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
MST1P2	11209	broad.mit.edu	37	1	16973855	16973855	+	RNA	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16973855G>A	uc009vow.2	+	5		c.665G>A			CROCCL1_uc001azg.1_5'Flank|CROCCL1_uc001azi.1_5'Flank|MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_Intron|MST1P2_uc009vox.2_5'Flank|MST1P2_uc001azm.3_5'Flank					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						CCGGGCTAGGGAAGGTCCAGG	0.692													4	5	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94548925	94548925	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94548925A>G	uc001dqh.2	-	7	945	c.841T>C	c.(841-843)TCA>CCA	p.S281P	ABCA4_uc010otn.1_Missense_Mutation_p.S281P	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	281	Extracellular.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances	p.S281L(1)		ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		ATTCTTGGTGACATATCAGAT	0.274													7	325	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158644146	158644146	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158644146A>T	uc001fst.1	-	10	1522	c.1323T>A	c.(1321-1323)CAT>CAA	p.H441Q		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	441	Spectrin 5.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					CAGAGGCTTCATGATTGGCAT	0.378													58	213	---	---	---	---	PASS
CRB1	23418	broad.mit.edu	37	1	197411309	197411309	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197411309A>C	uc001gtz.2	+	11	4027	c.3892A>C	c.(3892-3894)ATT>CTT	p.I1298L	CRB1_uc010poz.1_Missense_Mutation_p.I1274L|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Missense_Mutation_p.I1186L|CRB1_uc010ppb.1_Missense_Mutation_p.I762L|CRB1_uc010ppd.1_Missense_Mutation_p.I779L|CRB1_uc001gub.1_3'UTR	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	1298	Extracellular (Potential).|EGF-like 19; calcium-binding (Potential).				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9						TGAAAAGGACATTGATGAGTG	0.458													114	361	---	---	---	---	PASS
NUAK2	81788	broad.mit.edu	37	1	205275383	205275383	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205275383G>T	uc001hce.2	-	5	750	c.623C>A	c.(622-624)ACA>AAA	p.T208K		NM_030952	NP_112214	Q9H093	NUAK2_HUMAN	NUAK family, SNF1-like kinase, 2	208	Protein kinase.			T->A: Prevents phosphorylation and activation by STK11/LKB1 complex.	actin cytoskeleton organization|apoptosis|cellular response to glucose starvation|negative regulation of apoptosis		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|stomach(1)|breast(1)	5	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CCCACAGAATGTCTGCAGGAA	0.577													38	98	---	---	---	---	PASS
EIF2B4	8890	broad.mit.edu	37	2	27590158	27590158	+	Intron	SNP	C	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27590158C>A	uc002rkb.2	-						EIF2B4_uc002rjz.2_Intron|EIF2B4_uc002rka.2_Intron|EIF2B4_uc002rkc.2_Intron|EIF2B4_uc002rkd.2_Intron|EIF2B4_uc002rke.2_Intron|EIF2B4_uc002rkf.1_3'UTR	NM_001034116	NP_001029288	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B,						myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	translation initiation factor activity|translation initiation factor binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTATGATGACAAGCCTATAG	0.448													4	39	---	---	---	---	PASS
MSH6	2956	broad.mit.edu	37	2	48032086	48032086	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48032086A>G	uc002rwd.3	+	6	3628	c.3476A>G	c.(3475-3477)TAC>TGC	p.Y1159C	MSH6_uc010fbj.2_Missense_Mutation_p.Y857C|MSH6_uc010yoi.1_Missense_Mutation_p.Y1029C|MSH6_uc010yoj.1_Missense_Mutation_p.Y857C	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	1159					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ATGGGTTGTTACGTCCCTGCT	0.433			Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				5	321	---	---	---	---	PASS
SLC1A4	6509	broad.mit.edu	37	2	65217245	65217245	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65217245G>C	uc010yqa.1	+	1	790	c.468G>C	c.(466-468)GAG>GAC	p.E156D	SLC1A4_uc010ypy.1_Intron|SLC1A4_uc010ypz.1_Intron|SLC1A4_uc010fcv.2_Missense_Mutation_p.E156D	NM_003038	NP_003029	P43007	SATT_HUMAN	solute carrier family 1, member 4 isoform 1	156	Extracellular (Potential).				cellular nitrogen compound metabolic process|cognition|synaptic transmission, glutamatergic	intermediate filament|melanosome	chloride channel activity|L-alanine transmembrane transporter activity|L-cystine transmembrane transporter activity|L-hydroxyproline transmembrane transporter activity|L-proline transmembrane transporter activity|L-serine transmembrane transporter activity|L-threonine transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(1)	1					L-Alanine(DB00160)	TGGGGCTGGAGGACTCGGGGC	0.652													4	6	---	---	---	---	PASS
UNC50	25972	broad.mit.edu	37	2	99232913	99232913	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99232913C>G	uc002szc.3	+	5	712	c.560C>G	c.(559-561)ACA>AGA	p.T187R	C2orf64_uc002sza.2_Intron|UNC50_uc002szb.2_Missense_Mutation_p.T187R|UNC50_uc010yvl.1_Missense_Mutation_p.T204R	NM_014044	NP_054763	Q53HI1	UNC50_HUMAN	unc-50 homolog	187	Lumenal (Potential).				protein transport	Golgi membrane|integral to membrane|nuclear inner membrane	RNA binding				0						CTGACAGACACATTTATTGGA	0.363													163	575	---	---	---	---	PASS
ACVR2A	92	broad.mit.edu	37	2	148672763	148672763	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148672763C>T	uc002twg.2	+	6	801	c.532C>T	c.(532-534)CCA>TCA	p.P178S	ACVR2A_uc010zbn.1_Missense_Mutation_p.P70S|ACVR2A_uc002twh.2_Missense_Mutation_p.P178S	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	178	Cytoplasmic (Potential).				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TCTGTAGGACCCAGGACCACC	0.388													5	279	---	---	---	---	PASS
RNF25	64320	broad.mit.edu	37	2	219532832	219532832	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219532832G>A	uc002vit.2	-	4	345	c.257C>T	c.(256-258)CCC>CTC	p.P86L	RNF25_uc010fvw.2_5'UTR	NM_022453	NP_071898	Q96BH1	RNF25_HUMAN	ring finger protein 25	86	RWD.				positive regulation of NF-kappaB transcription factor activity	cytosol|nucleus	NF-kappaB binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AAGTCCTCGGGGATTTCGGAT	0.522													25	88	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188240	10188240	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188240T>A	uc003bvc.2	+	2	596	c.383T>A	c.(382-384)CTT>CAT	p.L128H	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	128	Involved in binding to CCT complex.		L -> F (in VHLD; type II).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.L128fs*31(5)|p.L128P(3)|p.L128fs*4(2)|p.L128R(2)|p.L128H(1)|p.L128I(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)		CACGATGGGCTTCTGGTTAAC	0.413		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				62	141	---	---	---	---	PASS
NBEAL2	23218	broad.mit.edu	37	3	47037324	47037324	+	Silent	SNP	C	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47037324C>G	uc003cqp.2	+	14	2198	c.2019C>G	c.(2017-2019)GCC>GCG	p.A673A	NBEAL2_uc010hjm.1_Silent_p.A234A	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	673							binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TGTCCTTTGCCGACTCTGCCT	0.577													19	60	---	---	---	---	PASS
CBLB	868	broad.mit.edu	37	3	105456081	105456081	+	Silent	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105456081C>T	uc003dwc.2	-	8	1327	c.1005G>A	c.(1003-1005)AGG>AGA	p.R335R	CBLB_uc011bhi.1_Silent_p.R357R|CBLB_uc003dwd.1_Silent_p.R335R|CBLB_uc003dwe.1_Silent_p.R335R|CBLB_uc011bhj.1_RNA	NM_170662	NP_733762	Q13191	CBLB_HUMAN	Cas-Br-M (murine) ecotropic retroviral	335	Cbl-PTB.|SH2-like.				cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9						GATTATAACTCCTCCCATCAG	0.264			Mis S		AML								7	551	---	---	---	---	PASS
SLC35A5	55032	broad.mit.edu	37	3	112300127	112300127	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112300127A>G	uc003dze.2	+	6	1408	c.1163A>G	c.(1162-1164)GAA>GGA	p.E388G		NM_017945	NP_060415	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5	388						Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity|sugar:hydrogen symporter activity			ovary(1)	1						CCTAGGCAAGAAAGGATCCGA	0.448													8	31	---	---	---	---	PASS
COPB2	9276	broad.mit.edu	37	3	139094452	139094452	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139094452C>A	uc003etf.3	-	6	639	c.509G>T	c.(508-510)TGG>TTG	p.W170L	COPB2_uc011bmv.1_Missense_Mutation_p.W141L|COPB2_uc010hui.2_Missense_Mutation_p.W141L|COPB2_uc011bmw.1_Missense_Mutation_p.W170L	NM_004766	NP_004757	P35606	COPB2_HUMAN	coatomer protein complex, subunit beta 2 (beta	170	WD 4.				COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(2)	2						GCCCAACTGCCACACCTGCAG	0.453													4	85	---	---	---	---	PASS
IFT80	57560	broad.mit.edu	37	3	159976407	159976407	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159976407T>C	uc011boy.1	-	20	2673	c.2240A>G	c.(2239-2241)GAG>GGG	p.E747G	IFT80_uc003fda.2_RNA|IFT80_uc003fdb.1_Missense_Mutation_p.E610G|IFT80_uc003fdd.1_Missense_Mutation_p.E430G|IFT80_uc003fde.1_Missense_Mutation_p.E610G	NM_020800	NP_065851	Q9P2H3	IFT80_HUMAN	WD repeat domain 56	747						cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TTTGATTTTCTCCCAATCTAT	0.333													8	603	---	---	---	---	PASS
TRA2B	6434	broad.mit.edu	37	3	185643314	185643314	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185643314G>C	uc003fpv.2	-	3	547	c.271C>G	c.(271-273)CGT>GGT	p.R91G	TRA2B_uc003fpt.2_5'Flank|TRA2B_uc003fpu.2_RNA|TRA2B_uc010hym.2_Translation_Start_Site|TRA2B_uc003fpw.2_Missense_Mutation_p.R91G	NM_004593	NP_004584	P62995	TRA2B_HUMAN	splicing factor, arginine/serine-rich 10	91	Arg/Ser-rich (RS1 domain).				nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|protein binding|RNA binding			ovary(2)	2						TGCCGTCTACGATAATCTCGA	0.522													60	50	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505836	195505836	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505836G>C	uc011bto.1	-	3	12691	c.12231C>G	c.(12229-12231)CAC>CAG	p.H4077Q	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.597													5	27	---	---	---	---	PASS
FYTTD1	84248	broad.mit.edu	37	3	197500330	197500330	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197500330A>G	uc003fyi.2	+	5	773	c.554A>G	c.(553-555)GAT>GGT	p.D185G	FYTTD1_uc011bui.1_Missense_Mutation_p.D159G|FYTTD1_uc011buj.1_RNA|FYTTD1_uc011buk.1_Missense_Mutation_p.D118G	NM_032288	NP_115664	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1 isoform 1	185					mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)		CATCAGAAAGATACTCGTCAG	0.348													6	338	---	---	---	---	PASS
GPR125	166647	broad.mit.edu	37	4	22389491	22389491	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22389491T>C	uc003gqm.1	-	19	4068	c.3803A>G	c.(3802-3804)AAG>AGG	p.K1268R	GPR125_uc010ieo.1_Missense_Mutation_p.K1124R|GPR125_uc003gql.1_Missense_Mutation_p.K395R	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor	1268	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)				CACAGCTGGCTTCCTTAACGC	0.443													7	320	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123183933	123183933	+	Silent	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123183933T>C	uc003ieh.2	+	41	6822	c.6777T>C	c.(6775-6777)TAT>TAC	p.Y2259Y	KIAA1109_uc003iel.1_Silent_p.Y194Y|KIAA1109_uc003iek.2_Silent_p.Y878Y	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	2259					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						TTCACCCATATCATTCTCTGA	0.428													5	128	---	---	---	---	PASS
HMGB2	3148	broad.mit.edu	37	4	174253302	174253302	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174253302G>A	uc011ckc.1	-	4	679	c.559C>T	c.(559-561)CCA>TCA	p.P187S	HMGB2_uc003ita.3_Missense_Mutation_p.P187S|HMGB2_uc003itb.2_Missense_Mutation_p.P187S|HMGB2_uc003itc.2_3'UTR	NM_001130689	NP_001124161	P26583	HMGB2_HUMAN	high-mobility group box 2	187	Asp/Glu-rich (acidic).				base-excision repair, DNA ligation|cell chemotaxis|cellular response to lipopolysaccharide|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|negative regulation of transcription, DNA-dependent|nucleosome assembly|phosphatidylinositol-mediated signaling|positive regulation of DNA binding|positive regulation of endothelial cell proliferation|positive regulation of erythrocyte differentiation|positive regulation of megakaryocyte differentiation|positive regulation of nuclease activity|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	condensed chromosome|extracellular space|nucleolus|nucleoplasm|perinuclear region of cytoplasm|protein complex	chemoattractant activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding|transcription regulatory region DNA binding				0		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		tcatcttctggttcgttcttc	0.274													6	451	---	---	---	---	PASS
DCTD	1635	broad.mit.edu	37	4	183812459	183812459	+	3'UTR	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183812459G>A	uc003ivf.2	-	6					DCTD_uc003ivg.2_3'UTR|DCTD_uc010irw.2_3'UTR|DCTD_uc003ivh.2_3'UTR	NM_001921	NP_001912	P32321	DCTD_HUMAN	dCMP deaminase isoform b						nucleotide biosynthetic process|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide metabolic process	cytosol	dCMP deaminase activity|zinc ion binding				0		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)		ATACTGGCTAGTAAGAAGTTA	0.368													6	107	---	---	---	---	PASS
CCDC110	256309	broad.mit.edu	37	4	186380044	186380044	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186380044C>T	uc003ixu.3	-	6	1773	c.1697G>A	c.(1696-1698)CGA>CAA	p.R566Q	CCDC110_uc003ixv.3_Missense_Mutation_p.R529Q|CCDC110_uc011ckt.1_Missense_Mutation_p.R566Q	NM_152775	NP_689988	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110 isoform a	566	Potential.					nucleus				central_nervous_system(1)	1		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		TATACTCATTCGATTATTTTC	0.294													6	681	---	---	---	---	PASS
ETF1	2107	broad.mit.edu	37	5	137848455	137848455	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137848455G>A	uc003ldc.3	-	6	895	c.730C>T	c.(730-732)CAG>TAG	p.Q244*	ETF1_uc011cyv.1_Nonsense_Mutation_p.Q230*|ETF1_uc010jex.2_RNA|ETF1_uc003ldd.3_Nonsense_Mutation_p.Q211*|ETF1_uc010jey.1_Nonsense_Mutation_p.Q50*	NM_004730	NP_004721	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	244					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|protein methylation|regulation of translational termination	cytoplasm	protein binding|ribosome binding|translation release factor activity, codon specific			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTACTTACCTGATCAAACATA	0.403													61	75	---	---	---	---	PASS
LRRTM2	26045	broad.mit.edu	37	5	138210719	138210719	+	5'UTR	SNP	G	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138210719G>T	uc011cyz.1	-	1					CTNNA1_uc003ldh.2_Intron|CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron|LRRTM2_uc010jez.2_RNA|LRRTM2_uc011cza.1_5'UTR|CTNNA1_uc003ldl.2_5'Flank	NM_015564	NP_056379	O43300	LRRT2_HUMAN	leucine rich repeat transmembrane neuronal 2							cell junction|integral to membrane|postsynaptic membrane					0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TGTGTCCCAGGCTTTCCAAGT	0.448													17	44	---	---	---	---	PASS
HMMR	3161	broad.mit.edu	37	5	162901154	162901154	+	Silent	SNP	A	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162901154A>G	uc003lzf.2	+	10	1175	c.993A>G	c.(991-993)GAA>GAG	p.E331E	HMMR_uc003lzh.2_Silent_p.E332E|HMMR_uc003lzg.2_Silent_p.E316E|HMMR_uc011dem.1_Silent_p.E245E	NM_012484	NP_036616	O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor isoform b	331				QER -> REH (in Ref. 1; AAC52049).		cell surface|cytoplasm	hyaluronic acid binding				0	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)		AACAACAGGAACGTGAAAAGC	0.313													7	520	---	---	---	---	PASS
C5orf60	285679	broad.mit.edu	37	5	179071892	179071892	+	Missense_Mutation	SNP	C	T	T	rs4990389	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179071892C>T	uc011dgo.1	-	1	156	c.130G>A	c.(130-132)GTT>ATT	p.V44I	C5orf60_uc003mki.2_Missense_Mutation_p.V44I	NM_001142306	NP_001135778	A6NFR6	CE060_HUMAN	hypothetical protein LOC285679	44	Helical; (Potential).					integral to membrane					0						CTGAACACAACAAAGAGGACG	0.517													4	108	---	---	---	---	PASS
C5orf60	285679	broad.mit.edu	37	5	179071893	179071893	+	Silent	SNP	A	G	G	rs4990388	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179071893A>G	uc011dgo.1	-	1	155	c.129T>C	c.(127-129)TTT>TTC	p.F43F	C5orf60_uc003mki.2_Silent_p.F43F	NM_001142306	NP_001135778	A6NFR6	CE060_HUMAN	hypothetical protein LOC285679	43	Helical; (Potential).					integral to membrane					0						TGAACACAACAAAGAGGACGA	0.517													4	106	---	---	---	---	PASS
DPCR1	135656	broad.mit.edu	37	6	30917913	30917913	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30917913G>C	uc003nsg.2	+	2	1672	c.1672G>C	c.(1672-1674)GAG>CAG	p.E558Q		NM_080870	NP_543146	Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						integral to membrane					0						ATCCCCAGCAGAGCCTACAGA	0.512													6	188	---	---	---	---	PASS
SCML4	256380	broad.mit.edu	37	6	108093542	108093542	+	5'UTR	SNP	G	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108093542G>C	uc010kdf.2	-	2					SCML4_uc003prz.3_Intron|SCML4_uc011eam.1_5'UTR|SCML4_uc003psa.3_5'UTR	NM_198081	NP_932347	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		TTCTGCTGGTGCCAGTCTTAC	0.473													20	67	---	---	---	---	PASS
NT5C3	51251	broad.mit.edu	37	7	33055308	33055308	+	Silent	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33055308G>A	uc003tdk.2	-	8	960	c.883C>T	c.(883-885)CTG>TTG	p.L295L	AVL9_uc011kai.1_Intron|NT5C3_uc003tdi.2_Silent_p.L256L|NT5C3_uc003tdj.2_Silent_p.L256L	NM_001002010	NP_001002010	Q9H0P0	5NT3_HUMAN	5'-nucleotidase, cytosolic III isoform 1	295					nucleotide metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol|endoplasmic reticulum	2'-phosphotransferase activity|5'-nucleotidase activity|magnesium ion binding|nucleotide binding			ovary(1)	1			GBM - Glioblastoma multiforme(11;0.0894)			CCAATTTTCAGAATGTGCTCA	0.328													87	238	---	---	---	---	PASS
BCAP29	55973	broad.mit.edu	37	7	107258848	107258848	+	3'UTR	SNP	A	G	G	rs141644610		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107258848A>G	uc003vej.2	+	8					BCAP29_uc011kly.1_3'UTR|BCAP29_uc011klz.1_Intron|BCAP29_uc011kma.1_Missense_Mutation_p.D282G	NM_018844	NP_061332	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein BAP29 isoform						apoptosis|intracellular protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|integral to membrane				large_intestine(1)|ovary(1)	2						TGTCAAAATGATAATTTTGTT	0.299													6	263	---	---	---	---	PASS
UBE3C	9690	broad.mit.edu	37	7	157018150	157018150	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157018150G>A	uc010lqs.2	+	17	2462	c.2150G>A	c.(2149-2151)GGT>GAT	p.G717D	UBE3C_uc003wni.3_Missense_Mutation_p.G80D	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	717					protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		CAAGGAGATGGTCCATTTCTG	0.318													145	462	---	---	---	---	PASS
XPO7	23039	broad.mit.edu	37	8	21857049	21857049	+	Silent	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21857049T>C	uc003xaa.3	+	24	2748	c.2646T>C	c.(2644-2646)GAT>GAC	p.D882D	XPO7_uc010lti.2_Silent_p.D891D|XPO7_uc010ltk.2_Silent_p.D883D	NM_015024	NP_055839	Q9UIA9	XPO7_HUMAN	exportin 7 isoform b	882					mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		TCCCACAGGATTACCCCAAGC	0.458													5	148	---	---	---	---	PASS
LEPROTL1	23484	broad.mit.edu	37	8	29994916	29994916	+	Silent	SNP	T	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29994916T>G	uc003xhx.2	+	4	515	c.408T>G	c.(406-408)ACT>ACG	p.T136T	MBOAT4_uc010lvg.2_Intron	NM_001128208	NP_001121680	O95214	LERL1_HUMAN	leptin receptor overlapping transcript-like 1	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		GAGTGTCCACTCAACCCGTGC	0.567													5	18	---	---	---	---	PASS
NKAIN3	286183	broad.mit.edu	37	8	63831061	63831061	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63831061A>T	uc010lyq.1	+	5	653	c.521A>T	c.(520-522)GAA>GTA	p.E174V		NM_173688	NP_775959	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3	174						integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)				TCCATGGAAGAAGAAGACACA	0.378													167	527	---	---	---	---	PASS
PI15	51050	broad.mit.edu	37	8	75757712	75757712	+	Silent	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75757712G>A	uc003yal.2	+	5	800	c.621G>A	c.(619-621)TTG>TTA	p.L207L	uc003yak.1_Intron|PI15_uc003yam.2_Silent_p.L207L	NM_015886	NP_056970	O43692	PI15_HUMAN	protease inhibitor 15 preproprotein	207						extracellular region	peptidase inhibitor activity			central_nervous_system(2)|ovary(1)	3	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)			CAGTTTACTTGGTATGCAACT	0.443													5	403	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110471954	110471954	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110471954T>C	uc003yne.2	+	47	7239	c.7135T>C	c.(7135-7137)TTT>CTT	p.F2379L		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	2379	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TGGAACTCTGTTTGAAGCAAG	0.378										HNSCC(38;0.096)			73	188	---	---	---	---	PASS
CTSL3	392360	broad.mit.edu	37	9	90387883	90387883	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90387883C>A	uc004apm.1	+	1	54	c.48C>A	c.(46-48)TTC>TTA	p.F16L		NR_027917				RecName: Full=Putative cathepsin L-like protein 3;          Short=Cathepsin L-like protein; AltName: Full=HCTSL-s;											ovary(1)	1						AACACAGCTTCACAATGGCCA	0.473													53	171	---	---	---	---	PASS
JMJD1C	221037	broad.mit.edu	37	10	64949144	64949144	+	Silent	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64949144T>C	uc001jmn.2	-	18	6654	c.6354A>G	c.(6352-6354)GAA>GAG	p.E2118E	JMJD1C_uc001jml.2_Silent_p.E1881E|JMJD1C_uc001jmm.2_Silent_p.E1830E|JMJD1C_uc010qiq.1_Silent_p.E1936E|JMJD1C_uc009xpi.2_Silent_p.E1936E|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc001jmo.2_Silent_p.E25E	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	2118					blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					GAATTTTGTTTTCAACAACTG	0.323													7	521	---	---	---	---	PASS
NAP1L4	4676	broad.mit.edu	37	11	2979718	2979718	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2979718T>C	uc001lxc.2	-	10	944	c.803A>G	c.(802-804)AAG>AGG	p.K268R	NAP1L4_uc009ydt.2_RNA|NAP1L4_uc010qxm.1_Missense_Mutation_p.K268R|NAP1L4_uc010qxn.1_Missense_Mutation_p.K268R	NM_005969	NP_005960	Q99733	NP1L4_HUMAN	nucleosome assembly protein 1-like 4	268	Nuclear localization signal (Potential).				nucleosome assembly	chromatin assembly complex|cytoplasm	unfolded protein binding			ovary(1)	1		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)		ATGCTTCTGCTTTTTCTTGAT	0.403													8	576	---	---	---	---	PASS
RRP8	23378	broad.mit.edu	37	11	6623330	6623330	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6623330T>C	uc001med.2	-	2	294	c.215A>G	c.(214-216)AAG>AGG	p.K72R	ILK_uc001mee.2_5'Flank|ILK_uc001mef.2_5'Flank|ILK_uc010rap.1_5'Flank|ILK_uc010raq.1_5'Flank|ILK_uc001meg.2_5'Flank|ILK_uc001meh.2_5'Flank	NM_015324	NP_056139	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase,	72					chromatin modification|chromatin silencing at rDNA|rRNA processing|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	methylated histone residue binding|S-adenosylmethionine-dependent methyltransferase activity				0						GCATTTCTTCTTCCTTTCCTC	0.517													5	141	---	---	---	---	PASS
NLRP14	338323	broad.mit.edu	37	11	7063767	7063767	+	Silent	SNP	C	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7063767C>G	uc001mfb.1	+	4	833	c.510C>G	c.(508-510)GTC>GTG	p.V170V		NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	170					cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|pancreas(1)|lung(1)|skin(1)	8				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		ATGTGGATGTCAAAACCGGTG	0.478													10	199	---	---	---	---	PASS
NLRP14	338323	broad.mit.edu	37	11	7064392	7064392	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7064392C>A	uc001mfb.1	+	4	1458	c.1135C>A	c.(1135-1137)CTG>ATG	p.L379M		NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	379	NACHT.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|pancreas(1)|lung(1)|skin(1)	8				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		TTGTACTTGTCTGAAGCAGCA	0.463													6	109	---	---	---	---	PASS
NLRP14	338323	broad.mit.edu	37	11	7064501	7064501	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7064501C>G	uc001mfb.1	+	4	1567	c.1244C>G	c.(1243-1245)TCT>TGT	p.S415C		NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	415	NACHT.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|pancreas(1)|lung(1)|skin(1)	8				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GATGGAGGCTCTCCTAGTCTA	0.463													4	84	---	---	---	---	PASS
KAT5	10524	broad.mit.edu	37	11	65480531	65480531	+	Splice_Site	SNP	T	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65480531T>G	uc001ofi.2	+	4	535	c.285_splice	c.e4+2	p.V95_splice	KAT5_uc001ofj.2_Splice_Site_p.V95_splice|KAT5_uc001ofk.2_Splice_Site_p.V128_splice|KAT5_uc010roo.1_Splice_Site_p.V128_splice|KAT5_uc001ofl.2_Splice_Site	NM_006388	NP_006379	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5 isoform 2						androgen receptor signaling pathway|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|double-strand break repair|interspecies interaction between organisms|negative regulation of interleukin-2 production|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nucleolus|perinuclear region of cytoplasm|Piccolo NuA4 histone acetyltransferase complex	androgen receptor binding|histone acetyltransferase activity|metal ion binding|repressing transcription factor binding|transcription coactivator activity				0						AGAGAGGTGGTGAGTAGGTCC	0.567													10	24	---	---	---	---	PASS
ANGPTL5	253935	broad.mit.edu	37	11	101777858	101777858	+	Nonsense_Mutation	SNP	G	A	A	rs140984722	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101777858G>A	uc001pgl.2	-	3	813	c.217C>T	c.(217-219)CGA>TGA	p.R73*		NM_178127	NP_835228	Q86XS5	ANGL5_HUMAN	angiopoietin-like 5 precursor	73					signal transduction	extracellular space	receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043)		BRCA - Breast invasive adenocarcinoma(274;0.0328)		TTTTCTTCTCGTGTAATTTTA	0.269													7	560	---	---	---	---	PASS
ARHGAP32	9743	broad.mit.edu	37	11	128840075	128840075	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128840075T>C	uc009zcp.2	-	22	4991	c.4991A>G	c.(4990-4992)GAT>GGT	p.D1664G	ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_Missense_Mutation_p.D623G|ARHGAP32_uc001qez.2_Missense_Mutation_p.D1315G	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1	1664	Interaction with GAB2.				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						CAGGGCCCCATCTGGACTGTA	0.493													4	52	---	---	---	---	PASS
STAT2	6773	broad.mit.edu	37	12	56748290	56748290	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56748290T>C	uc001slc.2	-	8	820	c.742A>G	c.(742-744)AGA>GGA	p.R248G	STAT2_uc001sld.2_Missense_Mutation_p.R244G|STAT2_uc010sqn.1_Missense_Mutation_p.R244G	NM_005419	NP_005410	P52630	STAT2_HUMAN	signal transducer and activator of transcription	248					interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3						ATGGGAGCTCTGATGCAGGCT	0.552													19	71	---	---	---	---	PASS
RDH16	8608	broad.mit.edu	37	12	57345981	57345981	+	Silent	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57345981C>T	uc001smi.3	-	4	958	c.786G>A	c.(784-786)TCG>TCA	p.S262S	RDH16_uc009zpa.2_Silent_p.S117S	NM_003708	NP_003699	O75452	RDH16_HUMAN	retinol dehydrogenase 16	262	Cytoplasmic (Potential).				lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	binding|electron carrier activity|retinol dehydrogenase activity				0						TGGTCACCAACGACAGATCCT	0.502													25	49	---	---	---	---	PASS
SYCP3	50511	broad.mit.edu	37	12	102131012	102131012	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102131012C>T	uc001tiq.2	-	3	330	c.198G>A	c.(196-198)ATG>ATA	p.M66I	SYCP3_uc001tir.2_Missense_Mutation_p.M66I|SYCP3_uc001tis.2_Missense_Mutation_p.M66I	NM_153694	NP_710161	Q8IZU3	SYCP3_HUMAN	synaptonemal complex protein 3	66					cell division|male meiosis I|spermatogenesis, exchange of chromosomal proteins	nucleus	DNA binding				0						CACGTTACCCCATATCTTCAA	0.308													5	292	---	---	---	---	PASS
RSRC2	65117	broad.mit.edu	37	12	122991416	122991416	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122991416G>T	uc001ucr.2	-	9	1236	c.1090C>A	c.(1090-1092)CAA>AAA	p.Q364K	RSRC2_uc001uco.2_Missense_Mutation_p.Q133K|RSRC2_uc001ucp.2_Missense_Mutation_p.Q305K|RSRC2_uc001ucq.2_Missense_Mutation_p.Q132K|RSRC2_uc001ucs.2_Missense_Mutation_p.Q133K|RSRC2_uc001uct.2_Missense_Mutation_p.Q316K|RSRC2_uc001ucu.2_Missense_Mutation_p.Q365K	NM_023012	NP_075388	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2 isoform a	364										ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)		TTGACATTTTGGTCCTTGTTT	0.289													6	537	---	---	---	---	PASS
