AAAC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128761521_128761524delAAAC								None (None upstream) : TMEM132C (137767 downstream)																							TTTTAAGACAAAACAAACAAACAA	0.328													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131257457	131257458	+	IGR	DEL	AT	-	-	rs150831558		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131257457_131257458delAT								RIMBP2 (56631 upstream) : STX2 (16691 downstream)																							GGGGGGACTCATGTGGAAATTC	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131431062	131431063	+	IGR	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131431062_131431063insT								RAN (70238 upstream) : GPR133 (7389 downstream)																							cttgagatggattttcttggtg	0.000													4	2	---	---	---	---	
IFT88	8100	broad.mit.edu	37	13	21192545	21192546	+	Intron	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21192545_21192546delTG	uc001unh.2	+						IFT88_uc001uni.2_Intron|IFT88_uc001unj.2_Intron|IFT88_uc010tcq.1_Intron|IFT88_uc001unk.2_Intron|IFT88_uc001unl.1_Intron	NM_175605	NP_783195	Q13099	IFT88_HUMAN	intraflagellar transport 88 homolog isoform 1						cilium morphogenesis	centriole|intraflagellar transport particle B|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		cCTACTATACTGTAACTCTTTA	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27573471	27573472	+	IGR	DEL	TC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27573471_27573472delTC								GPR12 (238549 upstream) : USP12 (68966 downstream)																							TAAAACACAGTCTCTCTCTCTC	0.322													4	2	---	---	---	---	
MTUS2	23281	broad.mit.edu	37	13	29937239	29937242	+	Intron	DEL	GGAC	-	-	rs35093974		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29937239_29937242delGGAC	uc001usl.3	+							NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						TGACTCTCAGGGACGGACTCGCGC	0.554											OREG0022329	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	47777807	47777807	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47777807delA								HTR2A (306757 upstream) : SUCLA2 (738985 downstream)																							tgataaaaagaaaaaaaaaca	0.000													4	2	---	---	---	---	
VPS36	51028	broad.mit.edu	37	13	53012278	53012278	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53012278delT	uc001vgs.2	-						VPS36_uc001vgq.2_Intron	NM_016075	NP_057159	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36						cellular membrane organization|endosome transport|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|late endosome|membrane|nucleus	lipid binding			skin(1)	1		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		atattttaaatttttttttta	0.294													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	57944271	57944272	+	IGR	INS	-	A	A	rs59191297		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57944271_57944272insA								PRR20B (199919 upstream) : PCDH17 (261517 downstream)																							AAAGAACAGAGGTAGGATCATG	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	57944272	57944273	+	IGR	INS	-	T	T	rs71875322		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57944272_57944273insT								PRR20B (199920 upstream) : PCDH17 (261516 downstream)																							AAGAACAGAGGTAGGATCATGA	0.317													4	2	---	---	---	---	
DIAPH3	81624	broad.mit.edu	37	13	60240491	60240492	+	3'UTR	INS	-	A	A	rs34390052		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60240491_60240492insA	uc001vht.2	-	28					DIAPH3_uc001vhs.2_RNA	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)		TACCAGGAGACAAAAAAAAAAA	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	80489011	80489012	+	Intron	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80489011_80489012insT	uc001vlh.2	+											Homo sapiens cDNA clone IMAGE:4825993.																		GTCATCTTGCCTTTTTTTTTCT	0.342													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85429690	85429691	+	IGR	INS	-	G	G	rs72512723	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85429690_85429691insG								SLITRK1 (973162 upstream) : SLITRK6 (937231 downstream)																							AGAAAGTTAAATTTAATTGTTA	0.332													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	87106488	87106488	+	IGR	DEL	C	-	-	rs7992200	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87106488delC								SLITRK6 (733005 upstream) : None (None downstream)																							TTTTCTTTTTCTTTTTTTTCA	0.323													6	3	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94575528	94575528	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94575528delA	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				GAATGAATCTAAAATGTTAAC	0.373													4	2	---	---	---	---	
CLDN10	9071	broad.mit.edu	37	13	96089956	96089956	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96089956delG	uc001vmg.2	+						CLDN10_uc010tii.1_Intron	NM_182848	NP_878268	P78369	CLD10_HUMAN	claudin 10 isoform a						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)			TTGTATTCCTGGAGGAAGGAT	0.473													4	2	---	---	---	---	
CLYBL	171425	broad.mit.edu	37	13	100267026	100267026	+	Intron	DEL	A	-	-	rs67385188		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100267026delA	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)					CCAAGGAGTCAGGGGGGGAGG	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	101703561	101703562	+	IGR	DEL	CA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101703561_101703562delCA								TMTC4 (376458 upstream) : NALCN (2568 downstream)																							CTCCTCTGATCACCACTCCACC	0.416													4	2	---	---	---	---	
ERCC5	2073	broad.mit.edu	37	13	103504185	103504186	+	Intron	INS	-	T	T	rs145456994	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103504185_103504186insT	uc001vpw.2	+						ERCC5_uc001vpu.1_Intron|ERCC5_uc010tjb.1_Intron|ERCC5_uc010tjc.1_5'Flank|ERCC5_uc010tjd.1_5'Flank	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein						negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					GCAATCACTTATTTTTTTTTAA	0.178			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				4	4	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108191714	108191714	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108191714delC	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						caaacccactcccacgataat	0.000													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108487973	108487974	+	Intron	INS	-	CA	CA	rs149110002	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108487973_108487974insCA	uc001vql.2	-						uc001vqm.2_5'Flank	NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						GGCACAAGACCCACACACACAC	0.376													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19450199	19450199	+	IGR	DEL	C	-	-	rs28718409	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19450199delC								OR11H12 (71627 upstream) : POTEG (103166 downstream)																							TAGGTCTTTTCAAAGTAAAAA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20066163	20066163	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20066163delG								P704P (45891 upstream) : OR4Q3 (149424 downstream)																							ACCAGTTTCAGGAAAGGCACT	0.493													3	4	---	---	---	---	
STXBP6	29091	broad.mit.edu	37	14	25507567	25507568	+	Intron	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25507567_25507568delAC	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpx.1_Intron	NM_014178	NP_054897	Q8NFX7	STXB6_HUMAN	amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)		gcagttgtagacacacacccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	29913809	29913810	+	IGR	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29913809_29913810insT								C14orf23 (649810 upstream) : PRKD1 (131879 downstream)																							TACTCTCCTCATTCTCTTCAGA	0.406													2	4	---	---	---	---	
NUBPL	80224	broad.mit.edu	37	14	32193519	32193519	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32193519delG	uc001wrk.3	+						NUBPL_uc010amj.2_Intron|NUBPL_uc010tpl.1_Intron	NM_025152	NP_079428	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like						mitochondrial respiratory chain complex I assembly|mitochondrion morphogenesis	mitochondrion	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding				0	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		GTGCTTGGTTGGGCTAATGAG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	34877319	34877319	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34877319delA								EGLN3 (457032 upstream) : C14orf147 (24826 downstream)																							aaagtgagggaaaaaaaaaaa	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	39314913	39314913	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39314913delA	uc001wun.2	-						uc001wuo.2_Intron					Homo sapiens cDNA FLJ43028 fis, clone BRTHA3000297.																		taatacctggaaatGACAATA	0.164													4	2	---	---	---	---	
