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
MTOR	2475	broad.mit.edu	37	1	11189845	11189845	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11189845G>C	uc001asd.2	-	40	5785	c.5664C>G	c.(5662-5664)TTC>TTG	p.F1888L	MTOR_uc001asc.2_Missense_Mutation_p.F93L	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	1888	FAT.				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						TGGAACGGAAGAAGCCCTGGA	0.468													33	39	---	---	---	---	PASS
KIAA1522	57648	broad.mit.edu	37	1	33236584	33236584	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33236584C>T	uc001bvv.2	+	6	1763	c.1627C>T	c.(1627-1629)CCT>TCT	p.P543S	KIAA1522_uc001bvu.1_Missense_Mutation_p.P602S|KIAA1522_uc010ohm.1_Missense_Mutation_p.P554S|KIAA1522_uc010ohn.1_Intron	NM_020888	NP_065939	Q9P206	K1522_HUMAN	hypothetical protein LOC57648	543	Pro-rich.										0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				GGCAGGTCCCCCTGCTTCCCC	0.647													4	19	---	---	---	---	PASS
MED8	112950	broad.mit.edu	37	1	43849988	43849988	+	3'UTR	SNP	G	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43849988G>T	uc001cje.1	-	8						NM_052877	NP_443109	Q96G25	MED8_HUMAN	mediator complex subunit 8 isoform 3						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ACATAGTCCTGCCTGGCAGAG	0.473													3	4	---	---	---	---	PASS
RPE65	6121	broad.mit.edu	37	1	68903915	68903915	+	Silent	SNP	G	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68903915G>C	uc001dei.1	-	10	1137	c.1083C>G	c.(1081-1083)CCC>CCG	p.P361P		NM_000329	NP_000320	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein	361					visual perception	cytoplasm|plasma membrane	all-trans-retinyl-palmitate hydrolase activity|metal ion binding|retinol isomerase activity			ovary(1)	1						CTTCAGGTTGGGGAGCCTTTC	0.348													30	108	---	---	---	---	PASS
LRRIQ3	127255	broad.mit.edu	37	1	74540469	74540469	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74540469T>C	uc001dfy.3	-	6	1065	c.873A>G	c.(871-873)ATA>ATG	p.I291M	LRRIQ3_uc001dfz.3_RNA	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	291										ovary(2)	2						CAGGATAATATATATTCTGTG	0.164													86	121	---	---	---	---	PASS
SLC44A5	204962	broad.mit.edu	37	1	76107473	76107473	+	Intron	SNP	C	G	G	rs211715	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76107473C>G	uc010oqz.1	-						SLC44A5_uc010orb.1_Intron|uc001dgv.2_RNA	NM_001130058	NP_001123530	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform B							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4						CTTTAGAGTGCAAAGAAAAAA	0.358													14	187	---	---	---	---	PASS
COL24A1	255631	broad.mit.edu	37	1	86252141	86252141	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86252141T>A	uc001dlj.2	-	48	3997	c.3955A>T	c.(3955-3957)ATC>TTC	p.I1319F	COL24A1_uc001dli.2_Missense_Mutation_p.I455F|COL24A1_uc010osd.1_Missense_Mutation_p.I619F|COL24A1_uc001dlk.2_RNA|COL24A1_uc010ose.1_RNA|COL24A1_uc010osf.1_RNA	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	1319	Collagen-like 15.				cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		CCGCCTCTGATGCCCTAAATA	0.493													6	31	---	---	---	---	PASS
TXNIP	10628	broad.mit.edu	37	1	145440274	145440274	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145440274G>A	uc001enn.3	+	5	921	c.580G>A	c.(580-582)GAG>AAG	p.E194K	NBPF10_uc001emp.3_Intron|TXNIP_uc001enm.1_Intron|TXNIP_uc010oys.1_Missense_Mutation_p.E139K	NM_006472	NP_006463	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	194					cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding			ovary(2)	2	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GCTAGGTGATGAGATTTCCAT	0.478													19	27	---	---	---	---	PASS
SYT11	23208	broad.mit.edu	37	1	155829511	155829511	+	5'UTR	SNP	C	T	T	rs3820594	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155829511C>T	uc001fmg.2	+	1					SYT11_uc010pgq.1_5'UTR|GON4L_uc001fly.1_5'Flank|GON4L_uc001flz.2_5'Flank|GON4L_uc009wrh.1_5'Flank|GON4L_uc001fma.1_5'Flank|GON4L_uc001fmc.2_5'Flank|GON4L_uc001fmd.3_5'Flank|GON4L_uc009wri.2_5'Flank	NM_152280	NP_689493	Q9BT88	SYT11_HUMAN	synaptotagmin XI							cell junction|synaptic vesicle membrane	protein binding|transporter activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;0.000162)			AGAGCTGTCTCACCATTGCAA	0.537													10	112	---	---	---	---	PASS
XPR1	9213	broad.mit.edu	37	1	180794054	180794054	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180794054A>G	uc001goi.2	+	8	1121	c.929A>G	c.(928-930)AAT>AGT	p.N310S	XPR1_uc009wxm.2_Missense_Mutation_p.N310S|XPR1_uc009wxn.2_Missense_Mutation_p.N310S	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor	310	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0						CCGAGAAGCAATTTGTCTCAT	0.383													67	239	---	---	---	---	PASS
XPR1	9213	broad.mit.edu	37	1	180849261	180849261	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180849261T>C	uc001goi.2	+	14	2050	c.1858T>C	c.(1858-1860)TGT>CGT	p.C620R	XPR1_uc009wxn.2_Missense_Mutation_p.C555R	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor	620	EXS.|Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0						TCTGAATAACTGTGGTGAATT	0.468													17	82	---	---	---	---	PASS
PCNXL2	80003	broad.mit.edu	37	1	233270864	233270864	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233270864C>G	uc001hvl.2	-	21	3967	c.3732G>C	c.(3730-3732)CAG>CAC	p.Q1244H	PCNXL2_uc001hvm.1_RNA|PCNXL2_uc009xfu.2_RNA|PCNXL2_uc001hvp.1_RNA|PCNXL2_uc009xfv.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1244	Helical; (Potential).					integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				AGTTAATAAACTGGTAAACCG	0.378													26	124	---	---	---	---	PASS
OR2L2	26246	broad.mit.edu	37	1	248202228	248202228	+	Missense_Mutation	SNP	T	C	C	rs138507569	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248202228T>C	uc001idw.2	+	1	755	c.659T>C	c.(658-660)GTT>GCT	p.V220A	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	220	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TATGGCCGGGTTCTCCTTGCT	0.512													35	148	---	---	---	---	PASS
INO80B	83444	broad.mit.edu	37	2	74682512	74682512	+	Intron	SNP	C	T	T	rs2268417	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74682512C>T	uc002slg.2	+						INO80B_uc002slf.1_Intron|INO80B_uc010yrr.1_Intron|WBP1_uc002slh.1_Intron|INO80B_uc002sli.1_Intron|INO80B_uc010yrs.1_Missense_Mutation_p.S31L	NM_031288	NP_112578	Q9C086	IN80B_HUMAN	high mobility group AT-hook 1-like 4						DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex|nucleolus	metal ion binding|protein binding			pancreas(1)	1						CAAACACTGTCGACAGGCTTT	0.498													4	18	---	---	---	---	PASS
CTNNA2	1496	broad.mit.edu	37	2	80136761	80136761	+	Silent	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80136761G>A	uc010ysh.1	+	6	899	c.894G>A	c.(892-894)AGG>AGA	p.R298R	CTNNA2_uc010yse.1_Silent_p.R298R|CTNNA2_uc010ysf.1_Silent_p.R298R|CTNNA2_uc010ysg.1_Silent_p.R298R	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	298					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						GCGAGGCCAGGTTCCGGCCGT	0.587													3	3	---	---	---	---	PASS
LOC401010	401010	broad.mit.edu	37	2	132201889	132201889	+	Missense_Mutation	SNP	C	A	A	rs2007096	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132201889C>A	uc002tst.2	-	1	579	c.113G>T	c.(112-114)AGT>ATT	p.S38I		NR_002826				SubName: Full=cDNA FLJ12694 fis, clone NT2RP1000358, highly similar to Homo sapiens mRNA; cDNA DKFZp564C186 (from clone DKFZp564C186);												0						GGCCTCAGCACTTTCCTGGTC	0.542													4	32	---	---	---	---	PASS
CXCR4	7852	broad.mit.edu	37	2	136872770	136872770	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136872770A>G	uc002tuz.2	-	2	823	c.728T>C	c.(727-729)ATC>ACC	p.I243T	CXCR4_uc002tuy.2_Missense_Mutation_p.I247T|CXCR4_uc010fnk.2_Missense_Mutation_p.I228T	NM_003467	NP_003458	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4 isoform b	243	Helical; Name=6.			VIL -> IIP (in Ref. 12; AAK29630).	activation of MAPK activity|apoptosis|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|inflammatory response|initiation of viral infection|regulation of chemotaxis|response to hypoxia|response to virus	cell leading edge|cell surface|cytoplasmic membrane-bounded vesicle|integral to membrane|plasma membrane	actin binding|C-X-C chemokine receptor activity|coreceptor activity|myosin light chain binding|ubiquitin binding|ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)	CAGGATGAGGATGACTGTGGT	0.512													30	39	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179401957	179401957	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179401957T>G	uc010zfg.1	-	305	92399	c.92175A>C	c.(92173-92175)AAA>AAC	p.K30725N	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.K24420N|TTN_uc010zfi.1_Missense_Mutation_p.K24353N|TTN_uc010zfj.1_Missense_Mutation_p.K24228N	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	31652							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCCTGTAGGTTTGTCTGGTT	0.398													21	110	---	---	---	---	PASS
SLC4A3	6508	broad.mit.edu	37	2	220502504	220502504	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220502504T>C	uc002vmp.3	+	17	3006	c.2737T>C	c.(2737-2739)TTC>CTC	p.F913L	SLC4A3_uc002vmo.3_Missense_Mutation_p.F940L|SLC4A3_uc010fwm.2_Missense_Mutation_p.F463L|SLC4A3_uc010fwn.1_Missense_Mutation_p.F422L	NM_005070	NP_005061	P48751	B3A3_HUMAN	solute carrier family 4, anion exchanger, member	913	Cytoplasmic (Potential).|Membrane (anion exchange).				bicarbonate transport	integral to plasma membrane|membrane fraction	inorganic anion exchanger activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	5		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTGCGCAAGTTCAGGAACAG	0.627													9	12	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52443568	52443568	+	Splice_Site	SNP	A	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52443568A>T	uc003ddx.2	-	3	237	c.122_splice	c.e3+1	p.G41_splice	PHF7_uc003ddy.2_5'Flank|PHF7_uc003ddz.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1						monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	p.?(1)		pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		ACAGCCACTCACCCCTGACAT	0.577			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								31	24	---	---	---	---	PASS
C3orf63	23272	broad.mit.edu	37	3	56703746	56703746	+	Silent	SNP	A	C	C	rs13094666	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56703746A>C	uc003did.3	-	5	818	c.717T>G	c.(715-717)GTT>GTG	p.V239V	C3orf63_uc003die.3_Silent_p.V239V	NM_015224	NP_056039	Q9UK61	CC063_HUMAN	retinoblastoma-associated protein 140 isoform b	239										ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)		TTTTAAAAATAACAACATCAC	0.318													9	103	---	---	---	---	PASS
KTELC1	56983	broad.mit.edu	37	3	119198873	119198873	+	Intron	SNP	G	A	A	rs4688007	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119198873G>A	uc003ecm.2	+						KTELC1_uc011biz.1_RNA|KTELC1_uc011bja.1_5'UTR	NM_152305	NP_689518	Q8NBL1	PGLT1_HUMAN	KTEL (Lys-Tyr-Glu-Leu) containing 1 precursor							endoplasmic reticulum lumen	UDP-glucosyltransferase activity				0				GBM - Glioblastoma multiforme(114;0.233)		ACTGATTTAGGACGACCTGTC	0.433													9	69	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	3	159819029	159819029	+	Intron	SNP	A	G	G	rs111766443	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159819029A>G	uc003fcw.1	-						uc003fcz.1_RNA					Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		CAAGAAGTAGAACAGACACCC	0.433													8	113	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513812	195513812	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513812T>A	uc011bto.1	-	2	5099	c.4639A>T	c.(4639-4641)ACA>TCA	p.T1547S	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)		GTGTCACCTGTGGATGCTGAG	0.582													3	3	---	---	---	---	PASS
GC	2638	broad.mit.edu	37	4	72649774	72649774	+	5'UTR	SNP	G	A	A	rs3733359	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72649774G>A	uc003hge.2	-	1					GC_uc010iie.2_5'Flank|GC_uc010iif.2_Intron	NM_000583	NP_000574	P02774	VTDB_HUMAN	vitamin D-binding protein precursor						hormone biosynthetic process|vitamin D metabolic process	cytosol|lysosomal lumen	actin binding|vitamin D binding|vitamin transporter activity			ovary(2)|upper_aerodigestive_tract(1)	3		all_hematologic(202;0.107)	Lung(101;0.148)		Cholecalciferol(DB00169)	CCTCTCTCCTGTAGGTGACCA	0.403													7	48	---	---	---	---	PASS
WDFY3	23001	broad.mit.edu	37	4	85722980	85722980	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85722980A>G	uc003hpd.2	-	17	3053	c.2645T>C	c.(2644-2646)TTA>TCA	p.L882S		NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	882						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		CAGGGATTGTAAAATATTTGC	0.443													17	47	---	---	---	---	PASS
ARHGAP24	83478	broad.mit.edu	37	4	86643155	86643155	+	Intron	SNP	A	C	C	rs17010697	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86643155A>C	uc003hpk.2	+						ARHGAP24_uc003hpi.1_3'UTR|ARHGAP24_uc003hpj.2_Intron	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		TGATTAAATTATTGTCATCCT	0.378													8	110	---	---	---	---	PASS
PTPN13	5783	broad.mit.edu	37	4	87662898	87662898	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87662898G>C	uc003hpz.2	+	16	2896	c.2416G>C	c.(2416-2418)GAA>CAA	p.E806Q	PTPN13_uc003hpy.2_Missense_Mutation_p.E806Q|PTPN13_uc003hqa.2_Missense_Mutation_p.E806Q|PTPN13_uc003hqb.2_Missense_Mutation_p.E806Q	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	806	FERM.					cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CCTTGTGTTTGAAGTTCACAA	0.403													75	105	---	---	---	---	PASS
HSPA4L	22824	broad.mit.edu	37	4	128732596	128732596	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128732596C>A	uc003ifm.2	+	12	1636	c.1383C>A	c.(1381-1383)AGC>AGA	p.S461R	HSPA4L_uc010iny.1_Missense_Mutation_p.S420R|HSPA4L_uc011cgr.1_Missense_Mutation_p.S428R	NM_014278	NP_055093	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	461					protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4						CTTAAGGGAGCTTCACTATTC	0.368													94	147	---	---	---	---	PASS
SPOCK3	50859	broad.mit.edu	37	4	167675635	167675635	+	Intron	SNP	G	A	A	rs2305593	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167675635G>A	uc003iri.1	-						SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjq.1_Intron|SPOCK3_uc011cjr.1_Intron|SPOCK3_uc003irj.1_Intron|SPOCK3_uc011cjs.1_Intron|SPOCK3_uc011cjt.1_Intron|SPOCK3_uc011cju.1_Intron|SPOCK3_uc011cjv.1_Intron|SPOCK3_uc003irk.3_3'UTR	NM_016950	NP_058646	Q9BQ16	TICN3_HUMAN	testican 3 isoform 2						signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		AACTATTTGCGTCTGTAAGGG	0.333													4	41	---	---	---	---	PASS
EGFLAM	133584	broad.mit.edu	37	5	38427225	38427225	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38427225G>A	uc003jlc.1	+	14	2249	c.1925G>A	c.(1924-1926)CGG>CAG	p.R642Q	EGFLAM_uc003jlb.1_Missense_Mutation_p.R642Q|EGFLAM_uc003jle.1_Missense_Mutation_p.R408Q|EGFLAM_uc003jlf.1_Missense_Mutation_p.R8Q	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G	642	Laminin G-like 2.					cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					ATCACATTTCGGCCAGACTCA	0.522													8	45	---	---	---	---	PASS
SLCO4C1	353189	broad.mit.edu	37	5	101597678	101597678	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101597678A>G	uc003knm.2	-	5	1246	c.959T>C	c.(958-960)CTA>CCA	p.L320P		NM_180991	NP_851322	Q6ZQN7	SO4C1_HUMAN	solute carrier organic anion transporter family,	320	Helical; Name=6; (Potential).				cell differentiation|multicellular organismal development|sodium-independent organic anion transport|spermatogenesis	basolateral plasma membrane|integral to membrane	sodium-independent organic anion transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		GATCCATGATAGAAGAAACCC	0.373													102	221	---	---	---	---	PASS
HIST1H2AA	221613	broad.mit.edu	37	6	25726774	25726774	+	5'UTR	SNP	A	C	C	rs4711095	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25726774A>C	uc003nfc.2	-	1					HIST1H2BA_uc003nfd.2_5'Flank	NM_170745	NP_734466	Q96QV6	H2A1A_HUMAN	histone cluster 1, H2aa						nucleosome assembly	nucleosome|nucleus	DNA binding				0						ATCAAATTGCAGCAACACGAG	0.517													16	253	---	---	---	---	PASS
TMEM63B	55362	broad.mit.edu	37	6	44107238	44107238	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44107238G>A	uc003owr.2	+	7	506	c.442G>A	c.(442-444)GCC>ACC	p.A148T	TMEM63B_uc003owq.1_Missense_Mutation_p.A148T|TMEM63B_uc010jyy.1_Missense_Mutation_p.A51T|TMEM63B_uc003ows.2_Missense_Mutation_p.A51T|TMEM63B_uc010jyz.2_5'Flank	NM_018426	NP_060896	Q5T3F8	TM63B_HUMAN	transmembrane protein 63B	148						integral to membrane	nucleotide binding|protein binding			pancreas(2)|central_nervous_system(1)	3	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			TGGGGGCGATGCCGTGCACTA	0.582													12	47	---	---	---	---	PASS
TDRD6	221400	broad.mit.edu	37	6	46661744	46661744	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46661744A>T	uc003oyj.2	+	1	5879	c.5879A>T	c.(5878-5880)CAT>CTT	p.H1960L	TDRD6_uc010jze.2_Missense_Mutation_p.H1954L	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	1960					cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)|skin(1)	6			Lung(136;0.192)			TTGCATCTACATGGAGCAGAT	0.393													86	101	---	---	---	---	PASS
ANKRD6	22881	broad.mit.edu	37	6	90340734	90340734	+	3'UTR	SNP	G	A	A	rs9344950	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90340734G>A	uc003pni.3	+	16					ANKRD6_uc003pne.3_3'UTR|ANKRD6_uc003pnf.3_3'UTR|ANKRD6_uc011dzy.1_3'UTR|ANKRD6_uc010kcd.2_3'UTR|LYRM2_uc010kce.1_Intron|LYRM2_uc003png.2_Intron|ANKRD6_uc003pnh.3_3'UTR|LYRM2_uc010kcf.1_Intron|ANKRD6_uc003pnj.3_3'UTR	NM_014942	NP_055757	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6								protein binding			ovary(2)|pancreas(1)	3		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		CACCAATAAAGAGGAAATATG	0.363													4	10	---	---	---	---	PASS
SYNJ2	8871	broad.mit.edu	37	6	158517224	158517224	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158517224G>A	uc003qqx.1	+	27	4394	c.4319G>A	c.(4318-4320)GGA>GAA	p.G1440E	SYNJ2_uc003qqy.1_Missense_Mutation_p.G1153E|SYNJ2_uc003qqz.1_Missense_Mutation_p.G1057E|SYNJ2_uc003qra.1_Missense_Mutation_p.G783E|SYNJ2_uc010kjp.1_Missense_Mutation_p.G323E	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	1440	Catalytic (By similarity).						nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		TTGGACTCAGGAACCAGGAGC	0.502													8	18	---	---	---	---	PASS
AQP1	358	broad.mit.edu	37	7	30963232	30963232	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30963232G>A	uc003tbv.1	+	4	855	c.798G>A	c.(796-798)ATG>ATA	p.M266I	AQP1_uc011kac.1_Missense_Mutation_p.M326I|AQP1_uc010kwf.1_Missense_Mutation_p.M183I|AQP1_uc010kwg.1_Missense_Mutation_p.M147I|AQP1_uc010kwh.1_Missense_Mutation_p.M215I	NM_198098	NP_932766	P29972	AQP1_HUMAN	aquaporin 1	266	Cytoplasmic.				ammonium transport|cell volume homeostasis|cellular hyperosmotic response|cellular response to cAMP|cellular response to copper ion|cellular response to dexamethasone stimulus|cellular response to hydrogen peroxide|cellular response to hypoxia|cellular response to mechanical stimulus|cellular response to mercury ion|cellular response to nitric oxide|cellular response to retinoic acid|cellular response to salt stress|cellular response to UV|cerebrospinal fluid secretion|cGMP biosynthetic process|establishment or maintenance of actin cytoskeleton polarity|lateral ventricle development|maintenance of symbiont-containing vacuole via substance secreted by host|negative regulation of apoptosis|odontogenesis|pancreatic juice secretion|positive regulation of angiogenesis|positive regulation of fibroblast proliferation|positive regulation of saliva secretion|renal water transport|response to drug|transepithelial water transport	apical plasma membrane|basal plasma membrane|brush border membrane|cytoplasm|integral to plasma membrane|nuclear membrane|sarcolemma|symbiont-containing vacuole	ammonia transmembrane transporter activity|carbon dioxide transmembrane transporter activity|glycerol transmembrane transporter activity|intracellular cGMP activated cation channel activity|nitric oxide transmembrane transporter activity|potassium channel activity|potassium ion transmembrane transporter activity|protein binding|water channel activity				0		Melanoma(862;0.16)			Acetazolamide(DB00819)	GGGTGGAGATGAAGCCCAAAT	0.632													5	37	---	---	---	---	PASS
TNS3	64759	broad.mit.edu	37	7	47384598	47384598	+	Silent	SNP	G	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47384598G>T	uc003tnv.2	-	19	2857	c.2490C>A	c.(2488-2490)ATC>ATA	p.I830I	TNS3_uc003tnw.2_Silent_p.I830I	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3	830						focal adhesion	protein binding			ovary(4)	4						TTCTGCCATCGATAATATCGA	0.478													32	58	---	---	---	---	PASS
ABCB1	5243	broad.mit.edu	37	7	87196210	87196210	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87196210C>A	uc003uiz.1	-	7	839	c.421G>T	c.(421-423)GGA>TGA	p.G141*	ABCB1_uc011khc.1_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	141	ABC transmembrane type-1 1.				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	ATTTGTCTTCCAGCTGCCAGG	0.433													37	183	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91631974	91631974	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91631974T>A	uc003ulg.2	+	8	2968	c.2743T>A	c.(2743-2745)TCT>ACT	p.S915T	AKAP9_uc003ule.2_Missense_Mutation_p.S927T|AKAP9_uc003ulf.2_Missense_Mutation_p.S915T|AKAP9_uc003uli.2_Missense_Mutation_p.S540T	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	927	Glu-rich.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AATGAAAAGTTCTGTCTTTGA	0.313			T	BRAF	papillary thyroid								38	59	---	---	---	---	PASS
CCDC132	55610	broad.mit.edu	37	7	92970752	92970752	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92970752A>G	uc003umo.2	+	23	2200	c.2072A>G	c.(2071-2073)GAT>GGT	p.D691G	CCDC132_uc003umq.2_RNA|CCDC132_uc003ump.2_Missense_Mutation_p.D661G|CCDC132_uc003umr.2_RNA|CCDC132_uc011khz.1_Missense_Mutation_p.D411G	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a	691											0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			GTTTCAGCTGATCCTACTGCC	0.383													71	131	---	---	---	---	PASS
ZNF394	84124	broad.mit.edu	37	7	99091034	99091034	+	3'UTR	SNP	C	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99091034C>A	uc003uqs.2	-	3					ZNF394_uc003uqt.2_3'UTR	NM_032164	NP_115540	Q53GI3	ZN394_HUMAN	zinc finger protein 394						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					catgcaccaccatgcccggct	0.000													3	2	---	---	---	---	PASS
GIGYF1	64599	broad.mit.edu	37	7	100281055	100281055	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100281055T>A	uc003uwg.1	-	18	3074	c.2065A>T	c.(2065-2067)AGA>TGA	p.R689*		NM_022574	NP_072096	O75420	PERQ1_HUMAN	PERQ amino acid rich, with GYF domain 1	689										large_intestine(1)|central_nervous_system(1)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					TCCACTTCTCTGCGCTCCTGG	0.667													10	14	---	---	---	---	PASS
PRKRIP1	79706	broad.mit.edu	37	7	102065632	102065632	+	3'UTR	SNP	T	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102065632T>C	uc003uzh.2	+	6					PRKRIP1_uc003uzf.2_3'UTR|PRKRIP1_uc003uzg.2_3'UTR|PRKRIP1_uc011kkq.1_3'UTR|PRKRIP1_uc011kkr.1_Silent_p.S188S|PRKRIP1_uc003uzi.1_3'UTR	NM_024653	NP_078929	Q9H875	PKRI1_HUMAN	PRKR interacting protein 1 (IL11 inducible)							nucleolus				ovary(1)	1						TGTTTGGCTCTTTCTCCCCCG	0.607													7	6	---	---	---	---	PASS
PNPLA8	50640	broad.mit.edu	37	7	108155935	108155935	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108155935T>C	uc003vff.1	-	4	408	c.1A>G	c.(1-3)ATG>GTG	p.M1V	PNPLA8_uc003vfg.1_RNA|PNPLA8_uc003vfh.1_Missense_Mutation_p.M1V|PNPLA8_uc003vfi.1_Intron|PNPLA8_uc003vfj.1_Missense_Mutation_p.M1V|PNPLA8_uc003vfk.1_Intron	NM_015723	NP_056538	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	1					fatty acid metabolic process|lipid catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|membrane fraction|perinuclear region of cytoplasm|peroxisomal membrane	ATP binding|calcium-independent phospholipase A2 activity|lysophospholipase activity			breast(2)	2						TTAATAGACATAACTTAAAAA	0.323													9	20	---	---	---	---	PASS
ZNF800	168850	broad.mit.edu	37	7	127013601	127013601	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127013601T>C	uc003vlx.1	-	5	2052	c.1789A>G	c.(1789-1791)AGT>GGT	p.S597G	ZNF800_uc003vlw.1_Missense_Mutation_p.S500G|ZNF800_uc003vly.1_Missense_Mutation_p.S597G|ZNF800_uc010lla.2_Missense_Mutation_p.S597G	NM_176814	NP_789784	Q2TB10	ZN800_HUMAN	zinc finger protein 800	597					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						TACTTTTTACTAGGAGAGTTA	0.363													70	365	---	---	---	---	PASS
MKLN1	4289	broad.mit.edu	37	7	131155588	131155588	+	Intron	SNP	G	T	T	rs1733861	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131155588G>T	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_Intron|MKLN1_uc003vqs.2_Intron|MKLN1_uc003vqu.2_Intron|MKLN1_uc003vqv.1_RNA	NM_013255	NP_037387	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)					TTATCCTTGTGTACATTTTCT	0.348													14	186	---	---	---	---	PASS
EPHA1	2041	broad.mit.edu	37	7	143097036	143097036	+	Silent	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143097036G>A	uc003wcz.2	-	4	630	c.543C>T	c.(541-543)CTC>CTT	p.L181L		NM_005232	NP_005223	P21709	EPHA1_HUMAN	ephrin receptor EphA1 precursor	181	Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(3)|lung(1)|breast(1)	5	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				AAGCGAGGTAGAGGCCACGGC	0.622													11	9	---	---	---	---	PASS
GATA4	2626	broad.mit.edu	37	8	11615820	11615820	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11615820A>C	uc003wuc.2	+	7	1719	c.1165A>C	c.(1165-1167)ATG>CTG	p.M389L	GATA4_uc003wub.1_Missense_Mutation_p.M183L|GATA4_uc011kxc.1_Missense_Mutation_p.M390L|uc003wud.1_5'Flank	NM_002052	NP_002043	P43694	GATA4_HUMAN	GATA binding protein 4	389					atrial septum primum morphogenesis|atrial septum secundum morphogenesis|blood coagulation|cardiac right ventricle morphogenesis|cell-cell signaling|embryonic foregut morphogenesis|embryonic heart tube anterior/posterior pattern formation|endocardial cushion development|endoderm development|heart looping|intestinal epithelial cell differentiation|male gonad development|positive regulation of angiogenesis|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|response to drug|transcription from RNA polymerase II promoter|ventricular septum development	nucleoplasm	activating transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		AGTCAGTGCGATGTCTGGCCA	0.622													6	9	---	---	---	---	PASS
PENK	5179	broad.mit.edu	37	8	57354188	57354188	+	Silent	SNP	C	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57354188C>T	uc003xsz.2	-	2	528	c.447G>A	c.(445-447)TCG>TCA	p.S149S	PENK_uc003xta.3_Silent_p.S149S	NM_006211	NP_006202	P01210	PENK_HUMAN	proenkephalin	149					neuropeptide signaling pathway	extracellular region	neuropeptide hormone activity|opioid peptide activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_lung(136;0.229)	Epithelial(17;0.000873)|all cancers(17;0.0069)			AATTGGCCAGCGAGTCGTCCT	0.532													40	43	---	---	---	---	PASS
KLF9	687	broad.mit.edu	37	9	73027890	73027890	+	Silent	SNP	T	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73027890T>C	uc004aht.2	-	1	1684	c.390A>G	c.(388-390)GGA>GGG	p.G130G		NM_001206	NP_001197	Q13886	KLF9_HUMAN	Kruppel-like factor 9	130					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TCGCAGCCACTCCAGGATGGA	0.607													3	11	---	---	---	---	PASS
SIRT3	23410	broad.mit.edu	37	11	216647	216647	+	3'UTR	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:216647G>A	uc001lok.3	-	7					SIRT3_uc010qvl.1_5'Flank|SIRT3_uc001loj.3_3'UTR|SIRT3_uc010qvm.1_3'UTR|SIRT3_uc010qvn.1_3'UTR|SIRT3_uc010qvo.1_3'UTR|SIRT3_uc010qvp.1_3'UTR|SIRT3_uc010qvq.1_3'UTR	NM_012239	NP_036371	Q9NTG7	SIRT3_HUMAN	sirtuin 3 isoform a						chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding			urinary_tract(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		TCAGAATTGGGATGTGGATGT	0.488													21	110	---	---	---	---	PASS