CENPJ	55835	broad.mit.edu	37	13	25457439	25457439	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25457439C>T	uc001upt.3	-	17	4146	c.3893G>A	c.(3892-3894)CGG>CAG	p.R1298Q	CENPJ_uc010tdf.1_RNA|CENPJ_uc010aae.2_RNA|CENPJ_uc010aaf.2_RNA	NM_018451	NP_060921	Q9HC77	CENPJ_HUMAN	centromere protein J	1298					cell division|centriole replication|G2/M transition of mitotic cell cycle|microtubule nucleation|microtubule polymerization	centriole|cytosol|gamma-tubulin small complex|microtubule	protein domain specific binding|tubulin binding			ovary(2)	2		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		TGGGTATTCCCGTCTCTTGAA	0.368													10	460	---	---	---	---	PASS
MTUS2	23281	broad.mit.edu	37	13	30071435	30071435	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30071435G>C	uc001usl.3	+	11	3728	c.3670G>C	c.(3670-3672)GAA>CAA	p.E1224Q	MTUS2_uc001usm.3_Missense_Mutation_p.E193Q|MTUS2_uc010aau.2_Missense_Mutation_p.E103Q|MTUS2_uc010tdq.1_5'UTR	NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a	1214	Potential.					cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						CCGCCGCTTCGAAGAGGCCTT	0.622													6	26	---	---	---	---	PASS
HSPH1	10808	broad.mit.edu	37	13	31711624	31711624	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31711624G>T	uc001utj.2	-	18	2806	c.2408C>A	c.(2407-2409)CCG>CAG	p.P803Q	HSPH1_uc001utk.2_Missense_Mutation_p.P759Q|HSPH1_uc010aaw.2_Missense_Mutation_p.P762Q|HSPH1_uc001utl.2_Missense_Mutation_p.P805Q|HSPH1_uc010tds.1_Missense_Mutation_p.P727Q	NM_006644	NP_006635	Q92598	HS105_HUMAN	heat shock 105kD	803					positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein	cytoplasm|extracellular region	ATP binding				0		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		TTTTGGTTTCGGTTGTGTTAC	0.343													7	682	---	---	---	---	PASS
FRY	10129	broad.mit.edu	37	13	32753054	32753054	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32753054C>A	uc001utx.2	+	22	3251	c.2755C>A	c.(2755-2757)CTA>ATA	p.L919I	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	919					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GAGAAATTACCTAATTCTTTG	0.433													5	263	---	---	---	---	PASS
G2E3	55632	broad.mit.edu	37	14	31074954	31074954	+	Silent	SNP	A	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31074954A>G	uc001wqk.2	+	11	1408	c.1254A>G	c.(1252-1254)CAA>CAG	p.Q418Q	G2E3_uc010tpe.1_Intron|G2E3_uc010tpf.1_Silent_p.Q372Q	NM_017769	NP_060239	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin ligase	418	HECT.				apoptosis|multicellular organismal development|protein modification process	Golgi apparatus|nucleolus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						TCTTAATGCAACATCTTGAGA	0.308													6	316	---	---	---	---	PASS
C14orf145	145508	broad.mit.edu	37	14	81259370	81259370	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81259370T>C	uc001xux.2	-	13	1465	c.1294A>G	c.(1294-1296)ACA>GCA	p.T432A	C14orf145_uc010asz.1_RNA	NM_152446	NP_689659	Q6ZU80	CE128_HUMAN	hypothetical protein LOC145508	432	Potential.					centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)		GCCTCACATGTGTCAAAGTGA	0.493													41	192	---	---	---	---	PASS
PAPOLA	10914	broad.mit.edu	37	14	97010550	97010550	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97010550C>A	uc001yfq.2	+	15	1564	c.1354C>A	c.(1354-1356)CTC>ATC	p.L452I	PAPOLA_uc001yfr.2_Missense_Mutation_p.L452I|PAPOLA_uc010twv.1_Missense_Mutation_p.L452I|PAPOLA_uc010avp.2_Missense_Mutation_p.L202I	NM_032632	NP_116021	P51003	PAPOA_HUMAN	poly(A) polymerase alpha	452					mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|RNA binding				0		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		CTCTGAAAACCTCAGTGTTGA	0.353													5	411	---	---	---	---	PASS
MIR1197	100302250	broad.mit.edu	37	14	101491920	101491920	+	RNA	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101491920T>C	hsa-mir-1197|MI0006656	+			c.20T>C			uc001yjy.1_5'Flank|MIR323_hsa-mir-323|MI0000807_5'Flank|MIR758_hsa-mir-758|MI0003757_5'Flank|MIR329-1_hsa-mir-329-1|MI0001725_5'Flank|MIR329-2_hsa-mir-329-2|MI0001726_5'Flank																	0						TATTTGAAGATGCGGTTGACC	0.488													6	275	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	33873834	33873834	+	Silent	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33873834C>T	uc001zhi.2	+	14	1633	c.1563C>T	c.(1561-1563)TAC>TAT	p.Y521Y	RYR3_uc010bar.2_Silent_p.Y521Y	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	521	Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ACCTCCTCTACAAATTGCTGG	0.458													12	130	---	---	---	---	PASS
ARPP19	10776	broad.mit.edu	37	15	52844224	52844224	+	Silent	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52844224C>T	uc002acd.1	-	3	370	c.246G>A	c.(244-246)CCG>CCA	p.P82P	ARPP19_uc002ace.1_Silent_p.P82P	NM_006628	NP_006619	P56211	ARP19_HUMAN	cyclic AMP phosphoprotein, 19 kD	82					cell division|G2/M transition of mitotic cell cycle|mitosis|positive regulation of gluconeogenesis|positive regulation of glucose import	cytoplasm	potassium channel regulator activity|protein phosphatase 2A binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity|receptor binding				0						CCGTCTTATCCGGAGCTGCAG	0.438													144	403	---	---	---	---	PASS
GOLGA6L5	374650	broad.mit.edu	37	15	85053188	85053188	+	RNA	SNP	C	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85053188C>G	uc002bkm.2	-	9		c.1859G>C			uc002bkl.1_5'Flank	NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						CCCTGTTCTCCGCAGCCCGAA	0.488													9	25	---	---	---	---	PASS
RAB11FIP3	9727	broad.mit.edu	37	16	532561	532561	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:532561G>A	uc002chf.2	+	4	1279	c.940G>A	c.(940-942)GAG>AAG	p.E314K	RAB11FIP3_uc010uuf.1_Missense_Mutation_p.E18K|RAB11FIP3_uc010uug.1_Missense_Mutation_p.E4K	NM_014700	NP_055515	O75154	RFIP3_HUMAN	rab11-family interacting protein 3 isoform 1	314					cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)				CATGGGCTCCGAGAGCACCTA	0.647													5	10	---	---	---	---	PASS
C16orf73	254528	broad.mit.edu	37	16	1884361	1884361	+	Silent	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1884361G>A	uc002cne.2	-	13	1343	c.1225C>T	c.(1225-1227)CTA>TTA	p.L409L	FAHD1_uc002cnd.2_Intron|FAHD1_uc010brz.2_Intron|C16orf73_uc010uvq.1_Silent_p.L438L|C16orf73_uc010uvr.1_Silent_p.L231L	NM_152764	NP_689977	Q8N635	CP073_HUMAN	hypothetical protein LOC254528 isoform 2	409					meiosis	cytoplasm					0						CTGTGTGATAGAACGAACTGC	0.383													5	222	---	---	---	---	PASS
ZNF200	7752	broad.mit.edu	37	16	3283545	3283545	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3283545C>G	uc002cuj.2	-	2	843	c.211G>C	c.(211-213)GTT>CTT	p.V71L	ZNF200_uc002cum.3_Missense_Mutation_p.V71L|ZNF200_uc010bti.2_Missense_Mutation_p.V71L|ZNF200_uc002cuk.2_Missense_Mutation_p.V71L|ZNF200_uc002cui.2_Missense_Mutation_p.V71L|ZNF200_uc002cul.3_Missense_Mutation_p.V71L	NM_003454	NP_003445	P98182	ZN200_HUMAN	zinc finger protein 200 isoform 1	71					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0						TTCATAATAACCAAGGTCTCC	0.517													9	122	---	---	---	---	PASS
TMC5	79838	broad.mit.edu	37	16	19451709	19451709	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19451709C>T	uc002dgc.3	+	3	1098	c.349C>T	c.(349-351)CCC>TCC	p.P117S	TMC5_uc010vaq.1_Missense_Mutation_p.P117S|TMC5_uc002dgb.3_Missense_Mutation_p.P117S|TMC5_uc010var.1_Missense_Mutation_p.P117S	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	117	Extracellular (Potential).					integral to membrane				skin(1)	1						TCAGAGTCATCCCTACCACCG	0.502													4	139	---	---	---	---	PASS
LOC100132247	100132247	broad.mit.edu	37	16	22503208	22503208	+	Intron	SNP	A	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22503208A>T	uc010bxg.2	+						LOC641298_uc010bxf.2_RNA	NM_001135865	NP_001129337	A8MRT5	K220L_HUMAN	hypothetical protein LOC100132247							integral to membrane					0						TTTTttttttaaattttgctt	0.129													5	20	---	---	---	---	PASS
CNOT1	23019	broad.mit.edu	37	16	58564211	58564211	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58564211T>C	uc002env.2	-	43	6511	c.6218A>G	c.(6217-6219)AAA>AGA	p.K2073R	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Missense_Mutation_p.K2068R|CNOT1_uc002ent.2_Missense_Mutation_p.K11R|CNOT1_uc010vik.1_Missense_Mutation_p.K1030R	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	2073					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CGCTAAATATTTGAATAAATC	0.338													50	163	---	---	---	---	PASS
LOC283922	283922	broad.mit.edu	37	16	74372644	74372644	+	Silent	SNP	A	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74372644A>G	uc002fcr.2	-	9	1661	c.315T>C	c.(313-315)CCT>CCC	p.P105P	LOC283922_uc010vms.1_RNA					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						TACCCTTGTCAGGGGGAACAA	0.443													9	106	---	---	---	---	PASS
C16orf55	124045	broad.mit.edu	37	16	89724745	89724745	+	Missense_Mutation	SNP	G	C	C	rs149646248		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89724745G>C	uc002fnw.1	+	2	124	c.124G>C	c.(124-126)GAC>CAC	p.D42H	CHMP1A_uc002fnu.2_5'Flank|CHMP1A_uc002fnv.2_5'Flank|C16orf55_uc002fnx.3_Missense_Mutation_p.D43H|C16orf55_uc010vpk.1_Missense_Mutation_p.D43H|C16orf55_uc002fny.1_Intron	NM_153025	NP_694570	Q96N06	CP055_HUMAN	hypothetical protein LOC124045	42											0		all_lung(18;0.000665)|all_hematologic(23;0.0355)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		CAGGCAGGCAGACAGGGAGTC	0.582													13	47	---	---	---	---	PASS
USP6	9098	broad.mit.edu	37	17	5076157	5076157	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5076157C>A	uc002gau.1	+	38	6335	c.4105C>A	c.(4105-4107)CAG>AAG	p.Q1369K	USP6_uc002gav.1_Missense_Mutation_p.Q1369K|USP6_uc010ckz.1_Missense_Mutation_p.Q1052K	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6	1369					protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5						CTATGAGCAGCAGGGGATAGA	0.418			T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								5	305	---	---	---	---	PASS
CLTC	1213	broad.mit.edu	37	17	57725743	57725743	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57725743G>T	uc002ixq.1	+	4	1105	c.662G>T	c.(661-663)CGG>CTG	p.R221L	CLTC_uc002ixp.2_Missense_Mutation_p.R221L|CLTC_uc002ixr.1_Missense_Mutation_p.R225L	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	221	Globular terminal domain.				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TTTGCAGTTCGGGGCCAAGCT	0.383			T	ALK|TFE3	ALCL|renal 								6	278	---	---	---	---	PASS
TLK2	11011	broad.mit.edu	37	17	60637441	60637441	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60637441G>A	uc010ddp.2	+	10	1053	c.785G>A	c.(784-786)CGA>CAA	p.R262Q	TLK2_uc002izx.3_Missense_Mutation_p.R110Q|TLK2_uc002izz.3_Missense_Mutation_p.R262Q|TLK2_uc002jaa.3_Missense_Mutation_p.R230Q|TLK2_uc010wpd.1_Missense_Mutation_p.R230Q	NM_006852	NP_006843	Q86UE8	TLK2_HUMAN	tousled-like kinase 2 isoform A	262	Potential.		R -> Q.		cell cycle|chromatin modification|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|kidney(1)	2						TACAAGGAACGATTAAATAGA	0.358													6	430	---	---	---	---	PASS
MARCH10	162333	broad.mit.edu	37	17	60813347	60813347	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60813347T>A	uc010ddr.2	-	6	2120	c.1882A>T	c.(1882-1884)AAG>TAG	p.K628*	MARCH10_uc002jag.3_Nonsense_Mutation_p.K628*|MARCH10_uc010dds.2_Nonsense_Mutation_p.K666*|MARCH10_uc002jah.2_Nonsense_Mutation_p.K627*|uc002jaj.1_RNA|uc002jak.2_Intron	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190	628							ligase activity|zinc ion binding				0						CTGGTTTCCTTTTCATCTGTG	0.383													22	62	---	---	---	---	PASS
ESCO1	114799	broad.mit.edu	37	18	19140877	19140877	+	Silent	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19140877T>C	uc002kth.1	-	8	2830	c.1896A>G	c.(1894-1896)GAA>GAG	p.E632E	ESCO1_uc002kti.1_RNA	NM_052911	NP_443143	Q5FWF5	ESCO1_HUMAN	establishment of cohesion 1 homolog 1	632	CCHH-type.				cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding				0						GTGTTTCATCTTCTGGATTTG	0.328													8	588	---	---	---	---	PASS
FHOD3	80206	broad.mit.edu	37	18	34323997	34323997	+	Silent	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34323997C>T	uc002kzt.1	+	19	3403	c.3306C>T	c.(3304-3306)GCC>GCT	p.A1102A	FHOD3_uc002kzs.1_Silent_p.A1119A|FHOD3_uc010dmz.1_Silent_p.A834A|FHOD3_uc010dnb.1_Silent_p.A98A	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1102	FH2.				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)				CAAAACAGGCCAAAGCGTTTG	0.453													4	137	---	---	---	---	PASS
GALR1	2587	broad.mit.edu	37	18	74962847	74962847	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74962847T>C	uc002lms.3	+	1	840	c.343T>C	c.(343-345)TTC>CTC	p.F115L		NM_001480	NP_001471	P47211	GALR1_HUMAN	galanin receptor 1	115	Helical; Name=3; (Potential).				digestion|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity			lung(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		CCACTACTTCTTCACCGTGTC	0.637													4	28	---	---	---	---	PASS
ZNF540	163255	broad.mit.edu	37	19	38090608	38090608	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38090608T>A	uc002ogq.2	+	3	423	c.91T>A	c.(91-93)TAC>AAC	p.Y31N	ZNF540_uc002ogu.2_Missense_Mutation_p.Y31N|ZNF540_uc010efq.2_Missense_Mutation_p.Y31N	NM_152606	NP_689819	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	31	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GAGGAAATTGTACAGAGATGT	0.418													7	640	---	---	---	---	PASS
PSG5	5673	broad.mit.edu	37	19	43690641	43690641	+	5'UTR	SNP	C	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43690641C>A	uc002ovu.2	-	1					PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_5'Flank|PSG5_uc002ovx.2_5'UTR|PSG5_uc002ovv.2_5'UTR|PSG5_uc002ovw.2_5'UTR	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5						female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)				GCTGTGCTGTCCTTCCTCCTT	0.617													5	24	---	---	---	---	PASS
LILRB1	10859	broad.mit.edu	37	19	55142960	55142960	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55142960C>T	uc002qgj.2	+	5	420	c.80C>T	c.(79-81)CCC>CTC	p.P27L	LILRB1_uc010erp.1_Intron|LILRB1_uc002qgl.2_Missense_Mutation_p.P27L|LILRB1_uc002qgk.2_Missense_Mutation_p.P27L|LILRB1_uc002qgm.2_Missense_Mutation_p.P27L|LILRB1_uc010erq.2_Missense_Mutation_p.P27L|LILRB1_uc010err.2_RNA	NM_006669	NP_006660	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor,	27	Ig-like C2-type 1.|Extracellular (Potential).				regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)|skin(1)	3				GBM - Glioblastoma multiforme(193;0.0188)		GGGCACCTCCCCAAGCCCACC	0.617										HNSCC(37;0.09)			6	49	---	---	---	---	PASS
MAGT1	84061	broad.mit.edu	37	X	77150869	77150869	+	Silent	SNP	G	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77150869G>T	uc004fof.2	-	1	197	c.135C>A	c.(133-135)ACC>ACA	p.T45T	MAGT1_uc004fog.3_RNA|MAGT1_uc004ect.3_Silent_p.T45T	NM_032121	NP_115497	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	13					protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				upper_aerodigestive_tract(1)	1						CCACCACCATGGTCACAGAGA	0.572													21	13	---	---	---	---	PASS
ZMAT1	84460	broad.mit.edu	37	X	101138822	101138822	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101138822T>C	uc004eim.2	-	2	4562	c.1064A>G	c.(1063-1065)AAT>AGT	p.N355S	ZMAT1_uc011mrl.1_Missense_Mutation_p.N526S|ZMAT1_uc004ein.2_Missense_Mutation_p.N355S|ZMAT1_uc011mrm.1_Missense_Mutation_p.N355S	NM_032441	NP_115817	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin type 1 isoform 3	355						nucleus	zinc ion binding			ovary(1)	1						GTCAGCAGTATTGTTTTCTGA	0.418													10	588	---	---	---	---	PASS
KIF1B	23095	broad.mit.edu	37	1	10350921	10350921	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10350921delA	uc001aqx.3	+						KIF1B_uc001aqv.3_Intron|KIF1B_uc001aqw.3_Intron|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		actccgtctcaaaaaaaaaaa	0.114													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	11036395	11036395	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11036395delT								C1orf127 (12137 upstream) : TARDBP (36284 downstream)																							ATTATAtttcttttttttttt	0.289													5	3	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21221636	21221636	+	Intron	DEL	A	-	-	rs3738150	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21221636delA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.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)		AATAAACATTAAAAAAAACCA	0.328													4	2	---	---	---	---	
ECE1	1889	broad.mit.edu	37	1	21663904	21663904	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21663904delG	uc001bem.2	-							NM_001113348	NP_001106819	P42892	ECE1_HUMAN	endothelin converting enzyme 1 isoform 4						bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		acctgctgcaggggactgatg	0.000													4	2	---	---	---	---	
FAM76A	199870	broad.mit.edu	37	1	28068394	28068394	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28068394delA	uc001boq.2	+						FAM76A_uc009vtb.2_Intron|FAM76A_uc001bor.2_Intron|FAM76A_uc001bos.2_Intron|FAM76A_uc001bot.2_Intron|FAM76A_uc010ofm.1_Intron	NM_152660	NP_689873	Q8TAV0	FA76A_HUMAN	hypothetical protein LOC199870 isoform 3												0		Colorectal(325;0.000147)|all_lung(284;0.00181)|Lung NSC(340;0.00278)|Renal(390;0.00357)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00253)|KIRC - Kidney renal clear cell carcinoma(1967;0.00292)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)		actctatctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	39304016	39304017	+	IGR	DEL	CA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39304016_39304017delCA								POU3F1 (791566 upstream) : RRAGC (998 downstream)																							CACTCCAAGTCACACTGTTAGC	0.366													4	2	---	---	---	---	
EDN2	1907	broad.mit.edu	37	1	41949065	41949065	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41949065delG	uc001cgx.2	-						EDN2_uc001cgu.2_Intron|EDN2_uc001cgv.2_Intron|EDN2_uc009vwh.2_Intron|EDN2_uc001cgw.2_Intron|EDN2_uc009vwi.2_Intron|EDN2_uc009vwj.2_Intron	NM_001956	NP_001947	P20800	EDN2_HUMAN	endothelin 2 preproprotein						artery smooth muscle contraction|calcium-mediated signaling|cytokine-mediated signaling pathway|elevation of cytosolic calcium ion concentration|hormonal regulation of the force of heart contraction|inositol phosphate-mediated signaling|macrophage activation|macrophage chemotaxis|neutrophil chemotaxis|positive regulation of cell proliferation|positive regulation of heart rate|positive regulation of leukocyte chemotaxis|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of the force of heart contraction by chemical signal|prostaglandin biosynthetic process|regulation of systemic arterial blood pressure by endothelin|regulation of vasoconstriction|vein smooth muscle contraction	extracellular space	endothelin B receptor binding|hormone activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTTGCAATTTGGGGAGGGGAA	0.552													4	2	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42194840	42194840	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42194840delG	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)				AGGTGGCTGTGGGAATAAAAC	0.567													4	2	---	---	---	---	
ST3GAL3	6487	broad.mit.edu	37	1	44300103	44300104	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44300103_44300104insT	uc001ckc.2	+						ST3GAL3_uc009vwu.1_Intron|ST3GAL3_uc010okj.1_Intron|ST3GAL3_uc001cjz.2_Intron|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Intron|ST3GAL3_uc001ckd.2_Intron|ST3GAL3_uc001cke.2_Intron|ST3GAL3_uc001ckf.2_Intron|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Intron|ST3GAL3_uc001ckj.2_Intron|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Intron|ST3GAL3_uc009vwy.2_Intron|ST3GAL3_uc009vwx.2_Intron|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Intron|ST3GAL3_uc009vxa.2_Intron|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Intron|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270	Q11203	SIAT6_HUMAN	sialyltransferase 6 isoform j						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				tcacctccacattccagtggaa	0.000													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49930158	49930159	+	Intron	DEL	AC	-	-	rs142187281	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49930158_49930159delAC	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		AGTTCTGAGTACACCTTCTTTG	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	55743892	55743892	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55743892delC								USP24 (63130 upstream) : None (None downstream)																							CCTCCTCTTGCCCCATCTTCT	0.517											OREG0013508	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
DOCK7	85440	broad.mit.edu	37	1	63127567	63127567	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63127567delC	uc001daq.2	-						DOCK7_uc001dap.2_Intron|DOCK7_uc009wah.1_Intron	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2						gagaggcgttcaagacaccaa	0.055													4	2	---	---	---	---	
MIER1	57708	broad.mit.edu	37	1	67394273	67394274	+	Intron	DEL	CA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67394273_67394274delCA	uc001dde.2	+						MIER1_uc001dda.3_Intron|MIER1_uc010opf.1_Intron|MIER1_uc009way.2_Intron|MIER1_uc001ddc.2_Intron|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Intron|MIER1_uc001ddg.2_Intron|MIER1_uc010opg.1_Intron|MIER1_uc001ddj.1_5'Flank|MIER1_uc001ddi.2_5'Flank	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1						TCTTTGCCTTCAGCTCTTTTCA	0.366													3	4	---	---	---	---	
MIER1	57708	broad.mit.edu	37	1	67394276	67394277	+	Intron	DEL	CT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67394276_67394277delCT	uc001dde.2	+						MIER1_uc001dda.3_Intron|MIER1_uc010opf.1_Intron|MIER1_uc009way.2_Intron|MIER1_uc001ddc.2_Intron|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Intron|MIER1_uc001ddg.2_Intron|MIER1_uc010opg.1_Intron|MIER1_uc001ddj.1_5'Flank|MIER1_uc001ddi.2_5'Flank	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1						TTGCCTTCAGCTCTTTTCATTA	0.361													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	75233735	75233735	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75233735delG								TYW3 (1377 upstream) : LHX8 (360384 downstream)																							CCACTCAACTGGGTGTTTAAC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	87311308	87311308	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87311308delG								SH3GLB1 (97442 upstream) : SEP15 (16822 downstream)																							GCAGCATTCCGGGGGTAGGTA	0.318													4	2	---	---	---	---	
HS2ST1	9653	broad.mit.edu	37	1	87387066	87387066	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87387066delT	uc010osk.1	+						HS2ST1_uc001dmc.3_Intron	NM_012262	NP_036394	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1 isoform							Golgi membrane|integral to membrane				central_nervous_system(1)	1		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		ggaccaacccttttttttata	0.000													4	2	---	---	---	---	
HFM1	164045	broad.mit.edu	37	1	91861409	91861410	+	Intron	DEL	TT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91861409_91861410delTT	uc001doa.3	-						HFM1_uc010osu.1_Intron|HFM1_uc010osv.1_Intron|HFM1_uc001doc.1_Intron	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AGTTTATTACtttttttttttt	0.114													11	5	---	---	---	---	
COL11A1	1301	broad.mit.edu	37	1	103555129	103555129	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103555129delA	uc001dul.2	-						COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		gatacactgtaaaccctctga	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	103766628	103766628	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103766628delG								COL11A1 (192576 upstream) : RNPC3 (301950 downstream)																							atgtgacagtgggagcaacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143540325	143540325	+	IGR	DEL	G	-	-	rs66944250		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143540325delG								None (None upstream) : LOC100286793 (107314 downstream)																							TGCTGTAGTAGTAACTGCTTC	0.368													6	4	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145028541	145028541	+	Intron	DEL	G	-	-	rs66503271		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145028541delG	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)		TCTCAGATGTGTTTTTTTCCT	0.418			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145078689	145078689	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145078689delC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_5'Flank|PDE4DIP_uc001emh.2_5'Flank|PDE4DIP_uc001emk.2_5'Flank			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						tacggatggtccccaacttac	0.000													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145148501	145148501	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145148501delA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						CTTTTACTTTAGAAGCTGAAA	0.214													4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145292408	145292408	+	5'Flank	DEL	C	-	-	rs59280816		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145292408delC	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Intron|NOTCH2NL_uc010oyh.1_Intron|NBPF10_uc001emq.1_5'Flank	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ATATAAATGACTTTGATCACT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148882683	148882683	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148882683delT	uc009wkv.1	+											Homo sapiens cDNA, FLJ17483.																		AACTGGAGTATTTAGTAAAAA	0.299													4	2	---	---	---	---	
LOC645166	645166	broad.mit.edu	37	1	148935064	148935064	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148935064delT	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0						tcttcttctcttttttctttt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	153531200	153531200	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153531200delC								S100A3 (9466 upstream) : S100A2 (2387 downstream)																							attgcggttgctagaagacag	0.030													4	2	---	---	---	---	
FCGR2A	2212	broad.mit.edu	37	1	161487382	161487382	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161487382delT	uc001gan.2	+						FCGR2A_uc001gam.2_Intron|FCGR2A_uc001gao.2_Intron	NM_001136219	NP_001129691	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor							integral to membrane|plasma membrane	IgG binding|receptor activity			ovary(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	ggaaattagatttttaggtta	0.000													4	2	---	---	---	---	
NOS1AP	9722	broad.mit.edu	37	1	162339261	162339262	+	3'UTR	INS	-	A	A	rs61332953		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162339261_162339262insA	uc001gbv.2	+	10					NOS1AP_uc010pks.1_RNA|NOS1AP_uc001gbw.2_3'UTR|NOS1AP_uc009wut.1_3'UTR	NM_014697	NP_055512	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			TCTGTTTTCTGACGTAAGCCGG	0.490													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	170282671	170282671	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170282671delT								LOC284688 (29322 upstream) : GORAB (218592 downstream)																							ACTGTCACCCTTTCACTTGGC	0.378													4	2	---	---	---	---	
C1orf129	80133	broad.mit.edu	37	1	170916976	170916976	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170916976delT	uc001ghg.2	+						C1orf129_uc009wvy.2_Intron|C1orf129_uc010plz.1_Intron	NM_025063	NP_079339	Q5TGP6	CA129_HUMAN	hypothetical protein LOC80133 isoform 2								binding			pancreas(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CATCCTACTATTTATCCCACC	0.423													4	2	---	---	---	---	
SLC9A11	284525	broad.mit.edu	37	1	173500622	173500622	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173500622delC	uc001giz.2	-						SLC9A11_uc009wwe.2_Intron|SLC9A11_uc010pmq.1_Intron	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11						sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2						ccaactaccaccagactcctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181328390	181328390	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181328390delC								IER5 (268413 upstream) : CACNA1E (124326 downstream)																							gacatataaacaaataagtac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181328393	181328394	+	IGR	DEL	AT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181328393_181328394delAT								IER5 (268416 upstream) : CACNA1E (124322 downstream)																							atataaacaaataagtacaagg	0.000													4	2	---	---	---	---	
KCNT2	343450	broad.mit.edu	37	1	196200641	196200642	+	Intron	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196200641_196200642insA	uc001gtd.1	-						KCNT2_uc009wyt.1_Intron|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7						TATAATGGAAGAAAAAAAAAGA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	198383385	198383388	+	IGR	DEL	AAAG	-	-	rs67690596		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198383385_198383388delAAAG								NEK7 (91839 upstream) : ATP6V1G3 (108968 downstream)																							aaagaaagaaaaagaaagaaagaa	0.000													4	2	---	---	---	---	