MAP4K5	11183	broad.mit.edu	37	14	50910066	50910067	+	Intron	INS	-	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50910066_50910067insG	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron|MAP4K5_uc010anv.1_Intron|MAP4K5_uc001wyc.1_Intron	NM_006575	NP_006566	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)					CTGACTGGCCAGGAAAATGCAT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	55586661	55586662	+	IGR	INS	-	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55586661_55586662insC								MAPK1IP1L (49749 upstream) : LGALS3 (9210 downstream)																							TGCTCTGGTTTCCCCTTTTAAC	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	56825521	56825521	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56825521delT								PELI2 (57491 upstream) : C14orf101 (220817 downstream)																							CTTGGGACCCTTTTCTTCTTG	0.373													4	2	---	---	---	---	
RAD51L1	5890	broad.mit.edu	37	14	69111470	69111470	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69111470delT	uc001xkg.1	+							NM_133510	NP_598194	O15315	RA51B_HUMAN	RAD51-like 1 isoform 2						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)		TGTCGTTTGCtttttttttta	0.224			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					5	3	---	---	---	---	
RGS6	9628	broad.mit.edu	37	14	72729589	72729590	+	Intron	INS	-	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72729589_72729590insC	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		gagctctgtgtccccccatgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	77366147	77366147	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77366147delG								C14orf166B (29502 upstream) : C14orf4 (124741 downstream)																							accttgagctggggagattct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88015501	88015501	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88015501delA								None (None upstream) : GALC (288663 downstream)																							agcagtgcagaaaaaaggtag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	91555595	91555595	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91555595delA								RPS6KA5 (28602 upstream) : C14orf159 (24762 downstream)																							GGAAACTGCCAAATGTCCAAC	0.502													4	2	---	---	---	---	
BRF1	2972	broad.mit.edu	37	14	105753567	105753567	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105753567delG	uc001yqp.2	-						BRF1_uc010tyo.1_Intron|BRF1_uc010typ.1_Intron|BRF1_uc010axg.1_Intron|BRF1_uc001yqr.2_Intron	NM_001519	NP_001510	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1						positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		AACATCAGGTGGACATTTGGA	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30897862	30897862	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30897862delT								FAM7A2 (4962 upstream) : ARHGAP11B (18835 downstream)																							TGCCTTTTTCTTTTTTTTTTC	0.423													6	3	---	---	---	---	
OTUD7A	161725	broad.mit.edu	37	15	31908526	31908526	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31908526delG	uc001zfq.2	-						OTUD7A_uc001zfr.2_Intron|OTUD7A_uc001zfs.1_Intron|OTUD7A_uc010baa.1_Intron	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		tgccttgtctggtgtgtgcgc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46315998	46315998	+	IGR	DEL	T	-	-	rs80012871		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46315998delT								SQRDL (332520 upstream) : None (None downstream)																							gatgttgagcttttttttttc	0.015													4	3	---	---	---	---	
COPS2	9318	broad.mit.edu	37	15	49429706	49429706	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49429706delA	uc001zxf.2	-						COPS2_uc001zxh.2_Intron|COPS2_uc010ufa.1_Intron	NM_004236	NP_004227	P61201	CSN2_HUMAN	COP9 constitutive photomorphogenic homolog						cullin deneddylation|transcription from RNA polymerase II promoter	cytoplasm|signalosome	protein binding|signal transducer activity			lung(1)	1		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		TAATTTGAACAAACTAAAAGT	0.279													252	141	---	---	---	---	
C15orf33	196951	broad.mit.edu	37	15	49657050	49657050	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49657050delT	uc001zxl.2	-							NM_152647	NP_689860	Q96M60	CO033_HUMAN	hypothetical protein LOC196951											ovary(1)	1		all_lung(180;0.00187)		all cancers(107;3.45e-08)|GBM - Glioblastoma multiforme(94;0.000124)		GGTCAAGGCATTTTTTTTTTT	0.294													3	3	---	---	---	---	
MYO5A	4644	broad.mit.edu	37	15	52681194	52681194	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52681194delA	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010uge.1_Intron	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		acgagttattaaaaaaaaaac	0.080													9	4	---	---	---	---	
PIGB	9488	broad.mit.edu	37	15	55612211	55612211	+	Intron	DEL	T	-	-	rs77286116		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55612211delT	uc002act.2	+						uc002acs.2_5'Flank|PIGB_uc010ugg.1_Intron	NM_004855	NP_004846	Q92521	PIGB_HUMAN	phosphatidylinositol glycan, class B						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	integral to membrane|intrinsic to endoplasmic reticulum membrane	glycolipid mannosyltransferase activity				0				all cancers(107;0.0255)		TAACCCACTCttttttttttg	0.333													7	4	---	---	---	---	
PIGB	9488	broad.mit.edu	37	15	55621518	55621519	+	Intron	DEL	AC	-	-	rs144123510		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55621518_55621519delAC	uc002act.2	+						PIGB_uc010ugg.1_Intron	NM_004855	NP_004846	Q92521	PIGB_HUMAN	phosphatidylinositol glycan, class B						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	integral to membrane|intrinsic to endoplasmic reticulum membrane	glycolipid mannosyltransferase activity				0				all cancers(107;0.0255)		CAACAAAAAAACAGTCATAATA	0.327													2	5	---	---	---	---	
TCF12	6938	broad.mit.edu	37	15	57343691	57343691	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57343691delT	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		CCTCTCCttctttttttttta	0.070			T	TEC	extraskeletal myxoid chondrosarcoma								3	3	---	---	---	---	
CA12	771	broad.mit.edu	37	15	63619700	63619700	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63619700delT	uc002amc.2	-						CA12_uc002amd.2_Intron|CA12_uc002ame.2_Intron	NM_001218	NP_001209	O43570	CAH12_HUMAN	carbonic anhydrase XII isoform 1 precursor						one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)	aaatgtagggttttttttttt	0.104													5	3	---	---	---	---	
TRIP4	9325	broad.mit.edu	37	15	64717359	64717359	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64717359delT	uc002anm.2	+							NM_016213	NP_057297	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ligand-dependent nuclear receptor binding|transcription coactivator activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3						CATTTTGATGTTTTTTTTTTC	0.318													2	4	---	---	---	---	
OAZ2	4947	broad.mit.edu	37	15	64989024	64989025	+	Intron	DEL	GC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64989024_64989025delGC	uc002anp.2	-									O95190	OAZ2_HUMAN	Homo sapiens ornithine decarboxylase antizyme 2 (OAZ2) mRNA, complete cds.						polyamine metabolic process|regulation of cellular amino acid metabolic process	cytosol|nucleus	ornithine decarboxylase inhibitor activity|protein binding				0					L-Ornithine(DB00129)	GTACAGCTGGGCAATGATGATG	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	66913531	66913531	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66913531delC	uc002aqe.2	+											Homo sapiens cDNA FLJ38816 fis, clone LIVER2007568.																		gtggctgtctcctgaggttgc	0.204													4	2	---	---	---	---	
MAP2K5	5607	broad.mit.edu	37	15	67921276	67921276	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67921276delG	uc002aqu.2	+						MAP2K5_uc002aqt.1_Intron|MAP2K5_uc002aqv.2_Intron|MAP2K5_uc002aqw.2_Intron	NM_145160	NP_660143	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5						nerve growth factor receptor signaling pathway		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)	2						caattttggaggtggtggAAG	0.204													4	2	---	---	---	---	
TMEM202	338949	broad.mit.edu	37	15	72695043	72695043	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72695043delG	uc002auq.2	+						TMEM202_uc002aur.2_Intron	NM_001080462	NP_001073931	A6NGA9	TM202_HUMAN	transmembrane protein 202							integral to membrane				central_nervous_system(1)|skin(1)	2						TGCAGAGCGTGGGAAAGAAAG	0.443													4	2	---	---	---	---	
NEO1	4756	broad.mit.edu	37	15	73447552	73447554	+	Intron	DEL	TGG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73447552_73447554delTGG	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						ggctgatgtttggtggtggtggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82031621	82031621	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82031621delC								TMC3 (365203 upstream) : MEX3B (302507 downstream)																							AAAACAAAAGCCCTCCAGCAA	0.433													4	2	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	87164042	87164042	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87164042delT	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						TATTAGCTCCTTTTTTTTTTT	0.418													4	2	---	---	---	---	