OR52J3	119679	broad.mit.edu	37	11	5068157	5068157	+	Silent	SNP	C	T	T	rs149427006		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5068157C>T	uc010qyv.1	+	1	402	c.402C>T	c.(400-402)TAC>TAT	p.Y134Y		NM_001001916	NP_001001916	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J,	134	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|lung(1)|skin(1)	3		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		CACTACATTACGCAACCATCT	0.488													31	123	---	---	---	---	PASS
SLC39A13	91252	broad.mit.edu	37	11	47433931	47433931	+	Silent	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47433931G>A	uc009ylq.2	+	4	621	c.450G>A	c.(448-450)CAG>CAA	p.Q150Q	SLC39A13_uc001nfd.2_Silent_p.Q150Q|SLC39A13_uc001nfe.1_RNA|SLC39A13_uc001nff.3_Silent_p.Q150Q|SLC39A13_uc001nfg.3_Silent_p.Q150Q	NM_001128225	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter),	150	Helical; (Potential).|Poly-Gln.				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				Lung(87;0.0936)		AGCAGCAACAGCTGGGGCTGT	0.547											OREG0020959	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	20	---	---	---	---	PASS
SNX32	254122	broad.mit.edu	37	11	65617711	65617711	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65617711G>C	uc001ofr.2	+	4	470	c.343G>C	c.(343-345)GAG>CAG	p.E115Q	SNX32_uc009yqt.2_3'UTR|SNX32_uc010rop.1_Missense_Mutation_p.K154N	NM_152760	NP_689973	Q86XE0	SNX32_HUMAN	sorting nexin 6B	115	PX.				cell communication|protein transport		phosphatidylinositol binding				0				READ - Rectum adenocarcinoma(159;0.171)		CACTCGGGAAGAGTTTGCCAA	0.577													12	26	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	103024178	103024178	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103024178G>T	uc001pho.2	+	22	3387	c.3243G>T	c.(3241-3243)AAG>AAT	p.K1081N	DYNC2H1_uc001phn.1_Missense_Mutation_p.K1081N|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1081	Potential.|Stem (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AAAGTGCAAAGTTAATAAAAG	0.303													22	174	---	---	---	---	PASS
RAB39	54734	broad.mit.edu	37	11	107833105	107833105	+	3'UTR	SNP	A	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107833105A>C	uc001pjt.2	+	2						NM_017516	NP_059986	Q14964	RB39A_HUMAN	RAB39, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0				BRCA - Breast invasive adenocarcinoma(274;3.04e-05)|Epithelial(105;8.56e-05)|all cancers(92;0.00179)		CTGACTTCAAACATGCTGAAG	0.398													11	38	---	---	---	---	PASS
USP2	9099	broad.mit.edu	37	11	119229962	119229962	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119229962G>A	uc001pwm.3	-	5	1335	c.1040C>T	c.(1039-1041)GCA>GTA	p.A347V	USP2_uc001pwl.3_Missense_Mutation_p.A138V|USP2_uc001pwn.3_Missense_Mutation_p.A104V	NM_004205	NP_004196	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2 isoform a	347					cell cycle|muscle organ development|negative regulation of transcription from RNA polymerase II promoter|positive regulation of mitotic cell cycle|protein deubiquitination|protein stabilization|ubiquitin-dependent protein catabolic process	nucleus|perinuclear region of cytoplasm	cyclin binding|cysteine-type endopeptidase activity|metal ion binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity			ovary(2)|urinary_tract(1)|skin(1)	4		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		AAAGCGCGGTGCGTATCTCTG	0.498													42	80	---	---	---	---	PASS
VWA5A	4013	broad.mit.edu	37	11	124016740	124016740	+	3'UTR	SNP	A	T	T	rs9326269	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124016740A>T	uc001pzu.2	+	19					VWA5A_uc001pzt.2_3'UTR	NM_001130142	NP_001123614	O00534	VMA5A_HUMAN	BCSC-1 isoform 1											upper_aerodigestive_tract(1)|ovary(1)	2						GTTCTTGTGTATTATAACTCT	0.363													6	56	---	---	---	---	PASS
OR8B3	390271	broad.mit.edu	37	11	124266328	124266328	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124266328A>T	uc010saj.1	-	1	920	c.920T>A	c.(919-921)ATT>AAT	p.I307N	OR8B2_uc001qab.3_Intron	NM_001005467	NP_001005467	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B,	307	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		TCTTCTCTGAATTTTAATCAG	0.328													24	51	---	---	---	---	PASS
DDX12	440081	broad.mit.edu	37	12	9574042	9574042	+	Missense_Mutation	SNP	C	A	A	rs7298124	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9574042C>A	uc010sgs.1	-	20	2189	c.1994G>T	c.(1993-1995)AGC>ATC	p.S665I	DDX12_uc001qvx.3_5'Flank|DDX12_uc001qvy.1_5'Flank	NM_004400	NP_004391			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12												0						GGAGACCCCGCTGCAGATGAC	0.592													7	46	---	---	---	---	PASS
WBP11	51729	broad.mit.edu	37	12	14943401	14943401	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14943401C>A	uc001rci.2	-	10	1459	c.1298G>T	c.(1297-1299)GGT>GTT	p.G433V		NM_016312	NP_057396	Q9Y2W2	WBP11_HUMAN	WW domain binding protein 11	433	Pro-rich.				mRNA processing|RNA splicing|rRNA processing	cytoplasm	single-stranded DNA binding|WW domain binding			ovary(1)|lung(1)	2						TGGAGGTGGACCAGGAGGAAG	0.463													18	40	---	---	---	---	PASS
ANKRD33	341405	broad.mit.edu	37	12	52282005	52282005	+	5'UTR	SNP	C	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52282005C>T	uc001rzf.3	+	1					ANKRD33_uc001rzh.3_Missense_Mutation_p.S12F|ANKRD33_uc001rzd.2_Missense_Mutation_p.S12F|ANKRD33_uc001rze.2_5'UTR|ANKRD33_uc001rzg.3_5'UTR|ANKRD33_uc001rzi.3_5'UTR	NM_001130015	NP_001123487	Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33 isoform 1												0				BRCA - Breast invasive adenocarcinoma(357;0.0969)		TGCGTTGCTTCCTGGGGAGGG	0.607													26	49	---	---	---	---	PASS
CCT2	10576	broad.mit.edu	37	12	69985846	69985846	+	Silent	SNP	G	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69985846G>T	uc001svb.1	+	8	751	c.657G>T	c.(655-657)CTG>CTT	p.L219L	CCT2_uc009zrm.1_RNA|CCT2_uc009zrn.1_Silent_p.L219L|CCT2_uc010stl.1_Silent_p.L172L	NM_006431	NP_006422	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2	219					'de novo' posttranslational protein folding	nucleus	ATP binding|unfolded protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			TAGGCTTCCTGTTGGATAAAA	0.284													25	100	---	---	---	---	PASS
MGAT4C	25834	broad.mit.edu	37	12	86383258	86383258	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86383258G>A	uc001tai.3	-	6	1317	c.67C>T	c.(67-69)CGT>TGT	p.R23C	MGAT4C_uc001tal.3_Missense_Mutation_p.R23C|MGAT4C_uc001taj.3_Missense_Mutation_p.R23C|MGAT4C_uc001tak.3_Missense_Mutation_p.R23C|MGAT4C_uc010sum.1_Missense_Mutation_p.R47C|MGAT4C_uc001tah.3_Missense_Mutation_p.R23C	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein	23	Cytoplasmic (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						ACTGTAGAACGTTTTCTCAGG	0.323													72	114	---	---	---	---	PASS
PLEKHG7	440107	broad.mit.edu	37	12	93131203	93131203	+	5'UTR	SNP	A	C	C	rs2036553	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93131203A>C	uc001tcj.2	+	2						NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1						CTCCCGACCGATCAATTAGAC	0.413													15	235	---	---	---	---	PASS
ACACB	32	broad.mit.edu	37	12	109689927	109689927	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109689927A>T	uc001tob.2	+	42	5986	c.5867A>T	c.(5866-5868)CAC>CTC	p.H1956L	ACACB_uc001toc.2_Missense_Mutation_p.H1956L|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Missense_Mutation_p.H622L	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	1956	Carboxyltransferase.				acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	GAGAATTCCCACATCATCCTC	0.562													21	38	---	---	---	---	PASS
PIWIL1	9271	broad.mit.edu	37	12	130845828	130845828	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130845828C>A	uc001uik.2	+	15	1859	c.1769C>A	c.(1768-1770)ACC>AAC	p.T590N	PIWIL1_uc001uij.1_Missense_Mutation_p.T590N	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	590	RNA-binding (By similarity).|Piwi.				gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|P granule	mRNA binding|piRNA binding|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		GTGGCCCGAACCTTAGGCAAA	0.488													54	87	---	---	---	---	PASS
OXA1L	5018	broad.mit.edu	37	14	23240790	23240790	+	3'UTR	SNP	G	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23240790G>C	uc001wgn.2	+	10					OXA1L_uc001wgo.2_RNA|OXA1L_uc010akc.2_3'UTR|OXA1L_uc001wgp.2_3'UTR|OXA1L_uc001wgq.2_3'UTR	NM_005015	NP_005006	Q15070	OXA1L_HUMAN	oxidase (cytochrome c) assembly 1-like						aerobic respiration|mitochondrial proton-transporting ATP synthase complex assembly|mitochondrial respiratory chain complex I assembly|negative regulation of ATPase activity|negative regulation of oxidoreductase activity|protein insertion into membrane|protein tetramerization	integral to mitochondrial membrane|mitochondrial respiratory chain|protein complex	protein homodimerization activity|ribosome binding			central_nervous_system(1)	1	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.0096)		GCGCATTCTGGCAGGAATTCT	0.478													22	50	---	---	---	---	PASS
DHRS1	115817	broad.mit.edu	37	14	24760009	24760009	+	3'UTR	SNP	G	A	A	rs4568	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24760009G>A	uc001woj.1	-	9					DHRS1_uc010aln.1_RNA|DHRS1_uc001wok.2_3'UTR	NM_138452	NP_612461	Q96LJ7	DHRS1_HUMAN	dehydrogenase/reductase (SDR family) member 1							endoplasmic reticulum	binding|oxidoreductase activity				0				GBM - Glioblastoma multiforme(265;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(311;0.0442)		GAGACAGGACGAACCACCAAG	0.512													4	36	---	---	---	---	PASS
LRFN5	145581	broad.mit.edu	37	14	42360818	42360818	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42360818C>T	uc001wvm.2	+	4	2949	c.1751C>T	c.(1750-1752)ACG>ATG	p.T584M	LRFN5_uc010ana.2_Intron	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	584	Cytoplasmic (Potential).					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TGTAGTGTAACGCTGCCCCAG	0.453										HNSCC(30;0.082)			17	38	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64565582	64565582	+	Intron	SNP	T	C	C	rs9323444	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64565582T>C	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc010apx.1_Missense_Mutation_p.S534P|SYNE2_uc010apz.1_Intron	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TAGAACCAGATCTCTAAAAGA	0.333													8	113	---	---	---	---	PASS
GALC	2581	broad.mit.edu	37	14	88429662	88429662	+	Intron	SNP	G	A	A	rs59068116	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88429662G>A	uc001xvt.2	-						GALC_uc010tvw.1_Intron|GALC_uc010tvx.1_Intron|GALC_uc010tvy.1_Intron|GALC_uc010tvz.1_Intron|GALC_uc001xvu.1_3'UTR	NM_000153	NP_000144	P54803	GALC_HUMAN	galactosylceramidase isoform a precursor						carbohydrate metabolic process|galactosylceramide catabolic process	lysosome	cation binding|galactosylceramidase activity				0						aaagtattcagttttatattt	0.154													6	78	---	---	---	---	PASS
NDUFB1	4707	broad.mit.edu	37	14	92582472	92582472	+	3'UTR	SNP	G	A	A	rs13350	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92582472G>A	uc001yaf.2	-	3						NM_004545	NP_004536	O75438	NDUB1_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.205)	NADH(DB00157)	AGACATTTCAGATTCTTCATG	0.274													7	114	---	---	---	---	PASS
DIO3	1735	broad.mit.edu	37	14	102028537	102028537	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102028537G>T	uc010txq.1	+	2	850	c.626G>T	c.(625-627)GGT>GTT	p.G209V	DIO3OS_uc001ykd.1_5'Flank|uc001yke.2_5'Flank|uc001ykf.2_5'Flank|uc001ykg.2_5'Flank|uc001ykh.3_5'Flank|MIR1247_hsa-mir-1247|MI0006382_5'Flank	NM_001362	NP_001353	P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III	209	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process	endosome membrane|integral to membrane|plasma membrane	thyroxine 5'-deiodinase activity|thyroxine 5-deiodinase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		all_neural(303;0.185)				CTGCAGCAAGGTGCACCCGGC	0.647													4	11	---	---	---	---	PASS
TGM5	9333	broad.mit.edu	37	15	43531237	43531237	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43531237G>A	uc001zrd.1	-	9	1131	c.1123C>T	c.(1123-1125)CCT>TCT	p.P375S	TGM5_uc001zrc.1_Missense_Mutation_p.P32S|TGM5_uc001zre.1_Missense_Mutation_p.P293S	NM_201631	NP_963925	O43548	TGM5_HUMAN	transglutaminase 5 isoform 1	375					epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	ACAGAGGCAGGGCCACAGCAG	0.592													12	31	---	---	---	---	PASS
ATP8B4	79895	broad.mit.edu	37	15	50211075	50211075	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50211075C>A	uc001zxu.2	-	19	2138	c.1996G>T	c.(1996-1998)GCC>TCC	p.A666S	ATP8B4_uc010ber.2_Missense_Mutation_p.A539S|ATP8B4_uc010ufd.1_Missense_Mutation_p.A476S|ATP8B4_uc010ufe.1_RNA	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4	666	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		TTAATATTGGCTAGTGATAAA	0.343													32	188	---	---	---	---	PASS
ERCC4	2072	broad.mit.edu	37	16	14041845	14041845	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14041845C>G	uc002dce.2	+	11	2401	c.2392C>G	c.(2392-2394)CTA>GTA	p.L798V	ERCC4_uc010uyz.1_Missense_Mutation_p.L348V	NM_005236	NP_005227	Q92889	XPF_HUMAN	excision repair cross-complementing rodent	798	Interaction with EME1 and ERCC1.				double-strand break repair via homologous recombination|meiotic mismatch repair|negative regulation of telomere maintenance|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|nucleotide-excision repair, DNA incision, 5'-to lesion|resolution of meiotic recombination intermediates|telomere maintenance via telomere shortening|transcription-coupled nucleotide-excision repair	nuclear chromosome, telomeric region|nucleoplasm|nucleotide-excision repair factor 1 complex	damaged DNA binding|protein C-terminus binding|protein N-terminus binding|single-stranded DNA binding|single-stranded DNA specific endodeoxyribonuclease activity			lung(4)|ovary(3)|skin(2)|pancreas(1)	10						CTTCCCCAGACTACGGATTCT	0.522			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				23	68	---	---	---	---	PASS
COG7	91949	broad.mit.edu	37	16	23400194	23400194	+	3'UTR	SNP	G	A	A	rs250587	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23400194G>A	uc002dlo.2	-	17						NM_153603	NP_705831	P83436	COG7_HUMAN	component of oligomeric golgi complex 7						intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)		CTGGTGAGTCGCGAAACAGCA	0.488													5	63	---	---	---	---	PASS
FBRS	64319	broad.mit.edu	37	16	30679940	30679940	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30679940G>A	uc002dzd.3	+	10	837	c.574G>A	c.(574-576)GGA>AGA	p.G192R	FBRS_uc002dzc.3_Missense_Mutation_p.G104R	NM_001105079	NP_001098549	Q9HAH7	FBRS_HUMAN	fibrosin	192										ovary(1)	1			Colorectal(24;0.103)			CGGGGCCTTTGGAGGCCTGGG	0.672													8	11	---	---	---	---	PASS
SMCR8	140775	broad.mit.edu	37	17	18219207	18219207	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18219207T>A	uc002gsy.3	+	1	614	c.104T>A	c.(103-105)TTC>TAC	p.F35Y		NM_144775	NP_658988	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region,	35										central_nervous_system(1)	1						GTGCCGCTCTTCCCCTTCGCC	0.557													25	52	---	---	---	---	PASS
EME1	146956	broad.mit.edu	37	17	48456585	48456585	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48456585G>C	uc002iqs.1	+	6	1303	c.1230G>C	c.(1228-1230)GAG>GAC	p.E410D	EME1_uc010dbp.1_Missense_Mutation_p.E423D|EME1_uc010dbq.1_5'Flank	NM_152463	NP_689676	Q96AY2	EME1_HUMAN	essential meiotic endonuclease 1 homolog 1	410					DNA recombination|DNA repair	nucleolus	DNA binding|endonuclease activity|metal ion binding|protein binding				0	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			ACGCTGAAGAGGTAAGAACGT	0.502								Direct_reversal_of_damage|Homologous_recombination					47	90	---	---	---	---	PASS
PTPN2	5771	broad.mit.edu	37	18	12814354	12814354	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12814354T>G	uc002krp.2	-	7	900	c.706A>C	c.(706-708)ATG>CTG	p.M236L	PTPN2_uc002krl.2_Missense_Mutation_p.M236L|PTPN2_uc002krn.2_Missense_Mutation_p.M259L|PTPN2_uc002kro.2_Missense_Mutation_p.M236L|PTPN2_uc002krm.2_Missense_Mutation_p.M236L	NM_002828	NP_002819	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type	236	Tyrosine-protein phosphatase.				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway	endoplasmic reticulum|nucleoplasm	protein binding			skin(2)	2		Lung NSC(161;8.94e-06)				CCTTTTTCCATCTGCAAGAAA	0.358													40	116	---	---	---	---	PASS
MBD1	4152	broad.mit.edu	37	18	47803544	47803544	+	Silent	SNP	A	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47803544A>C	uc010dow.1	-	3	578	c.141T>G	c.(139-141)GTT>GTG	p.V47V	MBD1_uc002lef.2_5'Flank|MBD1_uc002leg.2_Silent_p.V47V|MBD1_uc010xdi.1_Silent_p.V73V|MBD1_uc002leh.3_Silent_p.V47V|MBD1_uc002len.2_Silent_p.V47V|MBD1_uc002lei.3_Silent_p.V47V|MBD1_uc002lej.3_Silent_p.V47V|MBD1_uc002lek.3_Silent_p.V47V|MBD1_uc002lel.3_Silent_p.V47V|MBD1_uc002lem.3_Silent_p.V47V|MBD1_uc010xdj.1_Silent_p.V47V|MBD1_uc010xdk.1_Silent_p.V47V|MBD1_uc010dox.1_Silent_p.V47V|MBD1_uc002leo.2_Silent_p.V47V	NM_015846	NP_056671	Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1 isoform 1	47	MBD.				negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|nuclear speck	methyl-CpG binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						GAGTCAGCTCAACTTTGCTTC	0.527													20	66	---	---	---	---	PASS
ST8SIA3	51046	broad.mit.edu	37	18	55020027	55020027	+	5'UTR	SNP	C	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55020027C>A	uc002lgn.2	+	1						NM_015879	NP_056963	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			breast(1)|skin(1)	2				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		GAGCTGCTGGCCGCTCAATGG	0.463													3	5	---	---	---	---	PASS
C19orf38	255809	broad.mit.edu	37	19	10979899	10979899	+	Silent	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10979899G>A	uc010dxm.1	+	7	628	c.549G>A	c.(547-549)ACG>ACA	p.T183T	CARM1_uc002mpz.2_5'Flank|CARM1_uc010dxn.2_5'Flank	NM_001136482	NP_001129954	A8MVS5	HIDE1_HUMAN	hypothetical protein LOC255809 precursor	183	Cytoplasmic (Potential).					integral to membrane					0						CAAAGAAAACGATGCCAGAAG	0.547													14	38	---	---	---	---	PASS
ZNF607	84775	broad.mit.edu	37	19	38190296	38190296	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38190296T>A	uc002ohc.1	-	5	1332	c.736A>T	c.(736-738)ATT>TTT	p.I246F	ZNF607_uc002ohb.1_Missense_Mutation_p.I245F	NM_032689	NP_116078	Q96SK3	ZN607_HUMAN	zinc finger protein 607	246	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			CCAGTGTGAATACTCTGATGT	0.413													8	36	---	---	---	---	PASS
ATP5SL	55101	broad.mit.edu	37	19	41942328	41942328	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41942328A>G	uc002oqw.1	-	3	271	c.265T>C	c.(265-267)TTT>CTT	p.F89L	CYP2F1_uc010xvw.1_Intron|ATP5SL_uc002oqu.1_RNA|ATP5SL_uc002oqv.2_Missense_Mutation_p.F95L|ATP5SL_uc010xwa.1_Missense_Mutation_p.F95L|ATP5SL_uc002oqx.1_Intron|ATP5SL_uc002oqy.1_Missense_Mutation_p.F89L|ATP5SL_uc002oqz.1_Intron|ATP5SL_uc002ora.1_Missense_Mutation_p.F76L|ATP5SL_uc010xwb.1_Intron	NM_018035	NP_060505	Q9NW81	AT5SL_HUMAN	ATP5S-like	89										large_intestine(1)|breast(1)	2						AGGATGAAAAAGGCACCTGCG	0.532													16	39	---	---	---	---	PASS
ZNF284	342909	broad.mit.edu	37	19	44586259	44586259	+	Splice_Site	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44586259G>A	uc002oyg.1	+	4	451	c.235_splice	c.e4+1	p.G79_splice	ZNF284_uc010ejd.2_Splice_Site	NM_001037813	NP_001032902	Q2VY69	ZN284_HUMAN	zinc finger protein 284						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)				GGGAATTCAGGTAAGAACCAA	0.328													23	119	---	---	---	---	PASS
GPR77	27202	broad.mit.edu	37	19	47844249	47844249	+	Missense_Mutation	SNP	C	T	T	rs144687097		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47844249C>T	uc010ela.1	+	2	411	c.193C>T	c.(193-195)CGC>TGC	p.R65C	GPR77_uc002pgk.1_Missense_Mutation_p.R65C	NM_018485	NP_060955	Q9P296	C5ARL_HUMAN	G protein-coupled receptor 77	65	Cytoplasmic (Potential).				chemotaxis	integral to membrane|plasma membrane	C5a anaphylatoxin receptor activity			ovary(1)	1		all_cancers(25;1.72e-06)|all_lung(116;2.15e-05)|all_epithelial(76;3.44e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.0652)|Ovarian(192;0.086)		all cancers(93;0.000129)|OV - Ovarian serous cystadenocarcinoma(262;0.000415)|Epithelial(262;0.0109)|GBM - Glioblastoma multiforme(486;0.0138)		GAAGGTGGCCCGCCGGAGGGT	0.692													4	21	---	---	---	---	PASS
ZNF468	90333	broad.mit.edu	37	19	53345371	53345371	+	Missense_Mutation	SNP	G	A	A	rs148965254	byFrequency	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53345371G>A	uc002qaf.2	-	4	327	c.176C>T	c.(175-177)TCG>TTG	p.S59L	ZNF468_uc002qae.2_Missense_Mutation_p.S6L	NM_001008801	NP_001008801	Q5VIY5	ZN468_HUMAN	zinc finger protein ZNF468 isoform 2	59	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0358)		CCCTGTTGACGACAACGTCTT	0.368													14	29	---	---	---	---	PASS
ZNF160	90338	broad.mit.edu	37	19	53571306	53571306	+	3'UTR	SNP	T	C	C	rs2288421	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53571306T>C	uc010eqk.2	-	7					ZNF160_uc002qaq.3_3'UTR|ZNF160_uc002qar.3_3'UTR	NM_001102603	NP_001096073	Q9HCG1	ZN160_HUMAN	zinc finger protein 160						hemopoiesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(134;0.02)		AAGGAGTGAATTGTACCTAAT	0.403													6	47	---	---	---	---	PASS
LILRB3	11025	broad.mit.edu	37	19	54721109	54721109	+	Intron	SNP	C	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54721109C>A	uc002qef.1	-						LILRB3_uc002qee.1_Intron|LILRB3_uc002qeh.1_Intron|LILRB3_uc002qeg.1_Intron|LILRB3_uc002qei.1_Intron|LILRA6_uc002qek.1_Intron|LILRB3_uc010erh.1_Intron|LILRB3_uc002qej.1_Intron|LILRA6_uc002qel.1_Intron|LILRA6_uc002qem.1_Intron|LILRB3_uc002qen.1_Intron|LILRB3_uc002qeo.1_Intron|LILRB3_uc002qep.1_Intron|LILRB3_uc002qeq.1_Intron|LILRB3_uc002qer.1_Intron|LILRB3_uc002qes.1_Intron	NM_006864	NP_006855	O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor,						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	transmembrane receptor activity			skin(2)|ovary(1)	3	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ATGCAGCAGCCTGCAGCGGGG	0.632													25	51	---	---	---	---	PASS
LAIR2	3904	broad.mit.edu	37	19	55019389	55019389	+	Silent	SNP	G	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55019389G>T	uc002qgc.2	+	3	476	c.354G>T	c.(352-354)CTG>CTT	p.L118L	LAIR2_uc002qga.1_RNA|LAIR2_uc002qgb.1_RNA|LAIR2_uc002qgd.2_Silent_p.L118L|LAIR2_uc010erl.2_Intron	NM_002288	NP_002279	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like	118						extracellular region	receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		TCCTGGAGCTGCTGGTGAAAG	0.577													4	10	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	20	31497682	31497682	+	Missense_Mutation	SNP	G	T	T	rs78951406	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31497682G>T	uc010zub.1	+	15	1596	c.1502G>T	c.(1501-1503)AGG>ATG	p.R501M		NM_001143967	NP_001137439			EF-hand calcium binding domain 8																		GCAAGGAAGAGGACCACTCAT	0.562													5	48	---	---	---	---	PASS
ATP9A	10079	broad.mit.edu	37	20	50292728	50292728	+	Silent	SNP	A	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50292728A>T	uc002xwg.1	-	10	819	c.819T>A	c.(817-819)GTT>GTA	p.V273V	ATP9A_uc010gih.1_Silent_p.V137V|ATP9A_uc002xwf.1_5'UTR	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	273	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4						CAGTGTAAAGAACAACACCCA	0.408													39	80	---	---	---	---	PASS
PHACTR3	116154	broad.mit.edu	37	20	58318178	58318178	+	Silent	SNP	G	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58318178G>C	uc002yau.2	+	2	602	c.135G>C	c.(133-135)ACG>ACC	p.T45T	PHACTR3_uc002yat.2_Silent_p.T42T|PHACTR3_uc010zzw.1_Silent_p.T4T|PHACTR3_uc002yav.2_Silent_p.T4T|PHACTR3_uc002yaw.2_Silent_p.T4T|PHACTR3_uc002yax.2_Silent_p.T4T	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1	45						nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			TGGACCAAACGCCCCCGGCGC	0.582													16	46	---	---	---	---	PASS
YTHDF1	54915	broad.mit.edu	37	20	61827960	61827960	+	3'UTR	SNP	C	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61827960C>T	uc002yeh.2	-	5					YTHDF1_uc011aaq.1_3'UTR	NM_017798	NP_060268	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1											ovary(2)	2						ATGCAACACTCAACCCCCGCA	0.413													18	44	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11049593	11049593	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11049593G>A	uc002yit.1	-	4	516	c.308C>T	c.(307-309)GCG>GTG	p.A103V		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)		CCGGGCTGTCGCACACTGCAC	0.383													20	188	---	---	---	---	PASS
SETD4	54093	broad.mit.edu	37	21	37418187	37418187	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37418187G>A	uc002yuw.1	-	5	1792	c.419C>T	c.(418-420)CCT>CTT	p.P140L	SETD4_uc002yux.1_Missense_Mutation_p.P116L|SETD4_uc002yuu.2_RNA|SETD4_uc002yuv.2_Missense_Mutation_p.P140L|SETD4_uc002yuy.2_Missense_Mutation_p.P140L|SETD4_uc002yuz.2_Missense_Mutation_p.P116L|SETD4_uc002yva.2_Missense_Mutation_p.P116L	NM_017438	NP_059134	Q9NVD3	SETD4_HUMAN	SET domain containing 4 isoform a	140	SET.									large_intestine(1)|ovary(1)	2						CAAACAAACAGGGCAGGTATA	0.502													16	28	---	---	---	---	PASS
FOXRED2	80020	broad.mit.edu	37	22	36894120	36894120	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36894120T>C	uc003apn.3	-	5	1408	c.1300A>G	c.(1300-1302)AGC>GGC	p.S434G	FOXRED2_uc003apm.3_5'UTR|FOXRED2_uc003apo.3_Missense_Mutation_p.S434G|FOXRED2_uc003app.3_Missense_Mutation_p.S434G	NM_024955	NP_079231	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	434					ER-associated protein catabolic process	endoplasmic reticulum lumen	flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			lung(1)|kidney(1)	2						ACGATGGAGCTGGTCAGCTGT	0.632													10	24	---	---	---	---	PASS
ASB9	140462	broad.mit.edu	37	X	15266819	15266819	+	Intron	SNP	C	T	T	rs1139868	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15266819C>T	uc004cwl.2	-						ASB9_uc004cwk.2_3'UTR|ASB9_uc004cwm.2_3'UTR|ASB9_uc010ner.2_3'UTR|ASB9_uc004cwn.2_3'UTR	NM_001031739	NP_001026909	Q96DX5	ASB9_HUMAN	ankyrin repeat and SOCS box-containing 9 isoform						intracellular signal transduction						0	Hepatocellular(33;0.183)					TACTAGAGCCCCAAGGGATGT	0.473													7	35	---	---	---	---	PASS
TMEM47	83604	broad.mit.edu	37	X	34648280	34648280	+	3'UTR	SNP	G	A	A	rs10522027	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34648280G>A	uc004ddh.2	-	3					TMEM47_uc010ngs.2_RNA	NM_031442	NP_113630	Q9BQJ4	TMM47_HUMAN	transmembrane protein 47							integral to membrane				lung(1)	1						TGGTTATGATGTTGACAGCCA	0.348													6	35	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	5159045	5159046	+	IGR	DEL	CC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5159045_5159046delCC								AJAP1 (315195 upstream) : NPHP4 (763824 downstream)																							TTACACAACACCCAAGCAGCTG	0.366													4	2	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	6956410	6956410	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6956410delG	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TGTCCTTCCTGGGGCAGTGGG	0.478													4	2	---	---	---	---	
TMEM51	55092	broad.mit.edu	37	1	15517586	15517586	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15517586delC	uc001avw.3	+						TMEM51_uc010obk.1_Intron|TMEM51_uc001avz.2_Intron|TMEM51_uc001avy.2_Intron|TMEM51_uc001avx.2_Intron	NM_001136216	NP_001129688	Q9NW97	TMM51_HUMAN	transmembrane protein 51							integral to membrane					0		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		cccggccccacaagagttctt	0.000													4	2	---	---	---	---	
MST1P9	11223	broad.mit.edu	37	1	17088220	17088220	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17088220delT	uc010ock.1	-						CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_5'Flank	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						GCTCCCCGACTTTTTTCTCAT	0.587													4	2	---	---	---	---	