SRGAP2	23380	broad.mit.edu	37	1	206558835	206558835	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206558835delT	uc001hdy.2	+						SRGAP2_uc009xbt.2_Intron|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)					AATTCTTTTATTTTCCTGTAA	0.393													4	2	---	---	---	---	
CD55	1604	broad.mit.edu	37	1	207498723	207498723	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207498723delT	uc001hfq.3	+						CD55_uc001hfp.3_Intron|CD55_uc001hfr.3_Intron|CD55_uc010psf.1_Intron|CD55_uc009xcf.2_Intron|CD55_uc009xce.2_Intron|CD55_uc009xcg.2_5'Flank	NM_000574	NP_000565	P08174	DAF_HUMAN	decay accelerating factor for complement isoform						complement activation, classical pathway|elevation of cytosolic calcium ion concentration|innate immune response|respiratory burst	anchored to membrane|extracellular region|integral to plasma membrane|membrane raft|soluble fraction	receptor activity			ovary(1)	1					Chloramphenicol(DB00446)	ATATCAATGGTTCAGATGATG	0.104													5	7	---	---	---	---	
CR2	1380	broad.mit.edu	37	1	207641686	207641686	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207641686delT	uc001hfw.2	+						CR2_uc001hfv.2_Intron|CR2_uc009xch.2_Intron|CR2_uc009xci.1_5'Flank	NM_001877	NP_001868	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)						complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8						cattatgagattttttttttg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209440986	209440986	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209440986delT								None (None upstream) : LOC642587 (161182 downstream)																							TCCTGTTTACTTTTTTTTTTC	0.433													3	3	---	---	---	---	
FLVCR1	28982	broad.mit.edu	37	1	213062208	213062209	+	Intron	INS	-	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213062208_213062209insG	uc001hjt.2	+							NM_014053	NP_054772	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular						cell death|cellular iron ion homeostasis|heme export|transmembrane transport	integral to plasma membrane	heme transporter activity|protein binding|receptor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		tttttgttattttttgtagaga	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	218174367	218174370	+	IGR	DEL	CTGT	-	-	rs140654199		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218174367_218174370delCTGT								SPATA17 (133865 upstream) : RRP15 (284259 downstream)																							ctccacttgactgtcttatagtca	0.000													2	4	---	---	---	---	
RAB3GAP2	25782	broad.mit.edu	37	1	220367626	220367626	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220367626delA	uc010puk.1	-						RAB3GAP2_uc001hmf.2_Intron|RAB3GAP2_uc001hmg.2_Intron	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)		TCCCTCCACCAAAAAAAACTC	0.318													4	2	---	---	---	---	
MARK1	4139	broad.mit.edu	37	1	220728925	220728925	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220728925delA	uc001hmn.3	+						MARK1_uc001hml.2_Intron|MARK1_uc009xdw.2_Intron|MARK1_uc010pun.1_Intron|MARK1_uc001hmm.3_Intron	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1						intracellular protein kinase cascade	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(4)|central_nervous_system(2)|skin(2)|stomach(1)|lung(1)	10				GBM - Glioblastoma multiforme(131;0.0407)		gaggaagaagaaaaccaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222186794	222186794	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222186794delG								DUSP10 (271333 upstream) : HHIPL2 (508808 downstream)																							GCATCTACCAGGGAAGAAGAA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	231154124	231154124	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231154124delC								ARV1 (17653 upstream) : FAM89A (580 downstream)																							GAGGTGCCTTCCTCTCCCTAA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232815690	232815690	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232815690delA								SIPA1L2 (164447 upstream) : KIAA1383 (124948 downstream)																							caatctagctatggagctgag	0.000													4	2	---	---	---	---	
ZNF695	57116	broad.mit.edu	37	1	247129417	247129417	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247129417delG	uc001ibx.2	-						ZNF695_uc001ica.2_Intron|ZNF695_uc009xgt.1_Intron|ZNF695_uc001iby.2_Intron			Q8IW36	ZN695_HUMAN	RecName: Full=Zinc finger protein 695; AltName: Full=Zinc finger protein SBZF3;						regulation of transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			caaagagcctggggcagaggc	0.020													4	2	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29627685	29627685	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29627685delG	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)	TGAATTAACTGGGGAAAGAGA	0.443			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	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29883910	29883911	+	Intron	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29883910_29883911delTG	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)	TCTGGCTCCTTGTAACATAGTT	0.312			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	---	---	---	---	
GALNT14	79623	broad.mit.edu	37	2	31295995	31295996	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31295995_31295996insT	uc002rnr.2	-						GALNT14_uc002rnq.2_Intron|GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					taaccagctgcgtgatcttgag	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	31996835	31996835	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31996835delG								SRD5A2 (190795 upstream) : MEMO1 (96061 downstream)																							GTTACTAAAAGAAAAAATATT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34323490	34323490	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34323490delG								MYADML (370206 upstream) : None (None downstream)																							tacaggaagtggaaaaagcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35427742	35427742	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35427742delA								None (None upstream) : None (None downstream)																							CAAACAAAAGAAAAAAAATAG	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38692859	38692859	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38692859delA								ATL2 (88427 upstream) : HNRPLL (97469 downstream)																							CCCCTAACTTAAAAAAAAAAA	0.502											OREG0014555	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	52098738	52098739	+	IGR	INS	-	TGTA	TGTA	rs139914721	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:52098738_52098739insTGTA								NRXN1 (839064 upstream) : None (None downstream)																							TACGTTTACTGTGTATGTATGT	0.287													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	53804300	53804300	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53804300delG								None (None upstream) : ASB3 (92818 downstream)																							GGTCATGAAAGGGGGAGGTAG	0.428													4	2	---	---	---	---	
PNPT1	87178	broad.mit.edu	37	2	55885542	55885542	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55885542delG	uc002rzf.2	-						PNPT1_uc002rzg.2_Intron	NM_033109	NP_149100	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1						mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			agaacatggaggggcttttga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66556894	66556895	+	IGR	INS	-	A	A	rs150147317	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66556894_66556895insA								SPRED2 (897238 upstream) : MEIS1 (105637 downstream)																							TATACAATGGGAAAAAAAAATC	0.371													3	4	---	---	---	---	
PROKR1	10887	broad.mit.edu	37	2	68871963	68871963	+	5'Flank	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68871963delC	uc010yqj.1	+						PROKR1_uc002ses.2_Intron	NM_138964	NP_620414	Q8TCW9	PKR1_HUMAN	G protein-coupled receptor 73							integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(1)	1						GCAGCTGACACCCCCCTAGAC	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	69236067	69236067	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69236067delT								GKN1 (27956 upstream) : ANTXR1 (4209 downstream)																							TGACTGTTTCTAGGCTGAAGT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	70544194	70544194	+	IGR	DEL	A	-	-	rs35373031		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70544194delA								FAM136A (14974 upstream) : TGFA (130225 downstream)																							CCCTCTTATTACTGTGGTTGT	0.438													3	3	---	---	---	---	
TACR1	6869	broad.mit.edu	37	2	75386954	75386954	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75386954delA	uc002sng.2	-						TACR1_uc002snh.2_Intron	NM_001058	NP_001049	P25103	NK1R_HUMAN	tachykinin receptor 1 isoform long						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|detection of abiotic stimulus|mechanosensory behavior	integral to plasma membrane	protein binding			ovary(1)	1					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)	ACAGAGTCGTAGTGCATTCTG	0.423													4	2	---	---	---	---	
DNAH6	1768	broad.mit.edu	37	2	84820709	84820709	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84820709delT	uc010fgb.2	+							NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1						TCTTCTGCCCTTTAAGTACAG	0.284													4	2	---	---	---	---	
LOC654342	654342	broad.mit.edu	37	2	91828280	91828281	+	Intron	INS	-	T	T	rs146552335	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91828280_91828281insT	uc002sts.3	-						LOC654342_uc002stt.2_Intron|LOC654342_uc010yub.1_Intron					Homo sapiens cDNA clone IMAGE:4801360.												0						tctattctctatatGGGCCTCA	0.262													2	5	---	---	---	---	
VWA3B	200403	broad.mit.edu	37	2	98740747	98740747	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98740747delG	uc002syo.2	+						VWA3B_uc010yvh.1_Intron|VWA3B_uc002syj.2_Intron|VWA3B_uc002syk.1_Intron|VWA3B_uc002syl.1_Intron|VWA3B_uc002sym.2_Intron|VWA3B_uc002syn.1_Intron	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B											ovary(3)|large_intestine(2)|skin(1)	6						GGGAAGATGTGGGTCCCATTT	0.313													4	2	---	---	---	---	
INPP4A	3631	broad.mit.edu	37	2	99113317	99113317	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99113317delG	uc002syy.2	+						INPP4A_uc010yvj.1_Intron|INPP4A_uc010yvk.1_Intron|INPP4A_uc002syx.2_Intron|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696	Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type 1						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1						tttataatctggggttggagt	0.095													4	2	---	---	---	---	
AFF3	3899	broad.mit.edu	37	2	100416161	100416161	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100416161delA	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						gaaagattatactatttgata	0.000													4	2	---	---	---	---	
TGFBRAP1	9392	broad.mit.edu	37	2	105911139	105911140	+	Intron	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105911139_105911140insA	uc002tcq.2	-						TGFBRAP1_uc010fjc.2_Intron|TGFBRAP1_uc002tcr.3_Intron	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor						regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2						AAGAAACAAACAAACAAAAAAA	0.411											OREG0014858	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109808964	109808964	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109808964delA	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						GGATCAGAGTAAGCCTTTCTT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113582846	113582846	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113582846delT								IL1A (39875 upstream) : IL1B (4491 downstream)																							TCGGAAGCACTTGCCTTCTCC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	124733827	124733827	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124733827delG								None (None upstream) : CNTNAP5 (49037 downstream)																							attgcccctagggaggctgat	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133046453	133046454	+	IGR	INS	-	GACA	GACA	rs146739177		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133046453_133046454insGACA								NCRNA00164 (30911 upstream) : GPR39 (127693 downstream)																							CAAACCAATGTGACAGACAGAG	0.386													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	138559988	138559988	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138559988delA								THSD7B (124701 upstream) : HNMT (161602 downstream)																							ATCAAAAGCTAAAAGTCAAGA	0.229													4	2	---	---	---	---	
ACVR2A	92	broad.mit.edu	37	2	148675738	148675738	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148675738delA	uc002twg.2	+						ACVR2A_uc010zbn.1_Intron|ACVR2A_uc002twh.2_Intron	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor						activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)		ACTAGTCTTTAAAAAAAAAAA	0.274													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	150588744	150588744	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150588744delG								MMADHC (144414 upstream) : RND3 (735968 downstream)																							GCCCAAGCATGGGGGCAATCT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162426307	162426307	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162426307delC								TBR1 (144734 upstream) : SLC4A10 (54538 downstream)																							CTTTGTTTCTCCTTGGAAAGT	0.348													4	2	---	---	---	---	
ZNF804A	91752	broad.mit.edu	37	2	185573749	185573749	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185573749delA	uc002uph.2	+							NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A							intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11						TCCCCAGATGAAACCTTCCTG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	187988024	187988024	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187988024delT								ZSWIM2 (274127 upstream) : CALCRL (219827 downstream)																							ACCCTACATGTTGGATATAGA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	199796330	199796330	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199796330delT								PLCL1 (781724 upstream) : SATB2 (337894 downstream)																							TGCTATACAGTATGTTATAGA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	200721115	200721115	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200721115delT								FLJ32063 (379457 upstream) : C2orf69 (54864 downstream)																							TTTTGGTGCCTTTTTTTTTTA	0.129													4	2	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	205427350	205427350	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205427350delA	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		TAGTATTGGTAACTTTAAATA	0.343													4	2	---	---	---	---	
KLF7	8609	broad.mit.edu	37	2	208029390	208029390	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208029390delG	uc002vbz.1	-						KLF7_uc002vca.1_Intron	NM_003709	NP_003700	O75840	KLF7_HUMAN	Kruppel-like factor 7 (ubiquitous)						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			central_nervous_system(1)|skin(1)	2				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)		TCAGCATCCTGGGAGTTTCTT	0.507													4	2	---	---	---	---	
CRYGC	1420	broad.mit.edu	37	2	208993326	208993326	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208993326delT	uc002vco.3	-							NM_020989	NP_066269	P07315	CRGC_HUMAN	crystallin, gamma C						visual perception	cytoplasm|nucleus	protein binding|structural constituent of eye lens				0				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)		TTAGACAGTGTAAAATGTAGA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	219062795	219062796	+	IGR	INS	-	TTTC	TTTC	rs146442194	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219062795_219062796insTTTC								CXCR1 (31079 upstream) : ARPC2 (19078 downstream)																							CTATTCAtttttttctttcttt	0.248													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	220805694	220805694	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220805694delG								SLC4A3 (298993 upstream) : None (None downstream)																							taccaacagtggatgaacatt	0.000													4	2	---	---	---	---	
FARSB	10056	broad.mit.edu	37	2	223493835	223493836	+	Intron	INS	-	ATG	ATG			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223493835_223493836insATG	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	ACTTGAAAGGTTTATTTTCCAG	0.426													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	225927481	225927482	+	IGR	DEL	TC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225927481_225927482delTC								DOCK10 (20151 upstream) : KIAA1486 (338120 downstream)																							GTTCATGTCATCTCTCTGGCTT	0.406													4	2	---	---	---	---	
KIAA1486	57624	broad.mit.edu	37	2	226428007	226428008	+	Intron	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226428007_226428008insA	uc002voe.2	+						KIAA1486_uc010fxa.1_Intron	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624											ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)		gtccttgagtgaacattaaact	0.000													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	236720812	236720812	+	Intron	DEL	T	-	-	rs10715633		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236720812delT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						TCAAAAAAACTTTTTTTTTTT	0.517													8	4	---	---	---	---	
FBLN2	2199	broad.mit.edu	37	3	13659079	13659082	+	Intron	DEL	CCAT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13659079_13659082delCCAT	uc011avb.1	+						FBLN2_uc011auz.1_Intron|FBLN2_uc011ava.1_Intron|FBLN2_uc011avc.1_Intron	NM_001998	NP_001989	P98095	FBLN2_HUMAN	fibulin 2 isoform b precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			acccatccacccatccatccatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	14659639	14659639	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14659639delT								GRIP2 (76051 upstream) : C3orf19 (33614 downstream)																							accagagaggtttttccacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	20902104	20902104	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20902104delA								SGOL1 (674421 upstream) : VENTXP7 (545114 downstream)																							AAACAGAGGTAAAAAAAACTA	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	26586943	26586944	+	IGR	INS	-	A	A	rs150900551	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26586943_26586944insA								OXSM (750919 upstream) : LRRC3B (77356 downstream)																							AGACAAGTATCGGAAATTTTGG	0.262													2	4	---	---	---	---	
DNAH12	201625	broad.mit.edu	37	3	57400934	57400934	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57400934delA	uc003dit.2	-							NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2						TCTCAGGCTTAAAAAAAAAAC	0.299													3	3	---	---	---	---	
FHIT	2272	broad.mit.edu	37	3	59746559	59746559	+	Intron	DEL	T	-	-	rs148773057		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59746559delT	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003	P49789	FHIT_HUMAN	fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		TTAGAGGTAAttttttttttt	0.224			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				4	3	---	---	---	---	
ZNF717	100131827	broad.mit.edu	37	3	75832746	75832747	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75832746_75832747insT	uc011bgi.1	-						ZNF717_uc003dpw.3_Intron	NM_001128223	NP_001121695	C9JSV9	C9JSV9_HUMAN	zinc finger protein 717						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						TGCACAATTTATTTTGAATAAA	0.287													4	2	---	---	---	---	
CADM2	253559	broad.mit.edu	37	3	85485843	85485843	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85485843delT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		taaagtaaacttttttatttt	0.070													4	2	---	---	---	---	
DCBLD2	131566	broad.mit.edu	37	3	98531519	98531519	+	Intron	DEL	G	-	-	rs34899871		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98531519delG	uc003dtd.2	-						DCBLD2_uc003dte.2_Intron	NM_080927	NP_563615	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2						cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane				ovary(2)|central_nervous_system(1)	3						TTTATCAAAAGTTTATGAAAC	0.249													4	3	---	---	---	---	
PLCXD2	257068	broad.mit.edu	37	3	111413319	111413319	+	Intron	DEL	T	-	-	rs72352799		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111413319delT	uc003dya.2	+						PLCXD2_uc003dyb.2_Intron|PLCXD2_uc003dxz.2_Intron	NM_001134478	NP_001127950	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(1)	1						TGAAGAGAGCTTTTTTTTTTT	0.353													4	2	---	---	---	---	
GOLGB1	2804	broad.mit.edu	37	3	121431270	121431270	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121431270delA	uc003eei.3	-						GOLGB1_uc010hrc.2_Intron|GOLGB1_uc003eej.3_Intron|GOLGB1_uc011bjm.1_Intron|GOLGB1_uc010hrd.1_Intron	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,						Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)		caggacacagaaaaaaaaaac	0.000													3	3	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	123888060	123888061	+	Intron	DEL	GA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123888060_123888061delGA	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						TTCCCTTTCTGAGGGGTCAGTG	0.272													4	2	---	---	---	---	
ALDH1L1	10840	broad.mit.edu	37	3	125899007	125899007	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125899007delC	uc003eim.1	-						ALDH1L1_uc010hse.1_Intron|ALDH1L1_uc011bki.1_Intron|ALDH1L1_uc010hsf.1_Intron|ALDH1L1_uc011bkj.1_Intron|uc003eiq.2_5'Flank	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1						10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	GCAGTGCCCACCCCACAGGTT	0.632													4	2	---	---	---	---	
UROC1	131669	broad.mit.edu	37	3	126208376	126208376	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126208376delG	uc003eiz.1	-						UROC1_uc010hsi.1_Intron	NM_144639	NP_653240	Q96N76	HUTU_HUMAN	urocanase domain containing 1 isoform 1						histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)		TCTGTAGCCTGGAATAGATTC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	131170566	131170566	+	IGR	DEL	C	-	-	rs150256539		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131170566delC								NUDT16 (65637 upstream) : MRPL3 (10480 downstream)																							CAAAATTATACCCCCCATGCC	0.373													4	2	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	139678121	139678121	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139678121delC	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						gtagtggcctcctgccttgcc	0.000										HNSCC(16;0.037)			4	2	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140126913	140126914	+	Intron	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140126913_140126914delTG	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						ggagtccagttgagaagataca	0.000										HNSCC(16;0.037)			4	2	---	---	---	---	
ACPL2	92370	broad.mit.edu	37	3	141006394	141006394	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141006394delA	uc003etu.2	+						ACPL2_uc003etv.2_Intron|ACPL2_uc011bna.1_Intron|ACPL2_uc011bnb.1_Intron	NM_152282	NP_689495	Q8TE99	ACPL2_HUMAN	acid phosphatase-like 2 precursor							extracellular region	acid phosphatase activity			skin(1)	1						TGCAGCTCAGAGGGGGTAAGC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	148112943	148112943	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148112943delA								ZIC1 (978439 upstream) : AGTR1 (302715 downstream)																							AGCTTCTGTGAAAAAAGGAGA	0.348													4	2	---	---	---	---	
HLTF	6596	broad.mit.edu	37	3	148767867	148767867	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148767867delA	uc003ewq.1	-						HLTF_uc003ewr.1_Intron|HLTF_uc003ews.1_Intron|HLTF_uc010hve.1_Intron	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor						chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			GCAAAAAGTCAAAAAAAAAAA	0.318													8	4	---	---	---	---	
KCNAB1	7881	broad.mit.edu	37	3	155960332	155960332	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155960332delT	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			ttttatacactttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161639385	161639385	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161639385delC								OTOL1 (417657 upstream) : None (None downstream)																							ATACAGGTGGCTCCAGTGCCC	0.443													4	2	---	---	---	---	
ECT2	1894	broad.mit.edu	37	3	172484213	172484213	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172484213delT	uc003fii.2	+						ECT2_uc010hwv.1_Intron|ECT2_uc003fih.2_Intron|ECT2_uc003fij.1_Intron|ECT2_uc003fik.1_Intron|ECT2_uc003fil.1_Intron	NM_018098	NP_060568	Q9H8V3	ECT2_HUMAN	epithelial cell transforming sequence 2 oncogene						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|ovary(1)|skin(1)	4	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			ATTGATTGAATAGATAATTCA	0.348													4	2	---	---	---	---	
RPL39L	116832	broad.mit.edu	37	3	186856345	186856345	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186856345delG	uc003fre.1	-						RPL39L_uc003frf.1_Intron	NM_052969	NP_443201	Q96EH5	RL39L_HUMAN	ribosomal protein L39-like protein						spermatogenesis|translation	cytosolic large ribosomal subunit	structural constituent of ribosome				0	all_cancers(143;2.61e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.87e-18)	GBM - Glioblastoma multiforme(93;0.0745)		GAGCAGATGAGGCAGATAGGT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193692859	193692860	+	IGR	DEL	AC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193692859_193692860delAC								OPA1 (277260 upstream) : LOC100128023 (18024 downstream)																							GTGCGTGCATACACACACACAC	0.579											OREG0015991	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	55797	55797	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55797delC	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		aaaacattttcttgcagttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	11824534	11824534	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11824534delA								HS3ST1 (393997 upstream) : None (None downstream)																							attaaatgagaaaaaaaggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	15906870	15906871	+	IGR	DEL	AA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15906870_15906871delAA								CD38 (56164 upstream) : FGFBP1 (30324 downstream)																							ATGAAAGAGTAAATGAATCATG	0.317													4	2	---	---	---	---	
TAPT1	202018	broad.mit.edu	37	4	16190545	16190545	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16190545delA	uc010ied.1	-						TAPT1_uc011bxd.1_Intron|TAPT1_uc011bxe.1_Intron	NM_153365	NP_699196	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation							integral to membrane	growth hormone-releasing hormone receptor activity				0						tgactcaaccaaaaaaagaaa	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	17422665	17422665	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17422665delA								LDB2 (522241 upstream) : QDPR (65355 downstream)																							AAAGGGGCTTAAAAAAAAAAA	0.348													4	2	---	---	---	---	
LGI2	55203	broad.mit.edu	37	4	25006083	25006083	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25006083delA	uc003grf.2	-							NM_018176	NP_060646	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2							extracellular region					0		Breast(46;0.173)				gtatatacccaaaataattga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	42182126	42182127	+	IGR	INS	-	T	T	rs138411548	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42182126_42182127insT								BEND4 (27231 upstream) : SHISA3 (217729 downstream)																							atagttttttgttttgtttttt	0.035													4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54821898	54821898	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54821898delG	uc003haa.2	+							NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	TTTCTTATGTGCCCCATTCAG	0.129			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	62971330	62971330	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62971330delT								LPHN3 (33163 upstream) : None (None downstream)																							tgcatgtgtctttTTTTTTCC	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63194191	63194191	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63194191delA								LPHN3 (256024 upstream) : None (None downstream)																							ACTAAAGTAGAAAAAAAAAAT	0.368													4	2	---	---	---	---	
CENPC1	1060	broad.mit.edu	37	4	68411624	68411624	+	5'Flank	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68411624delT	uc003hdd.1	-						CENPC1_uc010ihk.1_5'Flank|CENPC1_uc010ihm.1_5'Flank	NM_001812	NP_001803	Q03188	CENPC_HUMAN	centromere protein C 1						mitotic prometaphase	condensed chromosome kinetochore|condensed nuclear chromosome, centromeric region|cytosol	DNA binding			urinary_tract(1)|lung(1)	2						TGCAGACGACTTTTTTTTTAA	0.358													4	2	---	---	---	---	
TMPRSS11F	389208	broad.mit.edu	37	4	68920031	68920031	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68920031delT	uc003hdt.1	-						LOC550112_uc003hdl.3_Intron|uc011cak.1_Intron	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						TATCCTTAGGTTTTTTTTTTC	0.299													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	78891163	78891164	+	IGR	INS	-	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78891163_78891164insC								MRPL1 (17219 upstream) : FRAS1 (87560 downstream)																							cttaaaaaaaaaaacctttgaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84776495	84776495	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84776495delG	uc010ikd.1	-											Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																		tcatccagctggacttcgcat	0.114													4	2	---	---	---	---	