AP3S2	10239	broad.mit.edu	37	15	90385433	90385433	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90385433delA	uc002boq.3	-						AP3S2_uc002bos.3_Intron|AP3S2_uc010bns.2_Intron|AP3S2_uc002bor.3_Intron|AP3S2_uc010bnt.2_Intron	NM_005829	NP_005820	P59780	AP3S2_HUMAN	adaptor-related protein complex 3, sigma 2						intracellular protein transport|vesicle-mediated transport	cytoplasmic vesicle membrane|Golgi apparatus|membrane coat	protein transporter activity				0	Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)			agagaaatggaaaaaaaaaat	0.000													9	4	---	---	---	---	
PCSK6	5046	broad.mit.edu	37	15	101951863	101951863	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101951863delA	uc002bwy.2	-						PCSK6_uc010bpd.2_Intron|PCSK6_uc010bpe.2_Intron|PCSK6_uc002bxa.2_Intron|PCSK6_uc002bxb.2_Intron|PCSK6_uc002bxc.1_Intron|PCSK6_uc002bxd.1_Intron|PCSK6_uc002bxe.2_Intron|PCSK6_uc002bxg.1_Intron	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4						glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GAACAAATGGAAAAAACCATA	0.413													4	2	---	---	---	---	
ADCY9	115	broad.mit.edu	37	16	4108468	4108468	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4108468delG	uc002cvx.2	-							NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6						ttgtctccaagaaaaaaaaaa	0.025													4	2	---	---	---	---	
LOC342346	342346	broad.mit.edu	37	16	4621857	4621857	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4621857delT	uc010uxn.1	+							NM_001145011	NP_001138483	C9JH24	C9JH24_HUMAN	hypothetical protein LOC342346												0						ttttcttttcttttttttttt	0.254													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	18086497	18086499	+	IGR	DEL	GAT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18086497_18086499delGAT								XYLT1 (521759 upstream) : NOMO2 (424684 downstream)																							GGTAATAGTGgatgatgatgatg	0.330													4	2	---	---	---	---	
ACSM5	54988	broad.mit.edu	37	16	20442103	20442104	+	Intron	INS	-	GGAAAGAAGGAAG	GGAAAGAAGGAAG	rs140995429	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20442103_20442104insGGAAAGAAGGAAG	uc002dhe.2	+							NM_017888	NP_060358	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2						gaaagaggaaaggaaggagtga	0.064													4	2	---	---	---	---	
ERN2	10595	broad.mit.edu	37	16	23702074	23702075	+	3'UTR	INS	-	CTGGCGGTCTTTT	CTGGCGGTCTTTT	rs146319386	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23702074_23702075insCTGGCGGTCTTTT	uc002dma.3	-	22					ERN2_uc010bxp.2_3'UTR	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2						apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|rRNA catabolic process|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		ctgcacccagccTGATTCTGAG	0.312													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	24466890	24466890	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24466890delA								CACNG3 (93154 upstream) : RBBP6 (82124 downstream)																							ttttttttttatttttctttt	0.000													4	2	---	---	---	---	
ZKSCAN2	342357	broad.mit.edu	37	16	25271210	25271211	+	5'Flank	INS	-	AAAC	AAAC	rs138822530	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25271210_25271211insAAAC	uc002dod.3	-						ZKSCAN2_uc010vcl.1_5'Flank|ZKSCAN2_uc002doe.2_5'Flank	NM_001012981	NP_001012999	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|breast(1)	4				GBM - Glioblastoma multiforme(48;0.0378)		acagaaaaaaaaaacaaaagaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26983801	26983801	+	IGR	DEL	T	-	-	rs111337492		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26983801delT								HS3ST4 (834793 upstream) : C16orf82 (94418 downstream)																							CTGATGTATCTTTTTTTTTTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	30549447	30549447	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30549447delA								ZNF768 (3228 upstream) : ZNF764 (15639 downstream)																							CTCCTTTGCCAAAAATGCCTG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	31693951	31693951	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31693951delC								CSDAP1 (113106 upstream) : KIAA0664P3 (17983 downstream)																							CCCATCACAGCCCAGATATTT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32847223	32847224	+	IGR	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32847223_32847224insT								TP53TG3B (158345 upstream) : SLC6A10P (41573 downstream)																							gttctcttctactacacattcc	0.000													4	4	---	---	---	---	
ANKRD26P1	124149	broad.mit.edu	37	16	46533886	46533886	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46533886delT	uc002eeb.3	-	11	2533	c.1078delA	c.(1078-1080)AGAfs	p.R360fs	ANKRD26P1_uc010cbd.2_RNA	NR_026556				Homo sapiens cDNA FLJ43980 fis, clone TESTI4018806.												0						TTATACAATCTTTTTTTTATG	0.264													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	48761670	48761670	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48761670delA								N4BP1 (117550 upstream) : CBLN1 (550541 downstream)																							atagcaATACAAAAAGAAAGC	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51401909	51401910	+	IGR	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51401909_51401910delTG								SALL1 (216726 upstream) : None (None downstream)																							CACAGTTGCCTGTGTGCTCTGT	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	53403273	53403273	+	RNA	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53403273delA	uc002ehh.2	-	2		c.1186delT								Homo sapiens mRNA; cDNA DKFZp313P036 (from clone DKFZp313P036).																		actccatctcaaaaaaaaaag	0.129													5	3	---	---	---	---	
RPGRIP1L	23322	broad.mit.edu	37	16	53702433	53702433	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53702433delG	uc002ehp.2	-						RPGRIP1L_uc002eho.3_Intron|RPGRIP1L_uc010vgy.1_Intron|RPGRIP1L_uc010cbx.2_Intron|RPGRIP1L_uc010vgz.1_Intron	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a						negative regulation of G-protein coupled receptor protein signaling pathway	cell-cell junction|centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)				TGGATGGTATGGGGGCAGAGG	0.294													4	2	---	---	---	---	
CES1	1066	broad.mit.edu	37	16	55844239	55844240	+	Intron	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55844239_55844240insT	uc002eim.2	-						CES1_uc010ccf.2_Intron|CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	ttgcctctggatttttttttct	0.149													5	3	---	---	---	---	
RSPRY1	89970	broad.mit.edu	37	16	57265167	57265167	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57265167delA	uc002elb.2	+	13	1743	c.1465delA	c.(1465-1467)ATGfs	p.M489fs	RSPRY1_uc002elc.2_Frame_Shift_Del_p.M489fs|RSPRY1_uc002eld.2_Frame_Shift_Del_p.M489fs	NM_133368	NP_588609	Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	489						extracellular region	zinc ion binding			ovary(1)	1						CCCACCATCTATGAAATTTAG	0.368													427	260	---	---	---	---	
CCDC113	29070	broad.mit.edu	37	16	58296667	58296668	+	Intron	INS	-	TAGA	TAGA	rs28479863	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58296667_58296668insTAGA	uc002ene.2	+						CCDC113_uc010vid.1_Intron	NM_014157	NP_054876	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113 isoform 1							protein complex					0						tagatgataggtagatagatag	0.292													3	4	---	---	---	---	
PMFBP1	83449	broad.mit.edu	37	16	72164874	72164874	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72164874delA	uc002fcc.3	-						PMFBP1_uc002fcd.2_Intron|PMFBP1_uc002fce.2_Intron|PMFBP1_uc002fcf.2_Intron|PMFBP1_uc010cgo.1_5'Flank	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1											ovary(2)	2		Ovarian(137;0.179)				TGTGCGACTCATTCTGTCACT	0.453													4	2	---	---	---	---	
CNTNAP4	85445	broad.mit.edu	37	16	76453039	76453039	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76453039delG	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron|CNTNAP4_uc002few.2_Intron	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						tatctctggtggtatagcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77577234	77577234	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77577234delT								ADAMTS18 (108223 upstream) : NUDT7 (179177 downstream)																							ataattgagcttatatctgaa	0.025													4	2	---	---	---	---	
LRRC50	123872	broad.mit.edu	37	16	84183630	84183630	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84183630delA	uc002fhl.3	+						LRRC50_uc010chi.1_Intron	NM_178452	NP_848547	Q8NEP3	DAAF1_HUMAN	leucine rich repeat containing 50						axonemal dynein complex assembly|cilium morphogenesis	cilium axoneme|cytoplasm|spindle pole	dynein binding				0						actctgtctcaaaaaaaaaaa	0.075									Kartagener_syndrome				4	4	---	---	---	---	