VWA5B1	127731	broad.mit.edu	37	1	20637005	20637005	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20637005delA	uc009vps.2	+						VWA5B1_uc001bdd.2_Intron|VWA5B1_uc010odc.1_Intron	NM_001039500	NP_001034589	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1							extracellular region					0						CTGAAACGGGAAAACTAGGTT	0.537													4	2	---	---	---	---	
NBPF3	84224	broad.mit.edu	37	1	21807368	21807368	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21807368delA	uc001ber.2	+						NBPF3_uc001bes.2_Intron|NBPF3_uc009vqb.2_Intron|NBPF3_uc010odm.1_Intron	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3							cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GTGGACTGTTAATGGGTGTAG	0.478													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25408046	25408046	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25408046delA								RUNX3 (116434 upstream) : SYF2 (140721 downstream)																							ATGTGCTGGCAAAAAAACTAC	0.438													4	2	---	---	---	---	
STMN1	3925	broad.mit.edu	37	1	26214190	26214190	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26214190delT	uc010oev.1	-						STMN1_uc001bky.2_Intron	NM_001145454	NP_001138926	P16949	STMN1_HUMAN	stathmin 1 isoform b						cell differentiation|intracellular signal transduction|microtubule depolymerization|mitotic spindle organization|nervous system development|response to virus	cytoplasm|microtubule	signal transducer activity|tubulin binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000163)|all_lung(284;0.000234)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.013)|READ - Rectum adenocarcinoma(331;0.0649)		ttttgttttgtttttttgaga	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35069422	35069424	+	IGR	DEL	CAA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35069422_35069424delCAA								C1orf94 (384693 upstream) : MIR552 (65776 downstream)																							CTTCCTGACTCAACTCCATTCTA	0.281													4	2	---	---	---	---	
PTPRF	5792	broad.mit.edu	37	1	44058316	44058317	+	Intron	DEL	AC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44058316_44058317delAC	uc001cjr.2	+						PTPRF_uc001cjs.2_Intron|PTPRF_uc001cju.2_Intron|PTPRF_uc009vwt.2_Intron|PTPRF_uc001cjv.2_Intron	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CTGGGCTGGGacacacacacac	0.564													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48058538	48058538	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48058538delA								FOXD2 (152176 upstream) : SKINTL (508849 downstream)																							GGATTCAGTGAAGGGCTGGCG	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	53655303	53655305	+	IGR	DEL	CAC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53655303_53655305delCAC								SLC1A7 (47014 upstream) : CPT2 (6796 downstream)																							tctgtcttttcacactgtcacct	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	73048755	73048755	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73048755delG								NEGR1 (300350 upstream) : None (None downstream)																							tagtgagtttggaagaggacc	0.000													4	2	---	---	---	---	
MCOLN2	255231	broad.mit.edu	37	1	85433861	85433861	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85433861delA	uc001dkm.2	-						MCOLN2_uc001dkn.2_Intron	NM_153259	NP_694991	Q8IZK6	MCLN2_HUMAN	mucolipin 2							integral to membrane	ion channel activity			ovary(3)|upper_aerodigestive_tract(1)	4				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		GAGTGGTTCCAAATCAAAGAA	0.403													4	2	---	---	---	---	
NTNG1	22854	broad.mit.edu	37	1	107866802	107866802	+	Intron	DEL	T	-	-	rs79614791		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107866802delT	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697	Q9Y2I2	NTNG1_HUMAN	netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		TGAAAACAGATTTTTTTTTTC	0.333													4	2	---	---	---	---	
NTNG1	22854	broad.mit.edu	37	1	107965211	107965211	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107965211delA	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvi.2_Intron|NTNG1_uc001dve.2_Intron|NTNG1_uc009wek.2_Intron|NTNG1_uc001dvg.2_Intron|NTNG1_uc009wem.2_Intron	NM_001113226	NP_001106697	Q9Y2I2	NTNG1_HUMAN	netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		ACAGCTACATAAGGATGCAAG	0.448													4	2	---	---	---	---	
SARS	6301	broad.mit.edu	37	1	109778186	109778186	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109778186delG	uc001dwu.1	+						SARS_uc001dwt.1_Intron|SARS_uc001dwv.1_Intron|SARS_uc001dww.1_Intron|SARS_uc001dwx.1_Intron|SARS_uc009wfa.1_Intron|SARS_uc001dwy.1_Intron|SARS_uc001dwz.1_Intron	NM_006513	NP_006504	P49591	SYSC_HUMAN	seryl-tRNA synthetase						seryl-tRNA aminoacylation|tRNA processing	cytosol	ATP binding|protein binding|RNA binding|serine-tRNA ligase activity			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)	CTGTGTTTCTGGGGAAGTgca	0.259													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145014292	145014292	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145014292delT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron|uc001emj.2_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)		AGCCTCTTGATTACCATGCAA	0.403			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145289011	145289012	+	Intron	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145289011_145289012delTG	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		gatatttagttgtcccaggacc	0.000													4	2	---	---	---	---	
ANKRD34A	284615	broad.mit.edu	37	1	145474846	145474846	+	3'UTR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145474846delG	uc001enq.1	+	4					NBPF10_uc001emp.3_Intron|LIX1L_uc001enr.2_5'Flank	NM_001039888	NP_001034977	Q69YU3	AN34A_HUMAN	ankyrin repeat domain 34												0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CAAGGAGGGTGGGGATTAGGA	0.597													4	2	---	---	---	---	
LOC645166	645166	broad.mit.edu	37	1	148932997	148932998	+	Intron	DEL	TT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148932997_148932998delTT	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0						GGTTTCCTTGTTAAGACAAGCG	0.574													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149302931	149302931	+	IGR	DEL	A	-	-	rs148824221		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149302931delA								LOC388692 (11189 upstream) : FCGR1C (66363 downstream)																							aaacagagataaaaaaaaaaa	0.000													3	3	---	---	---	---	
ILF2	3608	broad.mit.edu	37	1	153634744	153634746	+	3'UTR	DEL	ATG	-	-	rs146876548	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153634744_153634746delATG	uc001fcr.2	-	14					ILF2_uc010pdy.1_3'UTR|ILF2_uc009wok.2_3'UTR	NM_004515	NP_004506	Q12905	ILF2_HUMAN	interleukin enhancer binding factor 2						immune response|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|ribonucleoprotein complex	ATP binding|DNA binding|double-stranded RNA binding|protein binding|transferase activity				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGACACTTCTATGGAGTTTACTT	0.463													3	3	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154761743	154761744	+	Intron	DEL	CA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154761743_154761744delCA	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron|KCNN3_uc009wox.1_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			cctcccttttcacaaagacact	0.000													4	2	---	---	---	---	
PRCC	5546	broad.mit.edu	37	1	156754668	156754668	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156754668delG	uc001fqa.2	+						PRCC_uc001fqb.2_Intron	NM_005973	NP_005964	Q92733	PRCC_HUMAN	papillary renal cell carcinoma						cell cycle|mitotic cell cycle checkpoint	nucleus	protein binding		PRCC/TFE3(25)	kidney(25)|central_nervous_system(2)	27	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TAGGAACTCTGGATGGGCTGG	0.443			T	TFE3	papillary renal 								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158567731	158567732	+	IGR	DEL	CC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158567731_158567732delCC								OR10X1 (18042 upstream) : OR10Z1 (8497 downstream)																							atgccagcttccctgtgtcctg	0.000													4	2	---	---	---	---	
IGSF9	57549	broad.mit.edu	37	1	159906818	159906818	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159906818delT	uc001fur.2	-						IGSF9_uc001fuq.2_Intron	NM_001135050	NP_001128522	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform a							cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			CCCTGCCTCATAGGAGTCCTC	0.647											OREG0013921	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	1	165571194	165571195	+	IGR	DEL	CC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165571194_165571195delCC								LOC400794 (19853 upstream) : MGST3 (29255 downstream)																							CTCCCACATTCCGTAGTCAGTG	0.475											OREG0013963	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	1	181182111	181182111	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181182111delT								IER5 (122134 upstream) : CACNA1E (270605 downstream)																							TCTGAACAGGTTTTTTTTAAC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193419325	193419326	+	IGR	DEL	AT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193419325_193419326delAT								CDC73 (195385 upstream) : None (None downstream)																							TTGGAATTGGATAAGATCTTTT	0.381													4	2	---	---	---	---	
RAB7L1	8934	broad.mit.edu	37	1	205745678	205745678	+	5'Flank	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205745678delC	uc001hdf.3	-						RAB7L1_uc009xbp.2_5'Flank|RAB7L1_uc001hde.3_5'Flank|RAB7L1_uc010prr.1_5'Flank|RAB7L1_uc009xbq.2_5'Flank	NM_003929	NP_003920	O14966	RAB7L_HUMAN	RAB7, member RAS oncogene family-like 1 isoform						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding			ovary(1)	1	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			cttatgccttctatgacgctg	0.100													4	2	---	---	---	---	
PRSS38	339501	broad.mit.edu	37	1	228026724	228026725	+	Intron	DEL	GC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228026724_228026725delGC	uc001hrh.2	+							NM_183062	NP_898885	A1L453	PRS38_HUMAN	marapsin 2 precursor						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)|pancreas(1)	2						AAGTGTTCTGGCAGCACAAATT	0.297													4	2	---	---	---	---	
URB2	9816	broad.mit.edu	37	1	229770586	229770586	+	Intron	DEL	T	-	-	rs113038970		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229770586delT	uc001hts.1	+						URB2_uc009xfd.1_Intron	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog							nucleolus				central_nervous_system(2)|ovary(1)	3						AGTTTGTTGATTTTTTTTTTT	0.333													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	3610000	3610002	+	IGR	DEL	GTT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3610000_3610002delGTT								RNASEH1 (4060 upstream) : RPS7 (12851 downstream)																							TCTCTCAGGAGTTGAAAAAGGTG	0.448													4	2	---	---	---	---	
NBAS	51594	broad.mit.edu	37	2	15564789	15564790	+	Intron	INS	-	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15564789_15564790insC	uc002rcc.1	-						NBAS_uc010exl.1_5'Flank|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4						TAATTTATTTTCCCCCCGTTTT	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20038845	20038845	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20038845delT								OSR1 (480473 upstream) : TTC32 (57673 downstream)																							catcttctcattttcctcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	32048281	32048281	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32048281delC								SRD5A2 (242241 upstream) : MEMO1 (44615 downstream)																							CCAGAGCTGGCAATCTGGGCT	0.522													4	2	---	---	---	---	
MEMO1	51072	broad.mit.edu	37	2	32142809	32142809	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32142809delG	uc002rnx.2	-						MEMO1_uc010ymu.1_Intron|MEMO1_uc010ezq.2_Intron|MEMO1_uc002rny.2_Intron|MEMO1_uc002rnz.2_Intron|MEMO1_uc010ymv.1_Intron	NM_015955	NP_057039	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1 isoform 1						regulation of microtubule-based process	cytosol|nucleus				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)					ATGTCAATTCGTATGTTCAGC	0.338													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	33950284	33950284	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33950284delC								FAM98A (125922 upstream) : MYADML (848 downstream)																							ATGTGCACCACACACTCAAGC	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38409770	38409772	+	IGR	DEL	GCG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38409770_38409772delGCG								C2orf58 (779 upstream) : ATL2 (112259 downstream)																							agacgtgggtgcggagaaagggg	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	41262900	41262901	+	IGR	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41262900_41262901insT								SLC8A1 (523325 upstream) : None (None downstream)																							tagctgagtgattttttttcaa	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	46619841	46619841	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46619841delA								EPAS1 (6006 upstream) : LOC388946 (86863 downstream)																							CTgggggaagaaaaaaagagt	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	51345113	51345114	+	IGR	DEL	GC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51345113_51345114delGC								NRXN1 (85439 upstream) : None (None downstream)																							ACTCACAGGAGCAGAACACAGA	0.470													4	2	---	---	---	---	
VRK2	7444	broad.mit.edu	37	2	58245734	58245734	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58245734delA	uc002rzo.2	+						VRK2_uc010fcb.2_Intron	NM_001130482	NP_001123954	Q86Y07	VRK2_HUMAN	vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1						TATCCCCTCCAGGCTAGCTAA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66531286	66531286	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66531286delG								SPRED2 (871630 upstream) : MEIS1 (131246 downstream)																							AATGGTGGCAGGGCTCCAAGG	0.507													4	2	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71843722	71843722	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71843722delT	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						GACTTTGAACTTTCTGAGGGC	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	76176141	76176141	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76176141delT								C2orf3 (238030 upstream) : LRRTM4 (798717 downstream)																							agacttctgattttttaatat	0.000													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	80132081	80132081	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80132081delT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						TGCTAAATTATTTTAGGTTAA	0.358													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	80531228	80531228	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80531228delA	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysi.1_5'Flank|LRRTM1_uc002soj.3_Intron|LRRTM1_uc002sok.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						AAAAGGGAGGAAAAAAAAAAT	0.438													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	95629838	95629838	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95629838delA								TEKT4 (87270 upstream) : MAL (61641 downstream)																							CGGCAAGATCAAAAAGCAAAC	0.458													4	2	---	---	---	---	
VWA3B	200403	broad.mit.edu	37	2	98919885	98919886	+	Intron	DEL	GT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98919885_98919886delGT	uc002syo.2	+						VWA3B_uc002syn.1_Intron|VWA3B_uc010yvi.1_Intron|VWA3B_uc002syp.1_Intron|VWA3B_uc002syq.1_Intron|VWA3B_uc002syr.1_Intron|VWA3B_uc002sys.2_Intron	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B											ovary(3)|large_intestine(2)|skin(1)	6						TTATGTGAAGgtgtgtgtgtgt	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105437681	105437681	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105437681delT	uc002tck.1	-											Homo sapiens cDNA FLJ39179 fis, clone OCBBF2004147.																		GCAAATATGGTTTGGAACAAA	0.443													4	2	---	---	---	---	
CBWD2	150472	broad.mit.edu	37	2	114228975	114228976	+	Intron	DEL	TT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114228975_114228976delTT	uc002tju.2	+						CBWD2_uc002tjv.2_Intron|CBWD2_uc010fkv.2_Intron	NM_172003	NP_742000	Q8IUF1	CBWD2_HUMAN	COBW domain-containing protein 2								ATP binding|protein binding				0						ACATAGAAAATTTTAGCTTAGC	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	115142856	115142857	+	IGR	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115142856_115142857insA								ACTR3 (426689 upstream) : DPP10 (57042 downstream)																							tatctaaccccaaaagagccaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131143011	131143011	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131143011delG								PTPN18 (10030 upstream) : CFC1B (135825 downstream)																							CACCACAGATGGTGCAGGAAA	0.478													4	2	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	133009045	133009045	+	Intron	DEL	C	-	-	rs113324698		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133009045delC	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						gacacgttttcctccacccct	0.010													4	2	---	---	---	---	
R3HDM1	23518	broad.mit.edu	37	2	136466982	136466983	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136466982_136466983insT	uc002tuo.2	+						R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_Intron	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1								nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)		TCATTATGCTGTTTTTTTGTTT	0.282													52	34	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146421257	146421258	+	IGR	DEL	AC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146421257_146421258delAC								None (None upstream) : PABPC1P2 (923367 downstream)																							atacacacaaacacacacacac	0.149													4	2	---	---	---	---	
KIF5C	3800	broad.mit.edu	37	2	149639547	149639547	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149639547delG	uc010zbu.1	+							NM_004522	NP_004513	O60282	KIF5C_HUMAN	kinesin family member 5C						microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)		CTTTCTTCCAGGTTTTTTTTC	0.383													4	2	---	---	---	---	
KIF5C	3800	broad.mit.edu	37	2	149861716	149861718	+	Intron	DEL	CCT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149861716_149861718delCCT	uc010zbu.1	+						KIF5C_uc002tws.1_Intron|KIF5C_uc002twu.1_Intron	NM_004522	NP_004513	O60282	KIF5C_HUMAN	kinesin family member 5C						microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)		AGGCTCTGCACCTCAAGGTGCTC	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151466960	151466961	+	IGR	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151466960_151466961delTG								RND3 (122780 upstream) : RBM43 (637768 downstream)																							ctttgcaaaatgaATGTTACTA	0.010													4	2	---	---	---	---	
FMNL2	114793	broad.mit.edu	37	2	153233559	153233559	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153233559delT	uc002tye.2	+							NM_052905	NP_443137	Q96PY5	FMNL2_HUMAN	formin-like 2						actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3						ggaagcctggttttaccaatc	0.085													4	2	---	---	---	---	
FMNL2	114793	broad.mit.edu	37	2	153437214	153437215	+	Intron	DEL	TC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153437214_153437215delTC	uc002tye.2	+							NM_052905	NP_443137	Q96PY5	FMNL2_HUMAN	formin-like 2						actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3						AGATTATTCTTCTCAGAACTAG	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	160795123	160795124	+	IGR	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160795123_160795124insA								LY75 (33861 upstream) : PLA2R1 (2888 downstream)																							ACAGACTAcagattaaagcaac	0.228													4	2	---	---	---	---	
COBLL1	22837	broad.mit.edu	37	2	165548593	165548593	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165548593delG	uc010zcw.1	-						COBLL1_uc002ucp.2_Intron|COBLL1_uc002ucq.2_Intron|COBLL1_uc010zcx.1_Intron|COBLL1_uc002ucn.2_Intron|COBLL1_uc002uco.2_Intron	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1											ovary(2)|pancreas(1)	3						AACTCTTTCAGCTTATACTTC	0.348													4	3	---	---	---	---	
LRP2	4036	broad.mit.edu	37	2	170089678	170089680	+	Intron	DEL	GCC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170089678_170089680delGCC	uc002ues.2	-							NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	AGAGGTAGCAGCCAAATGCTGAA	0.419													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173096401	173096402	+	IGR	DEL	GA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173096401_173096402delGA								DLX2 (128923 upstream) : ITGA6 (195680 downstream)																							CTTTCACCTGGAGAACCTGTTA	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	180902910	180902910	+	IGR	DEL	T	-	-	rs111406265		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180902910delT								CWC22 (31070 upstream) : UBE2E3 (942202 downstream)																							CTTTTGTTTATTTTTTTTTTC	0.299													1	5	---	---	---	---	
COL5A2	1290	broad.mit.edu	37	2	189945893	189945893	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189945893delA	uc002uqk.2	-						COL5A2_uc010frx.2_Intron	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein						axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			TAAGAAGAACAAAAAAAAGCA	0.274													4	4	---	---	---	---	
NAB1	4664	broad.mit.edu	37	2	191538092	191538092	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191538092delT	uc002usb.2	+						NAB1_uc010fsc.2_Intron|NAB1_uc010fsd.2_Intron|NAB1_uc002usc.2_Intron|NAB1_uc010zgh.1_Intron	NM_005966	NP_005957	Q13506	NAB1_HUMAN	NGFI-A binding protein 1						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)			TTTTTTAAACttttttttcat	0.109													11	5	---	---	---	---	
ADAM23	8745	broad.mit.edu	37	2	207474545	207474546	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207474545_207474546insA	uc002vbq.2	+						ADAM23_uc010ziv.1_Intron	NM_003812	NP_003803	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23 preproprotein						cell adhesion|central nervous system development|proteolysis	extracellular region|integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		ACAGGATATTTACTTCCTGAAA	0.396													31	28	---	---	---	---	
UNC80	285175	broad.mit.edu	37	2	210840691	210840691	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210840691delT	uc010zjc.1	+						UNC80_uc002vdl.1_Intron|UNC80_uc010zjd.1_Intron|UNC80_uc010zje.1_Intron	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1							integral to membrane					0						CAGAATACTCTTGCTCGGGAA	0.353													4	2	---	---	---	---	
USP40	55230	broad.mit.edu	37	2	234394745	234394745	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234394745delC	uc010zmr.1	-						USP40_uc002vul.2_Intron|USP40_uc010zms.1_Intron	NM_018218	NP_060688	Q9NVE5	UBP40_HUMAN	ubiquitin thioesterase 40						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)|breast(1)	3		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		AGAGATTTTTCCCTAAATGCT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	236070257	236070257	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236070257delC								SH3BP4 (105901 upstream) : AGAP1 (332479 downstream)																							ttgctaagttccttctcactt	0.050													4	2	---	---	---	---	
LRRFIP1	9208	broad.mit.edu	37	2	238666866	238666867	+	Intron	INS	-	GT	GT	rs138141222	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238666866_238666867insGT	uc002vxe.2	+						LRRFIP1_uc002vxc.2_Intron|LRRFIP1_uc010znm.1_Intron|LRRFIP1_uc002vxd.2_Intron|LRRFIP1_uc002vxf.2_Intron	NM_001137552	NP_001131024	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|cytoskeleton|nucleus	DNA binding|double-stranded RNA binding|protein binding			breast(3)	3		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		AGCACTTAGGAgtgtgtgtgtg	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	500835	500835	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:500835delT								CHL1 (49740 upstream) : CNTN6 (633785 downstream)																							CTGGAATAACTTTGCCATTCA	0.418													4	2	---	---	---	---	
RBMS3	27303	broad.mit.edu	37	3	30013889	30013889	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30013889delT	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)				AGTTTCCAACTTTTTGTTTTC	0.368													4	2	---	---	---	---	
RBMS3	27303	broad.mit.edu	37	3	30032409	30032410	+	Intron	DEL	TA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30032409_30032410delTA	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)				ACTTAGCCCTTATCTAAATGTG	0.401													4	2	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41443507	41443508	+	Intron	DEL	CA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41443507_41443508delCA	uc003ckv.3	-							NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		ACTAAGCATTCACTTCATGGTT	0.332													4	2	---	---	---	---	
NBEAL2	23218	broad.mit.edu	37	3	47035311	47035311	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47035311delT	uc003cqp.2	+						NBEAL2_uc003cqq.1_Intron|NBEAL2_uc010hjm.1_5'Flank	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2								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)		GAGTTGCTGATCCAGCACATG	0.597													4	2	---	---	---	---	
IP6K1	9807	broad.mit.edu	37	3	49784918	49784918	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49784918delT	uc003cxm.1	-						IP6K1_uc003cxn.1_Intron|IP6K1_uc011bcv.1_Intron|IP6K1_uc003cxo.2_Intron	NM_153273	NP_695005	Q92551	IP6K1_HUMAN	inositol hexakisphosphate kinase 1 isoform 1						phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol hexakisphosphate 5-kinase activity|inositol trisphosphate 3-kinase activity				0						GAAGTATCCATTCCGCCTCCG	0.468													4	2	---	---	---	---	
FHIT	2272	broad.mit.edu	37	3	59908324	59908324	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59908324delC	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)		GTGCACTAAGCAAGAGAGAAC	0.428			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				4	3	---	---	---	---	
FHIT	2272	broad.mit.edu	37	3	60850295	60850296	+	Intron	DEL	GG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60850295_60850296delGG	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)		AGATGAGGTTGGAGCCTAAGTT	0.446			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				4	2	---	---	---	---	
ADAMTS9	56999	broad.mit.edu	37	3	64587520	64587521	+	Intron	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64587520_64587521delTG	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc003dmh.1_Intron|ADAMTS9_uc011bfp.1_Intron	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1						glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		GTCAATCCCTTGTAAAGAAAAA	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	120612320	120612321	+	IGR	INS	-	G	G	rs147019479	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120612320_120612321insG								GTF2E1 (110405 upstream) : STXBP5L (14729 downstream)																							TTCCAAGATTTATCACTCTGTG	0.356													4	2	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124069597	124069597	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124069597delT	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						TAAGACTGTATTTTTTTTGAA	0.403													6	3	---	---	---	---	
RPL32P3	132241	broad.mit.edu	37	3	129115712	129115713	+	Intron	INS	-	T	T	rs146775978	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129115712_129115713insT	uc003ema.2	-						RPL32P3_uc003emb.2_Intron|RPL32P3_uc003emd.1_Intron|SNORA7B_uc003eme.1_Intron	NR_003111				Homo sapiens cDNA FLJ36158 fis, clone TESTI2025757, weakly similar to Human mRNA for ribosomal protein L32.												0						ATCAAGAGACGTAAGTACCAGC	0.441													4	2	---	---	---	---	