MAPK10	5602	broad.mit.edu	37	4	87465300	87465300	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87465300delT	uc010ikh.1	-									P53779	MK10_HUMAN	Synthetic construct DNA, clone: pF1KB9001, Homo sapiens MAPK10 gene for mitogen-activated protein kinase 10, without stop codon, in Flexi system.						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		CGGAGACAGGTTTTTTTCCAC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	107398978	107398979	+	IGR	DEL	CT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107398978_107398979delCT								AIMP1 (128599 upstream) : DKK2 (443981 downstream)																							CATTTTCCTGCTCAGGTCCCTA	0.450													4	2	---	---	---	---	
SYNPO2	171024	broad.mit.edu	37	4	119841315	119841315	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119841315delA	uc003icm.3	+						SYNPO2_uc010ina.2_Intron|SYNPO2_uc010inb.2_Intron|SYNPO2_uc011cgh.1_Intron	NM_001128933	NP_001122405	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform b							nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2						aatgaaggagaaagaggaatc	0.000													4	2	---	---	---	---	
ZNF330	27309	broad.mit.edu	37	4	142145267	142145267	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142145267delC	uc003iiq.3	+						ZNF330_uc011chl.1_Intron	NM_014487	NP_055302	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330							chromosome, centromeric region|midbody|nucleolus	protein binding|zinc ion binding				0	all_hematologic(180;0.162)					TTAAGGGTCACCCACTTCATT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	143941356	143941356	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143941356delG								INPP4B (173752 upstream) : USP38 (164714 downstream)																							ttctaggggtggggtacaaca	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	145206987	145206987	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145206987delG								GYPA (145083 upstream) : HHIP (360186 downstream)																							ATGGTCCCCTGGTCACTTTTT	0.383													4	2	---	---	---	---	
ARHGAP10	79658	broad.mit.edu	37	4	148668946	148668946	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148668946delA	uc003ilf.2	+						ARHGAP10_uc003ile.1_Intron	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		GAAGCAAAAGAAAAAAAAAAG	0.358													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153121300	153121301	+	IGR	DEL	CA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153121300_153121301delCA								PET112L (439154 upstream) : FBXW7 (121110 downstream)																							TCATCTCCTTCACCAGGTCATG	0.500													4	2	---	---	---	---	
FNIP2	57600	broad.mit.edu	37	4	159710474	159710477	+	Intron	DEL	TGTG	-	-	rs11730562	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159710474_159710477delTGTG	uc003iqe.3	+						FNIP2_uc003iqd.2_Intron	NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2						DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		tgtgtgtgtatgtgtgtgtgtgtg	0.235													4	2	---	---	---	---	
LOC285501	285501	broad.mit.edu	37	4	178872853	178872854	+	Intron	INS	-	TCTT	TCTT	rs151009496	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178872853_178872854insTCTT	uc010iru.2	+							NR_028342				Homo sapiens cDNA clone IMAGE:4828874.												0		all_lung(41;6.03e-08)|Lung NSC(41;4.26e-07)|Breast(14;0.00066)|Melanoma(52;0.00168)|Prostate(90;0.0129)|all_hematologic(60;0.0202)|Renal(120;0.0246)|Colorectal(36;0.0508)|Hepatocellular(41;0.236)		all cancers(43;9.24e-25)|Epithelial(43;6.28e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.29e-10)|LUSC - Lung squamous cell carcinoma(1;2.61e-05)|Lung(1;3.22e-05)|GBM - Glioblastoma multiforme(59;0.000185)|Colorectal(24;0.000244)|STAD - Stomach adenocarcinoma(60;0.000777)|COAD - Colon adenocarcinoma(29;0.000884)		GAGTCTCTAAATCTTTATGAAT	0.396													2	4	---	---	---	---	
ZDHHC11	79844	broad.mit.edu	37	5	837172	837172	+	Intron	DEL	A	-	-	rs35847354		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:837172delA	uc011cma.1	-						ZDHHC11_uc003jbj.2_Intron|ZDHHC11_uc010itd.1_Intron	NM_024786	NP_079062	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11							integral to membrane	acyltransferase activity|zinc ion binding			skin(1)|pancreas(1)	2			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			actctgtctcaaaaaaaaaga	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2949243	2949243	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2949243delT								C5orf38 (193731 upstream) : IRX1 (646925 downstream)																							CCTAGTGACCTGGGACACTGC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3506706	3506707	+	Intron	INS	-	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3506706_3506707insC	uc003jdd.2	-											Homo sapiens cDNA clone IMAGE:4823480.																		TAATTATGTTTCCCTGCTCCGG	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5985755	5985756	+	IGR	INS	-	T	T	rs11381600		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5985755_5985756insT								KIAA0947 (495418 upstream) : FLJ33360 (324798 downstream)																							ACTCCTCTCTGTTTTTTTTTTT	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6804021	6804022	+	IGR	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6804021_6804022delTG								PAPD7 (46860 upstream) : ADCY2 (592321 downstream)																							AACTATAAATTGTGACAGCGTA	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	16411708	16411709	+	IGR	INS	-	ACAG	ACAG	rs10647155		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16411708_16411709insACAG								MARCH11 (231811 upstream) : ZNF622 (39920 downstream)																							cacacagacacacacacacaca	0.287													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24673556	24673556	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24673556delT								CDH10 (28645 upstream) : None (None downstream)																							tctttccttcttttttttttG	0.254													4	2	---	---	---	---	
MTMR12	54545	broad.mit.edu	37	5	32269140	32269140	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32269140delT	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1						tatttttaacttttttttttt	0.119													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	32889143	32889143	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32889143delT								C5orf23 (97324 upstream) : TARS (551659 downstream)																							ttgaaccttattttttttcct	0.000													4	2	---	---	---	---	
C5orf42	65250	broad.mit.edu	37	5	37142822	37142822	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37142822delT	uc011cpa.1	-						C5orf42_uc003jkp.1_Intron|C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TGccctttcataaaaacatag	0.129													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	37815423	37815423	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37815423delG								WDR70 (62651 upstream) : GDNF (331 downstream)																							CAGTGATGGTGGACTGTATCA	0.512													4	2	---	---	---	---	
DDX4	54514	broad.mit.edu	37	5	55082705	55082705	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55082705delC	uc003jqg.3	+						DDX4_uc010ivz.2_Intron|DDX4_uc003jqh.3_Intron|DDX4_uc003jqj.2_Intron	NM_001136034	NP_001129506	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform						multicellular organismal development|sperm motility	perinuclear region of cytoplasm|pi-body|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|skin(1)	2		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				GTGTTGCTGTCCATAGATGTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	55634745	55634745	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55634745delT								ANKRD55 (105559 upstream) : MAP3K1 (476155 downstream)																							caatgttatctggcaaagtta	0.000													4	2	---	---	---	---	
RAB3C	115827	broad.mit.edu	37	5	57979904	57979904	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57979904delA	uc003jrp.2	+							NM_138453	NP_612462	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		ccatgaactgaaaatatccag	0.000													4	2	---	---	---	---	
LOC100170939	100170939	broad.mit.edu	37	5	69515692	69515693	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69515692_69515693insT	uc003jyp.1	-						GUSBP3_uc003jxm.2_Intron|uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|LOC100170939_uc003jyl.2_Intron|LOC100170939_uc003jyo.1_Intron|uc003jyr.1_Intron|LOC100170939_uc003jys.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000370107;												0						GGGGAGGCAAGTGGCATCTCTG	0.446													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	79217372	79217372	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79217372delT								CMYA5 (121324 upstream) : MTX3 (55169 downstream)																							tctcagtttcttttttttttc	0.000													3	3	---	---	---	---	
RASGRF2	5924	broad.mit.edu	37	5	80255434	80255439	+	5'Flank	DEL	TGTGTT	-	-	rs5869061		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80255434_80255439delTGTGTT	uc003kha.1	+						RASGRF2_uc011ctn.1_5'Flank	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		catctgtgtgtgtgtttgattatctg	0.000													3	3	---	---	---	---	
MCTP1	79772	broad.mit.edu	37	5	94070520	94070520	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94070520delT	uc003kkx.2	-						MCTP1_uc003kkv.2_Intron|MCTP1_uc003kkw.2_Intron|MCTP1_uc003kku.2_Intron	NM_024717	NP_078993	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		atttccatgcttttttttctt	0.055													4	2	---	---	---	---	
RGMB	285704	broad.mit.edu	37	5	98106506	98106506	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98106506delA	uc003knc.2	+						RGMB_uc003knb.2_Intron|uc003knd.2_RNA|uc003kne.2_RNA	NM_001012761	NP_001012779	Q6NW40	RGMB_HUMAN	RGM domain family, member B						axon guidance|BMP signaling pathway|cell adhesion|positive regulation of transcription, DNA-dependent	anchored to plasma membrane|ER-Golgi intermediate compartment|membrane raft	identical protein binding				0		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		tcttgctctgaaaAAAAAAAT	0.254													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	102149858	102149858	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102149858delT								SLCO6A1 (315138 upstream) : PAM (51669 downstream)																							TCAGGTCCCCTTTAGTATTTA	0.413													4	2	---	---	---	---	
MAN2A1	4124	broad.mit.edu	37	5	109202857	109202858	+	3'UTR	DEL	AG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109202857_109202858delAG	uc003kou.1	+	22						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)		CAGTACAGTaagaaaaaaaaaa	0.307													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	109306668	109306668	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109306668delT								MAN2A1 (103239 upstream) : TMEM232 (318266 downstream)																							aggttgattcttttttcagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	111394335	111394335	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111394335delA								C5orf13 (81707 upstream) : EPB41L4A (83803 downstream)																							CATGTCAGACAAAAAAAAATC	0.234													4	2	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111738406	111738406	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111738406delG	uc003kpv.1	-						EPB41L4A_uc003kpw.1_Intron	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		GACACCAGATGGGAAGCATTT	0.388													4	2	---	---	---	---	
PRR16	51334	broad.mit.edu	37	5	119907047	119907047	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119907047delG	uc003ksq.2	+						PRR16_uc003ksp.2_Intron	NM_016644	NP_057728	Q569H4	PRR16_HUMAN	proline rich 16											pancreas(2)|ovary(1)	3		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)		tgaatgcagtgggagtgtgct	0.045													4	2	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127713774	127713774	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127713774delA	uc003kuu.2	-						FBN2_uc003kuv.2_Intron	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GTGGGAAAGGAAAAAAAAAAA	0.378													5	3	---	---	---	---	
RAD50	10111	broad.mit.edu	37	5	131968176	131968176	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131968176delT	uc003kxi.2	+						RAD50_uc003kxh.2_Intron	NM_005732	NP_005723	Q92878	RAD50_HUMAN	RAD50 homolog isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			tttttctgagtttttttttcc	0.124								Homologous_recombination					4	2	---	---	---	---	
CAMLG	819	broad.mit.edu	37	5	134086228	134086228	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134086228delA	uc003kzt.2	+						CAMLG_uc003kzu.2_Intron	NM_001745	NP_001736	P49069	CAMLG_HUMAN	calcium modulating ligand						defense response	endoplasmic reticulum|integral to membrane					0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Cyclosporine(DB00091)	actccatctcaaaaaaaaaaa	0.154													7	4	---	---	---	---	
PCDHAC2	56134	broad.mit.edu	37	5	140381322	140381322	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140381322delG	uc003lii.2	+						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTACAACCTGGGCTGTTTCA	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	144486170	144486170	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144486170delA								KCTD16 (629226 upstream) : PRELID2 (652412 downstream)																							actccatctcaaaaaaaaTTG	0.149													4	2	---	---	---	---	
SPARC	6678	broad.mit.edu	37	5	151059187	151059187	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151059187delC	uc003lui.2	-						GM2A_uc011dcs.1_Intron|uc003luj.2_Intron	NM_003118	NP_003109	P09486	SPRC_HUMAN	secreted protein, acidic, cysteine-rich						ossification|platelet activation|platelet degranulation|signal transduction	basement membrane|extracellular space|platelet alpha granule lumen	calcium ion binding|collagen binding			central_nervous_system(1)	1		Medulloblastoma(196;0.109)|all_hematologic(541;0.122)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;0.00118)	Becaplermin(DB00102)	TACATCGAGTCCCTTCCTTTT	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151987419	151987420	+	IGR	INS	-	GA	GA	rs147327416	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151987419_151987420insGA								NMUR2 (202579 upstream) : GRIA1 (881755 downstream)																							TGATAGAAATGGAGAGAGAGAG	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	158917632	158917632	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158917632delG								LOC285627 (24348 upstream) : ADRA1B (426108 downstream)																							AAAGTCTGCTGGCCCCTGGAA	0.478													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167204258	167204258	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167204258delA	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)		acagtgatggaaagaatggaa	0.045													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168713235	168713238	+	Intron	DEL	AAGC	-	-	rs72277881		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168713235_168713238delAAGC	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACTATAGAGGAAGCAAAATTATGT	0.343													1	7	---	---	---	---	
LCP2	3937	broad.mit.edu	37	5	169683269	169683270	+	Intron	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169683269_169683270delTG	uc003man.1	-						LCP2_uc011des.1_Intron|LCP2_uc011det.1_Intron	NM_005565	NP_005556	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2						immune response|platelet activation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	cytosol	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		tgtgtatgcatgtgtgtgtgtg	0.069													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	171888603	171888603	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171888603delA								SH3PXD2B (7076 upstream) : NEURL1B (179673 downstream)																							tctatctttcaagctttcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172803234	172803234	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172803234delA								STC2 (46728 upstream) : LOC285593 (203412 downstream)																							agtggatgccagagacatctg	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	175357459	175357459	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175357459delA								CPLX2 (46436 upstream) : THOC3 (29077 downstream)																							aaaaaaaaagaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	353069	353072	+	IGR	DEL	CATT	-	-	rs148332139		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:353069_353072delCATT								DUSP22 (1716 upstream) : IRF4 (38680 downstream)																							GCTGCCTCTCcattcattcattca	0.230													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14470821	14470822	+	IGR	INS	-	T	T	rs143063164	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14470821_14470822insT								CD83 (333675 upstream) : JARID2 (774912 downstream)																							ggagccttcccttcatgccact	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19239960	19239962	+	IGR	DEL	AAT	-	-	rs59317196	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19239960_19239962delAAT								MIR548A1 (667849 upstream) : ID4 (597655 downstream)																							cacaaagatgaataaaaaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	22453291	22453292	+	IGR	DEL	GT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22453291_22453292delGT								PRL (150209 upstream) : HDGFL1 (116386 downstream)																							Ttgtgtgtccgtgtgtgtgtgt	0.416													3	3	---	---	---	---	
LRRC16A	55604	broad.mit.edu	37	6	25339177	25339178	+	Intron	INS	-	A	A	rs148692912	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25339177_25339178insA	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						AATCCTCCTATGAGGGTCCCTA	0.322													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	33859356	33859356	+	5'Flank	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33859356delC	uc003ogg.2	-						uc003ogh.2_5'Flank|uc003ogi.1_RNA|uc003ogj.1_RNA|uc003ogk.2_5'Flank|uc011drx.1_5'Flank					DQ599581																		CTCTCTTCTTCCCTCTTTCTT	0.393													4	2	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38743908	38743908	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38743908delT	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						CACTAAAGGATTTTTTTTTGA	0.294													6	3	---	---	---	---	
ENPP4	22875	broad.mit.edu	37	6	46110832	46110833	+	Intron	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46110832_46110833delTG	uc003oxy.2	+							NM_014936	NP_055751	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase							integral to membrane	hydrolase activity			ovary(3)|skin(1)	4						TGTGTGTGTTTGTGTGTGTATG	0.401													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57375666	57375667	+	Intron	INS	-	T	T	rs11384142		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57375666_57375667insT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AAGTAACCTTGTATAACGCCTT	0.332													4	6	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57484232	57484233	+	Intron	DEL	TC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57484232_57484233delTC	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)		ccaaataagatcacatttttcg	0.000													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57511052	57511053	+	Intron	INS	-	TA	TA	rs140023671		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57511052_57511053insTA	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)		TTTTAAGTCTGACTTACTGGGT	0.213													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	83567849	83567852	+	IGR	DEL	TAGA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83567849_83567852delTAGA								TPBG (491235 upstream) : UBE2CBP (34334 downstream)																							cactacaatctagatagatagata	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	91404697	91404697	+	IGR	DEL	T	-	-	rs76799359		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91404697delT								MAP3K7 (107790 upstream) : None (None downstream)																							ACCAAAAGGATTAAGTGCAGA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	91438859	91438859	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91438859delG								MAP3K7 (141952 upstream) : None (None downstream)																							AGGTCAGACTGGGGCCTGGGG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	100742562	100742562	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100742562delT								MCHR2 (300448 upstream) : SIM1 (94189 downstream)																							ATACATTCTATTTCCAAACTA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	107241748	107241748	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107241748delT								MIR587 (9653 upstream) : C6orf203 (107659 downstream)																							TTCACTTTTATTTTATTTCCC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	110227317	110227317	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110227317delA								FIG4 (80683 upstream) : GPR6 (72192 downstream)																							CTTTCAGGACAAGTTAGAGAA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	113031423	113031424	+	IGR	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113031423_113031424delTG								RFPL4B (358925 upstream) : None (None downstream)																							GGGTGTCATATGTGTGTGTGTA	0.406													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	114723470	114723470	+	IGR	DEL	T	-	-	rs75050756	byFrequency	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114723470delT								HS3ST5 (59930 upstream) : None (None downstream)																							TTTCtaattatttttttttaa	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	115634193	115634193	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115634193delA								HS3ST5 (970653 upstream) : FRK (628500 downstream)																							ctctcttcacaaaaaaaagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	122098122	122098122	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122098122delA								GJA1 (327250 upstream) : HSF2 (622574 downstream)																							gttcacatttaaaggcacttc	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138910753	138910753	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138910753delT								NHSL1 (17085 upstream) : CCDC28A (183904 downstream)																							CCCAGCCTCCTTTTACCCTAA	0.532											OREG0017694	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
CCDC28A	25901	broad.mit.edu	37	6	139101310	139101311	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139101310_139101311insT	uc003qie.2	+							NM_015439	NP_056254	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A												0				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		CTGGGAAAAAGTTTTTTTTTAA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	139970023	139970023	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139970023delT								CITED2 (274238 upstream) : None (None downstream)																							agcaaggctcttcaaatgaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	141930326	141930326	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141930326delC	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																		TCCTAATTTTCCACATTGCTT	0.323													4	2	---	---	---	---	
SYNE1	23345	broad.mit.edu	37	6	152786895	152786896	+	Intron	INS	-	ACACAC	ACACAC	rs113781129		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152786895_152786896insACACAC	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_Intron|SYNE1_uc003qow.2_5'Flank|SYNE1_uc003qox.1_Intron|SYNE1_uc003qoz.2_Intron|SYNE1_uc003qoy.2_Intron	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CTCTTAGAAGAacacatacaca	0.287										HNSCC(10;0.0054)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156745023	156745024	+	IGR	DEL	GA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156745023_156745024delGA								MIR1202 (477010 upstream) : ARID1B (354062 downstream)																							cccttgaaatgagaaggccagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168129696	168129697	+	IGR	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168129696_168129697insA								TCP10 (331698 upstream) : C6orf123 (55524 downstream)																							gtgtcatcagggaaatgcaaat	0.000													4	2	---	---	---	---	
WIPI2	26100	broad.mit.edu	37	7	5272375	5272375	+	3'UTR	DEL	A	-	-	rs35935303		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5272375delA	uc003snv.2	+	13					WIPI2_uc003snw.2_3'UTR|WIPI2_uc003snx.2_3'UTR|WIPI2_uc003sny.2_3'UTR|WIPI2_uc010ksv.2_3'UTR|WIPI2_uc003soa.2_3'UTR|WIPI2_uc003sob.2_3'UTR	NM_015610	NP_056425	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2						autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)		GTGTGGGGGGAAAAAGTGTGC	0.532													4	4	---	---	---	---	
TAX1BP1	8887	broad.mit.edu	37	7	27798016	27798016	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27798016delT	uc003szl.2	+						TAX1BP1_uc011jzo.1_Intron|TAX1BP1_uc003szk.2_Intron|TAX1BP1_uc011jzp.1_Intron	NM_006024	NP_006015	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I)						anti-apoptosis|apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production	cytosol	identical protein binding|kinase binding|zinc ion binding			breast(1)	1			GBM - Glioblastoma multiforme(3;0.0823)			TTTTTGGAGATTTTTTTTTTT	0.289													5	4	---	---	---	---	
CREB5	9586	broad.mit.edu	37	7	28499841	28499841	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28499841delA	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron	NM_182898	NP_878901	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						AAAAGGAAATAAAAGGTTGCA	0.318													4	2	---	---	---	---	
AAA1	404744	broad.mit.edu	37	7	34402517	34402518	+	Intron	DEL	AC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34402517_34402518delAC	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						AGATGTCTCTACCTGCCACCTG	0.337													4	2	---	---	---	---	
ELMO1	9844	broad.mit.edu	37	7	37223765	37223765	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37223765delT	uc003tfk.1	-						ELMO1_uc011kbc.1_Intron|ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						ttttggattcttttccagata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	37545172	37545172	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37545172delG								ELMO1 (56642 upstream) : GPR141 (234824 downstream)																							TGTGCAACAAGGGGGGAAGGG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41619826	41619826	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41619826delT								C7orf10 (719469 upstream) : INHBA (108777 downstream)																							GGAATTCCTATTCTATTAGAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	42725149	42725149	+	IGR	DEL	A	-	-	rs34886054		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42725149delA								GLI3 (448531 upstream) : C7orf25 (223725 downstream)																							ACTGAGTTCCAAAAAAAAGTA	0.413													4	2	---	---	---	---	
NACAD	23148	broad.mit.edu	37	7	45128871	45128872	+	5'Flank	DEL	AA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45128871_45128872delAA	uc003tmt.2	-							NM_001146334	NP_001139806	O15069	NACAD_HUMAN	NAC alpha domain containing						protein transport	cytoplasm|nucleus					0						CGTGGCCAGGAAGAGGCGGGGA	0.653													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	48744707	48744708	+	IGR	DEL	AC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48744707_48744708delAC								ABCA13 (57616 upstream) : CDC14C (219449 downstream)																							CCCTTTCACTACAGCACTCAGA	0.465													4	2	---	---	---	---	
EGFR	1956	broad.mit.edu	37	7	55085608	55085608	+	5'Flank	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55085608delA	uc003tqk.2	+						EGFR_uc003tqh.2_5'Flank|EGFR_uc003tqi.2_5'Flank|EGFR_uc003tqj.2_5'Flank|EGFR_uc010kzg.1_5'Flank	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	CAGAGACAGCAAAGGGCAGGT	0.507		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57605238	57605239	+	IGR	INS	-	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57605238_57605239insG								ZNF716 (71973 upstream) : None (None downstream)																							TTCAATTACAAGTCCAGATGCT	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57670038	57670039	+	IGR	INS	-	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57670038_57670039insG								ZNF716 (136773 upstream) : None (None downstream)																							gatttttttttctattccatac	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61827624	61827624	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61827624delT								None (None upstream) : LOC643955 (924048 downstream)																							aagcaaatgctgagagatttg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62291398	62291398	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62291398delA								None (None upstream) : LOC643955 (460274 downstream)																							ggcctatatgaaaaatgaaat	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	66917154	66917154	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66917154delG								STAG3L4 (130642 upstream) : None (None downstream)																							GTATAAGTAAGGGGGGCGCTA	0.532													4	2	---	---	---	---	