FOXC2	2303	broad.mit.edu	37	16	86598125	86598128	+	5'Flank	DEL	TGTT	-	-	rs113305988		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86598125_86598128delTGTT	uc002fjq.2	+							NM_005251	NP_005242	Q99958	FOXC2_HUMAN	forkhead box C2						anti-apoptosis|artery morphogenesis|blood vessel remodeling|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|embryonic viscerocranium morphogenesis|insulin receptor signaling pathway|lymphangiogenesis|metanephros development|negative regulation of transcription from RNA polymerase II promoter|neural crest cell fate commitment|Notch signaling pathway|ossification|paraxial mesodermal cell fate commitment|patterning of blood vessels|positive regulation of cell adhesion mediated by integrin|positive regulation of cell migration involved in sprouting angiogenesis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of vascular wound healing|regulation of blood vessel size|regulation of organ growth|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|ureteric bud development|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding|transcription regulatory region DNA binding				0						TCGATTTAGGtgtttgtttgtttg	0.402									Late-onset_Hereditary_Lymphedema				4	2	---	---	---	---	
ZFPM1	161882	broad.mit.edu	37	16	88587956	88587957	+	Intron	INS	-	G	G	rs142044699	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88587956_88587957insG	uc002fkv.2	+							NM_153813	NP_722520	Q8IX07	FOG1_HUMAN	zinc finger protein, multitype 1						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|transcription factor binding|zinc ion binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GCTGTTCCCTCCCTCATGCTGT	0.624													4	3	---	---	---	---	
ZFPM1	161882	broad.mit.edu	37	16	88587959	88587960	+	Intron	INS	-	C	C			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88587959_88587960insC	uc002fkv.2	+							NM_153813	NP_722520	Q8IX07	FOG1_HUMAN	zinc finger protein, multitype 1						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|transcription factor binding|zinc ion binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GTTCCCTCCCTCATGCTGTTCC	0.629													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5532358	5532358	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5532358delC								NLRP1 (44526 upstream) : WSCD1 (440079 downstream)																							TCCACATTTTCCCCACAGTGT	0.498													4	2	---	---	---	---	
ASGR2	433	broad.mit.edu	37	17	7016705	7016706	+	Intron	DEL	AC	-	-	rs138132186		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7016705_7016706delAC	uc002gep.3	-						ASGR2_uc002gem.1_Intron|ASGR2_uc002gen.1_Intron|ASGR2_uc002geo.1_Intron|ASGR2_uc002ger.3_Intron|ASGR2_uc002geq.3_Intron|ASGR2_uc010clw.2_Intron|ASGR2_uc010vtl.1_Intron	NM_001181	NP_001172	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2 isoform a						cell surface receptor linked signaling pathway|endocytosis	focal adhesion|integral to membrane|nucleolus	asialoglycoprotein receptor activity|protein binding|sugar binding			ovary(1)	1					Antihemophilic Factor(DB00025)	ctcacaacatacacacacaaca	0.000													4	2	---	---	---	---	
MYH10	4628	broad.mit.edu	37	17	8512673	8512673	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8512673delA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955	P35580	MYH10_HUMAN	myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2						atcgagaaggaaagggaggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	10968078	10968078	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10968078delA								PIRT (226660 upstream) : SHISA6 (176662 downstream)																							cctgaataagaaaacctaggg	0.000													4	2	---	---	---	---	
PIGL	9487	broad.mit.edu	37	17	16229023	16229023	+	Intron	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16229023delG	uc002gpv.2	+							NM_004278	NP_004269	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminylphosphatidylinositol deacetylase activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		ATTAGTTCGAGGAAGGATTTA	0.453													26	28	---	---	---	---	
MPRIP	23164	broad.mit.edu	37	17	16994481	16994481	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16994481delT	uc002gqu.1	+						MPRIP_uc002gqv.1_Intron	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein							cytoplasm|cytoskeleton	actin binding				0						TTCCAGTGGGTTTTCAGCAAG	0.582													4	2	---	---	---	---	
MYO15A	51168	broad.mit.edu	37	17	18060834	18060834	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18060834delC	uc010vxh.1	+						MYO15A_uc010vxi.1_Intron|MYO15A_uc010vxj.1_3'UTR|MYO15A_uc010vxk.1_Intron|MYO15A_uc010vxl.1_5'Flank|MYO15A_uc002gsl.2_5'Flank|MYO15A_uc010vxm.1_5'Flank	NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV						sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					tgcttcacttcccctttatgg	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21223480	21223481	+	IGR	INS	-	G	G	rs2885712		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21223480_21223481insG								MAP2K3 (4931 upstream) : KCNJ12 (56218 downstream)																							AGCAGGGCCTTATCTGGGTTGT	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21223481	21223482	+	IGR	INS	-	CCCC	CCCC	rs78552764		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21223481_21223482insCCCC								MAP2K3 (4932 upstream) : KCNJ12 (56217 downstream)																							GCAGGGCCTTATCTGGGTTGTT	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21329284	21329284	+	IGR	DEL	C	-	-	rs67728666		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21329284delC								KCNJ12 (6105 upstream) : C17orf51 (102288 downstream)																							GGAGAGGGCACGGGGGTGGAA	0.358													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21341375	21341376	+	IGR	INS	-	A	A	rs142557330	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21341375_21341376insA								KCNJ12 (18196 upstream) : C17orf51 (90196 downstream)																							TTAGTATATACAAAAAGACTAA	0.411													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	27348180	27348180	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27348180delT								SEZ6 (14722 upstream) : PIPOX (21738 downstream)																							tttcttttccttttttttttt	0.239													2	4	---	---	---	---	
CPD	1362	broad.mit.edu	37	17	28708099	28708099	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28708099delT	uc002hfb.1	+						CPD_uc010wbo.1_Intron|CPD_uc010wbp.1_Intron	NM_001304	NP_001295	O75976	CBPD_HUMAN	carboxypeptidase D precursor						proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)|skin(1)	2						GTCTTCTATCTTTTACTTTAC	0.328													4	2	---	---	---	---	
NF1	4763	broad.mit.edu	37	17	29423150	29423150	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29423150delC	uc002hgg.2	+						NF1_uc002hge.1_Intron|NF1_uc002hgf.1_Intron|NF1_uc002hgh.2_Intron	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.0?(5)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GCAGTCTCTTCCCCCCCCCCT	0.453			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	30391685	30391685	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30391685delG								LRRC37B (11168 upstream) : RHOT1 (77788 downstream)																							attttaggcagggggaacagc	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33786250	33786250	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33786250delA								SLFN13 (10394 upstream) : SLFN12L (15676 downstream)																							ACTAAACATTAAAAAAAAAAG	0.308													6	4	---	---	---	---	
CACNB1	782	broad.mit.edu	37	17	37347528	37347529	+	Intron	INS	-	ACTTATTAT	ACTTATTAT	rs138131266	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37347528_37347529insACTTATTAT	uc002hrm.1	-						CACNB1_uc002hrl.1_Intron|CACNB1_uc002hrn.2_Intron|CACNB1_uc002hro.2_Intron|CACNB1_uc002hrp.1_Intron|CACNB1_uc010web.1_Intron	NM_000723	NP_000714	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1						axon guidance	voltage-gated calcium channel complex				large_intestine(1)|ovary(1)	2					Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Verapamil(DB00661)	taataacacgcacttattatac	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	42008271	42008271	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42008271delC								C17orf88 (12916 upstream) : PPY (9902 downstream)																							TTCCATCACTCCCTGCTTGCT	0.458													4	2	---	---	---	---	
SKAP1	8631	broad.mit.edu	37	17	46234243	46234244	+	Intron	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46234243_46234244insT	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron|MIR1203_hsa-mir-1203|MI0006335_5'Flank	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						TTCACTGGGTATTTTTTTTTGT	0.312													4	2	---	---	---	---	
ACSF2	80221	broad.mit.edu	37	17	48522284	48522284	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48522284delT	uc002iqu.2	+						ACSF2_uc010wml.1_Intron|ACSF2_uc010wmm.1_Intron|ACSF2_uc010wmn.1_Intron|ACSF2_uc010wmo.1_Intron	NM_025149	NP_079425	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2 precursor						fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			ATAATGTGGCttttttttgag	0.169													4	2	---	---	---	---	