GK5	256356	broad.mit.edu	37	3	141891560	141891561	+	Intron	DEL	AA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141891560_141891561delAA	uc003euq.1	-						GK5_uc003eup.1_Intron|GK5_uc010hus.1_Intron	NM_001039547	NP_001034636	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)						glycerol metabolic process		ATP binding|glycerol kinase activity				0						ACAAATTATTAAATGCTTAGCT	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	148384099	148384099	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148384099delA								None (None upstream) : AGTR1 (31559 downstream)																							ATAATCTTTTATAAATGAAGC	0.433													4	2	---	---	---	---	
SSR3	6747	broad.mit.edu	37	3	156261268	156261268	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156261268delA	uc003fau.2	-						SSR3_uc011bop.1_Intron	NM_007107	NP_009038	Q9UNL2	SSRG_HUMAN	signal sequence receptor gamma subunit						cotranslational protein targeting to membrane	integral to endoplasmic reticulum membrane|microsome|Sec61 translocon complex	protein binding|signal sequence binding				0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GTTCCAATTTAAAAAAAACAC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166461431	166461431	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166461431delA								BCHE (906178 upstream) : ZBBX (496650 downstream)																							ACAAAGGCACAATCAACAAAG	0.418													4	2	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170465234	170465234	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170465234delA	uc011bpt.1	+						uc003fha.1_Intron	NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			TCATTTTGTCAAAAAAACCTT	0.353													4	2	---	---	---	---	
SOX2	6657	broad.mit.edu	37	3	181431227	181431227	+	3'UTR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181431227delA	uc003fkx.2	+	1					SOX2OT_uc003fkv.2_Intron|SOX2OT_uc003fkw.3_Intron	NM_003106	NP_003097	P48431	SOX2_HUMAN	sex-determining region Y-box 2						cell cycle arrest|chromatin organization|eye development|glial cell fate commitment|inner ear development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell proliferation|negative regulation of neuron differentiation|osteoblast differentiation|pituitary gland development|positive regulation of MAPKKK cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of caspase activity|response to growth factor stimulus|response to wounding|somatic stem cell maintenance	cytosol|transcription factor complex	miRNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0	all_cancers(143;1.22e-16)|Ovarian(172;0.0283)		all cancers(12;1.82e-48)|Epithelial(37;9.85e-40)|OV - Ovarian serous cystadenocarcinoma(80;7.37e-23)|Lung(8;2.01e-21)|GBM - Glioblastoma multiforme(1;2.13e-08)			AAGAAAAAGGAAAAAAAAAAA	0.433			A		NSCLC|oesophageal squamous carcinoma		MICROPHTHALMIA AND ESOPHAGEAL ATRESIA SYNDROME						3	3	---	---	---	---	
C3orf21	152002	broad.mit.edu	37	3	194865230	194865231	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194865230_194865231insA	uc003fum.3	-						C3orf21_uc003ful.2_Intron	NM_152531	NP_689744	Q8NBI6	CC021_HUMAN	hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)		ctcagcctcccgagtagctggg	0.000													3	4	---	---	---	---	
C3orf21	152002	broad.mit.edu	37	3	194865235	194865235	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194865235delA	uc003fum.3	-						C3orf21_uc003ful.2_Intron	NM_152531	NP_689744	Q8NBI6	CC021_HUMAN	hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)		cctcccgagtagctgggatta	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197149794	197149795	+	IGR	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197149794_197149795insT								DLG1 (123651 upstream) : BDH1 (86860 downstream)																							TATTTTTTAAATTTTTTTGGGG	0.050													2	4	---	---	---	---	
C4orf44	345222	broad.mit.edu	37	4	3264509	3264509	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3264509delG	uc003ggt.2	+							NM_001012982	NP_001013000	Q6ZTZ1	CD044_HUMAN	hypothetical protein LOC345222 isoform b												0						CAGTCCACCTGGTGCCTTTCG	0.612													4	2	---	---	---	---	
CLNK	116449	broad.mit.edu	37	4	10600430	10600431	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10600430_10600431insT	uc003gmo.3	-						CLNK_uc003gmp.2_Intron	NM_052964	NP_443196	Q7Z7G1	CLNK_HUMAN	mast cell immunoreceptor signal transducer						immune response|intracellular signal transduction	intracellular	SH3/SH2 adaptor activity			ovary(1)	1						CTGACTGGTGATTTTTTTCCTC	0.238													4	2	---	---	---	---	
BOD1L	259282	broad.mit.edu	37	4	13575981	13575982	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13575981_13575982insA	uc003gmz.1	-							NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division								DNA binding			ovary(5)|breast(1)	6						AGAGCCCTGGGACTGATCAACC	0.218													4	2	---	---	---	---	
LDB2	9079	broad.mit.edu	37	4	16761028	16761028	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16761028delG	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron	NM_001290	NP_001281	O43679	LDB2_HUMAN	LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0						AAGGGTAGGTGGGCGGTCACT	0.388													4	2	---	---	---	---	
LDB2	9079	broad.mit.edu	37	4	16761032	16761032	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16761032delG	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron	NM_001290	NP_001281	O43679	LDB2_HUMAN	LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0						GTAGGTGGGCGGTCACTCTTC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18348032	18348032	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18348032delA								LCORL (324647 upstream) : None (None downstream)																							aatttatttgaaaaaaaaaaa	0.000													3	3	---	---	---	---	
TBC1D19	55296	broad.mit.edu	37	4	26718849	26718849	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26718849delT	uc003gsf.3	+						TBC1D19_uc010iew.2_Intron|TBC1D19_uc011bxu.1_Intron	NM_018317	NP_060787	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19							intracellular	Rab GTPase activator activity			breast(1)	1		Breast(46;0.0503)				CTTGGTAATATTTTTAGAATC	0.458													4	2	---	---	---	---	
C4orf34	201895	broad.mit.edu	37	4	39587740	39587740	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39587740delA	uc003guo.2	-						uc003gum.1_Intron|C4orf34_uc010ifm.2_5'Flank	NM_174921	NP_777581	Q96QK8	CD034_HUMAN	hypothetical protein LOC201895							integral to membrane	protein binding				0						cacaaatcttatcaagtggtt	0.085													4	2	---	---	---	---	
C4orf34	201895	broad.mit.edu	37	4	39587742	39587743	+	Intron	DEL	CA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39587742_39587743delCA	uc003guo.2	-						uc003gum.1_Intron|C4orf34_uc010ifm.2_5'Flank	NM_174921	NP_777581	Q96QK8	CD034_HUMAN	hypothetical protein LOC201895							integral to membrane	protein binding				0						caaatcttatcaagtggttagt	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	43373988	43373991	+	IGR	DEL	GTGC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43373988_43373991delGTGC								GRXCR1 (341315 upstream) : KCTD8 (801931 downstream)																							GTGTGTGTGTGTGCCTACATATGC	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49246538	49246539	+	IGR	DEL	AA	-	-	rs57295322		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49246538_49246539delAA								CWH43 (182445 upstream) : None (None downstream)																							TTAAAACAATAACATAATTATT	0.267													4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54783217	54783218	+	Intron	DEL	AC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54783217_54783218delAC	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)	CTCTCCGGCTACATGACCCTAC	0.554			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
ARL9	132946	broad.mit.edu	37	4	57385208	57385209	+	Intron	DEL	TA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57385208_57385209delTA	uc003hby.1	+							NM_206919	NP_996802	Q6T311	ARL9_HUMAN	ADP-ribosylation factor-like 9								GTP binding				0	Glioma(25;0.08)|all_neural(26;0.101)					taatacctagtatactgtcttg	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69018616	69018617	+	IGR	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69018616_69018617delTG								TMPRSS11F (23029 upstream) : FTLP10 (29393 downstream)																							CAtgtgtggctgtgtgtgtgtg	0.287													4	2	---	---	---	---	
C4orf37	285555	broad.mit.edu	37	4	99064518	99064518	+	5'Flank	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99064518delG	uc003htt.1	-							NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)		GTAAAGTAGAGGGGTGAGCGA	0.507											OREG0016268	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	4	100608467	100608467	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100608467delA								MTTP (63314 upstream) : DAPP1 (129514 downstream)																							ATCGTCATGGAAAAAAAAAGT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	105590730	105590730	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105590730delT	uc003hxh.1	+											Homo sapiens cDNA FLJ37242 fis, clone BRAMY2004335.																		ctcacttgcattccatgcctg	0.000													4	2	---	---	---	---	
ALPK1	80216	broad.mit.edu	37	4	113271670	113271670	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113271670delC	uc003iap.3	+						ALPK1_uc003iam.2_Intron|ALPK1_uc011cfw.1_Intron|ALPK1_uc003ian.3_Intron|ALPK1_uc011cfx.1_Intron|ALPK1_uc003iao.3_Intron	NM_025144	NP_079420	Q96QP1	ALPK1_HUMAN	alpha-kinase 1								ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CGTTGCCTCACCCACTGTAGC	0.453													4	2	---	---	---	---	
SYNPO2	171024	broad.mit.edu	37	4	119932522	119932523	+	Intron	DEL	TA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119932522_119932523delTA	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						CTGATTGCCTTATGACCTTACC	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	138376054	138376054	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138376054delG								None (None upstream) : PCDH18 (64022 downstream)																							tgtgtcttctgttctggtggc	0.000													4	2	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	143183482	143183482	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143183482delG	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_Intron|INPP4B_uc011cho.1_Intron|INPP4B_uc011chp.1_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					cagtcacactggcctatttgc	0.000													4	2	---	---	---	---	
MAP9	79884	broad.mit.edu	37	4	156281741	156281741	+	Intron	DEL	A	-	-	rs78652179		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156281741delA	uc003ios.2	-						MAP9_uc011cin.1_Intron|MAP9_uc010iqa.1_Intron|MAP9_uc003iot.1_Intron	NM_001039580	NP_001034669	Q49MG5	MAP9_HUMAN	aster-associated protein						cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		AGTGATTTACAAAAAAAAATA	0.254													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	160027852	160027852	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160027852delT								C4orf45 (3747 upstream) : RAPGEF2 (161146 downstream)																							ACATATGTAATTTTTTTTCCT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	167448373	167448373	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167448373delC								TLL1 (423380 upstream) : SPOCK3 (206163 downstream)																							CTGGAGATTACCCCATTACCC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	182179853	182179854	+	IGR	INS	-	T	T	rs139673795	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182179853_182179854insT								None (None upstream) : MGC45800 (880305 downstream)																							TACTGACTCTCTGACTCCCAGC	0.436													2	6	---	---	---	---	
WWC2	80014	broad.mit.edu	37	4	184208046	184208046	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184208046delG	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron|WWC2_uc003ivn.3_Intron|WWC2_uc010irz.2_Intron|WWC2_uc003ivo.3_Intron	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		GACAGCAGTTGGGGGGTCTCC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188108408	188108409	+	IGR	INS	-	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188108408_188108409insC								FAT1 (460558 upstream) : ZFP42 (808516 downstream)																							CCTCAAAGTGGCCCCCGATCAG	0.569													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190624464	190624465	+	IGR	DEL	AA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190624464_190624465delAA								None (None upstream) : FRG1 (237509 downstream)																							CCCTCTAAGTAAAGGAAATTAG	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6274450	6274450	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6274450delT								KIAA0947 (784113 upstream) : FLJ33360 (36104 downstream)																							ACTTAAGGGCTTTTTTTTAAA	0.468													5	3	---	---	---	---	
LOC285692	285692	broad.mit.edu	37	5	9871303	9871304	+	Intron	DEL	AA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9871303_9871304delAA	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0						AGGAAATCTTAAAAAGGAGAGA	0.421													4	2	---	---	---	---	
DAP	1611	broad.mit.edu	37	5	10693441	10693441	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10693441delT	uc003jez.3	-						DAP_uc011cmw.1_Intron	NM_004394	NP_004385	P51397	DAP1_HUMAN	death-associated protein						activation of caspase activity|cellular response to amino acid starvation|induction of apoptosis by extracellular signals|negative regulation of autophagy|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent		death domain binding				0		Ovarian(839;1.34e-05)|Breast(839;0.0634)|Lung NSC(810;0.0804)				TGCTGTCTCCTTTTCATGTAA	0.413													4	2	---	---	---	---	
FBXL7	23194	broad.mit.edu	37	5	15902193	15902194	+	Intron	DEL	GC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15902193_15902194delGC	uc003jfn.1	+							NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3						CAGGTTCCATGCAGCTGCCTCC	0.475													4	2	---	---	---	---	
FAM134B	54463	broad.mit.edu	37	5	16591657	16591657	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16591657delC	uc003jfs.2	-							NM_001034850	NP_001030022	Q9H6L5	F134B_HUMAN	hypothetical protein LOC54463 isoform 1						sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3						AGTGTTACCACCCCCTCCCAC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30671685	30671686	+	IGR	DEL	CC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30671685_30671686delCC								None (None upstream) : CDH6 (522110 downstream)																							CTGCAGGAAACCAAGACCAAAT	0.243													4	2	---	---	---	---	
NPR3	4883	broad.mit.edu	37	5	32748539	32748540	+	Intron	INS	-	GCAT	GCAT	rs146034103	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32748539_32748540insGCAT	uc003jhv.2	+						NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Intron	NM_000908	NP_000899	P17342	ANPRC_HUMAN	natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)	aacagcagaaagcattaccacc	0.000													4	2	---	---	---	---	
CAPSL	133690	broad.mit.edu	37	5	35919539	35919539	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35919539delC	uc003jjt.1	-						CAPSL_uc003jju.1_Intron	NM_001042625	NP_001036090	Q8WWF8	CAPSL_HUMAN	calcyphosine-like							cytoplasm	calcium ion binding			skin(1)	1	all_lung(31;0.000268)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.167)|Colorectal(62;0.202)			AATGAAGGTGCCAAGGTTATA	0.368													4	2	---	---	---	---	
TTC33	23548	broad.mit.edu	37	5	40754239	40754239	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40754239delA	uc003jma.2	-						TTC33_uc011cpm.1_Intron|TTC33_uc010ivg.2_Intron	NM_012382	NP_036514	Q6PID6	TTC33_HUMAN	tetratricopeptide repeat domain 33								binding			ovary(1)	1						ACCATATGTGAAAAAACCACG	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42218313	42218313	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42218313delT								FBXO4 (276650 upstream) : GHR (205713 downstream)																							TTTTTGCCCATCACTTTTATC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	43351706	43351706	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43351706delC								HMGCS1 (38111 upstream) : CCL28 (25044 downstream)																							CAAAAAGTGACCCAGAAGTTG	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	51793631	51793631	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51793631delT								None (None upstream) : ITGA1 (290143 downstream)																							GAATGTGATCTTTTGTTTTTC	0.259													0	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	55711282	55711283	+	IGR	INS	-	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55711282_55711283insC								ANKRD55 (182096 upstream) : MAP3K1 (399617 downstream)																							TACAGCCATCACCCCATTTCCC	0.480													4	2	---	---	---	---	
ZSWIM6	57688	broad.mit.edu	37	5	60686692	60686693	+	Intron	DEL	CC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60686692_60686693delCC	uc003jsr.2	+							NM_020928	NP_065979	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6								zinc ion binding				0						TTCTTGGTGTCCACCACACAGT	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	61107601	61107601	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61107601delC								FLJ37543 (105239 upstream) : KIF2A (494388 downstream)																							AGGGAGACCACCAGAAGATAA	0.458													4	2	---	---	---	---	
RGNEF	64283	broad.mit.edu	37	5	72947201	72947201	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72947201delC	uc003kcx.2	+							NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor						cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)		TCCAGATTTTCCAGATAGCAA	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	74244583	74244583	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74244583delA								FAM169A (52795 upstream) : GCNT4 (78707 downstream)																							tgcagatgataatagcactta	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87594335	87594337	+	Intron	DEL	TGT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87594335_87594337delTGT	uc003kjd.2	+						uc003kje.2_Intron					Homo sapiens cDNA clone IMAGE:4814828.																		tgccaaagcatgtaagagtcagt	0.167													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	91139420	91139423	+	IGR	DEL	ACTG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91139420_91139423delACTG								LOC100129716 (422889 upstream) : None (None downstream)																							ACCTGGAATCACTGACTGTTCAGG	0.324													16	12	---	---	---	---	
CHD1	1105	broad.mit.edu	37	5	98192710	98192710	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98192710delC	uc003knf.2	-						CHD1_uc010jbn.2_Intron	NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TTTTATTTTACACATCATTTA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	125432321	125432322	+	IGR	DEL	GT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125432321_125432322delGT								None (None upstream) : GRAMD3 (263466 downstream)																							GCAGTGATTGGTGATAATATAT	0.396													4	2	---	---	---	---	
TMEM173	340061	broad.mit.edu	37	5	138858169	138858170	+	Intron	INS	-	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138858169_138858170insC	uc003lep.2	-							NM_198282	NP_938023	Q86WV6	TM173_HUMAN	transmembrane protein 173						activation of innate immune response|apoptosis|cellular response to exogenous dsRNA|defense response to virus|innate immune response|interferon-beta production|positive regulation of defense response to virus by host|positive regulation of protein binding|positive regulation of protein import into nucleus, translocation|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane|perinuclear region of cytoplasm|plasma membrane	protein homodimerization activity|protein kinase binding|transcription factor binding			upper_aerodigestive_tract(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACCCAGGTCATTGGCCCCCGCA	0.589													3	3	---	---	---	---	
CSF1R	1436	broad.mit.edu	37	5	149454406	149454407	+	Intron	DEL	AC	-	-	rs67638436		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149454406_149454407delAC	uc003lrl.2	-						CSF1R_uc011dcd.1_Intron|CSF1R_uc010jhc.2_Intron|CSF1R_uc003lrm.2_Intron|CSF1R_uc011dce.1_Intron	NM_005211	NP_005202	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor precursor						cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|receptor complex	ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity			haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1)	54			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	cttccttcctacacacacacac	0.000													4	3	---	---	---	---	
ANXA6	309	broad.mit.edu	37	5	150516701	150516702	+	Intron	DEL	GG	-	-	rs145209340	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150516701_150516702delGG	uc003ltl.1	-						ANXA6_uc011dcp.1_Intron|ANXA6_uc003ltm.1_Intron|ANXA6_uc003ltn.1_Intron|ANXA6_uc003lto.1_Intron	NM_001155	NP_001146	P08133	ANXA6_HUMAN	annexin VI isoform 1							melanosome	calcium ion binding|calcium-dependent phospholipid binding|protein binding				0		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGGAGAGAAGGTAGATGGCTA	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151192191	151192192	+	IGR	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151192191_151192192insA								G3BP1 (7278 upstream) : GLRA1 (9883 downstream)																							TGCCCTGTTGGCAGAAACTAGC	0.426													4	2	---	---	---	---	
IL12B	3593	broad.mit.edu	37	5	158757805	158757805	+	5'Flank	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158757805delC	uc003lxr.1	-						uc003lxs.1_5'Flank	NM_002187	NP_002178	P29460	IL12B_HUMAN	interleukin 12B precursor						cell cycle arrest|cell migration|defense response to Gram-negative bacterium|interferon-gamma biosynthetic process|natural killer cell activation|negative regulation of interleukin-10 production|negative regulation of interleukin-17 production|negative regulation of smooth muscle cell proliferation|positive regulation of activated T cell proliferation|positive regulation of activation of JAK2 kinase activity|positive regulation of cell adhesion|positive regulation of defense response to virus by host|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-17 production|positive regulation of memory T cell differentiation|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target|positive regulation of natural killer cell proliferation|positive regulation of NF-kappaB import into nucleus|positive regulation of NK T cell activation|positive regulation of NK T cell proliferation|positive regulation of osteoclast differentiation|positive regulation of smooth muscle cell apoptosis|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat4 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|regulation of tyrosine phosphorylation of Stat1 protein|response to UV-B|sexual reproduction|T-helper 1 type immune response|T-helper cell differentiation	interleukin-12 complex|interleukin-23 complex|membrane	cytokine activity|cytokine receptor activity|interleukin-12 receptor binding|protein heterodimerization activity				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TAGGCAGATTCCCTGGGTTCC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	159079499	159079499	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159079499delA								LOC285627 (186215 upstream) : ADRA1B (264241 downstream)																							gaaccgtaacaaaaaaaagtt	0.055													4	2	---	---	---	---	
SH3PXD2B	285590	broad.mit.edu	37	5	171821317	171821317	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171821317delT	uc003mbr.2	-						SH3PXD2B_uc003mbs.1_Intron	NM_001017995	NP_001017995	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B						adipose tissue development|bone development|cell communication|cell differentiation|eye development|heart development|podosome assembly	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-5-phosphate binding|SH2 domain binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			agcaacaaaattacacataca	0.000													4	2	---	---	---	---	
COL23A1	91522	broad.mit.edu	37	5	177772457	177772457	+	Intron	DEL	T	-	-	rs78634385		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177772457delT	uc003mje.2	-							NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		GTATCATCTCTTTTTTTTTTC	0.289													4	2	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	2116239	2116240	+	Intron	INS	-	TT	TT			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2116239_2116240insTT	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		AAATGCTGTACTGATGGTTCTG	0.322													5	3	---	---	---	---	
TBC1D7	51256	broad.mit.edu	37	6	13326942	13326943	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13326942_13326943insT	uc003naj.2	-						TBC1D7_uc011dis.1_Intron|TBC1D7_uc003nan.2_Intron|TBC1D7_uc003nal.2_Intron|TBC1D7_uc003nam.2_Intron|TBC1D7_uc003nao.2_Intron|TBC1D7_uc010jpd.2_Intron|TBC1D7_uc003nap.2_Intron|TBC1D7_uc003naq.2_Intron	NM_016495	NP_057579	Q9P0N9	TBCD7_HUMAN	TBC1 domain family, member 7 isoform a						positive regulation of protein ubiquitination	cytoplasmic membrane-bounded vesicle	protein binding|Rab GTPase activator activity			ovary(1)	1	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)			GCTTCTGGATGTCTTTTAAGAA	0.327													104	60	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14019219	14019219	+	IGR	DEL	G	-	-	rs57251187		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14019219delG								RNF182 (38986 upstream) : CD83 (98646 downstream)																							catagaaaaagaaaaaactct	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14021063	14021064	+	IGR	DEL	GA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14021063_14021064delGA								RNF182 (40830 upstream) : CD83 (96801 downstream)																							CTGACTCAAGGAGGGCTGCATA	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27226933	27226934	+	IGR	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27226933_27226934delTG								PRSS16 (2684 upstream) : POM121L2 (49908 downstream)																							TGTGTGCATATGTGTGTGTGTT	0.366													4	2	---	---	---	---	
LY6G6F	259215	broad.mit.edu	37	6	31675443	31675444	+	Frame_Shift_Ins	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31675443_31675444insA	uc003nwa.1	+	2	261_262	c.261_262insA	c.(259-264)GGGAACfs	p.G87fs	BAT5_uc011dnz.1_Intron|LY6G6F_uc003nwb.1_Frame_Shift_Ins_p.G87fs	NM_001003693	NP_001003693	Q5SQ64	LY66F_HUMAN	G6f protein precursor	87_88	Extracellular (Potential).|Ig-like V-type.					integral to membrane|plasma membrane				breast(1)|central_nervous_system(1)	2						GACTGCTGGGGAACTATTCTTT	0.584													91	61	---	---	---	---	
TBC1D22B	55633	broad.mit.edu	37	6	37273889	37273889	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37273889delG	uc003onn.2	+						TBC1D22B_uc010jwt.2_Intron|TBC1D22B_uc003ono.1_5'UTR|TBC1D22B_uc003onp.2_5'UTR	NM_017772	NP_060242	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B							intracellular	Rab GTPase activator activity				0			OV - Ovarian serous cystadenocarcinoma(102;0.241)			TGCGTTTGGTGGGACAGTGGT	0.512													4	2	---	---	---	---	
CYP39A1	51302	broad.mit.edu	37	6	46607081	46607082	+	Intron	DEL	AT	-	-	rs138412044	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46607081_46607082delAT	uc003oyf.1	-						CYP39A1_uc011dwa.1_Intron|CYP39A1_uc010jzd.1_Intron	NM_016593	NP_057677	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A,						bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1						tcaaaaaaaaaTAATTTAAAAG	0.218													5	3	---	---	---	---	
OPN5	221391	broad.mit.edu	37	6	47748954	47748956	+	5'Flank	DEL	AAG	-	-	rs148539685		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47748954_47748956delAAG	uc003ozc.2	+							NM_181744	NP_859528	Q6U736	OPN5_HUMAN	opsin 5 isoform 1						phototransduction|protein-chromophore linkage|visual perception	integral to membrane	G-protein coupled receptor activity|photoreceptor activity			ovary(1)	1						AAACAGTACTAAGACCTGTGTAT	0.355													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50581345	50581345	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50581345delC								DEFB112 (564981 upstream) : TFAP2D (99912 downstream)																							acaacagaatccccaccctca	0.000													4	2	---	---	---	---	