PMS2L3	5387	broad.mit.edu	37	7	75142142	75142142	+	Intron	DEL	A	-	-	rs71519365		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75142142delA	uc003udp.2	-						PMS2L3_uc003udn.2_Intron|PMS2L3_uc003udq.2_Intron	NM_005395	NP_005386			SubName: Full=Postmeiotic segregation increased 2-like 3; SubName: Full=Postmeiotic segregation increased 2-like 3, isoform CRA_b;												0						tctcaaaaagaaaaaaaaaaa	0.129								Direct_reversal_of_damage|MMR					4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	83479741	83479741	+	IGR	DEL	A	-	-	rs34997594		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83479741delA								SEMA3E (201417 upstream) : SEMA3A (107924 downstream)																							TGAGGCAATCAAGAGTCAGGA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84415353	84415353	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84415353delC								SEMA3A (591136 upstream) : SEMA3D (209521 downstream)																							aatatacacaccccacttttt	0.124													4	2	---	---	---	---	
ZNF804B	219578	broad.mit.edu	37	7	88626301	88626302	+	Intron	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88626301_88626302delTG	uc011khi.1	+							NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			agtatgtgtatgtgtgtgtgta	0.267										HNSCC(36;0.09)			4	2	---	---	---	---	
FAM185A	222234	broad.mit.edu	37	7	102431465	102431466	+	Intron	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102431465_102431466delTG	uc011klf.1	+						FAM185A_uc011klg.1_Intron|FAM185A_uc011klh.1_Intron	NM_001145268	NP_001138740	Q8N0U4	F185A_HUMAN	hypothetical protein LOC222234 isoform 1												0						tataaacgtatgtacattgtac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	115182145	115182145	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115182145delT								MDFIC (522882 upstream) : TFEC (393057 downstream)																							CTAGTCCCACTTTTTTTTTAA	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	116888105	116888106	+	IGR	INS	-	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116888105_116888106insC								ST7 (18032 upstream) : WNT2 (28582 downstream)																							cgacctcaccgccccccacaac	0.000													4	2	---	---	---	---	
ASZ1	136991	broad.mit.edu	37	7	117069277	117069277	+	5'Flank	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117069277delT	uc003vjb.2	-						ASZ1_uc011kno.1_5'Flank|ASZ1_uc011knp.1_5'Flank	NM_130768	NP_570124	Q8WWH4	ASZ1_HUMAN	ankyrin repeat, SAM and basic leucine zipper						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)			AAAGAAGGCCTGAGGCTACAG	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	121949015	121949015	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121949015delT	uc003vkf.1	+											Homo sapiens cDNA FLJ32475 fis, clone SKNMC2000612.																		GAAAAACACGTTTTTTAATTC	0.438													4	2	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	121984888	121984889	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121984888_121984889insT	uc010lkp.2	-						CADPS2_uc011knx.1_Intron|CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						AATGGTGACAATTTTTATATAG	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128736164	128736164	+	IGR	DEL	T	-	-	rs66837005		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128736164delT								TPI1P2 (38871 upstream) : LOC407835 (30161 downstream)																							GGAATGAATCttttttttttt	0.174													4	3	---	---	---	---	
AHCYL2	23382	broad.mit.edu	37	7	128872823	128872823	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128872823delG	uc011kov.1	+						AHCYL2_uc003vot.2_Intron	NM_015328	NP_056143	Q96HN2	SAHH3_HUMAN	S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2						tGTACGggttgaacctaacca	0.015													4	2	---	---	---	---	
CPA5	93979	broad.mit.edu	37	7	130006964	130006964	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130006964delT	uc010lmd.1	+						CPA5_uc003vps.2_Intron|CPA5_uc003vpt.2_Intron|CPA5_uc010lme.1_Intron|CPA5_uc003vpu.1_Intron	NM_001127441	NP_001120913	Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5 isoform 1						proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2	Melanoma(18;0.0435)					ctatctagaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	131729445	131729445	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131729445delC								PODXL (488069 upstream) : PLXNA4 (78647 downstream)																							AACCAGTCAGCCCCCAAGGAA	0.468													4	2	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	132178276	132178276	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132178276delT	uc003vra.3	-						PLXNA4_uc003vrc.2_Intron|PLXNA4_uc003vrb.2_Intron	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						ACTCTGGATCTTTTTTCACTG	0.423													4	2	---	---	---	---	
CHCHD3	54927	broad.mit.edu	37	7	132491550	132491550	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132491550delC	uc003vre.2	-						CHCHD3_uc010lmi.2_Intron|CHCHD3_uc003vrf.2_Intron|CHCHD3_uc010lmj.2_Intron	NM_017812	NP_060282	Q9NX63	CHCH3_HUMAN	coiled-coil-helix-coiled-coil-helix domain						inner mitochondrial membrane organization|mitochondrial fusion	mitochondrial inner membrane	protein complex scaffold				0						CCATGACATTCCCATCAAGTA	0.343													4	2	---	---	---	---	
SLC35B4	84912	broad.mit.edu	37	7	133979173	133979173	+	3'UTR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133979173delA	uc003vrn.2	-	10					SLC35B4_uc010lmk.2_3'UTR|SLC35B4_uc010lml.1_Intron	NM_032826	NP_116215	Q969S0	S35B4_HUMAN	solute carrier family 35, member B4							Golgi membrane|integral to membrane	UDP-N-acetylglucosamine transmembrane transporter activity|UDP-xylose transmembrane transporter activity			skin(1)	1						GATGGGAGACAAAAGGGATAA	0.493													4	2	---	---	---	---	
ZNF777	27153	broad.mit.edu	37	7	149148380	149148381	+	Intron	DEL	GT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149148380_149148381delGT	uc003wfv.2	-							NM_015694	NP_056509	Q9ULD5	ZN777_HUMAN	zinc finger protein 777						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			GGGGGTGTGGGTGTGTGTGTGT	0.520													6	3	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151254556	151254556	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151254556delA	uc003wkk.2	-						PRKAG2_uc003wki.2_Intron|PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.2_Intron|PRKAG2_uc003wkl.2_3'UTR	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		CTTGGAAAACAAAAAAAAAGA	0.373													5	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151955436	151955436	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151955436delA	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		cagtattaataagtaagttta	0.000			N		medulloblastoma								3	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151981139	151981139	+	Intron	DEL	A	-	-	rs78183763		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151981139delA	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		AAATTGAAACAAAAACAATAA	0.229			N		medulloblastoma								4	4	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157988134	157988134	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157988134delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		ttcatgtttcttttttagggg	0.000													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	4165766	4165766	+	Intron	DEL	T	-	-	rs138912919	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4165766delT	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TCATGTATAGTTTTTTTtatg	0.219													4	2	---	---	---	---	
SGCZ	137868	broad.mit.edu	37	8	14822054	14822054	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14822054delG	uc003wwq.2	-							NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		accacttgctggagaggacag	0.129													4	2	---	---	---	---	
SGCZ	137868	broad.mit.edu	37	8	15028809	15028809	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15028809delC	uc003wwq.2	-							NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		AGTCCCAATTCCCAGCAGAGT	0.338													4	2	---	---	---	---	
LGI3	203190	broad.mit.edu	37	8	22007288	22007288	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22007288delC	uc003xav.2	-						LGI3_uc010ltu.2_Intron	NM_139278	NP_644807	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3						exocytosis	cell junction|extracellular region|synaptic vesicle|synaptosome				ovary(1)	1				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		CCCCACCTTTCCCCCAAGAGA	0.547													4	2	---	---	---	---	
ADAM28	10863	broad.mit.edu	37	8	24201545	24201545	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24201545delC	uc003xdy.2	+						ADAM28_uc011laa.1_Intron|ADAM28_uc010lua.2_Intron	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1						proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|lung(1)|central_nervous_system(1)	5		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		tagttttcttcaggatatgtg	0.169													4	2	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	25926668	25926668	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25926668delT	uc003xek.2	+							NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		agtgtggtactttttttatgg	0.164													4	2	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32229927	32229927	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32229927delA	uc003xip.2	+							NM_013962	NP_039256	Q02297	NRG1_HUMAN	neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TATTATGTATAAAAAAAAGTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	33062701	33062702	+	IGR	INS	-	T	T	rs5890715		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33062701_33062702insT								NRG1 (440143 upstream) : FUT10 (165644 downstream)																							TCTTGATTGCCTTTTTTTTTTT	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37100768	37100768	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37100768delG								KCNU1 (307127 upstream) : ZNF703 (452533 downstream)																							TTGAGGCTGTGGGGACAGTTT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37229450	37229451	+	IGR	DEL	GA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37229450_37229451delGA								KCNU1 (435809 upstream) : ZNF703 (323850 downstream)																							CTGAGTGCTTGAGAATAGTAGG	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37810046	37810046	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37810046delA								GOT1L1 (12399 upstream) : ADRB3 (10470 downstream)																							GCAAAGTTTTAAAAAAAAAAT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49052040	49052040	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49052040delG								UBE2V2 (77588 upstream) : EFCAB1 (571311 downstream)																							ccccagtggagggaaaaagag	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61812938	61812938	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61812938delT								CHD7 (33475 upstream) : CLVS1 (387587 downstream)																							TGCAATGTGCTTTTTTTATAC	0.388													4	2	---	---	---	---	
COPS5	10987	broad.mit.edu	37	8	67972671	67972671	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67972671delA	uc003xxe.2	-						COPS5_uc003xxd.2_5'UTR|COPS5_uc003xxf.2_Intron|COPS5_uc010lyu.1_5'Flank|COPS5_uc010lyv.1_Intron	NM_006837	NP_006828	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5						cullin deneddylation|transcription from RNA polymerase II promoter	eukaryotic translation initiation factor 3 complex|signalosome	metal ion binding|metallopeptidase activity|protein binding|transcription coactivator activity|translation initiation factor activity			ovary(1)|skin(1)	2	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)			CCACAGAAAGAATCCAAATTT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	72416959	72416959	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72416959delA	uc003xyw.2	-											Homo sapiens cDNA clone IMAGE:5264099.																		atctccatttAAAAAAAAATC	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79559020	79559020	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79559020delA								PKIA (43536 upstream) : FAM164A (19262 downstream)																							TATTATAGCTAAAAAACAGTG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	88756838	88756838	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88756838delT								CNBD1 (361883 upstream) : DCAF4L2 (126135 downstream)																							CTCTTCTCCCTTATTCTAGGG	0.239													4	2	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	102867906	102867906	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102867906delG	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			GGCCTCAGATGGAAGGTAGAG	0.398													4	2	---	---	---	---	
C8orf76	84933	broad.mit.edu	37	8	124244006	124244006	+	Intron	DEL	A	-	-	rs77482613		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124244006delA	uc003yqc.1	-						C8orf76_uc003yqd.2_Intron	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)			TCCTAAGGAGAAAAAAAAAAG	0.313													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138449921	138449922	+	IGR	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138449921_138449922insT								None (None upstream) : FAM135B (692346 downstream)																							CTGGAAAACTCTTTTTTTTTAA	0.351													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141074590	141074590	+	Intron	DEL	C	-	-	rs116558258	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141074590delC	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						ACGTTGCATGCCAGACCCAGA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142585630	142585630	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142585630delT								FLJ43860 (68300 upstream) : MIR1302-7 (281973 downstream)																							GGGGCTGGCATTTACACTGTG	0.229													4	2	---	---	---	---	
GLIS3	169792	broad.mit.edu	37	9	3892249	3892249	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3892249delA	uc003zhw.1	-						GLIS3_uc003zhx.1_Intron|GLIS3_uc010mhf.1_Intron|GLIS3_uc003zhv.1_Intron|GLIS3_uc003zhy.1_Intron	NM_152629	NP_689842	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform b						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		GAAGCAAGGCAAAAAAAAAGC	0.448													5	3	---	---	---	---	
KDM4C	23081	broad.mit.edu	37	9	6753003	6753003	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6753003delG	uc010mhu.2	+							NM_001146696	NP_001140168	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 4						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						CCTAGTTCCAGGGGACCACTG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	7508741	7508741	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7508741delA								KDM4C (333094 upstream) : C9orf123 (287752 downstream)																							gctgtggtggaaagaacactg	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	15310708	15310708	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15310708delC								TTC39B (3464 upstream) : SNAPC3 (112074 downstream)																							ctttctcgttcacttgtttac	0.020													4	2	---	---	---	---	
CNTLN	54875	broad.mit.edu	37	9	17352077	17352077	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17352077delT	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)		ATACAAAAACTTTTTTATTTC	0.318													4	2	---	---	---	---	
IFT74	80173	broad.mit.edu	37	9	27047931	27047931	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27047931delA	uc010mja.2	+						IFT74_uc010mjb.2_Intron|IFT74_uc003zqg.3_Intron	NM_001099223	NP_001092693	Q96LB3	IFT74_HUMAN	coiled-coil domain containing 2 isoform a							cytoplasmic membrane-bounded vesicle|intraflagellar transport particle B|microtubule-based flagellum				skin(1)	1		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		AAAGGAAATGAAAAAAAACCC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	32721930	32721931	+	IGR	INS	-	GGAC	GGAC	rs36004639		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32721930_32721931insGGAC								TAF1L (86263 upstream) : TMEM215 (61566 downstream)																							gatggatggatcaggtgatgga	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33608934	33608934	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33608934delG								SUGT1P1 (97887 upstream) : ANXA2P2 (15289 downstream)																							CTCATCTGTTGGGGGTGGCTG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	34084641	34084641	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34084641delC								UBAP2 (35694 upstream) : DCAF12 (1740 downstream)																							GGATGAGGAGCCAGCAGACTA	0.493													4	2	---	---	---	---	
CNTFR	1271	broad.mit.edu	37	9	34581129	34581131	+	5'UTR	DEL	TCC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34581129_34581131delTCC	uc003zup.1	-	2					CNTFR_uc003zuq.1_Intron|LOC415056_uc003zut.2_Intron|LOC415056_uc003zur.2_Intron|LOC415056_uc003zus.2_Intron	NM_147164	NP_671693	P26992	CNTFR_HUMAN	ciliary neurotrophic factor receptor						nervous system development	anchored to membrane|extrinsic to membrane|plasma membrane	ciliary neurotrophic factor receptor activity|receptor binding			ovary(3)|central_nervous_system(1)|skin(1)	5	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.00494)		CACATCAATGTCCTCCTCCTCCT	0.557													4	2	---	---	---	---	
ZCCHC7	84186	broad.mit.edu	37	9	37355052	37355052	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37355052delA	uc003zzq.2	+						ZCCHC7_uc011lqh.1_Intron|ZCCHC7_uc011lqi.1_Intron|ZCCHC7_uc010mlt.2_Intron	NM_032226	NP_115602	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7								nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.0137)		TCATTTTAGGAAATGTCCAGA	0.343													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67222190	67222191	+	IGR	DEL	CA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67222190_67222191delCA								LOC442421 (719163 upstream) : AQP7P1 (32076 downstream)																							TTTTATTTGTCACTACCACTGC	0.396													4	2	---	---	---	---	
TRPM3	80036	broad.mit.edu	37	9	73409009	73409009	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73409009delT	uc004aid.2	-						TRPM3_uc004ahu.2_Intron|TRPM3_uc004ahv.2_Intron|TRPM3_uc004ahw.2_Intron|TRPM3_uc004ahx.2_Intron|TRPM3_uc004ahy.2_Intron|TRPM3_uc004ahz.2_Intron|TRPM3_uc004aia.2_Intron|TRPM3_uc004aib.2_Intron|TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron|TRPM3_uc004aie.2_Intron|TRPM3_uc004aif.2_Intron|TRPM3_uc004aig.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						GGATAGCAGATTTTTTTTTTT	0.303													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82641334	82641334	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82641334delT								TLE4 (299677 upstream) : None (None downstream)																							ATTTTCTGCCTTTTTTTGCTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82678161	82678161	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82678161delT								TLE4 (336504 upstream) : None (None downstream)																							AGTGCACATATTTTTTTTCTT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85379248	85379248	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85379248delT								FLJ46321 (769078 upstream) : RASEF (218069 downstream)																							AAGGCAAGAATTTTTTTTTTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90068538	90068538	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90068538delA								C9orf170 (293897 upstream) : DAPK1 (44120 downstream)																							ACCCAGTGCTAAAACCTGTCT	0.328													4	2	---	---	---	---	
SYK	6850	broad.mit.edu	37	9	93658485	93658486	+	3'UTR	INS	-	A	A	rs113920845		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93658485_93658486insA	uc004aqz.2	+	14					SYK_uc004ara.2_3'UTR|SYK_uc004arb.2_3'UTR|SYK_uc004arc.2_3'UTR|SYK_uc011ltr.1_RNA|SYK_uc011lts.1_RNA|SYK_uc011ltt.1_RNA	NM_003177	NP_003168	P43405	KSYK_HUMAN	spleen tyrosine kinase isoform 1						cell proliferation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|neutrophil chemotaxis|organ morphogenesis|platelet activation|protein complex assembly	cytosol|T cell receptor complex	ATP binding|integrin binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5						aagaaagaaagaaaaaaaaaaa	0.332			T	ETV6|ITK	MDS|peripheral T-cell lymphoma								5	3	---	---	---	---	
ROR2	4920	broad.mit.edu	37	9	94661992	94661993	+	Intron	DEL	AC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94661992_94661993delAC	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20						CAACCCTTAGACACACACACCA	0.351													4	2	---	---	---	---	
SLC35D2	11046	broad.mit.edu	37	9	99147446	99147446	+	5'Flank	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99147446delA	uc004awc.2	-						SLC35D2_uc010msd.2_5'Flank|SLC35D2_uc010mse.2_5'Flank|SLC35D2_uc010msf.2_5'Flank|SLC35D2_uc004awd.2_5'Flank|SLC35D2_uc004awe.2_5'Flank	NM_007001	NP_008932	Q76EJ3	S35D2_HUMAN	solute carrier family 35, member D2							Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity				0		Acute lymphoblastic leukemia(62;0.0167)				AGTCCGTTTTAAAAGAGAAAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	101566197	101566198	+	IGR	DEL	AC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101566197_101566198delAC								ANKS6 (7403 upstream) : GALNT12 (3783 downstream)																							tgaaaaaaaaacaaataaatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102516852	102516853	+	Intron	INS	-	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102516852_102516853insC	uc004bad.1	-											Homo sapiens cDNA FLJ32889 fis, clone TESTI2004560.																		GAAAATCCTAACCCCCCTTCAT	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	108729048	108729048	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108729048delA								TMEM38B (191604 upstream) : ZNF462 (896330 downstream)																							GGGGTTGAGGAAAAAAAATGT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	112313807	112313807	+	IGR	DEL	T	-	-	rs79448349		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112313807delT								PTPN3 (53214 upstream) : PALM2 (89265 downstream)																							GTCTCCACAGTCATAGCAATT	0.473													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	116134313	116134313	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116134313delC								BSPRY (801 upstream) : HDHD3 (1385 downstream)																							AATCCACCAACCCAGCTCCTC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	116379031	116379031	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116379031delG								RGS3 (19014 upstream) : ZNF618 (259531 downstream)																							tcagatctcagggccccaggc	0.154													4	2	---	---	---	---	
ZNF618	114991	broad.mit.edu	37	9	116635759	116635759	+	5'Flank	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116635759delG	uc004bid.2	+						ZNF618_uc004bib.1_5'Flank|ZNF618_uc004bic.2_5'Flank|ZNF618_uc011lxi.1_5'Flank|ZNF618_uc011lxj.1_5'Flank	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AGACCCTCCTGGAATCTTCGC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	117588250	117588250	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117588250delG								TNFSF15 (19842 upstream) : TNFSF8 (76874 downstream)																							tagGATTGCTGAGTTTGGTCT	0.209													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	120129060	120129060	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120129060delT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						TCATCttctcttttttttttc	0.269													4	2	---	---	---	---	
TRAF1	7185	broad.mit.edu	37	9	123672681	123672681	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123672681delA	uc004bku.1	-						TRAF1_uc011lyg.1_Intron|TRAF1_uc010mvl.1_Intron	NM_005658	NP_005649	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1						apoptosis|positive regulation of NF-kappaB transcription factor activity|protein complex assembly|regulation of apoptosis|signal transduction	cytoplasm	protein binding|zinc ion binding			skin(2)|ovary(1)	3						CTGCCTCGTTAAAAAAAAAtt	0.289													4	2	---	---	---	---	
GSN	2934	broad.mit.edu	37	9	124028987	124028988	+	Intron	DEL	TC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124028987_124028988delTC	uc004bld.1	+						GSN_uc010mvq.1_5'Flank|GSN_uc010mvr.1_5'Flank|GSN_uc010mvu.1_5'Flank|GSN_uc010mvt.1_5'Flank|GSN_uc010mvs.1_5'Flank|GSN_uc004ble.1_5'Flank|GSN_uc010mvv.1_5'Flank	NM_198252	NP_937895	P06396	GELS_HUMAN	gelsolin isoform b						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3						ggcctgctcatctgaaaaatac	0.119													4	2	---	---	---	---	
RBM18	92400	broad.mit.edu	37	9	125010064	125010065	+	Intron	INS	-	T	T	rs34974193		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125010064_125010065insT	uc004bma.2	-						RBM18_uc004blz.2_Intron|RBM18_uc010mvy.2_Intron|RBM18_uc011lyp.1_Intron	NM_033117	NP_149108	Q96H35	RBM18_HUMAN	RNA binding motif protein 18								nucleotide binding|RNA binding				0						tttttttgttgttttttttttt	0.149													2	4	---	---	---	---	
ZBTB26	57684	broad.mit.edu	37	9	125682414	125682414	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125682414delA	uc004bnj.2	-						ZBTB26_uc004bnk.2_Intron	NM_020924	NP_065975	Q9HCK0	ZBT26_HUMAN	zinc finger and BTB domain containing 26						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TACCAATATCAAGTGCCAATT	0.353													4	2	---	---	---	---	
SCAI	286205	broad.mit.edu	37	9	127764004	127764005	+	Intron	DEL	GT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127764004_127764005delGT	uc004bpe.2	-						SCAI_uc004bpd.2_Intron|SCAI_uc010mwu.2_Intron	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2						negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5						ACATTTGATAGTGAAGCAAGCA	0.287													4	2	---	---	---	---	
GARNL3	84253	broad.mit.edu	37	9	130132402	130132403	+	Intron	DEL	TT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130132402_130132403delTT	uc011mae.1	+						GARNL3_uc011mad.1_Intron|GARNL3_uc010mxi.2_Intron	NM_032293	NP_115669	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3						AAGATAACTGTTTTACAAGGCA	0.450													4	2	---	---	---	---	
FNBP1	23048	broad.mit.edu	37	9	132725386	132725387	+	Intron	DEL	AG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132725386_132725387delAG	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848	Q96RU3	FNBP1_HUMAN	formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		AGGAACAAAAAGAGAAAACCCC	0.460			T	MLL	AML								4	2	---	---	---	---	
FNBP1	23048	broad.mit.edu	37	9	132769158	132769158	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132769158delA	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron	NM_015033	NP_055848	Q96RU3	FNBP1_HUMAN	formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		TGTGTGGGTTAAAAAAATAAA	0.279			T	MLL	AML								4	2	---	---	---	---	
KLF6	1316	broad.mit.edu	37	10	3824532	3824532	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3824532delA	uc001iha.2	-						KLF6_uc010qaj.1_Intron|KLF6_uc010qak.1_Intron|KLF6_uc010qal.1_Intron|KLF6_uc001ihb.2_Intron	NM_001300	NP_001291	Q99612	KLF6_HUMAN	Kruppel-like factor 6 isoform A						B cell differentiation	nucleus	zinc ion binding			central_nervous_system(3)|lung(1)	4				Colorectal(1;0.238)		CTACAGGGGCAAAACCTTTTG	0.418													4	2	---	---	---	---	
PFKFB3	5209	broad.mit.edu	37	10	6263013	6263014	+	Intron	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6263013_6263014delTG	uc001ije.2	+						PFKFB3_uc001ijd.2_Intron|PFKFB3_uc009xii.2_Intron|PFKFB3_uc010qaw.1_Intron|PFKFB3_uc001ijf.2_Intron	NM_004566	NP_004557	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(2)|central_nervous_system(1)	3						tgtatggctctgtgtgtgtgtg	0.059													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11038729	11038729	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11038729delT								LOC254312 (44603 upstream) : CELF2 (8530 downstream)																							CCAGATCCCATTTTTTTTTGT	0.498													3	3	---	---	---	---	
STAM	8027	broad.mit.edu	37	10	17718033	17718034	+	Intron	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17718033_17718034insA	uc001ipj.1	+						STAM_uc010qcf.1_Intron	NM_003473	NP_003464	Q92783	STAM1_HUMAN	signal transducing adaptor molecule 1						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	SH3/SH2 adaptor activity			large_intestine(1)|ovary(1)	2						TAGAATTCATTAAAAAAAAAAT	0.342													4	2	---	---	---	---	
ARMC3	219681	broad.mit.edu	37	10	23298061	23298061	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23298061delA	uc001irm.3	+						ARMC3_uc010qcv.1_Intron|ARMC3_uc010qcw.1_Intron	NM_173081	NP_775104	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3								binding				0						ggctctggccaaaaactctgg	0.000													4	2	---	---	---	---	