SUPT4H1	6827	broad.mit.edu	37	17	56430319	56430319	+	5'Flank	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56430319delG	uc002iwe.1	-						uc010dct.1_RNA|uc010dcu.1_RNA|uc002ivz.2_RNA|uc010dcv.1_RNA|uc002iwa.2_RNA|uc002iwb.2_RNA|uc002iwc.2_RNA|SUPT4H1_uc002iwd.1_5'Flank	NM_003168	NP_003159	P63272	SPT4H_HUMAN	suppressor of Ty 4 homolog 1						chromatin remodeling|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AACCTTTCTCGGGGAAGCAGA	0.527													4	2	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64495158	64495158	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64495158delT	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)	acatggaccattagcagacac	0.060													4	2	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64661622	64661623	+	Intron	INS	-	GGTCTCA	GGTCTCA	rs138595473	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64661622_64661623insGGTCTCA	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)	TGGCAAGAGGGGGTCCAAGTAC	0.550													4	2	---	---	---	---	
MAP2K6	5608	broad.mit.edu	37	17	67410476	67410476	+	5'Flank	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67410476delG	uc002jij.2	+						MAP2K6_uc002jii.2_5'Flank	NM_002758	NP_002749	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6						activation of MAPK activity|cell cycle arrest|DNA damage induced protein phosphorylation|innate immune response|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of muscle cell differentiation|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|pancreas(1)	5	Breast(10;6.05e-10)					AACGTCTACAGGCAAGAACAG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68431316	68431316	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68431316delC								KCNJ2 (255135 upstream) : None (None downstream)																							ctaagaaattccccattgtct	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68957488	68957489	+	IGR	DEL	AG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68957488_68957489delAG								KCNJ2 (781307 upstream) : None (None downstream)																							tagagagaaaagagagagaatg	0.173													4	2	---	---	---	---	
RAB37	326624	broad.mit.edu	37	17	72729568	72729568	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72729568delA	uc010dfu.2	+						RAB37_uc002jlc.2_Intron|RAB37_uc002jld.2_Intron	NM_175738	NP_783865	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family isoform 3						protein transport|small GTPase mediated signal transduction	ER-Golgi intermediate compartment	GTP binding			ovary(1)	1						gtgatttgagagtgtatgtgt	0.000													3	3	---	---	---	---	
RAB37	326624	broad.mit.edu	37	17	72729577	72729578	+	Intron	INS	-	GTT	GTT			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72729577_72729578insGTT	uc010dfu.2	+						RAB37_uc002jlc.2_Intron|RAB37_uc002jld.2_Intron	NM_175738	NP_783865	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family isoform 3						protein transport|small GTPase mediated signal transduction	ER-Golgi intermediate compartment	GTP binding			ovary(1)	1						gagtgtatgtgtgtgatgtgag	0.000													4	2	---	---	---	---	
RAB37	326624	broad.mit.edu	37	17	72729586	72729588	+	Intron	DEL	GAG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72729586_72729588delGAG	uc010dfu.2	+						RAB37_uc002jlc.2_Intron|RAB37_uc002jld.2_Intron	NM_175738	NP_783865	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family isoform 3						protein transport|small GTPase mediated signal transduction	ER-Golgi intermediate compartment	GTP binding			ovary(1)	1						tgtgtgatgtgaggtgtgtgtga	0.000													4	2	---	---	---	---	
RAB37	326624	broad.mit.edu	37	17	72729592	72729592	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72729592delT	uc010dfu.2	+						RAB37_uc002jlc.2_Intron|RAB37_uc002jld.2_Intron	NM_175738	NP_783865	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family isoform 3						protein transport|small GTPase mediated signal transduction	ER-Golgi intermediate compartment	GTP binding			ovary(1)	1						atgtgaggtgtgtgtgatttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75753052	75753052	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75753052delA								SEPT9 (256376 upstream) : FLJ45079 (122057 downstream)																							CAGGAATCACAAAAAAACCAC	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	78961357	78961357	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78961357delT								RPTOR (21184 upstream) : CHMP6 (4284 downstream)																							tcttgtaaccttttaatagtg	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	80562600	80562601	+	IGR	DEL	GC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80562600_80562601delGC								FOXK2 (119 upstream) : WDR45L (9839 downstream)																							CTGAGGACCAGCACTGCAGGCC	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	2473006	2473006	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2473006delT								None (None upstream) : METTL4 (64519 downstream)																							CTCCTGAGGGTCAGTGCACGA	0.498													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	4286003	4286004	+	Intron	DEL	AG	-	-	rs7231155	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4286003_4286004delAG	uc010wyz.1	-							NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				TACCCCACTCAGAGAGAGAGAG	0.347													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5936365	5936365	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5936365delA								TMEM200C (44262 upstream) : L3MBTL4 (18341 downstream)																							aagtgcatagaaaaaaaaaaa	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	19526403	19526404	+	IGR	DEL	TC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19526403_19526404delTC								MIB1 (75493 upstream) : GATA6 (223012 downstream)																							tcagcctctgtctctctctctc	0.000													4	2	---	---	---	---	
ZNF521	25925	broad.mit.edu	37	18	22680481	22680481	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22680481delT	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GGCCAAAATCTCTCTAATTTC	0.413			T	PAX5	ALL								2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	27739635	27739635	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27739635delA								None (None upstream) : MIR302F (139241 downstream)																							GGAAGCTTTTAAAAAAACACA	0.239													4	2	---	---	---	---	
ASXL3	80816	broad.mit.edu	37	18	31226008	31226008	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31226008delA	uc010dmg.1	+						ASXL3_uc002kxq.2_Intron	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						AAATTTATCCAAAAAAAAAAT	0.254													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	32992746	32992746	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32992746delT								ZNF396 (35445 upstream) : INO80C (40544 downstream)																							TGAATGAGGCTTGAGCATGAC	0.428													4	2	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34198943	34198943	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34198943delC	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron|FHOD3_uc002kzu.1_Intron|FHOD3_uc010dmz.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				TCTGTGTTGTCTGTCTATATT	0.522													4	2	---	---	---	---	
SETBP1	26040	broad.mit.edu	37	18	42565217	42565217	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42565217delA	uc010dni.2	+							NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AGAAAGTCTTAAAAAAAAAAG	0.294									Schinzel-Giedion_syndrome				5	4	---	---	---	---	
RNF165	494470	broad.mit.edu	37	18	43985982	43985983	+	Intron	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43985982_43985983delTG	uc002lcb.1	+						RNF165_uc002lby.1_Intron|RNF165_uc010dnn.1_Intron	NM_152470	NP_689683	Q6ZSG1	RN165_HUMAN	ring finger protein 165								zinc ion binding				0				READ - Rectum adenocarcinoma(1;0.0873)		TACATACCCCTGTGTGTGTGTa	0.302													4	2	---	---	---	---	
MAPK4	5596	broad.mit.edu	37	18	48211350	48211351	+	Intron	DEL	CA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48211350_48211351delCA	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)		CTTCTCTTCTCACCCCTTCTTG	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	49083366	49083366	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49083366delT	uc010xdq.1	+											Homo sapiens cDNA FLJ37617 fis, clone BRCOC2012229.																		tttgaggggattttttttttt	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	51258898	51258899	+	IGR	DEL	GA	-	-	rs35034968		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51258898_51258899delGA								DCC (201116 upstream) : MBD2 (421676 downstream)																							GTGGAAAATTGAGAGAGTTTGA	0.262													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53599335	53599335	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53599335delA								TCF4 (296150 upstream) : TXNL1 (670720 downstream)																							cagcaaatacaaaggccctaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	55565637	55565637	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55565637delA								ATP8B1 (166598 upstream) : NEDD4L (145982 downstream)																							cacctatcataagctccataa	0.174													4	2	---	---	---	---	