ELOVL5	60481	broad.mit.edu	37	6	53142586	53142587	+	Intron	INS	-	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53142586_53142587insC	uc003pbq.1	-						ELOVL5_uc003pbr.1_Intron|ELOVL5_uc011dwx.1_Intron|ELOVL5_uc003pbs.1_Intron	NM_021814	NP_068586	Q9NYP7	ELOV5_HUMAN	elongation of very long chain fatty acids-like						fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Lung NSC(77;0.116)					GCGTTGGAGGTCGGGGGAGGAA	0.535													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57372623	57372623	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57372623delA	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)		AACTTTACAGAAAGATCTCAA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57516345	57516346	+	IGR	INS	-	T	T	rs151188373		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57516345_57516346insT								PRIM2 (2970 upstream) : GUSBL2 (729813 downstream)																							TGGAAGCTGCGTTTTGGATAGG	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	64190432	64190432	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64190432delA								LGSN (160550 upstream) : PTP4A1 (41219 downstream)																							AAAGAAAGCCAAAAAAAAAAC	0.353													4	2	---	---	---	---	
ME1	4199	broad.mit.edu	37	6	84024802	84024803	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84024802_84024803insA	uc003pjy.2	-						ME1_uc011dzb.1_Intron|ME1_uc011dzc.1_Intron	NM_002395	NP_002386	P48163	MAOX_HUMAN	cytosolic malic enzyme 1						carbohydrate metabolic process|cellular lipid metabolic process|malate metabolic process|NADP biosynthetic process|response to carbohydrate stimulus|response to hormone stimulus	cytosol	ADP binding|electron carrier activity|malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|manganese ion binding|NAD binding|NADP binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)	NADH(DB00157)	AAGGTTCTTGTAAAAAAAAAAG	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	86691239	86691239	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86691239delG								SNHG5 (302788 upstream) : HTR1E (955785 downstream)																							aaggacccatggtacctcaat	0.000													4	2	---	---	---	---	
MDN1	23195	broad.mit.edu	37	6	90466282	90466282	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90466282delC	uc003pnn.1	-						MDN1_uc003pno.1_Intron	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GTAACCATTACCAAAAATATA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	114671541	114671542	+	IGR	DEL	CC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114671541_114671542delCC								HS3ST5 (8001 upstream) : None (None downstream)																							CCTTCCTCTTCCTTCAAATAAC	0.381													4	2	---	---	---	---	
ROS1	6098	broad.mit.edu	37	6	117708266	117708267	+	Intron	INS	-	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117708266_117708267insC	uc003pxp.1	-						ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor						transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		ATTTTCTATATAAAGTAAAAGA	0.248			T	GOPC|ROS1	glioblastoma|NSCLC								4	5	---	---	---	---	
HBS1L	10767	broad.mit.edu	37	6	135357649	135357649	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135357649delT	uc003qez.2	-						HBS1L_uc011ecy.1_Intron|HBS1L_uc011ecz.1_Intron|HBS1L_uc011eda.1_Intron|HBS1L_uc003qfa.2_3'UTR	NM_006620	NP_006611	Q9Y450	HBS1L_HUMAN	Hsp70 subfamily B suppressor 1-like protein						signal transduction		GTP binding|GTPase activity|translation elongation factor activity			skin(2)	2	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		AAGACTTTAATTAAAAATAAA	0.289													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	148128216	148128216	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148128216delT								SAMD5 (237059 upstream) : SASH1 (535513 downstream)																							atttctgttgtttttttttgt	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	154259550	154259550	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154259550delT								RGS17 (807161 upstream) : OPRM1 (72086 downstream)																							GATAAACAGGTTTTTTTTTTT	0.279													4	2	---	---	---	---	
ARID1B	57492	broad.mit.edu	37	6	157302936	157302936	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157302936delT	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron|ARID1B_uc003qqq.1_Intron	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		cattacctcgtttttttttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	126462	126463	+	IGR	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126462_126463delTG								None (None upstream) : FAM20C (66506 downstream)																							acatgtgggttgtttccagttt	0.000													4	2	---	---	---	---	
GET4	51608	broad.mit.edu	37	7	935755	935755	+	3'UTR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:935755delG	uc003sjl.1	+	9					GET4_uc003sjj.1_RNA	NM_015949	NP_057033	Q7L5D6	GET4_HUMAN	hypothetical protein LOC51608						tail-anchored membrane protein insertion into ER membrane|transport	BAT3 complex	protein binding				0						GGGATACCGTGGGACTCTGCC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	3123824	3123824	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3123824delC								CARD11 (40245 upstream) : SDK1 (217256 downstream)																							ATCTCATGGACACAAAGAAGG	0.522													4	2	---	---	---	---	
THSD7A	221981	broad.mit.edu	37	7	11574580	11574580	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11574580delG	uc003ssf.3	-							NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		agaccaacttgggcaacacag	0.154										HNSCC(18;0.044)			4	2	---	---	---	---	
MACC1	346389	broad.mit.edu	37	7	20254547	20254548	+	Intron	DEL	CC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20254547_20254548delCC	uc003sus.3	-						MACC1_uc010kug.2_Intron	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						GCACATTTTTCCAGGCCTGCTT	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25366268	25366268	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25366268delG								NPVF (98163 upstream) : MIR148A (623271 downstream)																							CAAGGAAAGTGGGCCTGGAAA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36175742	36175742	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36175742delA								SEPT7 (230827 upstream) : EEPD1 (17094 downstream)																							aacttattttaaaaaaaggaa	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	45292823	45292823	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45292823delC								RAMP3 (68976 upstream) : ADCY1 (320916 downstream)																							ATGCACCTGACCACCTTCTCC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	45308530	45308530	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45308530delC								RAMP3 (84683 upstream) : ADCY1 (305209 downstream)																							ggaacacagacccatacctgc	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	47716802	47716802	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47716802delG								C7orf65 (15556 upstream) : PKD1L1 (97488 downstream)																							tgtttcttcaggtgtgtcttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53667991	53667992	+	IGR	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53667991_53667992delTG								POM121L12 (563374 upstream) : HPVC1 (600925 downstream)																							gcatgagctctgtggagtcacg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	55345308	55345309	+	IGR	DEL	AA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55345308_55345309delAA								EGFR (70278 upstream) : LANCL2 (87832 downstream)																							TCTCACCAGCAAAGCAACAGAG	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	63816325	63816325	+	RNA	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63816325delG	uc003tsz.2	+	1		c.2957delG								Homo sapiens cDNA FLJ41146 fis, clone BRACE2036900.																		GGGTTGATTTGGGGGCAATTG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	66871049	66871050	+	IGR	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66871049_66871050delTG								STAG3L4 (84537 upstream) : None (None downstream)																							attgattttttgacccacaaag	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68681066	68681066	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68681066delG								None (None upstream) : AUTS2 (382839 downstream)																							TGCTTGTACTGGGGATGCTGT	0.403													4	2	---	---	---	---	
DTX2	113878	broad.mit.edu	37	7	76100474	76100474	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76100474delT	uc003uff.3	+						DTX2_uc011kgk.1_Intron|DTX2_uc003ufg.3_Intron|DTX2_uc003ufh.3_Intron|FDPSL2A_uc003ufi.2_RNA	NM_020892	NP_065943	Q86UW9	DTX2_HUMAN	deltex 2 isoform a						Notch signaling pathway	cytoplasm|nucleus	protein binding|zinc ion binding			ovary(1)|skin(1)	2						CCATTCGttcttttttttttt	0.219													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84255544	84255544	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84255544delA								SEMA3A (431327 upstream) : SEMA3D (369330 downstream)																							CAAGAAACAGAAAAAAATGAA	0.313													4	2	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90406573	90406573	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90406573delG	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						AAGTTTTCCAGTAAGGTGCTG	0.214													4	2	---	---	---	---	
ZKSCAN5	23660	broad.mit.edu	37	7	99125093	99125093	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99125093delT	uc003uqv.2	+						ZKSCAN5_uc010lfx.2_Intron|ZKSCAN5_uc003uqw.2_Intron|ZKSCAN5_uc003uqx.2_Intron|ZKSCAN5_uc003uqy.2_Intron	NM_145102	NP_659570	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					gtatgtttcctttttttttta	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	110177044	110177045	+	IGR	DEL	CA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110177044_110177045delCA								EIF3IP1 (576774 upstream) : IMMP2L (126065 downstream)																							GTCACCATCTCACACACACACT	0.391													4	2	---	---	---	---	
ST7	7982	broad.mit.edu	37	7	116653278	116653279	+	Intron	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116653278_116653279delTG	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_5'Flank	NM_021908	NP_068708	Q9NRC1	ST7_HUMAN	suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		TCAGGCATTTTGAGCTTACTAT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124937085	124937086	+	IGR	DEL	TC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124937085_124937086delTC								POT1 (367048 upstream) : None (None downstream)																							ATTTAGTTTATCTCTCTCTCTT	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	125892753	125892754	+	IGR	INS	-	CAT	CAT	rs143712589	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125892753_125892754insCAT								None (None upstream) : GRM8 (185898 downstream)																							ATTTCAACAAACATTTATACAA	0.361													4	2	---	---	---	---	
SND1	27044	broad.mit.edu	37	7	127584744	127584744	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127584744delC	uc003vmi.2	+						SND1_uc010lle.2_Intron	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						GTGAATTGAGCCCTGCATTGA	0.448													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128574023	128574024	+	IGR	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128574023_128574024insA								KCP (23250 upstream) : IRF5 (3745 downstream)																							GCATTAATCCTAAAAAAAAAGA	0.421													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146868581	146868583	+	Intron	DEL	GAC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146868581_146868583delGAC	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CTACACAAAAGACCAAAAAGTGA	0.369										HNSCC(39;0.1)			4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151956929	151956929	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151956929delC	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)		ACAGTAAACACTCAAAAGTTA	0.428			N		medulloblastoma								4	2	---	---	---	---	
VIPR2	7434	broad.mit.edu	37	7	158919789	158919789	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158919789delG	uc003woh.2	-						VIPR2_uc010lqx.2_Intron|VIPR2_uc010lqy.2_Intron	NM_003382	NP_003373	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2						cell-cell signaling	integral to plasma membrane				lung(1)|central_nervous_system(1)	2	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		TTAGAATGCTGCAGAGGATAC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	13695699	13695699	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13695699delT								C8orf48 (269903 upstream) : SGCZ (251675 downstream)																							gtagcacacattccctagcct	0.000													4	2	---	---	---	---	
MSR1	4481	broad.mit.edu	37	8	16000841	16000842	+	Intron	INS	-	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16000841_16000842insG	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron|MSR1_uc003wxb.2_Intron|MSR1_uc011kxz.1_Intron	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		TATTCATCACAAAAACAAAAGA	0.267													6	3	---	---	---	---	
SFTPC	6440	broad.mit.edu	37	8	22018629	22018629	+	5'Flank	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22018629delG	uc003xax.3	+						SFTPC_uc003xaw.3_Intron|SFTPC_uc011kza.1_5'Flank|SFTPC_uc003xaz.2_5'Flank|SFTPC_uc003xay.3_5'Flank	NM_003018	NP_003009	P11686	PSPC_HUMAN	surfactant protein C precursor						respiratory gaseous exchange	extracellular space					0				Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		GAGCAAAGAAGGAAGCACTGC	0.512													4	2	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	26171990	26171991	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26171990_26171991insT	uc003xeu.2	+						PPP2R2A_uc003xek.2_Intron|PPP2R2A_uc011laf.1_Intron	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)		tttctttcttgttttatgctat	0.000													4	2	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	26220031	26220031	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26220031delA	uc003xeu.2	+						PPP2R2A_uc003xek.2_Intron|PPP2R2A_uc011laf.1_Intron	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)		aataaaaattaaaaaaaaaaG	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	26579550	26579551	+	IGR	INS	-	TG	TG			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26579550_26579551insTG								DPYSL2 (63857 upstream) : ADRA1A (26116 downstream)																							GTAAATATTTATGTGTGTGTGT	0.361													4	2	---	---	---	---	
CHRNA2	1135	broad.mit.edu	37	8	27338313	27338314	+	5'Flank	DEL	CC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27338313_27338314delCC	uc010lur.2	-						CHRNA2_uc011lal.1_5'Flank|CHRNA2_uc010lus.2_5'Flank	NM_000742	NP_000733	Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha							cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(1)	1		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Gallamine Triethiodide(DB00483)|Levallorphan(DB00504)|Mecamylamine(DB00657)|Metocurine(DB01336)|Metocurine Iodide(DB00416)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Rocuronium(DB00728)|Tubocurarine(DB01199)	agttaattctcctccagccctg	0.020													4	2	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	31856562	31856562	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31856562delT	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)		TATATAGTTCTTTTTTTTTTC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	39721797	39721797	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39721797delG								ADAM2 (26018 upstream) : IDO1 (49531 downstream)																							AGTGAGGGCTGGAAAACCGTG	0.368													4	2	---	---	---	---	
ANK1	286	broad.mit.edu	37	8	41541906	41541906	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41541906delG	uc003xok.2	-						NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Intron|ANK1_uc003xoi.2_Intron|ANK1_uc003xoj.2_Intron|ANK1_uc003xol.2_Intron|ANK1_uc003xom.2_Intron	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1						axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CTGCTTCCCCGGAAAGGAGGA	0.602													4	2	---	---	---	---	
IKBKB	3551	broad.mit.edu	37	8	42143763	42143763	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42143763delC	uc003xow.1	+						IKBKB_uc003xov.2_Intron|IKBKB_uc010lxh.1_Intron|IKBKB_uc011lco.1_Intron|IKBKB_uc010lxj.1_Intron|IKBKB_uc003xox.1_Intron|IKBKB_uc011lcp.1_Intron|IKBKB_uc011lcq.1_Intron|IKBKB_uc010lxi.1_Intron|IKBKB_uc011lcr.1_Intron	NM_001556	NP_001547	O14920	IKKB_HUMAN	inhibitor of nuclear factor kappa B kinase beta						anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)	ACCTTTTTTTCTGAAGCTTTT	0.423													4	2	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48557493	48557493	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48557493delG	uc003xqd.2	+						KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				ctattgcaaagaaaaggatgg	0.000													4	2	---	---	---	---	
TCEA1	6917	broad.mit.edu	37	8	54924200	54924201	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54924200_54924201insA	uc003xru.2	-						TCEA1_uc003xrv.2_Intron|TCEA1_uc011ldw.1_Intron|TCEA1_uc003xrw.1_Intron	NM_006756	NP_006747	P23193	TCEA1_HUMAN	transcription elongation factor A 1 isoform 1						positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			GCTATCCCCCCAAAAAAACAGA	0.342			T	PLAG1	salivary adenoma								4	2	---	---	---	---	
ASPH	444	broad.mit.edu	37	8	62422428	62422429	+	Intron	DEL	TA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62422428_62422429delTA	uc003xuj.2	-						ASPH_uc011leg.1_Intron	NM_004318	NP_004309	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	GCTCCAGGCCTATCAAATCACG	0.554													4	2	---	---	---	---	
CPA6	57094	broad.mit.edu	37	8	68568239	68568239	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68568239delG	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			GGAGGCTTATGGGCTTTATGA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	76214551	76214551	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76214551delT								CRISPLD1 (267760 upstream) : HNF4G (105632 downstream)																							ACACAGATGCTTCCCTTTCTT	0.443													4	2	---	---	---	---	
STMN2	11075	broad.mit.edu	37	8	80544125	80544127	+	Intron	DEL	ATG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80544125_80544127delATG	uc003ybj.2	+						STMN2_uc010lzp.2_Intron|STMN2_uc011lfn.1_Intron	NM_007029	NP_008960	Q93045	STMN2_HUMAN	superiorcervical ganglia, neural specific 10						intracellular signal transduction|negative regulation of microtubule depolymerization|negative regulation of microtubule polymerization|negative regulation of neuron projection development|neuron differentiation|positive regulation of microtubule depolymerization|positive regulation of neuron projection development	axon|growth cone|membrane|membrane fraction|perinuclear region of cytoplasm|soluble fraction	protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)			TTATTTCCTTATGAAAAGAAAAG	0.330													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	83490482	83490482	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83490482delT								SNX16 (735961 upstream) : None (None downstream)																							tacaggagaataaaaagagga	0.000													4	2	---	---	---	---	
WWP1	11059	broad.mit.edu	37	8	87464566	87464567	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87464566_87464567insT	uc003ydt.2	+							NM_007013	NP_008944	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase						central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction	cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			lung(1)|liver(1)	2						TTTATTTTAAAAGCATCCTTTT	0.218													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	88756737	88756738	+	IGR	INS	-	TT	TT	rs148537266	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88756737_88756738insTT								CNBD1 (361782 upstream) : DCAF4L2 (126235 downstream)																							AGGAAAGTAACATTGCCAACCC	0.322													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94536901	94536901	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94536901delC								C8orf83 (507000 upstream) : FAM92A1 (175872 downstream)																							catccaaaaaccaacctcagg	0.000													4	2	---	---	---	---	
RPL30	6156	broad.mit.edu	37	8	99054249	99054250	+	Intron	DEL	GA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99054249_99054250delGA	uc003yif.2	-						RPL30_uc010mbk.1_Intron	NM_000989	NP_000980	P62888	RL30_HUMAN	ribosomal protein L30						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.192)			TCTTAAGGTTGACCAAAGATAA	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102275884	102275885	+	IGR	INS	-	C	C			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102275884_102275885insC								ZNF706 (57924 upstream) : NACAP1 (98137 downstream)																							TCTGGGTATTTCCCCCTTCTTT	0.475													6	3	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	102946906	102946906	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102946906delA	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)			atatgacaggaaaaaaaaaca	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103482506	103482507	+	IGR	DEL	GG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103482506_103482507delGG								UBR5 (58011 upstream) : ODF1 (81341 downstream)																							CAGTAACCTTGGATGGTTCTCT	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116800925	116800925	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116800925delT								TRPS1 (119697 upstream) : EIF3H (856131 downstream)																							ATCTGGTGGCTTTTTTTTTTA	0.284													5	3	---	---	---	---	
MAL2	114569	broad.mit.edu	37	8	120232946	120232946	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120232946delC	uc003yop.2	+							NM_052886	NP_443118	Q969L2	MAL2_HUMAN	MAL2 proteolipid protein							apical plasma membrane|endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding				0	all_cancers(13;1.91e-26)|Lung NSC(37;8.61e-08)|Ovarian(258;0.018)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000967)			tgccatggaacccccctttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	123539056	123539056	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123539056delC								HAS2AS (882123 upstream) : ZHX2 (254845 downstream)																							TCTTCTAACTCCCACACTTAG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125157641	125157641	+	Intron	DEL	C	-	-	rs36045593		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125157641delC	uc003yqy.1	-											Homo sapiens cDNA FLJ32770 fis, clone TESTI2001898.																		AATACCCATTCCCCCTCGCCT	0.458													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127423975	127423976	+	IGR	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127423975_127423976delTG								TRIB1 (973333 upstream) : FAM84B (140711 downstream)																							GATAGGCTGATGTGTGTGTGTA	0.431													4	2	---	---	---	---	
ADCY8	114	broad.mit.edu	37	8	132027685	132027685	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132027685delT	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			TAATGAGGAGTACAGATTCCA	0.184										HNSCC(32;0.087)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137655834	137655834	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137655834delG								KHDRBS3 (995988 upstream) : None (None downstream)																							ctaggatactgcagccctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143160732	143160733	+	IGR	INS	-	AC	AC	rs146417549	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143160732_143160733insAC								MIR1302-7 (293058 upstream) : NCRNA00051 (118984 downstream)																							tgtatgtacatacacacacata	0.000													3	3	---	---	---	---	
TSNARE1	203062	broad.mit.edu	37	8	143406913	143406913	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143406913delC	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron|TSNARE1_uc003ywl.3_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GACAGGCCAGCCCACGACCGG	0.438													4	2	---	---	---	---	
SCRIB	23513	broad.mit.edu	37	8	144873997	144873997	+	Intron	DEL	A	-	-	rs6982642		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144873997delA	uc003yzp.1	-						SCRIB_uc003yzn.1_Intron|SCRIB_uc003yzo.1_Intron	NM_015356	NP_056171	Q14160	SCRIB_HUMAN	scribble isoform b						activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction	cell-cell adherens junction|Scrib-APC-beta-catenin complex	protein binding			urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GCCAGACCCCACCCCCATGCC	0.677													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	22258169	22258169	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22258169delC								CDKN2BAS (137078 upstream) : DMRTA1 (188671 downstream)																							caagttagctccagggtgtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	35927824	35927824	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35927824delC								LOC158376 (16207 upstream) : OR2S2 (29282 downstream)																							tcctgagcagccaggtgagtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	37041134	37041136	+	IGR	DEL	TGC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37041134_37041136delTGC								PAX5 (6658 upstream) : ZCCHC7 (79333 downstream)																							CAAGAACATTTGCAGAGATGCCT	0.576													4	2	---	---	---	---	
FRMPD1	22844	broad.mit.edu	37	9	37746529	37746529	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37746529delG	uc004aag.1	+	16	4544	c.4500delG	c.(4498-4500)CTGfs	p.L1500fs	FRMPD1_uc004aah.1_Frame_Shift_Del_p.L1500fs	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1500						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		TGGTCCAGCTGGCCGGCCTGT	0.622													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69823244	69823245	+	IGR	INS	-	A	A	rs144648870	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69823244_69823245insA								LOC100133920 (158295 upstream) : FOXD4L5 (352464 downstream)																							TCAGATATAGTTCTACTATGTA	0.376													4	2	---	---	---	---	
VPS13A	23230	broad.mit.edu	37	9	79836376	79836376	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79836376delT	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10						TTTATTGACCTTTTCATCTCT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85122678	85122678	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85122678delA								FLJ46321 (512508 upstream) : RASEF (474639 downstream)																							tcagtggaagaaaaaaaaaaa	0.000													5	3	---	---	---	---	
HSD17B3	3293	broad.mit.edu	37	9	99059758	99059758	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99059758delA	uc004awa.1	-						HSD17B3_uc010msc.1_Intron	NM_000197	NP_000188	P37058	DHB3_HUMAN	estradiol 17 beta-dehydrogenase 3						androgen biosynthetic process|male genitalia development	endoplasmic reticulum membrane|microsome	binding|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity				0		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)			NADH(DB00157)	cctcccaagtagctgggatta	0.000													6	5	---	---	---	---	
LPAR1	1902	broad.mit.edu	37	9	113644295	113644296	+	Intron	DEL	CT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113644295_113644296delCT	uc004bfa.2	-						LPAR1_uc011lwm.1_Intron|LPAR1_uc004bfb.2_Intron|LPAR1_uc004bfc.2_Intron|LPAR1_uc011lwn.1_Intron|LPAR1_uc011lwo.1_Intron|LPAR1_uc010mub.2_Intron	NM_057159	NP_476500	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2						gctgggattactctctctgcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	118505383	118505383	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118505383delA								DEC1 (340460 upstream) : C9orf27 (145163 downstream)																							ctcaggatccaaactcaggtg	0.020													4	2	---	---	---	---	
DENND1A	57706	broad.mit.edu	37	9	126525536	126525537	+	Intron	DEL	CC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126525536_126525537delCC	uc004bnz.1	-						DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						ttgcagtagtccaggtgagact	0.000													4	2	---	---	---	---	