THNSL1	79896	broad.mit.edu	37	10	25311877	25311877	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25311877delT	uc001isi.3	+						ENKUR_uc001ish.1_Intron	NM_024838	NP_079114	Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1						threonine biosynthetic process		ATP binding|pyridoxal phosphate binding|shikimate kinase activity|threonine synthase activity			pancreas(1)	1					L-Threonine(DB00156)|Pyridoxal Phosphate(DB00114)	AAAGTTTTGATTTTTCAGTGT	0.244													4	2	---	---	---	---	
KIAA1462	57608	broad.mit.edu	37	10	30344832	30344832	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30344832delT	uc009xle.1	-						KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Intron	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608											ovary(4)	4						CTGACTCCTCTTTTTTTTCTT	0.343													4	2	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	34612274	34612275	+	Intron	DEL	CA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34612274_34612275delCA	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixo.1_Intron|PARD3_uc001ixp.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron|PARD3_uc001ixs.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				AAAAGGAAACCACACACACACA	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37693976	37693976	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37693976delA								ANKRD30A (172481 upstream) : ZNF248 (396471 downstream)																							aggatggggcaaaaaaaatat	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38223883	38223883	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38223883delG								ZNF248 (76871 upstream) : ZNF25 (14912 downstream)																							agcacatccaggaatgcactt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42648209	42648209	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42648209delC								None (None upstream) : LOC441666 (179106 downstream)																							TGAAGAAATGCCCCTTGCCTC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44189840	44189840	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44189840delG								ZNF32 (45514 upstream) : HNRNPA3P1 (93020 downstream)																							TCTTTCTGCTGGGGGAAAATC	0.532													4	2	---	---	---	---	
MARCH8	220972	broad.mit.edu	37	10	45991410	45991411	+	Intron	DEL	CA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45991410_45991411delCA	uc001jci.1	-						MARCH8_uc001jch.2_Intron|MARCH8_uc001jcj.1_Intron|MARCH8_uc001jck.1_Intron	NM_001002266	NP_001002266	Q5T0T0	MARH8_HUMAN	cellular modulator of immune recognition isoform							cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0						acatgggaaccacaaaaagatt	0.000													4	2	---	---	---	---	
C10orf11	83938	broad.mit.edu	37	10	77915797	77915797	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77915797delA	uc001jxi.2	+							NM_032024	NP_114413	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)					CTTTAACAGGAAAAAAAAATC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80477170	80477170	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80477170delG								RPS24 (660600 upstream) : LOC283050 (225914 downstream)																							GCTGGCATGTGGCAAGGACTT	0.378													4	2	---	---	---	---	
PANK1	53354	broad.mit.edu	37	10	91362139	91362139	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91362139delC	uc001kgp.1	-						PANK1_uc001kgn.1_Intron|PANK1_uc001kgo.1_Intron|PANK1_uc009xtu.1_Intron	NM_148977	NP_683878	Q8TE04	PANK1_HUMAN	pantothenate kinase 1 isoform alpha						coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity				0					Bezafibrate(DB01393)	GGTCATGCATCCCCAGACAGG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91785137	91785137	+	IGR	DEL	A	-	-	rs140844369		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91785137delA								KIF20B (250437 upstream) : HTR7 (715441 downstream)																							aagaagactgaaaaaaaaatt	0.000													4	2	---	---	---	---	
PLCE1	51196	broad.mit.edu	37	10	95797372	95797372	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95797372delG	uc001kjk.2	+						PLCE1_uc010qnx.1_Intron	NM_016341	NP_057425	Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1 isoform 1						activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)				CCTTCCTGCTGGGCACAGTGA	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	99855869	99855869	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99855869delG								CRTAC1 (65284 upstream) : C10orf28 (38512 downstream)																							tgtgtggagtggggtcagcag	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	101618883	101618884	+	IGR	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101618883_101618884delTG								ABCC2 (7221 upstream) : DNMBP (16450 downstream)																							CCGTGAGTTATGTGGCGACCAG	0.470													4	2	---	---	---	---	
C10orf76	79591	broad.mit.edu	37	10	103648350	103648350	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103648350delT	uc009xwy.1	-						C10orf76_uc009xwx.1_Intron	NM_024541	NP_078817	Q5T2E6	CJ076_HUMAN	hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		CAAACAAGGGTTACAAAGATG	0.488													4	2	---	---	---	---	
SUFU	51684	broad.mit.edu	37	10	104319839	104319839	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104319839delT	uc001kvy.1	+						SUFU_uc001kvw.1_Intron|SUFU_uc001kvx.2_Intron	NM_016169	NP_057253	Q9UMX1	SUFU_HUMAN	suppressor of fused						negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			central_nervous_system(4)|skin(2)|breast(1)	7		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		CTAACAGAGATTTTTTTTTGT	0.299			D|F|S		medulloblastoma	medulloblastoma			Medulloblastoma_associated_with_Germline_SUFU_Mutation				4	2	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	106921150	106921150	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106921150delC	uc001kyi.1	+							NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		AGGGTCCTTTCCCATATCCAT	0.552													4	2	---	---	---	---	
PDCD4	27250	broad.mit.edu	37	10	112654478	112654478	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112654478delT	uc001kzh.2	+						PDCD4_uc001kzg.2_Intron|PDCD4_uc010qre.1_Intron	NM_014456	NP_055271	Q53EL6	PDCD4_HUMAN	programmed cell death 4 isoform 1						apoptosis|cell aging|negative regulation of cell cycle|negative regulation of JUN kinase activity|negative regulation of transcription, DNA-dependent	cytosol|nucleus	protein binding|RNA binding			ovary(1)|breast(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		CACTGCAGTGTTTTTTTTTTT	0.279													4	2	---	---	---	---	
VTI1A	143187	broad.mit.edu	37	10	114470563	114470564	+	Intron	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114470563_114470564delTG	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron	NM_145206	NP_660207	Q96AJ9	VTI1A_HUMAN	SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		CAtgtgtatctgtgtgtgtgtg	0.307													4	2	---	---	---	---	
AFAP1L2	84632	broad.mit.edu	37	10	116103090	116103090	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116103090delT	uc001lbn.2	-						AFAP1L2_uc001lbo.2_Intron|AFAP1L2_uc010qse.1_Intron|AFAP1L2_uc001lbp.2_Intron|AFAP1L2_uc001lbr.1_Intron	NM_001001936	NP_001001936	Q8N4X5	AF1L2_HUMAN	KIAA1914 protein isoform 1						inflammatory response|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of transcription, DNA-dependent|regulation of interleukin-6 production|regulation of mitotic cell cycle	cytoplasm	protein tyrosine kinase activator activity|SH2 domain binding|SH3 domain binding			ovary(1)|breast(1)	2		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		CACCTCCTGCTTTCCTCGTGA	0.537													4	2	---	---	---	---	
INPP5F	22876	broad.mit.edu	37	10	121583100	121583101	+	Intron	INS	-	A	A	rs76438649	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121583100_121583101insA	uc001leo.2	+						INPP5F_uc001lep.2_Intron	NM_014937	NP_055752	Q9Y2H2	SAC2_HUMAN	inositol polyphosphate-5-phosphatase F								phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		AACAAACTTTTATTCCCCGATT	0.198													3	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	123045548	123045548	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123045548delT								WDR11 (376513 upstream) : FGFR2 (192297 downstream)																							GAAGAATGCATTTATGTAACT	0.443													4	2	---	---	---	---	
CHST15	51363	broad.mit.edu	37	10	125816936	125816937	+	Intron	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125816936_125816937insA	uc001lhm.2	-						CHST15_uc001lhn.2_Intron|CHST15_uc010que.1_Intron|CHST15_uc001lho.2_Intron	NM_015892	NP_056976	Q7LFX5	CHSTF_HUMAN	B cell RAG associated protein						hexose biosynthetic process	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity			ovary(1)	1						ACCTCtttatttaaacacctac	0.396													4	2	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127580879	127580879	+	Intron	DEL	A	-	-	rs112972524		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127580879delA	uc001ljg.1	-							NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				caacatctccaatttttttgt	0.000													7	4	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	128826994	128826994	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128826994delG	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GAACCAGCTAGGGCGTGGCAG	0.517													4	2	---	---	---	---	
AP2A2	161	broad.mit.edu	37	11	964708	964708	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:964708delA	uc001lss.2	+						AP2A2_uc001lst.1_Intron|AP2A2_uc009yco.1_Intron	NM_012305	NP_036437	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2						axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|cytosol	lipid binding|protein transporter activity				0		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		aaatgaagctaaaaaatacct	0.119													4	2	---	---	---	---	
BRSK2	9024	broad.mit.edu	37	11	1415072	1415072	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1415072delG	uc001lti.2	+						BRSK2_uc009ycv.1_Intron|BRSK2_uc001lth.1_Intron|BRSK2_uc001ltj.2_Intron|BRSK2_uc001ltk.2_Intron|BRSK2_uc001ltl.2_Intron	NM_003957	NP_003948	Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2						establishment of cell polarity|neuron differentiation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		GATGGGCTGTGGTGTGCAGGT	0.617													4	2	---	---	---	---	
ST5	6764	broad.mit.edu	37	11	8803163	8803164	+	Intron	DEL	AC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8803163_8803164delAC	uc001mgt.2	-						ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Intron|ST5_uc001mgw.1_Intron	NM_213618	NP_998783	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1						positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		atttaggaatacacacacacac	0.020													4	3	---	---	---	---	
USP47	55031	broad.mit.edu	37	11	11966549	11966549	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11966549delT	uc001mjs.2	+						USP47_uc001mjr.2_Intron	NM_017944	NP_060414	Q96K76	UBP47_HUMAN	ubiquitin specific protease 47						base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)		ATGGAGAATGTTGGCCATATT	0.159													4	2	---	---	---	---	
SPON1	10418	broad.mit.edu	37	11	14098659	14098659	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14098659delA	uc001mle.2	+							NM_006108	NP_006099	Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)		TGCCTTAGACAAGTCTTCACA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15729333	15729333	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15729333delT								INSC (460581 upstream) : SOX6 (258663 downstream)																							CCCTGTCGGATTTTGAGCCAG	0.458													4	2	---	---	---	---	
METT5D1	196074	broad.mit.edu	37	11	28140643	28140643	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28140643delT	uc001msh.2	+						METT5D1_uc001msg.2_Intron|METT5D1_uc001mse.2_Intron|METT5D1_uc001msf.1_Intron	NM_001113528	NP_001107000	A6NJ78	MET15_HUMAN	methyltransferase 5 domain containing 1 isoform								methyltransferase activity				0						aggttttacctttttatggga	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39803074	39803075	+	IGR	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39803074_39803075insA								None (None upstream) : LRRC4C (332678 downstream)																							TGAACTAAAGCAAAAAAGACAG	0.302													4	2	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	40314365	40314368	+	5'UTR	DEL	CTTC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40314365_40314368delCTTC	uc001mxa.1	-	1					LRRC4C_uc001mxc.1_Intron|LRRC4C_uc001mxd.1_Intron|LRRC4C_uc001mxb.1_5'UTR	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)				AAGCTTCGTTCTTCCTTCTCTCTT	0.466													4	2	---	---	---	---	
MYBPC3	4607	broad.mit.edu	37	11	47371843	47371843	+	Intron	DEL	T	-	-	rs11570049		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47371843delT	uc001nfa.3	-							NM_000256	NP_000247	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac						cardiac muscle contraction|cell adhesion|muscle filament sliding|regulation of muscle filament sliding|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis	C zone|cytosol|striated muscle myosin thick filament	actin binding|ATPase activator activity|metal ion binding|myosin heavy chain binding|structural constituent of muscle|titin binding			ovary(2)|central_nervous_system(1)	3				Lung(87;0.176)		gcccggctaatttttttgtat	0.000													6	6	---	---	---	---	
PTPRJ	5795	broad.mit.edu	37	11	48096372	48096372	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48096372delG	uc001ngp.3	+						PTPRJ_uc001ngo.3_Intron	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8						GGCCCTTGCTGGAATAATTAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49112409	49112410	+	IGR	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49112409_49112410insA								OR4A47 (601137 upstream) : FOLH1 (55778 downstream)																							AACCACTCAAGAAAAAAAAAAT	0.282													4	2	---	---	---	---	
OR5M10	390167	broad.mit.edu	37	11	56345405	56345406	+	5'Flank	DEL	CA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56345405_56345406delCA	uc001niz.1	-							NM_001004741	NP_001004741	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						ATCTCAAACCCACACACACACA	0.307													4	2	---	---	---	---	
UBE2L6	9246	broad.mit.edu	37	11	57319687	57319688	+	3'UTR	DEL	CA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57319687_57319688delCA	uc001nkn.1	-	4					UBE2L6_uc001nko.1_3'UTR	NM_004223	NP_004214	O14933	UB2L6_HUMAN	ubiquitin-conjugating enzyme E2L 6 isoform 1						negative regulation of type I interferon production	cytosol	protein binding|ubiquitin-protein ligase activity			ovary(1)	1						TTCCCTCCACCACACACACACA	0.535													4	2	---	---	---	---	
CTNND1	1500	broad.mit.edu	37	11	57496595	57496596	+	Intron	INS	-	AA	AA			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57496595_57496596insAA	uc001nlf.1	+						TMX2_uc001nlc.1_Intron|TMX2_uc001nld.1_Intron|TMX2_uc001nle.1_Intron	NM_001085462	NP_001078931	O60716	CTND1_HUMAN	catenin, delta 1 isoform 1A						adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)				cctctaaggagaaaaaaaaaag	0.000													4	2	---	---	---	---	
OSBP	5007	broad.mit.edu	37	11	59342781	59342781	+	3'UTR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59342781delC	uc001noc.1	-	14						NM_002556	NP_002547	P22059	OSBP1_HUMAN	oxysterol binding protein						lipid transport	Golgi membrane	oxysterol binding			large_intestine(1)	1		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GCAGTAGGCACCCCATGATAC	0.433													4	2	---	---	---	---	
GPHA2	170589	broad.mit.edu	37	11	64702169	64702169	+	3'UTR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64702169delG	uc001oca.2	-	4						NM_130769	NP_570125	Q96T91	GPHA2_HUMAN	glycoprotein hormone alpha 2 precursor							extracellular region	hormone activity				0						TCCAGTTTTTGAATCTTGAAC	0.493													7	5	---	---	---	---	
RELA	5970	broad.mit.edu	37	11	65422931	65422931	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65422931delT	uc001ofg.2	-						RELA_uc001ofh.2_Intron|RELA_uc010ron.1_Intron|RELA_uc009yqr.2_Intron|RELA_uc001ofe.2_3'UTR|RELA_uc001off.2_Intron	NM_021975	NP_068810	Q04206	TF65_HUMAN	v-rel reticuloendotheliosis viral oncogene						anti-apoptosis|cellular defense response|cytokine-mediated signaling pathway|defense response to virus|inflammatory response|innate immune response|interspecies interaction between organisms|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of inflammatory response|response to interleukin-1|response to UV-B|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|transcription factor complex	activating transcription factor binding|chromatin binding|identical protein binding|NF-kappaB binding|phosphate binding|protein kinase binding|protein N-terminus binding|repressing transcription factor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|ubiquitin protein ligase binding			lung(3)|ovary(1)	4						AGATTCTGCATTTTTAACTTC	0.294													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	66185457	66185458	+	IGR	DEL	AC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66185457_66185458delAC								SLC29A2 (45812 upstream) : NPAS4 (3017 downstream)																							AGTCAAATGAacacacacacac	0.396											OREG0021106	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SAPS3	55291	broad.mit.edu	37	11	68355147	68355148	+	Intron	INS	-	AG	AG			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68355147_68355148insAG	uc001onw.2	+						SAPS3_uc001onv.2_Intron|SAPS3_uc001ony.3_Intron|SAPS3_uc001onx.2_Intron|SAPS3_uc009ysh.2_Intron|SAPS3_uc001onu.2_Intron|SAPS3_uc010rqc.1_Intron|SAPS3_uc010rqd.1_Intron|SAPS3_uc001onz.2_Intron|SAPS3_uc001ooa.2_5'UTR	NM_001164161	NP_001157633	Q5H9R7	PP6R3_HUMAN	SAPS domain family, member 3 isoform 6						regulation of phosphoprotein phosphatase activity	cytoplasm|nucleus	protein phosphatase binding				0			LUAD - Lung adenocarcinoma(13;0.102)			CAATAGAGGACAGAGTGGTCAC	0.347													4	2	---	---	---	---	
DGAT2	84649	broad.mit.edu	37	11	75511694	75511694	+	3'UTR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75511694delT	uc001oxa.2	+	8					DGAT2_uc001oxb.2_3'UTR	NM_032564	NP_115953	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2						glycerol metabolic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	diacylglycerol O-acyltransferase activity				0	Ovarian(111;0.103)					ATGTTAGGTCTTTTTTAAGAA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76473774	76473774	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76473774delA								GUCY2E (40941 upstream) : TSKU (20511 downstream)																							GAGGAGTAAGAAAATGGCTTG	0.423													4	2	---	---	---	---	
RAB30	27314	broad.mit.edu	37	11	82693650	82693650	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82693650delA	uc001ozu.2	-						RAB30_uc009yve.2_Intron|RAB30_uc010rst.1_Intron|RAB30_uc001ozv.2_Intron	NM_014488	NP_055303	Q15771	RAB30_HUMAN	RAB30, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi stack|plasma membrane	GTP binding|GTPase activity				0						tcacacctgtaatcccagcac	0.129													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83449203	83449203	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83449203delG	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron	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)				GTGTTTTCCAGGGGGAGTTAA	0.428													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	84286046	84286047	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84286046_84286047insT	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.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)				tataaaacttccctggctagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	85857994	85857994	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85857994delC								PICALM (77094 upstream) : EED (97821 downstream)																							tggatcctgtcctcctgaagt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	88227127	88227127	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88227127delG								CTSC (156186 upstream) : GRM5 (10618 downstream)																							GCTAGGAAATGGGCACCAGTC	0.418													4	2	---	---	---	---	
PANX1	24145	broad.mit.edu	37	11	93883221	93883221	+	Intron	DEL	G	-	-	rs112312129		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93883221delG	uc001per.2	+						PANX1_uc001peq.2_Intron	NM_015368	NP_056183	Q96RD7	PANX1_HUMAN	pannexin 1						positive regulation of interleukin-1 beta secretion|protein hexamerization|synaptic transmission	bleb|endoplasmic reticulum membrane|gap junction|integral to membrane	calcium channel activity|gap junction hemi-channel activity|leak channel activity|receptor binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ggaagtcagtgggggaggaag	0.274													0	7	---	---	---	---	
FUT4	2526	broad.mit.edu	37	11	94274710	94274710	+	5'Flank	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94274710delC	uc001pez.2	+						PIWIL4_uc010rue.1_5'Flank	NM_002033	NP_002024	P22083	FUT4_HUMAN	fucosyltransferase 4						L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane|membrane fraction	alpha(1,3)-fucosyltransferase activity			skin(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TCGCCTACTGCCCCAGTCTTC	0.502													4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	95980376	95980376	+	Intron	DEL	A	-	-	rs75115900		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95980376delA	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)				CAGACCATGCAAAAAAAAAAT	0.378			T	MECT1|CRTC3	salivary gland mucoepidermoid								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	96762839	96762839	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96762839delC								JRKL (636112 upstream) : None (None downstream)																							TAACACAGATCCAGGAATTTA	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107024419	107024419	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107024419delT								GUCY1A2 (135248 upstream) : CWF19L2 (172655 downstream)																							cttaaagacattttttttaaa	0.000													4	2	---	---	---	---	
ATM	472	broad.mit.edu	37	11	108183414	108183415	+	Intron	DEL	CT	-	-	rs147088513		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108183414_108183415delCT	uc001pkb.1	+						ATM_uc009yxr.1_Intron|C11orf65_uc010rvx.1_Intron|ATM_uc001pke.1_Intron|ATM_uc001pkg.1_Intron|ATM_uc009yxt.1_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		ctaatactgactctgccacttC	0.178			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			3	4	---	---	---	---	
SCN2B	6327	broad.mit.edu	37	11	118047359	118047360	+	5'Flank	DEL	GA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118047359_118047360delGA	uc001psf.2	-							NM_004588	NP_004579	O60939	SCN2B_HUMAN	sodium channel, voltage-gated, type II, beta						synaptic transmission	voltage-gated sodium channel complex	voltage-gated sodium channel activity				0	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.19e-05)|Epithelial(105;0.00117)		gtgtgtaaaggagagagagaga	0.287													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	129128098	129128098	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129128098delA								ARHGAP32 (66005 upstream) : BARX2 (117783 downstream)																							CTATCATATTAAAATCTAAAC	0.289													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133402361	133402362	+	5'UTR	DEL	GC	-	-	rs7106694	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133402361_133402362delGC	uc001qgu.2	-	1						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)		GAGAGAGAGAGCGCGCGAGAGA	0.446													6	3	---	---	---	---	
KDM5A	5927	broad.mit.edu	37	12	405996	405996	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:405996delA	uc001qif.1	-						KDM5A_uc001qie.1_Intron	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						ttaggactctaaaactctatG	0.159			T 	NUP98	AML								4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2747419	2747419	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2747419delG	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	gagcagtgatggcaggcattg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	3477330	3477331	+	IGR	DEL	AG	-	-	rs146093330		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3477330_3477331delAG								TSPAN9 (81601 upstream) : PRMT8 (13184 downstream)																							AGGGAAGAACAGAGGTGGGAAC	0.455													4	4	---	---	---	---	
GDF3	9573	broad.mit.edu	37	12	7848473	7848473	+	5'Flank	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7848473delT	uc001qte.2	-							NM_020634	NP_065685	Q9NR23	GDF3_HUMAN	growth differentiation factor 3 precursor						eye development|growth|skeletal system development	extracellular space	cytokine activity|growth factor activity			skin(3)|ovary(1)|lung(1)|central_nervous_system(1)	6						GAAGAGGGAATTTTTTTTTCT	0.388													4	2	---	---	---	---	
RPL13AP20	387841	broad.mit.edu	37	12	13026020	13026020	+	5'Flank	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13026020delC	uc010sho.1	+							NR_003932				SubName: Full=Ribosomal protein L13a variant; Flags: Fragment;												0						CACCCACCCTCTACTCCCTTT	0.483													4	2	---	---	---	---	
PYROXD1	79912	broad.mit.edu	37	12	21590884	21590884	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21590884delC	uc001rew.2	+						PYROXD1_uc009ziq.2_Intron|PYROXD1_uc009zir.2_Intron	NM_024854	NP_079130	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase								oxidoreductase activity			ovary(1)	1						ACTTATTGCTCCCAGATTTTA	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	23363376	23363376	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23363376delG								ETNK1 (519769 upstream) : SOX5 (321856 downstream)																							AAAGGTTTGTGGGGGAAAGTT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	28178801	28178801	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28178801delA								PTHLH (53885 upstream) : CCDC91 (153409 downstream)																							agactctgtcaaaaaaaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30658033	30658033	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30658033delT								TMTC1 (720341 upstream) : IPO8 (123890 downstream)																							CTGTTAGTGATTTTTTTTTGG	0.338													4	2	---	---	---	---	
DENND5B	160518	broad.mit.edu	37	12	31630951	31630952	+	Intron	INS	-	T	T	rs142172766	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31630951_31630952insT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.1_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2						TAAAAAATGGATTTTTTTTTTA	0.322													11	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	43089200	43089201	+	IGR	DEL	TT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43089200_43089201delTT								PRICKLE1 (105628 upstream) : ADAMTS20 (658812 downstream)																							ggcaggaaacttaaggccattt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	43127779	43127779	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43127779delT								PRICKLE1 (144207 upstream) : ADAMTS20 (620234 downstream)																							ATTCCCGCTCTTTTTTTTCCC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	46874738	46874738	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46874738delG								SLC38A2 (108093 upstream) : SLC38A4 (283806 downstream)																							gaaggacaatgggggccagag	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47117224	47117226	+	IGR	DEL	TGC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47117224_47117226delTGC								SLC38A2 (350579 upstream) : SLC38A4 (41318 downstream)																							TAGATCCTGTTGCTGCTGCTGCT	0.384													4	2	---	---	---	---	
ATF7	11016	broad.mit.edu	37	12	53964397	53964398	+	Intron	DEL	TC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53964397_53964398delTC	uc001sdy.2	-						ATF7_uc010sok.1_Intron|ATF7_uc001sdz.2_Intron|ATF7_uc010sol.1_Intron|ATF7_uc001sea.3_Intron|ATF7_uc001seb.3_Intron	NM_001130059	NP_001123531	P17544	ATF7_HUMAN	activating transcription factor 7 isoform 1						interspecies interaction between organisms	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2						gttggtttcttctgaaggatgt	0.000													4	2	---	---	---	---	
GLS2	27165	broad.mit.edu	37	12	56866122	56866123	+	Intron	INS	-	G	G			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56866122_56866123insG	uc001slj.2	-						GLS2_uc009zos.2_Intron|GLS2_uc001slk.2_Intron|GLS2_uc009zot.2_Intron	NM_013267	NP_037399	Q9UI32	GLSL_HUMAN	glutaminase 2 precursor						cellular amino acid biosynthetic process|glutamate secretion|glutamine metabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity|protein binding			ovary(1)|central_nervous_system(1)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	AATAATCTTTTTTCCATATCCA	0.411													8	5	---	---	---	---	
SRGAP1	57522	broad.mit.edu	37	12	64303255	64303255	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64303255delT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		TTGTATGTGCTTTTTCCTTTC	0.418													4	2	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	66752609	66752610	+	Intron	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66752609_66752610insA	uc001stk.2	-						GRIP1_uc001stj.2_Intron	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TGAGAGAAGGGAAAAAATGAGA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80420949	80420949	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80420949delG								PPP1R12A (91714 upstream) : PTPRQ (417177 downstream)																							gttcctgggtgggcagaactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	91584540	91584541	+	IGR	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91584540_91584541insA								DCN (7734 upstream) : BTG1 (794325 downstream)																							GCAGTTTTATGAAAAAAAGGAA	0.322													4	2	---	---	---	---	