RTTN	25914	broad.mit.edu	37	18	67871057	67871057	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67871057delA	uc002lkp.2	-						RTTN_uc010xfb.1_Intron|RTTN_uc002lkq.1_Intron	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin								binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)				TGTTATTGCCAAAAAAATAAT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73187173	73187173	+	IGR	DEL	C	-	-	rs72977869		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73187173delC								C18orf62 (47584 upstream) : ZNF516 (884446 downstream)																							ATTGATCACTCTTAAAAAAAA	0.333													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76697142	76697142	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76697142delT								None (None upstream) : SALL3 (43133 downstream)																							AAACCTGACCTAACCTTTTCC	0.323													4	2	---	---	---	---	
TLE2	7089	broad.mit.edu	37	19	3000822	3000823	+	Intron	INS	-	T	T	rs4061734		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3000822_3000823insT	uc002lww.2	-						TLE2_uc010xhb.1_Intron|TLE2_uc010dth.2_Intron|TLE2_uc010xhc.1_Intron|TLE2_uc010dti.2_Intron	NM_003260	NP_003251	Q04725	TLE2_HUMAN	transducin-like enhancer protein 2 isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGCCTCTCCCttttttttttt	0.337													7	4	---	---	---	---	
SH3GL1	6455	broad.mit.edu	37	19	4380290	4380290	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4380290delA	uc002maj.2	-						SH3GL1_uc002mak.2_Intron|SH3GL1_uc010xig.1_Intron	NM_003025	NP_003016	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1						central nervous system development|endocytosis|signal transduction	early endosome membrane	lipid binding|protein binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		GGTACAGTGGAAAAGGAAAGA	0.552			T	MLL	AL								4	2	---	---	---	---	
RANBP3	8498	broad.mit.edu	37	19	5965833	5965834	+	Intron	INS	-	CCAC	CCAC	rs139121680	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5965833_5965834insCCAC	uc002mdw.2	-						RANBP3_uc002mdx.2_Intron|RANBP3_uc002mdy.2_Intron|RANBP3_uc002mdz.2_Intron|RANBP3_uc010duq.2_Intron|RANBP3_uc002mea.2_Intron|RANBP3_uc010xix.1_Intron	NM_007322	NP_015561	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3 isoform RANBP3-d						intracellular transport|protein transport	cytoplasm|nucleus	Ran GTPase binding			breast(1)	1						TTTCATATACGTGGccagcgtt	0.233													4	3	---	---	---	---	
KRI1	65095	broad.mit.edu	37	19	10673741	10673741	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10673741delT	uc002moy.1	-						KRI1_uc002mow.1_5'Flank|KRI1_uc002mox.1_Intron	NM_023008	NP_075384	Q8N9T8	KRI1_HUMAN	KRI1 homolog											ovary(1)	1			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			tatttacttatttttttttga	0.164													4	2	---	---	---	---	
NFIX	4784	broad.mit.edu	37	19	13153749	13153749	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13153749delC	uc010xmx.1	+						NFIX_uc002mwd.2_Intron|NFIX_uc002mwe.2_Intron|NFIX_uc002mwf.2_Intron|NFIX_uc002mwg.1_Intron			Q14938	NFIX_HUMAN	RecName: Full=Nuclear factor 1;						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			aaaCTTGACACCCTCAGGCAG	0.274													4	2	---	---	---	---	
MRI1	84245	broad.mit.edu	37	19	13875312	13875312	+	5'Flank	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13875312delG	uc002mxe.2	+						MRI1_uc002mxf.2_5'Flank	NM_001031727	NP_001026897	Q9BV20	MTNA_HUMAN	translation initiation factor eIF-2B subunit						L-methionine salvage from methylthioadenosine	cell projection|cytoplasm|nucleus	identical protein binding|S-methyl-5-thioribose-1-phosphate isomerase activity			ovary(1)	1						CTCTTTTTCCGGGGGAGGCTC	0.682													4	2	---	---	---	---	
CYP4F8	11283	broad.mit.edu	37	19	15729400	15729400	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15729400delT	uc002nbi.2	+						CYP4F8_uc010xoi.1_3'UTR|CYP4F8_uc010xoj.1_Intron	NM_007253	NP_009184	P98187	CP4F8_HUMAN	cytochrome P450, family 4, subfamily F,						prostaglandin metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	alkane 1-monooxygenase activity|aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding			large_intestine(1)	1						tgagtgataattTTTTTTTTA	0.264													4	2	---	---	---	---	
ZNF429	353088	broad.mit.edu	37	19	21724489	21724492	+	Intron	DEL	CTCA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21724489_21724492delCTCA	uc010ecu.1	+									Q86V71	ZN429_HUMAN	Homo sapiens KRAB zinc finger protein HZF26 (HZF26) mRNA, partial cds.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						CAACAGTTTTCTCACTGTTGTCTT	0.245													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	22780028	22780028	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22780028delA	uc002nqu.3	+											Homo sapiens cDNA FLJ60031 complete cds, moderately similar to Golgin subfamily A member 2.																		taaaaactgtaaaggcagatg	0.234													13	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	28297113	28297113	+	RNA	DEL	T	-	-	rs77586400		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28297113delT	uc002nry.1	+	2		c.758delT								Homo sapiens cDNA clone IMAGE:3867353.																		GGGATGCAGATTTTTTTTTTC	0.328													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	28927087	28927087	+	RNA	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28927087delC	uc002nsa.1	-	10		c.2321delG								Homo sapiens cDNA clone IMAGE:5297319, with apparent retained intron.																		CTGTGCCCTTCCTCCAGTCTT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29982897	29982897	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29982897delA	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		GAACAACAACAAAAAAAAAAC	0.468													4	4	---	---	---	---	
VSTM2B	342865	broad.mit.edu	37	19	30030849	30030850	+	Intron	DEL	AG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30030849_30030850delAG	uc010xrl.1	+							NM_001146339	NP_001139811	A6NLU5	VTM2B_HUMAN	V-set and transmembrane domain containing 2B							integral to membrane					0						GTAATCGTATAGCTCTAGAGAC	0.604													4	2	---	---	---	---	
ZNF536	9745	broad.mit.edu	37	19	30926610	30926610	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30926610delC	uc002nsu.1	+						ZNF536_uc010edd.1_Intron	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					TTCTTTCCATCCCCAGCAGCT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	34467132	34467132	+	IGR	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34467132delC								KCTD15 (160467 upstream) : LSM14A (196220 downstream)																							TTCTAATGTTCAGTCACTTCT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	47407159	47407159	+	IGR	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47407159delT								AP2S1 (52956 upstream) : GRLF1 (14774 downstream)																							GAAATTCGCCTTTTTTTTTTT	0.328													4	2	---	---	---	---	
CCDC9	26093	broad.mit.edu	37	19	47763878	47763878	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47763878delG	uc010xym.1	+	5	451	c.244delG	c.(244-246)GGGfs	p.G82fs		NM_015603	NP_056418	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	82											0		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		GAGGTCTCCTGGGACCCCTCG	0.701													4	2	---	---	---	---	
SPHK2	56848	broad.mit.edu	37	19	49127159	49127159	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49127159delA	uc002pjr.2	+						SPHK2_uc010xzt.1_Intron|SPHK2_uc002pjs.2_Intron|SPHK2_uc002pjt.2_Intron|SPHK2_uc002pju.2_5'Flank|SPHK2_uc002pjv.2_5'Flank|SPHK2_uc002pjw.2_5'Flank|SPHK2_uc010xzu.1_5'Flank	NM_020126	NP_064511	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|cell proliferation|sphinganine-1-phosphate biosynthetic process	cytosol|lysosomal membrane|membrane fraction	ATP binding|D-erythro-sphingosine kinase activity|diacylglycerol kinase activity|Ras GTPase binding|sphinganine kinase activity			lung(1)	1		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		TAACTGTCCGAAAAAAAAGTA	0.458													6	3	---	---	---	---	
NR1H2	7376	broad.mit.edu	37	19	50835593	50835593	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50835593delT	uc002prv.3	+						KCNC3_uc002pru.1_5'Flank			P55055	NR1H2_HUMAN	Homo sapiens NR1H2 mRNA for liver X receptor beta, complete cds.						negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of pinocytosis|negative regulation of transcription, DNA-dependent|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		TAAATCAGCGTTTTTTTGCAG	0.552													4	2	---	---	---	---	