RALGPS1	9649	broad.mit.edu	37	9	129773017	129773017	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129773017delA	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron	NM_014636	NP_055451	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1						GGCTCCTGCTAATTGATGGCC	0.512													4	2	---	---	---	---	
BAT2L1	84726	broad.mit.edu	37	9	134349749	134349749	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134349749delT	uc004can.3	+						BAT2L1_uc010mzj.1_Intron|BAT2L1_uc004cao.3_Intron	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like								protein binding				0						tttgtttttgtttttTCTTTT	0.234													4	2	---	---	---	---	
ADAMTS13	11093	broad.mit.edu	37	9	136294729	136294730	+	Intron	INS	-	T	T	rs143601101	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136294729_136294730insT	uc004cdv.3	+						ADAMTS13_uc004cdp.3_Intron|ADAMTS13_uc004cdt.1_Intron|ADAMTS13_uc004cdu.1_Intron|ADAMTS13_uc004cdw.3_Intron|ADAMTS13_uc004cdx.3_Intron|ADAMTS13_uc004cdy.1_Intron|ADAMTS13_uc004cdz.3_5'Flank|ADAMTS13_uc004cdq.1_Intron|ADAMTS13_uc004cds.1_Intron|ADAMTS13_uc004cdr.1_Intron	NM_139025	NP_620594	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1						cell-matrix adhesion|glycoprotein metabolic process|integrin-mediated signaling pathway|peptide catabolic process|platelet activation|protein processing|proteolysis	cell surface|proteinaceous extracellular matrix	calcium ion binding|integrin binding|metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|kidney(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		ACACCCCTATCTCCCCCACCCG	0.579													6	4	---	---	---	---	
SNAPC4	6621	broad.mit.edu	37	9	139288494	139288495	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139288494_139288495insA	uc004chh.2	-							NM_003086	NP_003077	Q5SXM2	SNPC4_HUMAN	small nuclear RNA activating complex,						snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter	snRNA-activating protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		ctcagcctcccgagtagctggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	139600493	139600493	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139600493delG								AGPAT2 (18582 upstream) : FAM69B (6531 downstream)																							gtgatcttgtgggtgtggcat	0.000													4	2	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1506164	1506164	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1506164delC	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		caaacgcaaacccccataaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	1817193	1817194	+	IGR	INS	-	A	A	rs150111362	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1817193_1817194insA								ADARB2 (37475 upstream) : None (None downstream)																							GAGGTGATAATAAAAAAACGAT	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3585414	3585414	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3585414delG	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																		TACCCTCTCTGTGCTCGCTCC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	22578361	22578362	+	IGR	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22578361_22578362insA								DNAJC1 (285711 upstream) : COMMD3 (26937 downstream)																							aaaaagaaaagaaaaaaaaatg	0.000													4	2	---	---	---	---	
MPP7	143098	broad.mit.edu	37	10	28552284	28552285	+	Intron	INS	-	C	C	rs141047282	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28552284_28552285insC	uc001iua.1	-						MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1						tttgcatagttctgcaaataaa	0.238													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	28924505	28924506	+	IGR	INS	-	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28924505_28924506insG								WAC (14584 upstream) : BAMBI (41918 downstream)																							ggagatgaggaagagagaaggg	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	34153682	34153682	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34153682delA								NRP1 (529676 upstream) : PARD3 (246416 downstream)																							TGTAAAAAAGAAAAAAAAAAC	0.388													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38019472	38019472	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38019472delT								ANKRD30A (497977 upstream) : ZNF248 (70975 downstream)																							AGTTTATGCATTTTATTGACT	0.318													4	2	---	---	---	---	
GPRIN2	9721	broad.mit.edu	37	10	47002410	47002411	+	3'UTR	DEL	CA	-	-	rs140058802		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47002410_47002411delCA	uc010qfq.1	+	1						NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth												0						CATACACAGGCACACATGTGTG	0.559													2	5	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47041869	47041869	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47041869delT	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						tgtttctgtctttgcattcag	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64470355	64470356	+	IGR	DEL	CT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64470355_64470356delCT								ZNF365 (38584 upstream) : ADO (94160 downstream)																							tagaaagggcctcaactaacaa	0.000													4	2	---	---	---	---	
SGPL1	8879	broad.mit.edu	37	10	72634824	72634824	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72634824delT	uc001jrm.2	+						SGPL1_uc009xqk.2_Intron	NM_003901	NP_003892	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1						apoptosis|carboxylic acid metabolic process|ceramide metabolic process|sphingolipid catabolic process	integral to endoplasmic reticulum membrane	carboxy-lyase activity|pyridoxal phosphate binding|sphinganine-1-phosphate aldolase activity				0					Pyridoxal Phosphate(DB00114)	TTTCCAGAAATTTTTTTAGTA	0.378													4	2	---	---	---	---	
KCNMA1	3778	broad.mit.edu	37	10	78727559	78727559	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78727559delT	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxk.1_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxl.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)	GCTTGGCAAGTTTCCACTCAC	0.547													4	2	---	---	---	---	
ZCCHC24	219654	broad.mit.edu	37	10	81176599	81176599	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81176599delA	uc001kak.2	-						ZCCHC24_uc010qlr.1_Intron|ZCCHC24_uc009xrw.2_Intron	NM_153367	NP_699198	Q8N2G6	ZCH24_HUMAN	zinc finger, CCHC domain containing 24								nucleic acid binding|zinc ion binding			breast(1)	1						gggccatgagaagattagagg	0.095													4	2	---	---	---	---	
GOT1	2805	broad.mit.edu	37	10	101165548	101165549	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101165548_101165549delGA	uc001kpr.2	-	5	814_815	c.606_607delTC	c.(604-609)ACTCCGfs	p.T202fs	GOT1_uc009xwh.2_RNA|GOT1_uc001kpq.1_5'UTR	NM_002079	NP_002070	P17174	AATC_HUMAN	aspartate aminotransferase 1	202_203					aspartate catabolic process|cellular response to insulin stimulus|gluconeogenesis|response to glucocorticoid stimulus	cytosol	L-aspartate:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding				0		Ovarian(717;0.028)|Colorectal(252;0.234)		Epithelial(162;4.76e-10)|all cancers(201;3.84e-08)	L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	CACTGCTCCGGAGTTGGGTCAA	0.431													132	71	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102429352	102429353	+	IGR	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102429352_102429353insA								HIF1AN (115672 upstream) : PAX2 (76115 downstream)																							TGACCTATGGGAACCAAAGCAC	0.609													4	2	---	---	---	---	
FBXW4	6468	broad.mit.edu	37	10	103399046	103399047	+	Intron	INS	-	G	G	rs143359606	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103399046_103399047insG	uc001kto.2	-							NM_022039	NP_071322	P57775	FBXW4_HUMAN	F-box and WD repeat domain containing 4						ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	ubiquitin ligase complex				skin(1)	1		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)		TAGAATATGGCGGGTTTTGCTA	0.480													4	3	---	---	---	---	
GPAM	57678	broad.mit.edu	37	10	113918297	113918297	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113918297delC	uc009xxy.1	-						GPAM_uc001kzp.2_Intron|GPAM_uc001kzq.1_Intron	NM_020918	NP_065969	Q9HCL2	GPAT1_HUMAN	mitochondrial glycerol 3-phosphate						phospholipid biosynthetic process|triglyceride biosynthetic process	integral to membrane|mitochondrial outer membrane	glycerol-3-phosphate O-acyltransferase activity			ovary(1)|skin(1)	2				Epithelial(162;0.0306)|all cancers(201;0.123)		ATTCCCAGTGCCCACTGTCTT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	120771128	120771129	+	IGR	DEL	CG	-	-	rs115685587	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120771128_120771129delCG								C10orf46 (256370 upstream) : NANOS1 (18099 downstream)																							CAGCAATATCCGTGATAATAAA	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122381408	122381408	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122381408delA								PPAPDC1A (32041 upstream) : WDR11 (229287 downstream)																							ggtacaattcaaatccaaatc	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	128589057	128589058	+	IGR	DEL	GC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128589057_128589058delGC								C10orf90 (229978 upstream) : DOCK1 (4965 downstream)																							CGTAGGGTCTGCCTTAATGATC	0.465													4	2	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	128835774	128835774	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128835774delA	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)		ATTTCATGGTAAATGTCGTTG	0.348													4	2	---	---	---	---	
BNIP3	664	broad.mit.edu	37	10	133785543	133785544	+	Intron	INS	-	TG	TG	rs147043799	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133785543_133785544insTG	uc001lkv.1	-						BNIP3_uc001lku.1_5'Flank|BNIP3_uc010qut.1_Intron	NM_004052	NP_004043	Q12983	BNIP3_HUMAN	BCL2/adenovirus E1B 19kD-interacting protein 3						cellular response to cobalt ion|cellular response to hypoxia|cellular response to mechanical stimulus|chromatin remodeling|defense response to virus|DNA fragmentation involved in apoptotic nuclear change|induction of apoptosis|interspecies interaction between organisms|mitochondrial fragmentation involved in apoptosis|negative regulation of membrane potential|negative regulation of mitochondrial fusion|negative regulation of survival gene product expression|neuron apoptosis|positive regulation of mitochondrial fission|positive regulation of protein complex disassembly|positive regulation of release of cytochrome c from mitochondria|reactive oxygen species metabolic process|regulation of mitochondrial membrane permeability	dendrite|integral to mitochondrial outer membrane|nuclear envelope|nucleoplasm	GTPase binding|protein heterodimerization activity|protein homodimerization activity			lung(1)|skin(1)	2		all_cancers(35;4e-11)|all_epithelial(44;5.07e-08)|Ovarian(717;2.61e-05)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Breast(234;0.023)|all_neural(114;0.0299)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)		Epithelial(32;1.59e-12)|all cancers(32;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(35;2.57e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CAAGAAAACACATCGCGCATCT	0.505													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	4442698	4442698	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4442698delA								TRIM21 (27772 upstream) : OR52K2 (27872 downstream)																							aacctcagttaaaaaaatctc	0.149													4	2	---	---	---	---	
BTBD10	84280	broad.mit.edu	37	11	13461498	13461498	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13461498delG	uc001mkz.2	-						BTBD10_uc010rcl.1_Frame_Shift_Del_p.L20fs|BTBD10_uc001mla.2_Intron|BTBD10_uc009ygn.2_Intron|BTBD10_uc010rcm.1_Intron|BTBD10_uc010rcn.1_Intron|BTBD10_uc009ygo.2_Intron	NM_032320	NP_115696	Q9BSF8	BTBDA_HUMAN	K+ channel tetramerization protein							nucleus					0				Epithelial(150;0.0214)		AGAGTATAAAGGGACTCTGCT	0.363													4	2	---	---	---	---	
USH1C	10083	broad.mit.edu	37	11	17528181	17528181	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17528181delT	uc001mnf.2	-						USH1C_uc001mne.2_Intron|USH1C_uc009yhb.2_Intron|USH1C_uc001mng.2_Intron|USH1C_uc001mnd.2_Intron	NM_005709	NP_005700	Q9Y6N9	USH1C_HUMAN	harmonin isoform a						equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1						actgcctagctttagcctcaa	0.000													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	20856359	20856359	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20856359delG	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						AGAAAGGACTGGAGTTAGAGG	0.388													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21345428	21345428	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21345428delA	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						agggttgagcaaaaatatgtt	0.164													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21426753	21426753	+	Intron	DEL	C	-	-	rs113010567		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21426753delC	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						GGTTTTGTTGCTGCTCCTTGG	0.468													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21426755	21426756	+	Intron	DEL	GC	-	-	rs66537440		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21426755_21426756delGC	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						TTTTGTTGCTGCTCCTTGGCTT	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	33440837	33440837	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33440837delA								HIPK3 (64898 upstream) : C11orf41 (123040 downstream)																							AGAATTGAGTAATGAGCCTGG	0.333													4	2	---	---	---	---	
HSD17B12	51144	broad.mit.edu	37	11	43738401	43738401	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43738401delG	uc001mxq.3	+						HSD17B12_uc001mxp.2_Intron	NM_016142	NP_057226	Q53GQ0	DHB12_HUMAN	hydroxysteroid (17-beta) dehydrogenase 12						long-chain fatty-acyl-CoA biosynthetic process|steroid biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	estradiol 17-beta-dehydrogenase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity				0						cccaggtgaaggaggcagggg	0.045													4	2	---	---	---	---	
EXT2	2132	broad.mit.edu	37	11	44102399	44102399	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44102399delA	uc010rfo.1	+						ACCS_uc009yks.1_Intron|ACCS_uc001mxx.2_Intron	NM_207122	NP_997005	Q93063	EXT2_HUMAN	exostosin 2 isoform 2						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5						gtcatttgctaacccctgCTC	0.209			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				4	2	---	---	---	---	
SLC39A13	91252	broad.mit.edu	37	11	47377894	47377895	+	Intron	DEL	CA	-	-	rs141558426		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47377894_47377895delCA	uc001nfd.2	+						SPI1_uc001nfb.1_Intron|SPI1_uc001nfc.1_Intron			Q96H72	S39AD_HUMAN	RecName: Full=Zinc transporter ZIP13; AltName: Full=Zrt- and Irt-like protein 13;          Short=ZIP-13; AltName: Full=Solute carrier family 39 member 13; AltName: Full=LIV-1 subfamily of ZIP zinc transporter 9; AltName: Full=LZT-Hs9;						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				Lung(87;0.0936)		ACAACCCACTCACACACACCTG	0.139													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59059111	59059111	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59059111delT								MPEG1 (78617 upstream) : OR5AN1 (72821 downstream)																							ACTGTCTCACTTACACCACTT	0.383													4	2	---	---	---	---	
AHNAK	79026	broad.mit.edu	37	11	62215824	62215825	+	Intron	INS	-	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62215824_62215825insG	uc001ntk.1	-							NM_024060	NP_076965	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 2						nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				tggatggaagaggaaagatcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	64199892	64199893	+	IGR	DEL	AG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64199892_64199893delAG								RPS6KA4 (60206 upstream) : SLC22A11 (123205 downstream)																							agagacagacagagagagagag	0.000													3	3	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70510841	70510841	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70510841delC	uc001oqc.2	-						SHANK2_uc010rqn.1_5'Flank|SHANK2_uc001opz.2_5'Flank|SHANK2_uc010rqp.1_5'Flank	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			AGGGGGGCTGCCCAGACACTT	0.413													4	2	---	---	---	---	
ARHGEF17	9828	broad.mit.edu	37	11	73066671	73066671	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73066671delC	uc001otu.2	+	4	3568	c.3547delC	c.(3547-3549)CCTfs	p.P1183fs		NM_014786	NP_055601	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1183	DH.				actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0						GGAGGCGAGGCCTGCCTTTCT	0.557													65	38	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	77323260	77323260	+	IGR	DEL	T	-	-	rs111330259		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77323260delT								AQP11 (2569 upstream) : CLNS1A (3937 downstream)																							gaaTAGCAGCTTTTTTTTTTT	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	80712232	80712232	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80712232delA								None (None upstream) : None (None downstream)																							tggaccaggcaatggggtgcc	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	85997423	85997423	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85997423delA								EED (7645 upstream) : C11orf73 (15830 downstream)																							GTTTCGAAGGAAAAAAAATGG	0.259													4	2	---	---	---	---	
FAM55B	120406	broad.mit.edu	37	11	114550089	114550089	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114550089delG	uc009yyy.2	+							NM_182495	NP_872301	Q96DL1	FA55B_HUMAN	hypothetical protein LOC120406							integral to membrane				ovary(1)	1						CTAAAACCTTGTTGTCCATGC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116575320	116575320	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116575320delC								None (None upstream) : BUD13 (43568 downstream)																							CACAGGGACACCCCCAGACAC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	121563173	121563174	+	IGR	DEL	CA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121563173_121563174delCA								SORL1 (58702 upstream) : LOC399959 (396637 downstream)																							cacctgGCTTCAACCTACAGTT	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	125951641	125951641	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125951641delG								CDON (18454 upstream) : RPUSD4 (120349 downstream)																							ttgatattttgggccagataa	0.095													4	2	---	---	---	---	
TIRAP	114609	broad.mit.edu	37	11	126160676	126160677	+	Intron	DEL	TC	-	-	rs147593820	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126160676_126160677delTC	uc001qdm.1	+						TIRAP_uc001qdl.1_Intron|TIRAP_uc009zcb.1_Intron|TIRAP_uc001qdn.1_Intron|TIRAP_uc001qdo.1_Intron	NM_001039661	NP_001034750	P58753	TIRAP_HUMAN	Toll-interleukin 1 receptor domain-containing						3'-UTR-mediated mRNA stabilization|cellular response to bacterial lipopeptide|cellular response to lipoteichoic acid|defense response to Gram-positive bacterium|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|myeloid cell differentiation|negative regulation of growth of symbiont in host|positive regulation of B cell proliferation|positive regulation of chemokine (C-X-C motif) ligand 1 production|positive regulation of chemokine (C-X-C motif) ligand 2 production|positive regulation of ERK1 and ERK2 cascade|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-12 production|positive regulation of interleukin-15 production|positive regulation of interleukin-6 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of JNK cascade|positive regulation of neutrophil chemotaxis|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein homodimerization activity|positive regulation of toll-like receptor 2 signaling pathway|positive regulation of toll-like receptor 3 signaling pathway|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|regulation of interferon-beta production|response to lipopolysaccharide|TIRAP-dependent toll-like receptor 4 signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway	endocytic vesicle|intrinsic to membrane|ruffle membrane	phosphatidylinositol-4,5-bisphosphate binding|protein binding, bridging|protein heterodimerization activity|protein homodimerization activity|protein kinase C delta binding|Toll-like receptor 2 binding|Toll-like receptor 4 binding|transmembrane receptor activity			ovary(1)	1	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		CCTTTGTGATTCTCTCTCTCTA	0.525													4	2	---	---	---	---	
VPS26B	112936	broad.mit.edu	37	11	134114477	134114478	+	Intron	DEL	GG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134114477_134114478delGG	uc001qhe.2	+							NM_052875	NP_443107	Q4G0F5	VP26B_HUMAN	vacuolar protein sorting 26 homolog B						protein transport|vacuolar transport	cytosol|retromer complex					0	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;2.43e-10)|all cancers(11;2.94e-09)|BRCA - Breast invasive adenocarcinoma(10;9.57e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00164)|Lung(977;0.216)		CAGAACTGCTGGGTGAAGTGGT	0.361											OREG0021548	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
WNK1	65125	broad.mit.edu	37	12	957526	957526	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:957526delA	uc001qio.3	+						WNK1_uc001qip.3_Intron	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			ATTGGAGATGAAGAGAATGGA	0.353													4	2	---	---	---	---	
CD4	920	broad.mit.edu	37	12	6928158	6928160	+	Intron	DEL	AGC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6928158_6928160delAGC	uc001qqv.1	+						CD4_uc010sfj.1_Intron|CD4_uc009zfc.1_Intron|CD4_uc010sfk.1_Intron|CD4_uc010sfl.1_Intron|CD4_uc010sfm.1_Intron|GPR162_uc010sfn.1_5'Flank|GPR162_uc001qqw.1_5'Flank|GPR162_uc001qqx.1_5'Flank|GPR162_uc009zfd.1_5'Flank	NM_000616	NP_000607	P01730	CD4_HUMAN	CD4 antigen precursor						cell adhesion|entry into host cell|immune response|induction by virus of host cell-cell fusion|initiation of viral infection|maintenance of protein location in cell|positive regulation of interleukin-2 biosynthetic process|positive regulation of protein kinase activity|protein palmitoleylation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|T cell selection|transmembrane receptor protein tyrosine kinase signaling pathway	early endosome|endoplasmic reticulum membrane|integral to membrane|T cell receptor complex	coreceptor activity|extracellular matrix structural constituent|glycoprotein binding|MHC class II protein binding|protein homodimerization activity|protein kinase binding|transmembrane receptor activity|zinc ion binding				0		Myeloproliferative disorder(1001;0.0122)				gaggaaggggagCAaaggggggc	0.089													9	4	---	---	---	---	
AICDA	57379	broad.mit.edu	37	12	8757273	8757274	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8757273_8757274insA	uc001qur.2	-						AICDA_uc001qup.1_Intron|AICDA_uc001quq.1_Intron|AICDA_uc009zgd.1_Intron	NM_020661	NP_065712	Q9GZX7	AICDA_HUMAN	activation-induced cytidine deaminase						B cell differentiation|DNA demethylation|mRNA processing|negative regulation of methylation-dependent chromatin silencing	cytoplasm	cytidine deaminase activity|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung SC(5;0.184)					CTGATGTGGAGGAGAAATAAAG	0.342									Immune_Deficiency_with_Hyper-IgM				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	22141338	22141339	+	IGR	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22141338_22141339delTG								ABCC9 (47002 upstream) : CMAS (57820 downstream)																							ATAGGAACACTGTGATACTCTC	0.505													4	2	---	---	---	---	
FAR2	55711	broad.mit.edu	37	12	29352635	29352636	+	Intron	INS	-	A	A	rs144775521	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29352635_29352636insA	uc001ris.3	+							NM_018099	NP_060569	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2						ether lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane	binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor				0						acataaaagatggcaggcagag	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34120583	34120583	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34120583delA								SYT10 (527829 upstream) : ALG10 (54633 downstream)																							cataaaggctaagaaagaaag	0.000													4	2	---	---	---	---	
LRRK2	120892	broad.mit.edu	37	12	40668195	40668195	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40668195delC	uc001rmg.3	+						LRRK2_uc001rmh.1_Intron	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2						activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				aacaagctctccttaattgta	0.070													4	2	---	---	---	---	
ANO6	196527	broad.mit.edu	37	12	45629350	45629351	+	Intron	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45629350_45629351delTG	uc001roo.2	+						ANO6_uc010sld.1_Intron|ANO6_uc010sle.1_Intron|ANO6_uc010slf.1_Intron	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a						activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2						TTGAGTGGCATGACATCTGAGC	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	49268337	49268337	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49268337delC								RND1 (8684 upstream) : CCDC65 (29556 downstream)																							CAGAGAGGAGCAGAGGGCAGC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55454289	55454290	+	IGR	DEL	AA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55454289_55454290delAA								NEUROD4 (30489 upstream) : OR9K2 (69263 downstream)																							cagacaaaggaaagagagtatg	0.020													4	2	---	---	---	---	
GLS2	27165	broad.mit.edu	37	12	56866122	56866123	+	Intron	INS	-	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-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													4	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	67461662	67461662	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67461662delC								GRIP1 (263768 upstream) : CAND1 (201399 downstream)																							CGCCCACCTACCCACGCTGCG	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	67821981	67821981	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67821981delG								CAND1 (113593 upstream) : DYRK2 (220531 downstream)																							ctgccctcttggcagttcTTG	0.219													4	2	---	---	---	---	
ZFC3H1	196441	broad.mit.edu	37	12	72032512	72032512	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72032512delA	uc001swo.2	-							NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2						RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5						ACTAATAATTAGTCCCTCAAA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	73626340	73626341	+	IGR	DEL	CC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73626340_73626341delCC								TRHDE (566919 upstream) : None (None downstream)																							aggttgttttccacaaaagctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77631918	77631919	+	IGR	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77631918_77631919delTG								E2F7 (172558 upstream) : NAV3 (593150 downstream)																							TGTGGTGCTCTGTGTGAACTAC	0.465													4	2	---	---	---	---	
LIN7A	8825	broad.mit.edu	37	12	81231679	81231679	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81231679delT	uc001szj.1	-						LIN7A_uc001szk.1_Intron	NM_004664	NP_004655	O14910	LIN7A_HUMAN	lin-7 homolog A						exocytosis|protein complex assembly|protein transport	basolateral plasma membrane|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	L27 domain binding			ovary(1)|skin(1)	2						ATTATAACCCTttttttttgt	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82340953	82340954	+	IGR	DEL	CA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82340953_82340954delCA								PPFIA2 (187844 upstream) : CCDC59 (405136 downstream)																							CCCAAACCAGCACACACACACA	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	91470008	91470008	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91470008delT								KERA (17877 upstream) : LUM (27225 downstream)																							TTTCTGAGACTTTTTTTTCCC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	91584478	91584479	+	IGR	DEL	TC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91584478_91584479delTC								DCN (7672 upstream) : BTG1 (794387 downstream)																							TATTTTAAGTTCTCTAATCAGT	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	91907461	91907462	+	IGR	DEL	AA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91907461_91907462delAA								DCN (330655 upstream) : BTG1 (471404 downstream)																							CCACATTGATAAAGAAAAATCA	0.401													4	2	---	---	---	---	