BTG1	694	broad.mit.edu	37	12	92495163	92495164	+	Intron	INS	-	A	A	rs56166966		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92495163_92495164insA	uc001tbv.1	-						BTG1_uc001tbw.1_Intron|BTG1_uc001tbx.1_Intron|BTG1_uc009zss.1_Intron			P62324	BTG1_HUMAN	Homo sapiens full length insert cDNA clone YW25A12.						cell migration|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of endothelial cell differentiation|positive regulation of myoblast differentiation|regulation of apoptosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|transcription cofactor activity				0		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				gaaagagaaagaagaaagaaag	0.000			T	MYC	BCLL								5	4	---	---	---	---	
MRPL42	28977	broad.mit.edu	37	12	93888549	93888550	+	Intron	INS	-	T	T	rs149836750	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93888549_93888550insT	uc001tcr.2	+						MRPL42_uc001tcq.2_Intron|MRPL42_uc001tcs.2_Intron|MRPL42_uc001tct.2_Intron	NM_172177	NP_751917	Q9Y6G3	RM42_HUMAN	mitochondrial ribosomal protein L42 isoform a						translation	mitochondrial small ribosomal subunit	structural constituent of ribosome			ovary(2)	2						agtccaaggactgattcttggg	0.025													2	5	---	---	---	---	
DRAM1	55332	broad.mit.edu	37	12	102311883	102311883	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102311883delA	uc001tix.2	+						DRAM1_uc010svv.1_Intron	NM_018370	NP_060840	Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1						apoptosis|autophagy	integral to membrane|lysosomal membrane				ovary(1)	1						CAAAGGATGTAAAAAAATTTC	0.338													4	2	---	---	---	---	
C12orf42	374470	broad.mit.edu	37	12	103749945	103749947	+	Intron	DEL	CAG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103749945_103749947delCAG	uc001tjt.2	-						C12orf42_uc001tjs.2_Intron|C12orf42_uc009zuf.1_Intron|C12orf42_uc001tju.2_Intron	NM_198521	NP_940923	Q96LP6	CL042_HUMAN	hypothetical protein LOC374470											ovary(1)|central_nervous_system(1)	2						catggcttctcagcttcctccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	110131647	110131648	+	IGR	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110131647_110131648insA								MVK (96577 upstream) : C12orf34 (20542 downstream)																							gtcgggtgcagaaaaaaaAACA	0.183													4	2	---	---	---	---	
NAA25	80018	broad.mit.edu	37	12	112504306	112504307	+	Intron	DEL	CT	-	-	rs149040836		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112504306_112504307delCT	uc001ttm.2	-						NAA25_uc001ttn.3_Intron|NAA25_uc009zvz.1_Intron|NAA25_uc009zwa.1_Intron	NM_024953	NP_079229	Q14CX7	NAA25_HUMAN	mitochondrial distribution and morphology 20							cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3						ctgctggtccctgttttcctcc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116774548	116774548	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116774548delA								MED13L (59557 upstream) : NCRNA00173 (196679 downstream)																							tcaaacaaacaaaaaaaaGAT	0.224													3	4	---	---	---	---	
SPATA13	221178	broad.mit.edu	37	13	24738376	24738376	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24738376delA	uc001upg.1	+						SPATA13_uc001upd.1_Intron|C1QTNF9_uc001upe.2_Intron|SPATA13_uc001upf.1_Intron	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		AAAGAGCAGTAAAGGGGGAGC	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	35476542	35476542	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35476542delG								RFC3 (935848 upstream) : NBEA (39914 downstream)																							TGGTGTTTGTGGGAGTTTAAA	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	39537165	39537165	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39537165delT								FREM2 (75900 upstream) : STOML3 (2898 downstream)																							TTCCAAGAGGTTTTTAAAAGG	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	39903553	39903557	+	IGR	DEL	TTTGT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39903553_39903557delTTTGT								NHLRC3 (279311 upstream) : LHFP (13473 downstream)																							TTTTCATTTCTTTGTTTTGTTTTGT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	45899581	45899581	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45899581delT								GTF2F2 (41344 upstream) : TPT1 (11723 downstream)																							agtgcaaggattaggcctaag	0.000													4	2	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	48922817	48922817	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48922817delT	uc001vcb.2	+						RB1_uc010acs.1_Intron	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(5)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TTTTTCTTAATTTTTTTTTTT	0.204		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59888030	59888030	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59888030delA								None (None upstream) : DIAPH3 (351695 downstream)																							catttcacagaaaaaaaaaga	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	64071919	64071919	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64071919delA								None (None upstream) : OR7E156P (239649 downstream)																							aatccactggaaaaaaaaatg	0.000													4	2	---	---	---	---	
C13orf34	79866	broad.mit.edu	37	13	73309572	73309573	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73309572_73309573insT	uc001viv.1	+						C13orf34_uc010thq.1_Intron|C13orf34_uc010aen.1_Intron|C13orf34_uc010thr.1_Intron|C13orf34_uc001viw.1_Intron	NM_024808	NP_079084	Q6PGQ7	BORA_HUMAN	aurora borealis						cell division|mitosis|regulation of mitosis|regulation of mitotic spindle organization|regulation of protein localization		protein kinase binding				0		Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.000227)		ATGGCTTTGTCTTTTTTTGTTA	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78383037	78383037	+	IGR	DEL	T	-	-	rs111800868		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78383037delT								SLAIN1 (44660 upstream) : EDNRB (86579 downstream)																							AATTTTAAGGTTTTTTTTTTC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	79797047	79797047	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79797047delA								RNF219 (562347 upstream) : RBM26 (97053 downstream)																							TGGATTTCACAAAAAAAAGTA	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	88811816	88811816	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88811816delG								SLITRK5 (479948 upstream) : None (None downstream)																							aatgtatgatgggcagctcag	0.000													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94121908	94121908	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94121908delT	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)				tgggtcatgcttttggtgtca	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	97700256	97700256	+	IGR	DEL	C	-	-	rs61356507		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97700256delC								OXGR1 (53652 upstream) : MBNL2 (174318 downstream)																							caaaaaaaaacaaaaacaaaa	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	104962730	104962730	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104962730delT								None (None upstream) : None (None downstream)																							gtagtgtcaaTTTTTTTTTTA	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105360908	105360908	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105360908delC								None (None upstream) : DAOA (757308 downstream)																							CATACCTGAACCCCAACAATC	0.368													4	2	---	---	---	---	
ANKRD10	55608	broad.mit.edu	37	13	111533256	111533256	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111533256delC	uc001vrn.2	-						ANKRD10_uc001vrm.2_Intron|ANKRD10_uc001vrl.2_RNA	NM_017664	NP_060134	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10											central_nervous_system(1)	1	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			ATTAAAATGACCATGGCAGCC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	21316980	21316981	+	IGR	INS	-	GA	GA	rs149443444	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21316980_21316981insGA								RNASE1 (45944 upstream) : RNASE3 (42581 downstream)																							GTGGTGTTTCTGAGAGACTTGG	0.505													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	24489715	24489715	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24489715delA								DHRS4 (14100 upstream) : DHRS4L1 (15995 downstream)																							gacatcatggaaaaaaacctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	27807933	27807934	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27807933_27807934insT	uc010amc.1	-											Homo sapiens cDNA clone IMAGE:40107853.																		tttgatcacaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	29345200	29345200	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29345200delT								C14orf23 (81201 upstream) : PRKD1 (700489 downstream)																							TTATGAATTCTTACCAGCCTT	0.333													4	2	---	---	---	---	
HECTD1	25831	broad.mit.edu	37	14	31669129	31669130	+	Intron	DEL	GA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31669129_31669130delGA	uc001wrc.1	-							NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		acaggtgcttgactctaaaatt	0.015													4	2	---	---	---	---	
SOS2	6655	broad.mit.edu	37	14	50593532	50593532	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50593532delG	uc001wxs.3	-						SOS2_uc010ans.2_Intron|SOS2_uc010tql.1_Intron	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)					agaacatgctgggggaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51903655	51903657	+	IGR	DEL	GAG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51903655_51903657delGAG								TMX1 (179285 upstream) : FRMD6 (52198 downstream)																							AGGGGAGGGAGAGGAGGATGAAG	0.163													4	2	---	---	---	---	
ERO1L	30001	broad.mit.edu	37	14	53150337	53150337	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53150337delC	uc001wzv.2	-						ERO1L_uc001wzw.2_Intron|ERO1L_uc010aof.2_Intron	NM_014584	NP_055399	Q96HE7	ERO1A_HUMAN	ERO1-like precursor						chaperone mediated protein folding requiring cofactor|electron transport chain|protein thiol-disulfide exchange|response to temperature stimulus|transport	endoplasmic reticulum lumen|endoplasmic reticulum membrane|microsome	disulfide oxidoreductase activity|flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor				0	Breast(41;0.226)					TTAAAATTATCCAATGGATGG	0.269													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57150085	57150085	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57150085delT								C14orf101 (33855 upstream) : OTX2 (117342 downstream)																							caatataaactttTTTTTTTA	0.179													4	3	---	---	---	---	
SMOC1	64093	broad.mit.edu	37	14	70356023	70356024	+	Intron	DEL	CA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70356023_70356024delCA	uc001xls.1	+						SMOC1_uc001xlt.1_Intron	NM_022137	NP_071420	Q9H4F8	SMOC1_HUMAN	secreted modular calcium-binding protein 1						cell differentiation|eye development|limb development|regulation of osteoblast differentiation|signal transduction	basement membrane	calcium ion binding			upper_aerodigestive_tract(1)|pancreas(1)	2				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GCCCATCATTCAAAAGGTTCAG	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	71848481	71848482	+	IGR	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71848481_71848482delTG								PCNX (266382 upstream) : SNORD56B (16572 downstream)																							TCTGATAGACTGTGTGTGCTGG	0.342													4	2	---	---	---	---	
NEK9	91754	broad.mit.edu	37	14	75562428	75562428	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75562428delA	uc001xrl.2	-						NEK9_uc001xrk.2_Intron	NM_033116	NP_149107	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9						cell division|mitosis	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|stomach(2)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00718)		cccaatctctaaaaaaaaatg	0.020													4	2	---	---	---	---	
TTLL5	23093	broad.mit.edu	37	14	76373489	76373490	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76373489_76373490insT	uc001xrx.2	+						TTLL5_uc001xsa.2_Intron	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)		GAGGGAACAAATTTTTTTTCAA	0.312													4	2	---	---	---	---	
VASH1	22846	broad.mit.edu	37	14	77244485	77244485	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77244485delT	uc001xst.2	+							NM_014909	NP_055724	Q7L8A9	VASH1_HUMAN	vasohibin 1						cell cycle arrest|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|negative regulation of endothelial cell proliferation	endoplasmic reticulum|extracellular space					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0283)		TGTGGGTCCCTTTTTTTTTTT	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	77447959	77447959	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77447959delA								C14orf166B (111314 upstream) : C14orf4 (42929 downstream)																							catcgaatctaagactctatt	0.189													4	2	---	---	---	---	
C14orf102	55051	broad.mit.edu	37	14	90783321	90783322	+	Intron	DEL	GC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90783321_90783322delGC	uc001xyi.1	-						C14orf102_uc001xyj.1_Intron	NM_017970	NP_060440	Q9H7Z3	CN102_HUMAN	hypothetical protein LOC55051 isoform 1								protein binding			ovary(2)|lung(1)	3		all_cancers(154;0.118)		COAD - Colon adenocarcinoma(157;0.218)		CACCTCACCTGCAAGACTTAGG	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98053196	98053197	+	IGR	DEL	AT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98053196_98053197delAT								VRK1 (705246 upstream) : C14orf64 (338750 downstream)																							TGGAGTAATAATAAAAATGTGT	0.371													4	2	---	---	---	---	
EML1	2009	broad.mit.edu	37	14	100293215	100293215	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100293215delC	uc001ygs.2	+						EML1_uc010avt.1_Intron|EML1_uc010tww.1_Intron|EML1_uc001ygq.2_Intron|EML1_uc001ygr.2_Intron	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				GAATATTCTACACAACAAAGG	0.438													4	2	---	---	---	---	
EML1	2009	broad.mit.edu	37	14	100293217	100293217	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100293217delC	uc001ygs.2	+						EML1_uc010avt.1_Intron|EML1_uc010tww.1_Intron|EML1_uc001ygq.2_Intron|EML1_uc001ygr.2_Intron	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				ATATTCTACACAACAAAGGAC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101703984	101703984	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101703984delT								MIR656 (170846 upstream) : DIO3OS (314576 downstream)																							TGCCTCCACATTTTTTTTTTT	0.323													2	4	---	---	---	---	
C14orf73	91828	broad.mit.edu	37	14	103571696	103571697	+	Intron	DEL	TG	-	-	rs113889693		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103571696_103571697delTG	uc001ymk.2	+							NM_001077594	NP_001071062	Q17RC7	EX3L4_HUMAN	hypothetical protein LOC91828												0		Melanoma(154;0.155)	Epithelial(46;0.221)			AGCTGAGGGCtgtgtgtgtgtg	0.089											OREG0022947	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	104735405	104735405	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104735405delT								KIF26A (88171 upstream) : C14orf180 (310651 downstream)																							gagttacaggtttttgaagga	0.000													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106607572	106607572	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106607572delG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						aatgtggggtgggtgctttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20867625	20867628	+	IGR	DEL	GAGT	-	-	rs61049442		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20867625_20867628delGAGT								GOLGA8C (86599 upstream) : BCL8 (2428 downstream)																							AAGAAAATAAGAGTAAGTTTAATG	0.157													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23685826	23685828	+	IGR	DEL	TCT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23685826_23685828delTCT								GOLGA8E (237403 upstream) : MKRN3 (124626 downstream)																							tgctgccacatcttcttctgctc	0.207													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23783158	23783158	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23783158delA								GOLGA8E (334735 upstream) : MKRN3 (27296 downstream)																							AAGAGAAAGGAAAAAAAATAG	0.403													4	2	---	---	---	---	
SNRPN	6638	broad.mit.edu	37	15	25179002	25179003	+	Intron	DEL	AC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25179002_25179003delAC	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron|SNRPN_uc001yws.1_Intron|SNRPN_uc001ywt.1_Intron	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		TAATTGGAAAACAGAAAGAATG	0.342									Prader-Willi_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26257481	26257482	+	IGR	DEL	AT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26257481_26257482delAT								ATP10A (147164 upstream) : GABRB3 (531213 downstream)																							attccaccacatcctttgacga	0.000													4	2	---	---	---	---	
GABRB3	2562	broad.mit.edu	37	15	26888589	26888589	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26888589delA	uc001zaz.2	-						GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	AGCAAACTCCAAAAACAACAG	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30897862	30897862	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30897862delT								FAM7A2 (4962 upstream) : ARHGAP11B (18835 downstream)																							TGCCTTTTTCTTTTTTTTTTC	0.423													6	4	---	---	---	---	
TRPM1	4308	broad.mit.edu	37	15	31369450	31369450	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31369450delG	uc001zfm.2	-						TRPM1_uc001zfn.3_Intron	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,						cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		GCACGGTTCTGGGGTGGGAGC	0.448													4	2	---	---	---	---	
OTUD7A	161725	broad.mit.edu	37	15	32032826	32032827	+	Intron	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32032826_32032827insA	uc001zfr.2	-						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)		gcataagtgagagggggaaaaa	0.149													2	4	---	---	---	---	
OTUD7A	161725	broad.mit.edu	37	15	32163486	32163486	+	5'Flank	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32163486delC	uc001zfr.2	-						OTUD7A_uc001zfs.1_5'Flank|OTUD7A_uc010baa.1_5'Flank	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)		TTTCACGCCACCCCTTCAGAT	0.507													4	2	---	---	---	---	
TUBGCP4	27229	broad.mit.edu	37	15	43693650	43693651	+	Intron	DEL	AA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43693650_43693651delAA	uc001zro.2	+						TUBGCP4_uc001zrn.2_Intron|TUBGCP4_uc010bdh.2_Intron	NM_014444	NP_055259	Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	structural constituent of cytoskeleton			ovary(3)	3		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		actccgtctcaaaaaaaaaaaa	0.203													4	2	---	---	---	---	
FRMD5	84978	broad.mit.edu	37	15	44479765	44479766	+	Intron	INS	-	T	T	rs34597404		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44479765_44479766insT	uc001ztl.2	-						FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		GCTTTTGGCAAttttttttttt	0.188													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	53325067	53325067	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53325067delT								ONECUT1 (242858 upstream) : WDR72 (480871 downstream)																							TGGTGTGGTGTTTTTTTTTCT	0.383													3	3	---	---	---	---	
UNC13C	440279	broad.mit.edu	37	15	54711982	54711982	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54711982delT	uc002ack.2	+							NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CTTTCTCACATTTTTTTGTTT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	57881076	57881076	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57881076delG								CGNL1 (38156 upstream) : GCOM1 (3038 downstream)																							GAATGGGAGAGAAAGAAAGAG	0.453													4	2	---	---	---	---	
ALDH1A2	8854	broad.mit.edu	37	15	58447900	58447900	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58447900delT	uc010ugw.1	-						AQP9_uc010ugx.1_Intron|AQP9_uc002aez.2_Intron	NM_170697	NP_733798	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 3						negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	TATTTTCACCTGATCTCCTGA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	58679808	58679810	+	IGR	DEL	AGA	-	-	rs71884092		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58679808_58679810delAGA								ALDH1A2 (108346 upstream) : LIPC (22965 downstream)																							tggcatacacagaagaacatgta	0.138													6	4	---	---	---	---	
ANXA2	302	broad.mit.edu	37	15	60678567	60678567	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60678567delC	uc002agn.2	-						ANXA2_uc002agk.2_Intron|ANXA2_uc002agl.2_Intron|ANXA2_uc002agm.2_Intron|ANXA2_uc010uhd.1_Intron|ANXA2_uc010bgj.2_Intron	NM_001136015	NP_001129487	P07355	ANXA2_HUMAN	annexin A2 isoform 2						angiogenesis|positive regulation of vesicle fusion|skeletal system development	basement membrane|melanosome|midbody|soluble fraction	calcium ion binding|calcium-dependent phospholipid binding|cytoskeletal protein binding|phospholipase inhibitor activity			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Tenecteplase(DB00031)	ACAAAATGTTCCCCATGGCTA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62776242	62776242	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62776242delC								C2CD4B (318760 upstream) : MGC15885 (153129 downstream)																							GGCCTTGCTGCCCCCAGTTTA	0.572													4	2	---	---	---	---	
HIGD2B	123346	broad.mit.edu	37	15	72970646	72970646	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72970646delT	uc002ava.2	-							NR_002780				Homo sapiens HIG1 domain family, member 2B pseudogene, mRNA (cDNA clone IMAGE:5742106).												0						ttttcttttctttttttttta	0.080													4	2	---	---	---	---	
PTPN9	5780	broad.mit.edu	37	15	75815801	75815801	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75815801delA	uc002bal.2	-							NM_002833	NP_002824	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2						CTGTGGTAAGAAAAAAAAAAC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	76078004	76078005	+	5'Flank	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76078004_76078005insT	uc002bbb.1	-											DQ577530																		TATGCTCTTGGTTTCCCACCTT	0.609													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78251471	78251472	+	IGR	INS	-	TG	TG	rs144414157	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78251471_78251472insTG								LOC645752 (32283 upstream) : LOC91450 (34104 downstream)																							TGTATCCTAGCTGTGTAATCAC	0.465											OREG0023323	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82330278	82330278	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82330278delG								TMC3 (663860 upstream) : MEX3B (3850 downstream)																							GCCGCACCACGGCAACTCCGC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88822550	88822550	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88822550delT								NTRK3 (22889 upstream) : MRPL46 (180158 downstream)																							ttgagcctccttttgcctggt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94129351	94129351	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94129351delA								RGMA (496918 upstream) : MCTP2 (645450 downstream)																							gttcattgtgaaaaaaatagg	0.154													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7189762	7189762	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7189762delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		GATTGGATTCTTTTTTTTTTA	0.408													4	3	---	---	---	---	
PDXDC1	23042	broad.mit.edu	37	16	15132211	15132212	+	Intron	INS	-	AAAGTTG	AAAGTTG	rs147448533	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15132211_15132212insAAAGTTG	uc002ddc.2	+						NTAN1_uc002ddd.2_Intron|NTAN1_uc010uzo.1_Intron	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	TTAGTAAGAAAAAAGTTGATTG	0.361													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20621035	20621035	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20621035delT								ACSM2B (33340 upstream) : ACSM1 (13524 downstream)																							GTCAAAAGTATTTTTTTTTTT	0.299													4	2	---	---	---	---	
HS3ST4	9951	broad.mit.edu	37	16	26017712	26017712	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26017712delT	uc002dof.2	+							NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)		GTTTGTTGGCTTTTTTTAAGG	0.149													4	2	---	---	---	---	
SRCAP	10847	broad.mit.edu	37	16	30725221	30725222	+	Intron	INS	-	T	T	rs71374028		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30725221_30725222insT	uc002dze.1	+						SRCAP_uc002dzf.2_Intron|SRCAP_uc002dzg.1_Intron|SRCAP_uc010bzz.1_Intron	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein						interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			CATCAAttctgttttttttttt	0.223													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33980320	33980320	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33980320delT								MIR1826 (14728 upstream) : UBE2MP1 (423482 downstream)																							ttgttggacatttgggttggt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49056530	49056530	+	IGR	DEL	T	-	-	rs34542074		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49056530delT								N4BP1 (412410 upstream) : CBLN1 (255681 downstream)																							CAATACTCCATTTTTTTAAAG	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	50429486	50429486	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50429486delT								BRD7 (26657 upstream) : NKD1 (152755 downstream)																							TTTTGTTTTGTTTTTTTTTGG	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52215964	52215964	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52215964delT								None (None upstream) : TOX3 (255954 downstream)																							cctacttcccttttgtaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58093619	58093620	+	IGR	DEL	GG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58093619_58093620delGG								MMP15 (12817 upstream) : C16orf80 (53877 downstream)																							CTTACAGGGTGGAAGGATCTGG	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64265549	64265549	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64265549delA								None (None upstream) : CDH11 (715136 downstream)																							TATTTTCAGGAAAAAAAAAAT	0.254													6	3	---	---	---	---	
SMPD3	55512	broad.mit.edu	37	16	68436159	68436160	+	Intron	DEL	TC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68436159_68436160delTC	uc002ewa.2	-							NM_018667	NP_061137	Q9NY59	NSMA2_HUMAN	neutral sphingomyelin phosphodiesterase 3						cell cycle|multicellular organismal development|sphingomyelin catabolic process	Golgi membrane|integral to membrane|plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity			skin(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	ggcctccatttctctcctctat	0.228													4	2	---	---	---	---	
ADAMTS18	170692	broad.mit.edu	37	16	77317610	77317610	+	3'UTR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77317610delT	uc002ffc.3	-	23						NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						AAATCAAAGATTTTTTTTAAA	0.433													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80944825	80944825	+	IGR	DEL	T	-	-	rs5818316		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80944825delT								CDYL2 (106650 upstream) : C16orf61 (64876 downstream)																							cttaggttcctagaacacccc	0.239													4	2	---	---	---	---	
TOM1L2	146691	broad.mit.edu	37	17	17806475	17806476	+	Intron	DEL	TC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17806475_17806476delTC	uc002grz.3	-						TOM1L2_uc002gry.3_Intron|TOM1L2_uc010vwy.1_Intron|TOM1L2_uc010cpr.2_Intron|TOM1L2_uc010vwz.1_Intron|TOM1L2_uc010vxa.1_Intron|TOM1L2_uc010vxb.1_Intron	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3						intracellular protein transport	intracellular					0	all_neural(463;0.228)					atatatagcttctctctctctc	0.010													4	2	---	---	---	---	
CCDC144NL	339184	broad.mit.edu	37	17	20769282	20769282	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20769282delT	uc002gyf.2	-						uc002gyg.1_5'Flank|uc002gyh.1_5'Flank	NM_001004306	NP_001004306	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family,												0						TCAGTTTTGGTTTGTTAAGGC	0.184													3	5	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21311089	21311090	+	Intron	INS	-	TCTT	TCTT	rs59325871		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21311089_21311090insTCTT	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	ccatccatccatccatcctatt	0.000										Prostate(3;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21548362	21548374	+	IGR	DEL	AAAAGGCCTGTGG	-	-	rs112577776	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21548362_21548374delAAAAGGCCTGTGG								C17orf51 (70631 upstream) : FAM27L (276996 downstream)																							AATGTAAGAAAAAAGGCCTGTGGGAAGGACTAT	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25303981	25303981	+	IGR	DEL	G	-	-	rs76252330		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25303981delG								None (None upstream) : WSB1 (317125 downstream)																							CTCAAGATTTGATCCCCATTA	0.308													2	5	---	---	---	---	