ZNF175	7728	broad.mit.edu	37	19	52084427	52084427	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52084427delA	uc002pxb.2	+							NM_007147	NP_009078	Q9Y473	ZN175_HUMAN	zinc finger protein 175						response to virus	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		CTCATTTTTGAAAAAAAAAAA	0.348													4	2	---	---	---	---	
ZNF528	84436	broad.mit.edu	37	19	52905663	52905663	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52905663delT	uc002pzh.2	+						ZNF528_uc002pzi.2_Intron	NM_032423	NP_115799	Q3MIS6	ZN528_HUMAN	zinc finger protein 528						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		ttcttctttcttttttttttt	0.204													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	55028636	55028636	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55028636delA								LAIR2 (6741 upstream) : KIR3DX1 (15273 downstream)																							TGTACAGTAGAAAAAAAAATG	0.363													4	2	---	---	---	---	
ZNF343	79175	broad.mit.edu	37	20	2470205	2470205	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2470205delT	uc002wge.1	-						ZNF343_uc010gao.1_Intron|ZNF343_uc002wgd.1_Intron	NM_024325	NP_077301	Q6P1L6	ZN343_HUMAN	zinc finger protein 343						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						atcattgctctttttccctct	0.000													4	2	---	---	---	---	
ATRN	8455	broad.mit.edu	37	20	3471778	3471779	+	Intron	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3471778_3471779insT	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2						TTATCTGCAGATTATTAGCTCT	0.198													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	20712334	20712334	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20712334delA								RALGAPA2 (19068 upstream) : PLK1S1 (394290 downstream)																							CCCCAGCTTTAAAAAAAATCC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26200814	26200814	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26200814delA								MIR663 (11900 upstream) : None (None downstream)																							CATACACAACAAAAAGACTGA	0.164													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26248600	26248601	+	IGR	DEL	AC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26248600_26248601delAC								MIR663 (59686 upstream) : None (None downstream)																							agtggagaaaacatatataaag	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29595756	29595757	+	IGR	INS	-	T	T	rs1973439		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29595756_29595757insT								None (None upstream) : FRG1B (16122 downstream)																							tgtggtggctcttgcctgtcat	0.203													4	3	---	---	---	---	
PLAGL2	5326	broad.mit.edu	37	20	30782872	30782873	+	3'UTR	INS	-	G	G			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30782872_30782873insG	uc002wxn.2	-	3						NM_002657	NP_002648	Q9UPG8	PLAL2_HUMAN	pleiomorphic adenoma gene-like 2							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			AAACTGGAGGCGGGGGTGGGGG	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	40482751	40482752	+	IGR	INS	-	T	T	rs143479498	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40482751_40482752insT								CHD6 (235618 upstream) : PTPRT (218641 downstream)																							GAGCTTGACAATTTTTTTTTAA	0.416													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41600175	41600176	+	Intron	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41600175_41600176insT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				catttcttccatttttttttca	0.000													4	2	---	---	---	---	
EYA2	2139	broad.mit.edu	37	20	45586785	45586785	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45586785delT	uc002xsm.2	+						EYA2_uc010ghp.2_Intron	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				AGTGATGGCATTTTTTGCTTA	0.502													4	2	---	---	---	---	
EYA2	2139	broad.mit.edu	37	20	45766385	45766385	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45766385delT	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				TTTTTTTTTCTTTTAGTTTCT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46802896	46802896	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46802896delG								SULF2 (387536 upstream) : LOC284749 (185758 downstream)																							AGAGATGCGTGGAGAGGCAGA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	47199192	47199193	+	IGR	INS	-	T	T	rs72534978	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47199192_47199193insT								LOC284749 (199811 upstream) : PREX1 (41600 downstream)																							aaatttcaacaagactccccac	0.163													1	6	---	---	---	---	
CSE1L	1434	broad.mit.edu	37	20	47707098	47707098	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47707098delA	uc002xty.2	+						CSE1L_uc010zyg.1_Intron|CSE1L_uc010ghx.2_Intron|CSE1L_uc010ghy.2_Intron|CSE1L_uc010zyh.1_Intron	NM_001316	NP_001307	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like protein						apoptosis|cell proliferation|intracellular protein transport	cytoplasm|nucleus	importin-alpha export receptor activity			large_intestine(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			cgtctcaaagaaaaaaaaaaT	0.154													12	6	---	---	---	---	
ZFP64	55734	broad.mit.edu	37	20	50788760	50788761	+	Intron	INS	-	TG	TG			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50788760_50788761insTG	uc002xwl.2	-						ZFP64_uc002xwk.2_Intron|ZFP64_uc002xwm.2_Intron|ZFP64_uc002xwn.2_Intron	NM_018197	NP_060667	Q9NPA5	ZF64A_HUMAN	zinc finger protein 64 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						gtgtgtgtgtttgtgtgtgtgt	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50951978	50951979	+	IGR	INS	-	AG	AG	rs140783718	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50951978_50951979insAG								ZFP64 (143454 upstream) : TSHZ2 (636898 downstream)																							gacaggcaaacagagagagaga	0.000													2	4	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	52039256	52039256	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52039256delA	uc002xwo.2	+						uc002xwp.1_Intron	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)			TCTCGAGTCCAAAAAAATAGG	0.443													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60347872	60347872	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60347872delT	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			TCTCACTTGATTTTTTTTTTT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9851113	9851113	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9851113delA								None (None upstream) : None (None downstream)																							atgaaaaattaaaaaaaaaac	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9856378	9856380	+	IGR	DEL	CTC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9856378_9856380delCTC								None (None upstream) : None (None downstream)																							CCTCTGCCTTCTCCTCCAGGGCA	0.581													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10700256	10700257	+	IGR	DEL	AA	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10700256_10700257delAA								None (None upstream) : TPTE (206486 downstream)																							gcctactgtgaaagagaaatat	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10710970	10710972	+	IGR	DEL	TAT	-	-	rs144798371	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10710970_10710972delTAT								None (None upstream) : TPTE (195771 downstream)																							ctacttttaatatgaagatattt	0.000													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10779270	10779279	+	IGR	DEL	TGGAGTGGAA	-	-	rs72130995		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10779270_10779279delTGGAGTGGAA								None (None upstream) : TPTE (127464 downstream)																							tggagtgtagtggagtggaatggagtggaa	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11062214	11062214	+	Intron	DEL	C	-	-	rs113361486		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11062214delC	uc002yit.1	-						BAGE_uc002yiw.1_5'Flank|BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		taaaaagaaaccccccaaaaa	0.035													8	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11069012	11069013	+	Intron	INS	-	C	C	rs150046862		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-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													5	6	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11088434	11088434	+	Intron	DEL	A	-	-	rs71272578		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11088434delA	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)		CTAGTATGCCAAAAAAAAGTA	0.184													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11088831	11088831	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11088831delT	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)		TATGTCTGTATTTTTTTTCTA	0.209													4	2	---	---	---	---	
NCRNA00157	54075	broad.mit.edu	37	21	19221216	19221217	+	Intron	DEL	TC	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19221216_19221217delTC	uc011aca.1	-							NR_024354				Homo sapiens non-protein coding RNA 157 (NCRNA00157), non-coding RNA.												0						GCACATACATTCTCTCTCTCTC	0.257													4	2	---	---	---	---	