APAF1	317	broad.mit.edu	37	12	99110110	99110110	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99110110delT	uc001tfz.2	+						APAF1_uc001tfy.2_Intron|APAF1_uc001tga.2_Intron|APAF1_uc001tgb.2_Intron|APAF1_uc001tgc.2_Intron|APAF1_uc009zto.2_Intron	NM_181861	NP_863651	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1 isoform						activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)	CAGACACTCATTTATCAATCC	0.294													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99175092	99175093	+	Intron	DEL	AC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99175092_99175093delAC	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron|ANKS1B_uc010svd.1_Intron|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc009ztq.2_Intron|ANKS1B_uc010sve.1_Intron|ANKS1B_uc001tgh.3_Intron|ANKS1B_uc001tgi.2_Intron|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc009ztp.2_Intron|ANKS1B_uc010svf.1_Intron|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		AACAACAACAacacacacacac	0.292													8	5	---	---	---	---	
DAO	1610	broad.mit.edu	37	12	109274019	109274019	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109274019delT	uc001tnr.3	+						DAO_uc001tnp.1_Intron|DAO_uc001tnq.3_Intron|DAO_uc009zvb.2_Intron	NM_001917	NP_001908	P14920	OXDA_HUMAN	D-amino-acid oxidase						glyoxylate metabolic process	peroxisomal matrix	binding|D-amino-acid oxidase activity			ovary(1)|skin(1)	2						CAGATGCACCTTTGAGCTGGG	0.547													6	3	---	---	---	---	
VPS29	51699	broad.mit.edu	37	12	110934255	110934256	+	Intron	DEL	TA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110934255_110934256delTA	uc001tqy.2	-						VPS29_uc001tqw.2_Intron|VPS29_uc001tqx.2_Intron|VPS29_uc001tqz.2_Intron	NM_016226	NP_057310	Q9UBQ0	VPS29_HUMAN	vacuolar protein sorting 29 isoform 1						protein transport	endosome membrane	metal ion binding|phosphoserine phosphatase activity				0						CAGACATACTTATGGTAATGTA	0.307													4	2	---	---	---	---	
TRAFD1	10906	broad.mit.edu	37	12	112578536	112578537	+	Intron	DEL	GT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112578536_112578537delGT	uc001ttp.2	+						TRAFD1_uc001tto.2_Intron|TRAFD1_uc009zwb.2_Intron|TRAFD1_uc010syj.1_Intron	NM_006700	NP_006691	O14545	TRAD1_HUMAN	TRAF-type zinc finger domain containing 1						negative regulation of innate immune response	intracellular	protein binding|zinc ion binding				0						GAAGATTGCAGTAGATACTCTT	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115637335	115637335	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115637335delT								TBX3 (515366 upstream) : MED13L (759048 downstream)																							CAACTTCAGCTTTACTGCTGC	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	117640789	117640790	+	IGR	INS	-	T	T	rs142971823	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117640789_117640790insT								FBXO21 (12489 upstream) : NOS1 (10189 downstream)																							TCTCAAACttgttttttttatt	0.183													4	2	---	---	---	---	
CIT	11113	broad.mit.edu	37	12	120128329	120128329	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120128329delG	uc001txi.1	-						CIT_uc001txh.1_Intron|CIT_uc001txj.1_Intron	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron						intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		CTTCTTACCTGAGCAACCCCC	0.542													4	2	---	---	---	---	
MSI1	4440	broad.mit.edu	37	12	120797085	120797085	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120797085delA	uc001tye.1	-							NM_002442	NP_002433	O43347	MSI1H_HUMAN	musashi 1						nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ttgtcctcccaacattccctg	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128303748	128303749	+	IGR	DEL	TA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128303748_128303749delTA								None (None upstream) : TMEM132C (595542 downstream)																							tcagcatagctataaaagggtg	0.040													4	2	---	---	---	---	
GALNT9	50614	broad.mit.edu	37	12	132873869	132873869	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132873869delG	uc001ukc.3	-						GALNT9_uc009zys.2_Intron	NM_001122636	NP_001116108	Q9HCQ5	GALT9_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		TCAAGACACTGCCAAGATAAC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19810544	19810544	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19810544delT								TUBA3C (54608 upstream) : LOC100101938 (26397 downstream)																							AAAAGAAGAGTACCTGTCCTG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31422325	31422325	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31422325delA								ALOX5AP (83769 upstream) : C13orf33 (57987 downstream)																							TGCTGGGAGGAAAAAAAAAAC	0.398													6	3	---	---	---	---	
NBEA	26960	broad.mit.edu	37	13	35950817	35950818	+	Intron	DEL	AT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35950817_35950818delAT	uc001uvb.2	+						NBEA_uc010abi.2_Intron	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AGGAGGAGGAATAGGATTCCCC	0.426													4	2	---	---	---	---	
WBP4	11193	broad.mit.edu	37	13	41643065	41643065	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41643065delC	uc001uxt.2	+						WBP4_uc010tfd.1_Intron	NM_007187	NP_009118	O75554	WBP4_HUMAN	WW domain-containing binding protein 4						nuclear mRNA cis splicing, via spliceosome	nuclear speck|spliceosomal complex	nucleic acid binding|proline-rich region binding|zinc ion binding			breast(2)|kidney(1)	3		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		GACTAAGTGTCATACTTAGTC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	74238561	74238561	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74238561delC								KLF5 (586886 upstream) : KLF12 (21589 downstream)																							ttcgttaaggccagtagaaaa	0.000													4	2	---	---	---	---	
LMO7	4008	broad.mit.edu	37	13	76401589	76401590	+	Intron	DEL	TA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76401589_76401590delTA	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc001vjt.1_Intron|LMO7_uc010thw.1_Intron|LMO7_uc001vjw.1_Intron	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AATATGGTCTTATTTAAAATCT	0.401													4	2	---	---	---	---	
MYCBP2	23077	broad.mit.edu	37	13	77664533	77664533	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77664533delC	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron|MYCBP2_uc001vke.2_Intron	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		GATAATCTCTCTTTAAATCAT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	79486567	79486567	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79486567delA								RNF219 (251867 upstream) : RBM26 (407533 downstream)																							ttctcagcataaaaacaaact	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	81001497	81001497	+	IGR	DEL	A	-	-	rs11318203		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81001497delA								SPRY2 (86411 upstream) : None (None downstream)																							GTGAAAAAGGAAAAAAAATGA	0.343													3	3	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94988935	94988937	+	Intron	DEL	CAA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94988935_94988937delCAA	uc001vlt.2	+							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)				GCTTTCTCTGcaacaacaacaac	0.325													4	2	---	---	---	---	
HS6ST3	266722	broad.mit.edu	37	13	97274264	97274265	+	Intron	INS	-	A	A	rs148424163	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97274264_97274265insA	uc001vmw.2	+							NM_153456	NP_703157	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					gcaaagggtgtaacatcaattc	0.000													4	2	---	---	---	---	
COL4A2	1284	broad.mit.edu	37	13	111089403	111089404	+	Intron	DEL	AA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111089403_111089404delAA	uc001vqx.2	+							NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein						angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			TCTGGGAACTAAAATAGAAACC	0.277													4	2	---	---	---	---	
TFDP1	7027	broad.mit.edu	37	13	114287754	114287755	+	Intron	INS	-	G	G			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114287754_114287755insG	uc001vtw.2	+						TFDP1_uc010tkd.1_Intron|TFDP1_uc010tke.1_Intron|TFDP1_uc001vty.3_Intron|TFDP1_uc001vtx.2_Intron|TFDP1_uc010agx.2_Intron	NM_007111	NP_009042	Q14186	TFDP1_HUMAN	transcription factor Dp-1						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding			lung(4)|ovary(2)|skin(1)	7	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)			AAGTGTGTGCCGGGGCCGAGAG	0.450										TSP Lung(29;0.18)			10	5	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	33450294	33450294	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33450294delG	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		CTTTCAGCCAGGAGTTAGCAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49617525	49617525	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49617525delA								None (None upstream) : SDCCAG1 (415502 downstream)																							CACTCAGCATAATCACAAGCT	0.413													4	2	---	---	---	---	
MAP4K5	11183	broad.mit.edu	37	14	50923042	50923043	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50923042_50923043insT	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron|MAP4K5_uc010anv.1_Intron	NM_006575	NP_006566	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)					taactggaaaataaaaATTATT	0.153													4	2	---	---	---	---	
ERO1L	30001	broad.mit.edu	37	14	53150340	53150343	+	Intron	DEL	ATGG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53150340_53150343delATGG	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)					AAATTATCCAATGGATGGTTTCAG	0.260													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	54857976	54857977	+	IGR	DEL	GC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54857976_54857977delGC								BMP4 (434422 upstream) : CDKN3 (5696 downstream)																							AGTTGAAACAGCAGAAACTCAG	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	71648743	71648743	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71648743delA								PCNX (66644 upstream) : SNORD56B (216311 downstream)																							GCTAACCCCTAAAAGGAAttt	0.224													4	2	---	---	---	---	
DPF3	8110	broad.mit.edu	37	14	73179108	73179109	+	Intron	DEL	GG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73179108_73179109delGG	uc001xnc.2	-						DPF3_uc001xnd.1_Intron|DPF3_uc001xnf.2_Intron|DPF3_uc010ari.1_Intron|DPF3_uc010ttq.1_Intron	NM_012074	NP_036206	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3						chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		AGGCAAAGGTGGGAGGAGAGGA	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	85917843	85917843	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85917843delT								None (None upstream) : FLRT2 (78645 downstream)																							GCTCTCATTGTTTCACTGGGC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	87368742	87368742	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87368742delC								None (None upstream) : GALC (935422 downstream)																							atggagaaggccggaggcact	0.000													4	2	---	---	---	---	
EVL	51466	broad.mit.edu	37	14	100599303	100599303	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100599303delC	uc001ygt.2	+						EVL_uc001ygv.2_Intron|EVL_uc001ygu.2_Intron|EVL_uc010avu.2_Intron	NM_016337	NP_057421	Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)				CAGCAGCAGGCCTGCCCTCAC	0.682													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20866888	20866889	+	IGR	INS	-	A	A	rs148671060		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20866888_20866889insA								GOLGA8C (85862 upstream) : BCL8 (3167 downstream)																							ATCACCAACTGAAAAAAAACGA	0.332													3	3	---	---	---	---	
CYFIP1	23191	broad.mit.edu	37	15	22936583	22936583	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22936583delG	uc001yus.2	+						CYFIP1_uc001yut.2_Intron|CYFIP1_uc010aya.1_Intron	NM_014608	NP_055423	Q7L576	CYFP1_HUMAN	cytoplasmic FMR1 interacting protein 1 isoform						axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		tttttggggtggggggatatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	25699213	25699213	+	IGR	DEL	A	-	-	rs8025120	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25699213delA								UBE3A (15085 upstream) : ATP10A (224649 downstream)																							GATCTCGTTTAAAAAAAAAGC	0.333													4	2	---	---	---	---	
ATP10A	57194	broad.mit.edu	37	15	25964472	25964472	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25964472delA	uc010ayu.2	-							NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		aaatggggataaaaaagggga	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	36785934	36785934	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36785934delC								ATPBD4 (947530 upstream) : C15orf41 (85878 downstream)																							GCAGTAATTGCAATATAACAT	0.358													4	2	---	---	---	---	
GPR176	11245	broad.mit.edu	37	15	40137795	40137795	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40137795delT	uc001zkj.1	-						GPR176_uc001zkk.1_Intron	NM_007223	NP_009154	Q14439	GP176_HUMAN	G protein-coupled receptor 176						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)		aaaactgggctttgggatctg	0.035													4	2	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62167305	62167305	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62167305delG	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						AATATGGATAGAATATCTATT	0.299													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	66672095	66672095	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66672095delT								TIPIN (23041 upstream) : MAP2K1 (7116 downstream)																							CCAGAGCCTCTTTTTTTTTCT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70539857	70539857	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70539857delT								TLE3 (149601 upstream) : UACA (407038 downstream)																							GTACTTGGGGTCCCCAACCAA	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78601061	78601061	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78601061delC								WDR61 (9121 upstream) : CRABP1 (31605 downstream)																							CATTATGGGACCCCTCGTAAA	0.448											OREG0023332	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
KIAA1199	57214	broad.mit.edu	37	15	81171440	81171441	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81171440_81171441insT	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						TTATTGGTGTCTTGAGTAATTC	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82014723	82014723	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82014723delC								TMC3 (348305 upstream) : MEX3B (319405 downstream)																							cttaaagccacccagcctatt	0.000													3	3	---	---	---	---	
ADAMTSL3	57188	broad.mit.edu	37	15	84660127	84660127	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84660127delC	uc002bjz.3	+						ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)			atctaactctcaagggtgagg	0.095													4	2	---	---	---	---	
ALPK3	57538	broad.mit.edu	37	15	85375844	85375845	+	Intron	DEL	TC	-	-	rs73437935	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85375844_85375845delTC	uc002ble.2	+							NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3						heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)			tgtttacacatctctctctctc	0.005													4	2	---	---	---	---	
SLC28A1	9154	broad.mit.edu	37	15	85434150	85434151	+	Intron	DEL	CA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85434150_85434151delCA	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron|SLC28A1_uc002blf.2_Intron	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)			acagaggagtcacaggagcaaa	0.000													4	2	---	---	---	---	
AKAP13	11214	broad.mit.edu	37	15	86047223	86047224	+	Intron	DEL	AG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86047223_86047224delAG	uc002blv.1	+						AKAP13_uc002bls.2_Intron|AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						GGACATGCTCAGGCATAGGGCT	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87608327	87608327	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87608327delT								AGBL1 (36044 upstream) : NCRNA00052 (511833 downstream)																							ttcagagcacttgaaggtgaa	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96104822	96104822	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96104822delA								LOC145820 (53748 upstream) : NR2F2 (764335 downstream)																							CCCCTACTTCAACCTTTTCCC	0.378													4	2	---	---	---	---	
CLCN7	1186	broad.mit.edu	37	16	1507521	1507522	+	Intron	INS	-	ACATGG	ACATGG			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1507521_1507522insACATGG	uc002clv.2	-						CLCN7_uc002clw.2_Intron	NM_001287	NP_001278	P51798	CLCN7_HUMAN	chloride channel 7 isoform a							integral to membrane|lysosomal membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4		Hepatocellular(780;0.0893)				CTCAGAGACACGCGTGACGCGG	0.653													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5263613	5263614	+	IGR	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5263613_5263614insT								FAM86A (115824 upstream) : A2BP1 (805518 downstream)																							ttctttttttcttttttttttt	0.208													3	3	---	---	---	---	
SHISA9	729993	broad.mit.edu	37	16	13219806	13219806	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13219806delG	uc010uyy.1	+							NM_001145204	NP_001138676	B4DS77	SHSA9_HUMAN	shisa homolog 9 isoform 1						regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0						ACCAGGGTCAGAGTACAGAAG	0.403													4	2	---	---	---	---	
TMC5	79838	broad.mit.edu	37	16	19508771	19508771	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19508771delA	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron|TMC5_uc002dge.3_Intron|TMC5_uc002dgf.3_Intron|TMC5_uc002dgg.3_Intron	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1						TCAACTTCTTATATCTTCTCA	0.353													4	2	---	---	---	---	
ZP2	7783	broad.mit.edu	37	16	21214744	21214744	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21214744delC	uc002dii.2	-						ZP2_uc010bwn.1_Intron	NM_003460	NP_003451	Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 preproprotein						binding of sperm to zona pellucida|intracellular protein transport	endoplasmic reticulum|Golgi apparatus|integral to membrane|multivesicular body|plasma membrane|proteinaceous extracellular matrix|stored secretory granule	acrosin binding|coreceptor activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(48;0.0573)		CTGGATGTATCCCCAGGCAGA	0.438													4	2	---	---	---	---	
XPO6	23214	broad.mit.edu	37	16	28119167	28119168	+	Intron	DEL	TT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28119167_28119168delTT	uc002dpa.1	-						XPO6_uc002dpb.1_Intron|XPO6_uc010vcp.1_Intron	NM_015171	NP_055986	Q96QU8	XPO6_HUMAN	exportin 6						protein export from nucleus		protein binding|protein transporter activity			ovary(1)|skin(1)	2						TCTCTTTATGTTTTAGTTTTTG	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	31543455	31543456	+	IGR	INS	-	CT	CT			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31543455_31543456insCT								AHSP (3332 upstream) : CSDAP1 (35632 downstream)																							cctcaccctgactctaTAAGGA	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46400003	46400004	+	IGR	INS	-	AATTC	AATTC	rs66536434		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46400003_46400004insAATTC								None (None upstream) : ANKRD26P1 (103245 downstream)																							atccattcgataattcaagtcc	0.000													10	5	---	---	---	---	
PHKB	5257	broad.mit.edu	37	16	47581176	47581176	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47581176delA	uc002eev.3	+						PHKB_uc010vgi.1_Intron|PHKB_uc002eeu.3_Intron	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				tgtattttttagtagagatga	0.015													3	10	---	---	---	---	
ABCC12	94160	broad.mit.edu	37	16	48158479	48158481	+	Intron	DEL	TTG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48158479_48158481delTTG	uc002efc.1	-						ABCC12_uc002eey.1_Intron|ABCC12_uc002eez.1_Intron|ABCC12_uc002efa.1_Intron|ABCC12_uc002efb.1_Intron|ABCC12_uc002efd.1_Intron|ABCC12_uc002efe.1_Intron	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)				TGAAACAGCCTTGTGCTGGTCTG	0.483													4	2	---	---	---	---	
AMFR	267	broad.mit.edu	37	16	56401620	56401620	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56401620delG	uc002eiy.2	-						AMFR_uc002eix.2_Intron	NM_001144	NP_001135	Q9UKV5	AMFR2_HUMAN	autocrine motility factor receptor						endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|protein oligomerization|protein polyubiquitination	integral to endoplasmic reticulum membrane|integral to membrane of membrane fraction	protein binding|protein binding|receptor activity|ubiquitin-protein ligase activity|zinc ion binding			breast(2)	2						AAAGGAGCCTGGGGCCTAACC	0.403													4	2	---	---	---	---	
MT2A	4502	broad.mit.edu	37	16	56643363	56643363	+	3'UTR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56643363delT	uc002ejh.2	+	3					MT1A_uc002eji.2_Intron	NM_005953	NP_005944	P02795	MT2_HUMAN	metallothionein 2A						cellular copper ion homeostasis|interferon-gamma-mediated signaling pathway		metal ion binding|protein binding				0						GCTATATTCCTTTTTCTATGA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66139279	66139280	+	IGR	DEL	AC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66139279_66139280delAC								LOC283867 (529076 upstream) : CDH5 (261245 downstream)																							GGACTTCCCTACATAATGGAGC	0.495													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	81328220	81328221	+	IGR	DEL	AA	-	-	rs75295231		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81328220_81328221delAA								BCMO1 (3473 upstream) : GAN (20350 downstream)																							CGAAAAATCTAAGTGTGTTGGC	0.411													2	4	---	---	---	---	
SLC38A8	146167	broad.mit.edu	37	16	84067078	84067078	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84067078delC	uc002fhg.1	-							NM_001080442	NP_001073911	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8						amino acid transport|sodium ion transport	integral to membrane					0						TCACACACTGCCAGAGACACG	0.657													4	2	---	---	---	---	
LOC732275	732275	broad.mit.edu	37	16	86371988	86371988	+	5'Flank	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86371988delC	uc010chq.2	-						LOC732275_uc002fjj.2_RNA|LOC732275_uc010chr.2_RNA|LOC732275_uc010von.1_RNA					Homo sapiens cDNA FLJ35925 fis, clone TESTI2010734.												0						ATGCCACTCACCCAGGTGTCA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	2678786	2678786	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2678786delG								MIR1253 (27310 upstream) : RAP1GAP2 (20946 downstream)																							gtggtggggagggggcacggg	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5542908	5542908	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5542908delT								NLRP1 (55076 upstream) : WSCD1 (429529 downstream)																							TGTTTGGCTGTGAGCTCAGTC	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	10162586	10162586	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10162586delA								GAS7 (60718 upstream) : MYH13 (41597 downstream)																							CTAAAAAAACAAAAAAAACAA	0.388													4	2	---	---	---	---	
TMEM220	388335	broad.mit.edu	37	17	10628611	10628611	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10628611delC	uc002gmx.2	-						TMEM220_uc002gmy.2_Intron	NM_001004313	NP_001004313	Q6QAJ8	TM220_HUMAN	transmembrane protein 220							integral to membrane					0						ACAGAGGTCACAGCACTAATT	0.244													4	2	---	---	---	---	
SHISA6	388336	broad.mit.edu	37	17	11374084	11374085	+	Intron	DEL	TG	-	-	rs140386799		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11374084_11374085delTG	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269	Q6ZSJ9	SHSA6_HUMAN	shisa homolog 6							integral to membrane				breast(1)	1						CCCTGACAAATGTGTGCAGCAT	0.327													4	4	---	---	---	---	
PEMT	10400	broad.mit.edu	37	17	17495717	17495717	+	5'Flank	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17495717delA	uc002grl.2	-						PEMT_uc010vwx.1_5'Flank	NM_148172	NP_680477	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase						cell proliferation|phosphatidylcholine biosynthetic process	endoplasmic reticulum membrane|integral to membrane|mitochondrial membrane	phosphatidylethanolamine N-methyltransferase activity				0				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)		actgtggtggaaaaaacgggg	0.000													4	2	---	---	---	---	
C17orf39	79018	broad.mit.edu	37	17	17957824	17957824	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17957824delC	uc002gsg.1	+							NM_024052	NP_076957	Q8IVV7	CQ039_HUMAN	hypothetical protein LOC79018											skin(1)	1	all_neural(463;0.228)					TTAACAGTGTCCCCCCATCCT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21339354	21339355	+	IGR	INS	-	GCAG	GCAG	rs34586616		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21339354_21339355insGCAG								KCNJ12 (16175 upstream) : C17orf51 (92217 downstream)																							aggcacagcaagcaggcaggca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	27632614	27632614	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27632614delT								NUFIP2 (11448 upstream) : TAOK1 (85329 downstream)																							cgtgtaactatttttttttcc	0.000													4	2	---	---	---	---	
RHBDL3	162494	broad.mit.edu	37	17	30647869	30647869	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30647869delG	uc002hhe.1	+						RHBDL3_uc010csw.1_Intron|RHBDL3_uc010csx.1_Intron|RHBDL3_uc010csy.1_Intron|RHBDL3_uc002hhf.1_Intron	NM_138328	NP_612201	P58872	RHBL3_HUMAN	rhomboid protease 3						proteolysis	integral to membrane	calcium ion binding|serine-type endopeptidase activity			ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)				tgcagagaatggtgcttggcc	0.239													4	2	---	---	---	---	
MED1	5469	broad.mit.edu	37	17	37571595	37571595	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37571595delA	uc002hrv.3	-						MED1_uc010wee.1_Intron|MED1_uc002hru.2_Intron	NM_004774	NP_004765	Q15648	MED1_HUMAN	mediator complex subunit 1						androgen biosynthetic process|androgen receptor signaling pathway|cellular lipid metabolic process|fat cell differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|estrogen receptor binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|receptor activity|retinoic acid receptor binding|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			lung(2)|ovary(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	8		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		AGGAGAATCTAAAAGGCAAAG	0.318										HNSCC(31;0.082)			68	43	---	---	---	---	
CDC6	990	broad.mit.edu	37	17	38456339	38456340	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38456339_38456340insA	uc002huj.1	+							NM_001254	NP_001245	Q99741	CDC6_HUMAN	cell division cycle 6 protein						cell division|DNA replication|DNA replication checkpoint|M/G1 transition of mitotic cell cycle|mitosis|negative regulation of cell proliferation|negative regulation of DNA replication|positive regulation of cell cycle cytokinesis|positive regulation of chromosome segregation|regulation of cyclin-dependent protein kinase activity|regulation of mitotic anaphase|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm|spindle midzone|spindle pole	ATP binding|kinase binding|nucleoside-triphosphatase activity			ovary(2)|breast(1)	3						ctcaacctcccaagtagctggg	0.000													3	3	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44278275	44278276	+	Intron	INS	-	T	T	rs112647480		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44278275_44278276insT	uc010dav.2	-							NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				AAGGGAATTACttttttttttt	0.218													4	2	---	---	---	---	