KSR1	8844	broad.mit.edu	37	17	25938896	25938896	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25938896delT	uc010crg.2	+						KSR1_uc002gzm.2_Intron|KSR1_uc002gzn.2_Intron	NM_014238	NP_055053	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras						Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		CCTTTCAGTCTTTTTTTTTTC	0.328													4	2	---	---	---	---	
DDX52	11056	broad.mit.edu	37	17	35993686	35993687	+	Intron	DEL	AA	-	-	rs77997237		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35993686_35993687delAA	uc002hoi.1	-						DDX52_uc002hoh.1_Intron|DDX52_uc002hoj.1_Intron	NM_007010	NP_008941	Q9Y2R4	DDX52_HUMAN	ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)				accttgtctcaaaaaaaaaaaa	0.144													3	3	---	---	---	---	
G6PC	2538	broad.mit.edu	37	17	41061695	41061695	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41061695delT	uc002icb.1	+						G6PC_uc010whf.1_Intron	NM_000151	NP_000142	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit						gluconeogenesis|glucose homeostasis|transmembrane transport	integral to endoplasmic reticulum membrane	glucose-6-phosphatase activity|phosphate binding			ovary(1)|breast(1)|kidney(1)|skin(1)	4		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		ATCTCAGAGCTTTTTACAATC	0.333									Glycogen_Storage_Disease_type_Ia				4	2	---	---	---	---	
FMNL1	752	broad.mit.edu	37	17	43314486	43314486	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43314486delA	uc002iin.2	+							NM_005892	NP_005883	O95466	FMNL_HUMAN	formin-like 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			pancreas(1)	1						ctccatcttgaaaaaaaaaat	0.065													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	47549396	47549397	+	IGR	DEL	CG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47549396_47549397delCG								PHB (57154 upstream) : NGFR (23258 downstream)																							caccatctgtcgcagcccccag	0.000													4	2	---	---	---	---	
SAMD14	201191	broad.mit.edu	37	17	48192222	48192222	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48192222delC	uc002iqg.2	-						SAMD14_uc002iqd.2_Intron|SAMD14_uc002iqe.2_Intron|SAMD14_uc002iqf.2_Intron	NM_174920	NP_777580	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14												0						TTCTCCTCTGCCCAGCTGCAC	0.299											OREG0024555	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51816924	51816924	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51816924delA								None (None upstream) : KIF2B (83315 downstream)																							AGATGAAGCTAAAAAAAAGCT	0.363													4	2	---	---	---	---	
CCDC45	90799	broad.mit.edu	37	17	62516456	62516456	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62516456delG	uc002jem.2	+						CCDC45_uc002jen.2_Intron|CCDC45_uc010wqb.1_Intron	NM_138363	NP_612372	Q96GE4	CEP95_HUMAN	coiled-coil domain containing 45							centrosome|spindle pole	protein binding				0	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			CAAGGTGTTTGGGTTTGATGT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	74970013	74970013	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74970013delC								MGAT5B (23543 upstream) : C17orf86 (114712 downstream)																							taaacattttcccccagcttt	0.025													4	2	---	---	---	---	
GCGR	2642	broad.mit.edu	37	17	79767531	79767534	+	Intron	DEL	CTGT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79767531_79767534delCTGT	uc010wuw.1	+						GCGR_uc010wuv.1_Intron|GCGR_uc010wux.1_Intron	NM_000160	NP_000151	P47871	GLR_HUMAN	glucagon receptor precursor						cellular response to glucagon stimulus|energy reserve metabolic process|regulation of blood pressure|response to nutrient	integral to membrane|plasma membrane	glucagon receptor activity				0					Glucagon recombinant(DB00040)	gcctgtctgcctgtctgtctgcct	0.005													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	94412	94412	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:94412delT								None (None upstream) : USP14 (64071 downstream)																							CTAtcttttcttttttttttt	0.139													5	3	---	---	---	---	
PTPRM	5797	broad.mit.edu	37	18	8273864	8273864	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8273864delA	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)				CAAAAGCCCCATATGGTTTGC	0.428													4	2	---	---	---	---	
KIAA0802	23255	broad.mit.edu	37	18	8716985	8716986	+	5'Flank	DEL	GG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8716985_8716986delGG	uc002knr.2	+						KIAA0802_uc002knq.2_Intron	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255												0						TTTCATCACTGGGCTGCAAGAC	0.450													4	2	---	---	---	---	
KIAA1012	22878	broad.mit.edu	37	18	29429382	29429382	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29429382delA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0						TTTTTAGGCCAAAAAAAAATA	0.264													13	6	---	---	---	---	
DTNA	1837	broad.mit.edu	37	18	32374847	32374847	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32374847delT	uc010dmn.1	+						DTNA_uc002kxu.2_Intron|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc002kxx.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dmk.1_Intron|DTNA_uc010dml.2_Intron|DTNA_uc002kyb.3_Intron|DTNA_uc010dmm.2_Intron	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						acatatctcattttacagatg	0.100													4	2	---	---	---	---	
SETBP1	26040	broad.mit.edu	37	18	42382120	42382120	+	Intron	DEL	T	-	-	rs35056117		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42382120delT	uc010dni.2	+						SETBP1_uc002lay.2_Intron	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)		GCTTCCATCATTTTTTTTGCA	0.428									Schinzel-Giedion_syndrome				4	2	---	---	---	---	
SIGLEC15	284266	broad.mit.edu	37	18	43403136	43403136	+	5'Flank	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43403136delG	uc002lbl.1	+							NM_213602	NP_998767	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15 precursor							integral to membrane					0						tcaatggggtgggagtggtgg	0.134													4	2	---	---	---	---	
HAUS1	115106	broad.mit.edu	37	18	43700206	43700206	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43700206delT	uc002lbu.2	+						HAUS1_uc002lbv.2_Intron	NM_138443	NP_612452	Q96CS2	HAUS1_HUMAN	coiled-coil domain containing 5						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole				ovary(1)	1						CTTTTCCAGCttttttttttt	0.169													3	4	---	---	---	---	
HDHD2	84064	broad.mit.edu	37	18	44663022	44663023	+	Intron	INS	-	A	A	rs2571003		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44663022_44663023insA	uc002lcs.2	-						HDHD2_uc002lct.2_Intron	NM_032124	NP_115500	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain								hydrolase activity				0						GGtttttttttaaaaaaaaaaa	0.277													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	49083366	49083366	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49083366delT	uc010xdq.1	+											Homo sapiens cDNA FLJ37617 fis, clone BRCOC2012229.																		tttgaggggattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	55206603	55206604	+	IGR	INS	-	AC	AC	rs145734344	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55206603_55206604insAC								ONECUT2 (48074 upstream) : FECH (5470 downstream)																							cacacaaacatacacacacaca	0.356													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58506578	58506578	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58506578delT								MC4R (466577 upstream) : CDH20 (494410 downstream)																							gataatagcattttttttcct	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	63601669	63601670	+	IGR	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63601669_63601670insT								CDH7 (53495 upstream) : CDH19 (569651 downstream)																							tcagggaaatattttattaagg	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	63637388	63637388	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63637388delT								CDH7 (89214 upstream) : CDH19 (533933 downstream)																							AGACTTTCACTTTTTTTTTGG	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68988673	68988673	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68988673delC								SOCS6 (991239 upstream) : None (None downstream)																							TTGCTGTCTGCCCATGCACAC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73415525	73415525	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73415525delA	uc002lmc.2	-											Homo sapiens cDNA clone IMAGE:4830327.																		GTCCATAAAGAAAAAAACAGC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73616354	73616354	+	IGR	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73616354delG								C18orf62 (476765 upstream) : ZNF516 (455265 downstream)																							AGGAAGCCCAGGGGCCACAGG	0.622													4	2	---	---	---	---	
ZNF236	7776	broad.mit.edu	37	18	74618752	74618753	+	Intron	DEL	GC	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74618752_74618753delGC	uc002lmi.2	+						ZNF236_uc002lmj.2_Intron	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236						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)		GCCTGTTGTTGCAGAGCTGCAG	0.446													4	2	---	---	---	---	
PIN1	5300	broad.mit.edu	37	19	9956668	9956668	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9956668delA	uc002mml.1	+						PIN1_uc002mmk.1_Intron|PIN1_uc002mmm.1_Intron|PIN1_uc002mmn.1_Intron	NM_006221	NP_006212	Q13526	PIN1_HUMAN	protein (peptidyl-prolyl cis/trans isomerase)						cell cycle|negative regulation of cell motility|negative regulation of ERK1 and ERK2 cascade|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of type I interferon production|positive regulation of Rho GTPase activity|positive regulation of ubiquitin-protein ligase activity|protein folding|regulation of mitosis|regulation of pathway-restricted SMAD protein phosphorylation	nucleoplasm	GTPase activating protein binding|mitogen-activated protein kinase kinase binding|peptidyl-prolyl cis-trans isomerase activity|phosphoserine binding|phosphothreonine binding			skin(1)	1						GTCCAGACAGAAGGGGGGACA	0.617													4	2	---	---	---	---	
RAD23A	5886	broad.mit.edu	37	19	13058448	13058448	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13058448delG	uc002mvw.1	+						RAD23A_uc002mvx.1_Intron|RAD23A_uc002mvz.1_Intron|RAD23A_uc002mwa.1_Intron|RAD23A_uc002mvy.1_Intron|RAD23A_uc010xmw.1_Intron	NM_005053	NP_005044	P54725	RD23A_HUMAN	UV excision repair protein RAD23 homolog A						interspecies interaction between organisms|nucleotide-excision repair|positive regulation of viral genome replication|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			central_nervous_system(1)	1						aacagcacctggcacataatg	0.085								NER					4	2	---	---	---	---	
UCA1	652995	broad.mit.edu	37	19	15944490	15944490	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15944490delA	uc002nbr.3	+							NR_015379				Homo sapiens cDNA FLJ14241 fis, clone OVARC1000533.												0						ctcctcttctaaaaaacctgc	0.000													4	2	---	---	---	---	
MYO9B	4650	broad.mit.edu	37	19	17236428	17236428	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17236428delG	uc010eak.2	+						MYO9B_uc002nfi.2_Intron|MYO9B_uc002nfj.1_Intron	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1						actin filament-based movement	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1						TCCTAGCCCTGGGAGTCCTTG	0.532													4	2	---	---	---	---	
PDE4C	5143	broad.mit.edu	37	19	18338354	18338354	+	Intron	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18338354delC	uc010xqc.1	-						PDE4C_uc002nik.3_Intron|PDE4C_uc002nil.3_Intron|PDE4C_uc002nii.3_5'Flank|PDE4C_uc010ebl.2_Intron|PDE4C_uc010xqd.1_5'Flank|PDE4C_uc002nim.1_Intron	NM_001098819	NP_001092289	Q08493	PDE4C_HUMAN	phosphodiesterase 4C isoform PDE4C-2						signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|skin(2)|central_nervous_system(1)	5					Dyphylline(DB00651)	TGGGAGGATTCCCAGAGTCTG	0.473													4	2	---	---	---	---	
ZNF493	284443	broad.mit.edu	37	19	21589141	21589141	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21589141delT	uc002npx.2	+						ZNF493_uc002npu.2_Intron|ZNF493_uc002npw.2_Intron|ZNF493_uc002npy.2_Intron	NM_175910	NP_787106	Q6ZR52	ZN493_HUMAN	zinc finger protein 493 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GCCTTTGGCATTTTTTTGTTT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	23520274	23520274	+	IGR	DEL	A	-	-	rs34046756		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23520274delA								ZNF99 (567490 upstream) : ZNF91 (1145 downstream)																							taataacttcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	32976299	32976300	+	IGR	DEL	GT	-	-	rs35801162		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32976299_32976300delGT								DPY19L3 (1063 upstream) : PDCD5 (95804 downstream)																							CGTGACAGGAgtgtgtgtgtgt	0.351													5	3	---	---	---	---	
HIPK4	147746	broad.mit.edu	37	19	40895262	40895263	+	Intron	INS	-	A	A			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40895262_40895263insA	uc002onp.2	-							NM_144685	NP_653286	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4							cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)|stomach(1)	2			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			tttaaaaaattaaaaaaaaaat	0.183													4	2	---	---	---	---	
LTBP4	8425	broad.mit.edu	37	19	41131714	41131714	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41131714delG	uc002ooh.1	+						LTBP4_uc002oog.1_Intron|LTBP4_uc002ooi.1_Intron|LTBP4_uc002ooj.1_Intron|LTBP4_uc002ook.1_Intron|LTBP4_uc002ool.1_Intron|LTBP4_uc010xvp.1_Intron	NM_001042544	NP_001036009	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding						growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCCCCTGGGAGGACCTGAGTG	0.587													4	2	---	---	---	---	
SHANK1	50944	broad.mit.edu	37	19	51216434	51216434	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51216434delG	uc002psx.1	-							NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1						cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		AGCCCATCCTGACCCTCATGT	0.552													4	2	---	---	---	---	
ZNF432	9668	broad.mit.edu	37	19	52539550	52539550	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52539550delA	uc002pyk.2	-							NM_014650	NP_055465	O94892	ZN432_HUMAN	zinc finger protein 432						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|pancreas(1)	3		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)		acgaaggaacaaaaaaagaag	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53091404	53091405	+	IGR	DEL	TG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53091404_53091405delTG								ZNF701 (3355 upstream) : ZNF137 (8532 downstream)																							AGGTCTCCCCTGTGTGTGTGTT	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	8917496	8917496	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8917496delT								PLCB1 (51951 upstream) : PLCB4 (132205 downstream)																							TTTTCTTTTCTTTTTTTTTTT	0.388													6	6	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	14281509	14281511	+	Intron	DEL	ATT	-	-	rs75929526		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14281509_14281511delATT	uc002wou.2	+						MACROD2_uc002wot.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				GTGAGCCATCATTGTCACATTAG	0.355													3	3	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19398954	19398954	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19398954delA	uc002wrl.2	+							NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						catgctgtataaaaagaacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23439885	23439886	+	IGR	DEL	GA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23439885_23439886delGA								CST11 (6403 upstream) : CST8 (31880 downstream)																							ACCTCACTTTGAATCCCTTGGG	0.292													4	2	---	---	---	---	
TMEM90B	79953	broad.mit.edu	37	20	24512059	24512059	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24512059delA	uc002wtw.1	+							NM_024893	NP_079169	Q9H7V2	SYNG1_HUMAN	transmembrane protein 90B						response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0						ATAGACTTTTAAAAAAAATCT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29584721	29584725	+	IGR	DEL	TGCTG	-	-	rs148627987	by1000genomes	TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29584721_29584725delTGCTG								None (None upstream) : FRG1B (27154 downstream)																							TGTTCATTAATGCTGTTTCTAATTT	0.351													6	3	---	---	---	---	
PIGU	128869	broad.mit.edu	37	20	33201688	33201688	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33201688delG	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron|PIGU_uc010gev.1_Intron	NM_080476	NP_536724	Q9H490	PIGU_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0						agatactgatggtggcactgc	0.000													4	2	---	---	---	---	
DLGAP4	22839	broad.mit.edu	37	20	34961731	34961731	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34961731delG	uc002xff.2	+							NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a						cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				AGTTAATAGAGGGTTTTTTTT	0.219													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36048877	36048878	+	IGR	INS	-	C	C			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36048877_36048878insC								SRC (15058 upstream) : BLCAP (96942 downstream)																							GCCCAGACTTGCCCCCAGATCG	0.639													4	2	---	---	---	---	
KIAA0406	9675	broad.mit.edu	37	20	36628269	36628269	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36628269delT	uc002xhl.2	-						KIAA0406_uc002xhm.2_Intron	NM_014657	NP_055472	O43156	TTI1_HUMAN	hypothetical protein LOC9675								binding				0		Myeloproliferative disorder(115;0.00874)				ttgttaggaattttttttatt	0.000													4	2	---	---	---	---	
LPIN3	64900	broad.mit.edu	37	20	39978357	39978357	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39978357delT	uc002xjx.2	+						LPIN3_uc010ggh.2_Intron|LPIN3_uc010zwf.1_Intron	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3						fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)				CTGGCTGGGGTGGGCAGCAGC	0.458													4	2	---	---	---	---	
STK4	6789	broad.mit.edu	37	20	43607423	43607423	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43607423delT	uc002xnb.2	+						STK4_uc010ggx.2_Intron|STK4_uc010ggy.2_Intron|STK4_uc010ggw.1_Intron	NM_006282	NP_006273	Q13043	STK4_HUMAN	serine/threonine kinase 4						apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)				TGGTGTTTTGTTttttttttt	0.154													5	3	---	---	---	---	
PREX1	57580	broad.mit.edu	37	20	47324230	47324230	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47324230delA	uc002xtw.1	-							NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CTAATAATCTAAGGAAGGCAA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59481862	59481864	+	IGR	DEL	TGA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59481862_59481864delTGA								MIR646 (598237 upstream) : CDH4 (345695 downstream)																							atgatgacactgatgatgatgat	0.034													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59644691	59644692	+	IGR	DEL	TT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59644691_59644692delTT								MIR646 (761066 upstream) : CDH4 (182867 downstream)																							TAAACCCCAGTTAAGAAAACAA	0.381													4	2	---	---	---	---	
LSM14B	149986	broad.mit.edu	37	20	60705076	60705077	+	Intron	INS	-	T	T			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60705076_60705077insT	uc010gjy.1	+						LSM14B_uc010gjx.1_Intron|LSM14B_uc002ybv.2_Intron|LSM14B_uc010gjz.1_Intron|LSM14B_uc010zzz.1_Intron	NM_144703	NP_653304	Q9BX40	LS14B_HUMAN	LSM14 homolog B						multicellular organismal development|regulation of translation	ribonucleoprotein complex					0	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			TTCCTGGGCtattttttttttt	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9443256	9443258	+	IGR	DEL	ATG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9443256_9443258delATG								None (None upstream) : None (None downstream)																							atgaaataaaatgatgaagtgaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9735165	9735166	+	Intron	DEL	AG	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9735165_9735166delAG	uc011abu.1	+											Homo sapiens, clone IMAGE:4720764, mRNA.																		CTATTCTGGAAGAAAAAAGAAC	0.431													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10714113	10714113	+	IGR	DEL	T	-	-	rs2885374		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10714113delT								None (None upstream) : TPTE (192630 downstream)																							aacagtttcctgactgatcac	0.000													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11071942	11071942	+	Intron	DEL	G	-	-	rs150796084		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11071942delG	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)		acatacacctgggagtagtaa	0.000													8	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11074016	11074017	+	Intron	INS	-	AACT	AACT	rs142631439		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11074016_11074017insAACT	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)		catgtaagaacaacaaaccaca	0.000													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11093534	11093534	+	Intron	DEL	A	-	-	rs111962813		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11093534delA	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)		GAACTTGCCTAAAGCCACATC	0.313													4	3	---	---	---	---	
TIAM1	7074	broad.mit.edu	37	21	32604955	32604955	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32604955delT	uc002yow.1	-						TIAM1_uc011adk.1_Intron|TIAM1_uc011adl.1_Intron|TIAM1_uc002yox.1_Intron	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10						CTCTCCAGGATTTAAATTCTG	0.463													4	2	---	---	---	---	
CRKL	1399	broad.mit.edu	37	22	21303368	21303368	+	Intron	DEL	G	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21303368delG	uc002ztf.2	+						CRKL_uc002ztg.1_Intron	NM_005207	NP_005198	P46109	CRKL_HUMAN	v-crk sarcoma virus CT10 oncogene homolog						JNK cascade|Ras protein signal transduction	cytosol	protein tyrosine kinase activity|SH3/SH2 adaptor activity|signal transducer activity				0	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			GGTGTGGGGTGGGGAGCTGCT	0.308													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	23042544	23042545	+	Intron	INS	-	T	T	rs146717696		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23042544_23042545insT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						ccttaaggatcggttaagatgc	0.139													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27714079	27714079	+	IGR	DEL	C	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27714079delC								MIAT (599130 upstream) : MN1 (430187 downstream)																							ATTCCTATAACCATAAAACAA	0.478													4	2	---	---	---	---	
XBP1	7494	broad.mit.edu	37	22	29194291	29194293	+	Intron	DEL	TTT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29194291_29194293delTTT	uc011akl.1	-						XBP1_uc003aec.2_5'Flank|XBP1_uc003aed.2_Intron|XBP1_uc003aef.2_Intron	NM_001079539	NP_001073007	P17861	XBP1_HUMAN	X-box binding protein 1 isoform XBP1(S)						immune response	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1						TTAGATTAACttttttttttttt	0.207													4	2	---	---	---	---	
TCN2	6948	broad.mit.edu	37	22	31019284	31019284	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31019284delA	uc003aip.1	+						TCN2_uc003aiq.1_Intron|TCN2_uc003air.1_Intron	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor						cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GACAGATTACAAAAAAAAAAA	0.239													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35773440	35773440	+	IGR	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35773440delT								TOM1 (29455 upstream) : HMOX1 (3647 downstream)																							agttctctacttttTTTgcct	0.030													4	2	---	---	---	---	
CACNG2	10369	broad.mit.edu	37	22	37012098	37012098	+	Intron	DEL	T	-	-	rs11289424		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37012098delT	uc003aps.1	-							NM_006078	NP_006069	Q9Y698	CCG2_HUMAN	voltage-dependent calcium channel gamma-2						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0						ccaaagaccctcaactcagaa	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45049109	45049110	+	IGR	INS	-	TG	TG	rs71756993		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45049109_45049110insTG								NCRNA00207 (80780 upstream) : PRR5 (15483 downstream)																							aagatgtagactgaagaaggtg	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	6286517	6286518	+	IGR	DEL	GT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6286517_6286518delGT								NLGN4X (139811 upstream) : VCX3A (165142 downstream)																							TCCCCCAGTAGTGTGTGTGAGG	0.257													4	2	---	---	---	---	
OTC	5009	broad.mit.edu	37	X	38226428	38226428	+	Intron	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38226428delA	uc004def.3	+							NM_000531	NP_000522	P00480	OTC_HUMAN	ornithine carbamoyltransferase precursor						arginine biosynthetic process|urea cycle	mitochondrial matrix|ornithine carbamoyltransferase complex	ornithine carbamoyltransferase activity			ovary(1)|breast(1)	2					L-Citrulline(DB00155)|L-Ornithine(DB00129)	aacctgtctcaaaaaaaaaaa	0.119													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	106559145	106559146	+	IGR	DEL	GA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106559145_106559146delGA								CXorf41 (71673 upstream) : PRPS1 (312508 downstream)																							TGGCATATTGGAGAGAGAGAGA	0.243													4	3	---	---	---	---	
AIFM1	9131	broad.mit.edu	37	X	129267606	129267606	+	Intron	DEL	T	-	-	rs66532248		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129267606delT	uc004evg.2	-						AIFM1_uc011mur.1_Intron|AIFM1_uc011mus.1_Intron|AIFM1_uc004evh.2_Intron|AIFM1_uc004evi.2_Intron|AIFM1_uc004evk.2_Intron	NM_004208	NP_004199	O95831	AIFM1_HUMAN	programmed cell death 8 isoform 1						activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(4)|central_nervous_system(1)	5						CCCATTTAAAttttttttttt	0.179													6	4	---	---	---	---	
NSDHL	50814	broad.mit.edu	37	X	152002904	152002904	+	Intron	DEL	T	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152002904delT	uc004fgt.1	+						NSDHL_uc004fgs.1_Intron	NM_001129765	NP_001123237	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like						cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|C-3 sterol dehydrogenase (C-4 sterol decarboxylase) activity|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity				0	Acute lymphoblastic leukemia(192;6.56e-05)				NADH(DB00157)	AGCTGGCGACTTTTTTTGTCC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	155252987	155252988	+	In_Frame_Ins	INS	-	CAGCACCAC	CAGCACCAC			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155252987_155252988insCAGCACCAC	uc004fnw.1	+	7	1602_1603	c.943_944insCAGCACCAC	c.(943-945)ACA>ACAGCACCACCA	p.315_316insAPP	uc004fnx.3_In_Frame_Ins_p.101_102insAPP	NM_182905	NP_878908			WAS protein family homolog 1																		TGGGGTactaacaccaccccca	0.530													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9931514	9931515	+	IGR	DEL	TT	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9931514_9931515delTT								TTTY22 (280660 upstream) : None (None downstream)																							tttctttatctttgacttttgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9945244	9945244	+	IGR	DEL	A	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9945244delA								TTTY22 (294390 upstream) : None (None downstream)																							agattgaaataaaaagaataa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59009655	59009656	+	IGR	INS	-	A	A	rs71218032		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59009655_59009656insA								None (None upstream) : None (None downstream)																							gatccctgatcatgccactgtg	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59011870	59011871	+	IGR	DEL	TA	-	-			TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59011870_59011871delTA								None (None upstream) : None (None downstream)																							TTAGCCACCTTATGAAAGACTT	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59022489	59022490	+	IGR	INS	-	A	A	rs28547130		TCGA-CZ-5458-01A-01D-1501-10	TCGA-CZ-5458-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59022489_59022490insA								None (None upstream) : None (None downstream)																							aaaagaaaaagaaaaaaCTCca	0.010													4	2	---	---	---	---	