ADAMTS5	11096	broad.mit.edu	37	21	28301061	28301061	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28301061delT	uc002ymg.2	-							NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						ctctttcttcttttttttTTC	0.095													3	3	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36777131	36777132	+	Intron	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36777131_36777132delTG	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						TGATGTTCTCTGTGTGTGTGTG	0.351			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
DOPEY2	9980	broad.mit.edu	37	21	37649590	37649590	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37649590delT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						AGGACTGCACttttttttttg	0.289													5	3	---	---	---	---	
LCA5L	150082	broad.mit.edu	37	21	40785756	40785756	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40785756delA	uc002yxu.2	-						LCA5L_uc002yxv.2_Intron	NM_152505	NP_689718	O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like												0		Prostate(19;1.2e-06)				tgattacctgaaaaattcagt	0.224													4	2	---	---	---	---	
HIRA	7290	broad.mit.edu	37	22	19370834	19370834	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19370834delA	uc002zpf.1	-						HIRA_uc011agx.1_Intron|HIRA_uc010grn.1_Intron|HIRA_uc010gro.1_Intron|HIRA_uc010grp.2_Intron	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective						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)					GAAAAAAAAGAAAAAAAAAAT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	22261443	22261444	+	IGR	INS	-	T	T			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22261443_22261444insT								MAPK1 (39473 upstream) : PPM1F (12349 downstream)																							CTACTTTACAATTTTTTTTTAA	0.386													4	2	---	---	---	---	
RAB36	9609	broad.mit.edu	37	22	23488568	23488568	+	Intron	DEL	G	-	-	rs147076751	by1000genomes	TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23488568delG	uc002zwv.1	+						RAB36_uc010gtw.1_Intron	NM_004914	NP_004905	O95755	RAB36_HUMAN	RAB36, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)		taatttttttggttttttttt	0.000													4	3	---	---	---	---	
EWSR1	2130	broad.mit.edu	37	22	29686700	29686700	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29686700delT	uc003aet.2	+						EWSR1_uc003aev.2_Intron|EWSR1_uc003aew.2_Intron|EWSR1_uc003aex.2_Intron|EWSR1_uc003aey.2_Intron|EWSR1_uc003aez.2_5'UTR	NM_005243	NP_005234	Q01844	EWS_HUMAN	Ewing sarcoma breakpoint region 1 isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	calmodulin binding|nucleotide binding|RNA binding|zinc ion binding		EWSR1/FLI1(2266)|EWSR1/ATF1(323)|EWSR1/WT1(231)|EWSR1/ERG(162)|EWSR1/NR4A3(140)|EWSR1/DDIT3(43)|EWSR1/CREB1(42)|EWSR1/FEV(10)|EWSR1/POU5F1(10)|EWSR1/ETV1(7)|EWSR1/ETV4(6)|EWSR1/ZNF384(4)|EWSR1/PBX1(3)|EWSR1/SP3(3)|EWSR1/PATZ1(2)	bone(2526)|soft_tissue(702)|skin(8)|autonomic_ganglia(4)|haematopoietic_and_lymphoid_tissue(4)|salivary_gland(2)|central_nervous_system(2)|NS(2)|pancreas(2)|lung(1)|ovary(1)	3254						TGGTGTGTACTTTTAAAAAGG	0.353			T	FLI1|ERG|ZNF278|NR4A3|FEV|ATF1|ETV1|ETV4|WT1|ZNF384|CREB1|POU5F1| PBX1	Ewing sarcoma| desmoplastic small round cell tumor |ALL|clear cell sarcoma|sarcoma|myoepithelioma								4	2	---	---	---	---	
C22orf23	84645	broad.mit.edu	37	22	38340062	38340062	+	3'UTR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38340062delG	uc003auj.1	-	7					C22orf23_uc003auk.1_3'UTR	NM_032561	NP_115950	Q9BZE7	EVG1_HUMAN	hypothetical protein LOC84645												0	Melanoma(58;0.045)					GCAGTGCTATGCCACCACCTG	0.637													17	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	42625177	42625177	+	IGR	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42625177delA								TCF20 (13732 upstream) : NFAM1 (151238 downstream)																							GGTCCCAAGCAAATGTGACAT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	44719141	44719144	+	IGR	DEL	CCAT	-	-	rs145338668		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44719141_44719144delCCAT								KIAA1644 (10410 upstream) : LDOC1L (169306 downstream)																							catccatccaccatccatccatcc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45048978	45048979	+	IGR	INS	-	G	G	rs71800987		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45048978_45048979insG								NCRNA00207 (80649 upstream) : PRR5 (15614 downstream)																							GTgaagaaggtaagatgaaagt	0.015													4	2	---	---	---	---	
TBC1D22A	25771	broad.mit.edu	37	22	47396733	47396734	+	Intron	DEL	AA	-	-	rs67546552		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47396733_47396734delAA	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		AAGCaaaaagaaaaaaaaaaaa	0.342													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48095717	48095717	+	Intron	DEL	T	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48095717delT	uc003bik.1	+											Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																		gtttacttgattttttttcta	0.000													4	2	---	---	---	---	
MID1	4281	broad.mit.edu	37	X	10427708	10427708	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10427708delC	uc004cte.3	-	8	1616	c.1425delG	c.(1423-1425)GAGfs	p.E475fs	MID1_uc004ctd.3_Frame_Shift_Del_p.E186fs|MID1_uc004ctg.3_Frame_Shift_Del_p.E475fs|MID1_uc004cth.3_Frame_Shift_Del_p.E437fs|MID1_uc004ctk.3_Frame_Shift_Del_p.E475fs|MID1_uc004cti.3_Frame_Shift_Del_p.E475fs|MID1_uc004ctj.3_Frame_Shift_Del_p.E475fs|MID1_uc011mie.1_RNA|MID1_uc004csz.3_Frame_Shift_Del_p.E147fs|MID1_uc004cta.3_Frame_Shift_Del_p.E231fs|MID1_uc004ctb.3_Frame_Shift_Del_p.E135fs|MID1_uc004ctc.3_Frame_Shift_Del_p.E242fs	NM_033290	NP_150632	O15344	TRI18_HUMAN	midline 1	475	Fibronectin type-III.				microtubule cytoskeleton organization|pattern specification process|positive regulation of stress-activated MAPK cascade	cytoplasm|microtubule|microtubule associated complex|spindle	ligase activity|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|pancreas(1)	3						ACTTCCCAGGCTCACTGCTGC	0.522													13	52	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	14113348	14113348	+	IGR	DEL	G	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14113348delG								GEMIN8 (65313 upstream) : GLRA2 (434072 downstream)																							gcaggactctggggattgctc	0.129													4	2	---	---	---	---	
ZMAT1	84460	broad.mit.edu	37	X	101138798	101138799	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101138798_101138799delTG	uc004eim.2	-	2	4585_4586	c.1087_1088delCA	c.(1087-1089)CATfs	p.H363fs	ZMAT1_uc011mrl.1_Frame_Shift_Del_p.H534fs|ZMAT1_uc004ein.2_Frame_Shift_Del_p.H363fs|ZMAT1_uc011mrm.1_Frame_Shift_Del_p.H363fs	NM_032441	NP_115817	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin type 1 isoform 3	363						nucleus	zinc ion binding			ovary(1)	1						TTTCTGTTTATGACCTGCTTGA	0.391													134	133	---	---	---	---	
ZMAT1	84460	broad.mit.edu	37	X	101138801	101138810	+	Frame_Shift_Del	DEL	CCTGCTTGAT	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101138801_101138810delCCTGCTTGAT	uc004eim.2	-	2	4574_4583	c.1076_1085delATCAAGCAGG	c.(1075-1086)CATCAAGCAGGTfs	p.H359fs	ZMAT1_uc011mrl.1_Frame_Shift_Del_p.H530fs|ZMAT1_uc004ein.2_Frame_Shift_Del_p.H359fs|ZMAT1_uc011mrm.1_Frame_Shift_Del_p.H359fs	NM_032441	NP_115817	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin type 1 isoform 3	359_362						nucleus	zinc ion binding			ovary(1)	1						CTGTTTATGACCTGCTTGATGGTCAGCAGT	0.400													129	132	---	---	---	---	
MID2	11043	broad.mit.edu	37	X	107070729	107070729	+	Intron	DEL	C	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107070729delC	uc004enl.2	+						MID2_uc004enk.2_Intron	NM_012216	NP_036348	Q9UJV3	TRIM1_HUMAN	midline 2 isoform 1							centrosome|microtubule	ligase activity|zinc ion binding			ovary(1)	1						TGAGGATGAGCCCTTATAAAG	0.463													4	2	---	---	---	---	
WDR44	54521	broad.mit.edu	37	X	117519621	117519621	+	Intron	DEL	A	-	-			TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117519621delA	uc004eqn.2	+						WDR44_uc004eqo.2_Intron|WDR44_uc011mtr.1_Intron|MIR1277_hsa-mir-1277|MI0006419_5'Flank	NM_019045	NP_061918	Q5JSH3	WDR44_HUMAN	WD repeat domain 44 protein							cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm				lung(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5						acttaaagttaaaaaaaaaaa	0.005													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9960320	9960321	+	IGR	INS	-	A	A	rs148334492		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9960320_9960321insA								TTTY22 (309466 upstream) : None (None downstream)																							CACCAAGCCTGAAAAATGTATA	0.342													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9987492	9987493	+	IGR	DEL	CA	-	-	rs111703981		TCGA-CZ-5453-01A-01D-1501-10	TCGA-CZ-5453-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9987492_9987493delCA								TTTY22 (336638 upstream) : None (None downstream)																							GCATCATAAGCACACACCGTGC	0.366													6	3	---	---	---	---	