NPEPPS	9520	broad.mit.edu	37	17	45663680	45663681	+	Intron	INS	-	TA	TA			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45663680_45663681insTA	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010wkv.1_5'Flank	NM_006310	NP_006301	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0						TGATGCAAGAGtatatatatat	0.282													4	4	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64525916	64525916	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64525916delC	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)	TGGCTCATGTCTTAGCTGGCT	0.398													4	2	---	---	---	---	
WIPI1	55062	broad.mit.edu	37	17	66453573	66453581	+	5'UTR	DEL	GCCCGGGAA	-	-	rs71142184		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66453573_66453581delGCCCGGGAA	uc010dey.2	-	1					WIPI1_uc002jhd.3_RNA|WIPI1_uc010wqo.1_5'UTR|WIPI1_uc002jhe.3_RNA	NM_017983	NP_060453	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting						macroautophagy|vesicle targeting, trans-Golgi to endosome	autophagic vacuole membrane|clathrin-coated vesicle|cytosol|endosome membrane|PAS complex|pre-autophagosomal structure membrane|trans-Golgi network	androgen receptor binding|estrogen receptor binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding				0						CGGGGGCTCGGCCCGGGAAGCCGCAGCTC	0.651													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	72146027	72146027	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72146027delT								C17orf54 (321351 upstream) : RPL38 (53768 downstream)																							AAGATCTCTGTTTTGTGGGAG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75922536	75922537	+	IGR	INS	-	AT	AT	rs145111837	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75922536_75922537insAT								FLJ45079 (42367 upstream) : TNRC6C (77781 downstream)																							GGGCTCTGCTGATCATGGAAAA	0.515													4	2	---	---	---	---	
ENGASE	64772	broad.mit.edu	37	17	77075375	77075375	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77075375delA	uc002jwv.2	+						ENGASE_uc002jwu.1_Intron|ENGASE_uc010wtz.1_Intron|ENGASE_uc002jww.2_5'Flank	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase							cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1						cctcccaagtagctgggacta	0.000													4	2	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78858712	78858712	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78858712delG	uc002jyt.1	+						RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						AAGCGCCTGTGGGGTTGGATT	0.667													4	2	---	---	---	---	
BAHCC1	57597	broad.mit.edu	37	17	79426022	79426022	+	Intron	DEL	C	-	-	rs34202212		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79426022delC	uc002kaf.2	+						BAHCC1_uc002kae.2_Intron	NM_001080519	NP_001073988	Q9P281	BAHC1_HUMAN	BAH domain and coiled-coil containing 1								DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)			AGGGTGCCAGCCGCCTGGGGA	0.592													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	871409	871409	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:871409delT								YES1 (58867 upstream) : ADCYAP1 (33535 downstream)																							GGACCTGGCCTTCACTCAAAC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	9869238	9869238	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9869238delG								RAB31 (6685 upstream) : TXNDC2 (16485 downstream)																							CCGAGTGAGAGGGTGTGTGTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14399400	14399400	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14399400delG								LOC284233 (56878 upstream) : CXADRP3 (78556 downstream)																							ACTATACCCAGGGGTAGCTTA	0.328													6	3	---	---	---	---	
CELF4	56853	broad.mit.edu	37	18	35076495	35076496	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35076495_35076496insT	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						ACAACAATAAATTTTTTTTAAA	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35204808	35204809	+	IGR	DEL	CT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35204808_35204809delCT								CELF4 (58808 upstream) : None (None downstream)																							GTTTCCCCAGCTAGTCCTGGAG	0.554													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35468051	35468051	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35468051delG								CELF4 (322051 upstream) : None (None downstream)																							GGTGAAATTTGGCAGACACAT	0.209													4	2	---	---	---	---	
SETBP1	26040	broad.mit.edu	37	18	42426363	42426374	+	Intron	DEL	ACTCATACTCAT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42426363_42426374delACTCATACTCAT	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)		cccaaaagaaactcatactcattttccattcc	0.000									Schinzel-Giedion_syndrome				10	5	---	---	---	---	
SLC14A2	8170	broad.mit.edu	37	18	42894542	42894542	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42894542delG	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4						gttgccttgaggtcctctcct	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	51791308	51791309	+	IGR	DEL	TG	-	-	rs35359886		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51791308_51791309delTG								MBD2 (40150 upstream) : POLI (4540 downstream)																							tcttttcttttGTGTGTGTGTG	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	61201979	61201979	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61201979delC								SERPINB5 (29662 upstream) : SERPINB12 (21414 downstream)																							AGTTGCTTTTCCAGTAGTGGT	0.408													4	2	---	---	---	---	
DOT1L	84444	broad.mit.edu	37	19	2194294	2194295	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2194294_2194295insA	uc002lvb.3	+							NM_032482	NP_115871	Q8TEK3	DOT1L_HUMAN	DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ctcagcctcccgagtagctggg	0.000													4	2	---	---	---	---	
DOT1L	84444	broad.mit.edu	37	19	2194299	2194299	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2194299delA	uc002lvb.3	+							NM_032482	NP_115871	Q8TEK3	DOT1L_HUMAN	DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		cctcccgagtagctgggacta	0.000													4	2	---	---	---	---	
GNA15	2769	broad.mit.edu	37	19	3141041	3141041	+	Intron	DEL	T	-	-	rs147633876	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3141041delT	uc002lxf.2	+						GNA15_uc010xhf.1_Intron	NM_002068	NP_002059	P30679	GNA15_HUMAN	guanine nucleotide binding protein (G protein),						activation of phospholipase C activity by dopamine receptor signaling pathway|activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)		CCAAAAGCTGTTTTTTTTTTA	0.498													4	2	---	---	---	---	
GIPC3	126326	broad.mit.edu	37	19	3590339	3590340	+	3'UTR	DEL	TC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3590339_3590340delTC	uc002lyd.3	+	6						NM_133261	NP_573568	Q8TF64	GIPC3_HUMAN	GIPC PDZ domain containing family, member 3											breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCCAACCCTTCTCTAGAATCC	0.446													4	2	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	9080245	9080246	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9080245_9080246insA	uc002mkp.2	-							NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						aaagaagaaagaaagagaaaga	0.050													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	9148901	9148901	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9148901delC								MUC16 (56883 upstream) : OR1M1 (55020 downstream)																							gactacgccaccccaaaatat	0.194													4	2	---	---	---	---	
CCDC151	115948	broad.mit.edu	37	19	11532993	11532994	+	Intron	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11532993_11532994delTG	uc002mrs.2	-						CCDC151_uc002mrr.2_Intron|CCDC151_uc010dxz.2_Intron|RGL3_uc002mrn.2_5'Flank|RGL3_uc002mrm.2_5'Flank|RGL3_uc002mro.2_5'Flank|RGL3_uc002mrp.2_5'Flank|RGL3_uc002mrq.2_5'Flank	NM_145045	NP_659482	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151											ovary(1)	1						GGGCTTCCCCTGTGGGCGGGGC	0.678													5	3	---	---	---	---	
ZNF442	79973	broad.mit.edu	37	19	12474598	12474598	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12474598delC	uc002mtr.1	-						ZNF442_uc010xmk.1_Intron	NM_030824	NP_110451	Q9H7R0	ZN442_HUMAN	zinc finger protein 442						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(2)|breast(1)|kidney(1)	4						CTCTGTGAGGCCCCACCCCAA	0.522													4	2	---	---	---	---	
NFIX	4784	broad.mit.edu	37	19	13105916	13105917	+	5'Flank	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13105916_13105917delTG	uc002mwd.2	+							NM_002501	NP_002492	Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			CCCAGACTGCTGTGTGTGTGTG	0.564													4	2	---	---	---	---	
NWD1	284434	broad.mit.edu	37	19	16857851	16857852	+	Intron	DEL	TT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16857851_16857852delTT	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron			Q149M9	NWD1_HUMAN	RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7						tttttctttctttttttttttt	0.010													4	2	---	---	---	---	
CPAMD8	27151	broad.mit.edu	37	19	17081408	17081408	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17081408delA	uc002nfb.2	-							NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						actccatctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
PGLS	25796	broad.mit.edu	37	19	17628004	17628005	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17628004_17628005insT	uc002ngw.2	+							NM_012088	NP_036220	O95336	6PGL_HUMAN	6-phosphogluconolactonase							cytosol	6-phosphogluconolactonase activity				0						AGCTACTTGTATTTTTTTATCT	0.287													4	2	---	---	---	---	
ATP13A1	57130	broad.mit.edu	37	19	19767096	19767096	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19767096delA	uc002nnh.3	-						ATP13A1_uc002nnf.3_5'Flank|ATP13A1_uc002nng.2_Intron	NM_020410	NP_065143	Q9HD20	AT131_HUMAN	ATPase type 13A1						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(3)|large_intestine(2)|central_nervous_system(1)	6						AGCCAGGGGGATCCCCACCCG	0.602													4	3	---	---	---	---	
ZNF253	56242	broad.mit.edu	37	19	20003795	20003795	+	3'UTR	DEL	T	-	-	rs141633713		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20003795delT	uc002noj.2	+	4					ZNF253_uc002nok.2_3'UTR|ZNF253_uc002nol.2_RNA	NM_021047	NP_066385	O75346	ZN253_HUMAN	zinc finger protein 253						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TCTCAATTCCtttttttttga	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30771463	30771463	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30771463delA								C19orf2 (264852 upstream) : ZNF536 (91865 downstream)																							TGCTGCTCTCATATCCTCCAA	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31382811	31382812	+	IGR	DEL	TT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31382811_31382812delTT								ZNF536 (333846 upstream) : DKFZp566F0947 (257971 downstream)																							attcctaaggtttagggcttag	0.040													4	2	---	---	---	---	
ACTN4	81	broad.mit.edu	37	19	39167858	39167858	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39167858delA	uc002oja.1	+						ACTN4_uc010egc.1_Intron	NM_004924	NP_004915	O43707	ACTN4_HUMAN	actinin, alpha 4						platelet activation|platelet degranulation|positive regulation of cellular component movement|positive regulation of sodium:hydrogen antiporter activity|protein transport|regulation of apoptosis	extracellular region|nucleolus|perinuclear region of cytoplasm|platelet alpha granule lumen|protein complex|pseudopodium|ribonucleoprotein complex	actin filament binding|calcium ion binding|integrin binding|nucleoside binding|protein homodimerization activity				0	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			ttctccttttaactccaacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	43177347	43177348	+	IGR	DEL	TT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43177347_43177348delTT								CEACAM8 (78265 upstream) : PSG3 (48447 downstream)																							tgtctgcctctttttcttggtg	0.059													4	2	---	---	---	---	
PSG3	5671	broad.mit.edu	37	19	43228338	43228338	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43228338delT	uc002oue.2	-						PSG3_uc002ouf.2_Intron|PSG3_uc010eil.2_Intron	NM_021016	NP_066296	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3						defense response|female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)				ATTCTTGCAGTTTTTTTTTCC	0.383													4	2	---	---	---	---	
DHX34	9704	broad.mit.edu	37	19	47884820	47884821	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47884820_47884821insT	uc010xyn.1	+						DHX34_uc010xyo.1_Intron	NM_014681	NP_055496	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34							intracellular	ATP binding|ATP-dependent helicase activity|RNA binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		gtgttgctgtctttgtctctgt	0.460													4	2	---	---	---	---	
ELSPBP1	64100	broad.mit.edu	37	19	48510210	48510210	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48510210delG	uc002pht.2	+							NM_022142	NP_071425	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1 precursor						single fertilization	extracellular region					0		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		AAAAAAGTTTGGGGCGTGTTG	0.468													4	2	---	---	---	---	
LIG1	3978	broad.mit.edu	37	19	48625577	48625577	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48625577delG	uc002pia.1	-						LIG1_uc010xze.1_Intron|LIG1_uc002phz.1_Intron|LIG1_uc002pib.1_Intron|LIG1_uc010xzf.1_Intron|LIG1_uc010xzg.1_Intron	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I						anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	ctgacttcctgaaaccttcaa	0.199								NER					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	51110673	51110674	+	IGR	DEL	TC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51110673_51110674delTC								SNAR-F (2331 upstream) : SYT3 (14562 downstream)																							TTCACTGTCTTCTCTCTCTGGT	0.520													4	2	---	---	---	---	
KLK11	11012	broad.mit.edu	37	19	51530200	51530205	+	Intron	DEL	CCTATG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51530200_51530205delCCTATG	uc002pvd.1	-						KLK11_uc002pvb.1_5'Flank|KLK11_uc002pve.1_Intron|KLK11_uc002pvf.1_Intron|KLK11_uc002pvc.3_5'Flank|KLK11_uc010eom.2_5'Flank	NM_144947	NP_659196	Q9UBX7	KLK11_HUMAN	kallikrein 11 isoform 2 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|GBM - Glioblastoma multiforme(134;0.00878)		tctttctgtccctatgtgtctgtctg	0.180													8	4	---	---	---	---	
ATRN	8455	broad.mit.edu	37	20	3598146	3598146	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3598146delC	uc002wim.2	+							NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2						gctctttctactttttaaaaa	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	4419522	4419522	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4419522delG								ADRA1D (189863 upstream) : PRNP (247275 downstream)																							gagtgcatgagggtctaagat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	6333411	6333412	+	IGR	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6333411_6333412delTG								FERMT1 (229220 upstream) : BMP2 (415333 downstream)																							tgagccatcttgagtacagatc	0.000													4	2	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9094904	9094904	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9094904delA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						ACACATTTCTAACGAGATAAT	0.313													4	2	---	---	---	---	
BFSP1	631	broad.mit.edu	37	20	17534301	17534301	+	Intron	DEL	G	-	-	rs145104791	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17534301delG	uc002wpp.2	-						BFSP1_uc010zrn.1_Intron|BFSP1_uc010zro.1_Intron	NM_001161705	NP_001155177	Q12934	BFSP1_HUMAN	filensin isoform 2							cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens			central_nervous_system(1)	1						ggaggcaagtggggtggcaaa	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22485011	22485011	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22485011delG								LOC284788 (83730 upstream) : C20orf56 (56183 downstream)																							TCCTGGACATGCCACACCGCC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25582346	25582347	+	IGR	DEL	AC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25582346_25582347delAC								NINL (16193 upstream) : NANP (11228 downstream)																							acacctacatacacacacacaa	0.030													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	30403279	30403279	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30403279delT								TPX2 (13676 upstream) : MYLK2 (3899 downstream)																							ACTCTTTGGATTTTCCATCAC	0.527													4	2	---	---	---	---	
C20orf203	284805	broad.mit.edu	37	20	31257027	31257028	+	Intron	DEL	TG	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31257027_31257028delTG	uc002wxz.2	-							NR_026959		Q8NBC4	CT203_HUMAN	Homo sapiens cDNA FLJ33706 fis, clone BRAWH2007808.							cytoplasm					0						gtGCTGAACTTGTGTTAACTGG	0.297													4	2	---	---	---	---	
DSN1	79980	broad.mit.edu	37	20	35399863	35399864	+	5'UTR	INS	-	GA	GA			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35399863_35399864insGA	uc010gfr.2	-	2					DSN1_uc002xfz.2_5'UTR|DSN1_uc002xfy.3_Intron|DSN1_uc002xga.2_5'UTR|DSN1_uc010zvs.1_5'UTR|DSN1_uc002xgc.2_Intron|DSN1_uc002xgb.2_5'UTR	NM_001145316	NP_001138788	Q9H410	DSN1_HUMAN	DSN1, MIND kinetochore complex component,						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			ovary(2)	2		Myeloproliferative disorder(115;0.00874)				TGAAGTCATCCTAGGTGGTAAA	0.421													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	38645649	38645649	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38645649delG								LOC339568 (792258 upstream) : MAFB (668870 downstream)																							GTGTGTTGCTGGGCCTTGTTT	0.358													4	2	---	---	---	---	
SPINLW1	57119	broad.mit.edu	37	20	44171758	44171758	+	Intron	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44171758delG	uc002xou.2	-						SPINLW1_uc010zxc.1_Intron|SPINLW1_uc002xot.2_Intron|SPINLW1_uc002xov.1_3'UTR	NM_020398	NP_065131	O95925	EPPI_HUMAN	serine peptidase inhibitor-like, with Kunitz and							extracellular region	serine-type endopeptidase inhibitor activity			pancreas(1)	1		Myeloproliferative disorder(115;0.0122)				aaaatagggtgggcccctata	0.040													4	2	---	---	---	---	
EYA2	2139	broad.mit.edu	37	20	45562915	45562916	+	Intron	DEL	TC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45562915_45562916delTC	uc002xsm.2	+						EYA2_uc010ghp.2_Intron	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				atcaacatagtctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48845144	48845145	+	IGR	DEL	AC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48845144_48845145delAC								CEBPB (35932 upstream) : PTPN1 (281746 downstream)																							ttttgtagagacagggtcttgc	0.000													2	4	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51763240	51763240	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51763240delT	uc002xwo.2	+							NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			CAGCATAAAATTTTATTAGGC	0.373													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60319654	60319657	+	Intron	DEL	AGAC	-	-	rs75238513		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60319654_60319657delAGAC	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			ggagagagagagacagacagaCAG	0.270													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	61504408	61504409	+	IGR	DEL	GC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61504408_61504409delGC								TCFL5 (11293 upstream) : DIDO1 (4681 downstream)																							TGCTGAAGAGGCGGGAGAAGAG	0.535													4	2	---	---	---	---	
PRIC285	85441	broad.mit.edu	37	20	62205121	62205121	+	Intron	DEL	G	-	-	rs67354507		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62205121delG	uc002yfm.2	-						PRIC285_uc002yfn.2_Intron	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285						cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)			AGGAAGAGATGGGTCCCCGGG	0.602													2	6	---	---	---	---	
ZBTB46	140685	broad.mit.edu	37	20	62396474	62396475	+	Intron	DEL	GT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62396474_62396475delGT	uc002ygv.1	-						ZBTB46_uc002ygu.2_Intron	NM_025224	NP_079500	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					gtgtgtgtgcgtgtgtgtgtgt	0.074													4	2	---	---	---	---	
PCMTD2	55251	broad.mit.edu	37	20	62899380	62899381	+	Intron	INS	-	TA	TA			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62899380_62899381insTA	uc002yil.3	+						PCMTD2_uc002yim.3_Intron	NM_018257	NP_060727	Q9NV79	PCMD2_HUMAN	protein-L-isoaspartate (D-aspartate)							cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					ATACCAATCTTTACTTATTTTA	0.347													94	45	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9839615	9839615	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9839615delG								None (None upstream) : None (None downstream)																							taagcaaaaagaacaaagctg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10703387	10703387	+	IGR	DEL	C	-	-	rs143834133		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10703387delC								None (None upstream) : TPTE (203356 downstream)																							caagaaatttctttgtgatgt	0.000													3	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11091176	11091177	+	Intron	INS	-	A	A	rs60485999		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11091176_11091177insA	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)		aaaTATTTTTTAAAAAAATGGT	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26196788	26196789	+	IGR	DEL	GT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26196788_26196789delGT								None (None upstream) : NCRNA00158 (561345 downstream)																							CTATCTGGCAGTGAATAATCAT	0.396													4	2	---	---	---	---	
PCP4	5121	broad.mit.edu	37	21	41270694	41270695	+	Intron	INS	-	CA	CA			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41270694_41270695insCA	uc002yyp.2	+							NM_006198	NP_006189	P48539	PCP4_HUMAN	Purkinje cell protein 4						central nervous system development	cytosol|nucleus				large_intestine(1)	1		Prostate(19;2.65e-06)|all_epithelial(19;0.138)				TTTTGGGCAACATGGTAATTAC	0.347													4	2	---	---	---	---	
LOC284837	284837	broad.mit.edu	37	21	45225896	45225896	+	RNA	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45225896delT	uc002zdt.1	-	4		c.1632delA			LOC284837_uc010gpn.1_RNA|LOC284837_uc002zdu.1_RNA					Homo sapiens cDNA FLJ36091 fis, clone TESTI2020515.												0						cacagtcaactttagaccatt	0.259													4	2	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45824842	45824843	+	Intron	INS	-	TGA	TGA	rs72346173		TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45824842_45824843insTGA	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						gacagtgactgtgatgatagtg	0.020													3	5	---	---	---	---	
C22orf42	150297	broad.mit.edu	37	22	32550003	32550004	+	Intron	DEL	CA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32550003_32550004delCA	uc003amd.2	-							NM_001010859	NP_001010859	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42											ovary(1)|skin(1)	2						gagaccttTTcacacacacaca	0.099													4	2	---	---	---	---	
LOC646851	646851	broad.mit.edu	37	22	39003590	39003591	+	Intron	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39003590_39003591insT	uc011anx.1	-						LOC646851_uc011anw.1_Intron			B7Z7C6	B7Z7C6_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000348086;												0						TTTCTTTGCTATTTCTTACTGT	0.252													20	12	---	---	---	---	
TAB1	10454	broad.mit.edu	37	22	39771852	39771854	+	5'UTR	DEL	GCT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39771852_39771854delGCT	uc003axr.2	+	2					SYNGR1_uc003axo.3_Intron|SYNGR1_uc003axp.3_Intron|SYNGR1_uc003axq.3_Intron|SYNGR1_uc003axs.3_Intron	NM_006116	NP_006107	Q15750	TAB1_HUMAN	mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|activation of MAPKKK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB 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|endosome membrane	catalytic activity|protein binding			breast(1)	1						CCTGCATCTGGCTGGCTTCCCTC	0.635													3	3	---	---	---	---	
TNRC6B	23112	broad.mit.edu	37	22	40719315	40719315	+	3'UTR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40719315delT	uc011aor.1	+	23					TNRC6B_uc003aym.2_3'UTR|TNRC6B_uc003ayn.3_3'UTR	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0						GACCTTTTCGTTTTTTTTTTC	0.393													5	3	---	---	---	---	
PPARA	5465	broad.mit.edu	37	22	46582338	46582339	+	Intron	DEL	GC	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46582338_46582339delGC	uc003bgw.1	+						PPARA_uc003bgx.1_Intron|PPARA_uc010hab.1_Intron|PPARA_uc003bgy.1_Intron|PPARA_uc003bgz.1_Intron|PPARA_uc003bha.2_Intron|PPARA_uc003bhb.1_Intron	NM_005036	NP_005027	Q07869	PPARA_HUMAN	peroxisome proliferative activated receptor,						fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)	AGAGAGAAGAGCATGATTCAAG	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	11867252	11867252	+	IGR	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11867252delA								MSL3 (73382 upstream) : FRMPD4 (289333 downstream)																							atcaacatgcaaaaatcagtt	0.000													4	2	---	---	---	---	
DMD	1756	broad.mit.edu	37	X	31205678	31205679	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31205678_31205679insA	uc004dda.1	-						DMD_uc004dcq.1_Intron|DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc004dcm.1_Intron|DMD_uc004dcn.1_Intron|DMD_uc004dco.1_Intron|DMD_uc004dcp.1_Intron|DMD_uc011mkb.1_Intron|DMD_uc010ngm.2_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				gatcaatcgtccagcaaaatgc	0.134													4	2	---	---	---	---	
DMD	1756	broad.mit.edu	37	X	32977863	32977864	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32977863_32977864insA	uc004dda.1	-						DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron|DMD_uc004ddf.2_Intron|DMD_uc010ngr.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				ccaagaacttgatataaacttc	0.163													4	2	---	---	---	---	
LANCL3	347404	broad.mit.edu	37	X	37511546	37511546	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37511546delT	uc011mkd.1	+						LANCL3_uc004ddp.1_Intron	NM_198511	NP_940913	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3								catalytic activity				0						TTTTATTGACTTTTTTTTTTC	0.284													2	4	---	---	---	---	
SRPX	8406	broad.mit.edu	37	X	38055368	38055369	+	Intron	INS	-	A	A			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38055368_38055369insA	uc004ddy.1	-						SRPX_uc004ddz.1_Intron|SRPX_uc011mkh.1_Intron|SRPX_uc011mki.1_Intron	NM_006307	NP_006298	P78539	SRPX_HUMAN	sushi-repeat-containing protein, X-linked						cell adhesion	cell surface|membrane					0						agattattaacaaaaaaaatag	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	38391853	38391855	+	IGR	DEL	CTT	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38391853_38391855delCTT								OTC (111151 upstream) : TSPAN7 (28876 downstream)																							GCAGTTTCTCCTTCTTCTTTATG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	45464831	45464831	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45464831delC								CXorf36 (404685 upstream) : MIR221 (140754 downstream)																							aagtattgttcccctcactgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	46753391	46753391	+	IGR	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46753391delT								RP2 (11602 upstream) : PHF16 (18345 downstream)																							ACCCAATTCCTTTTTAATTTC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	53782756	53782757	+	IGR	INS	-	T	T			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53782756_53782757insT								HUWE1 (69083 upstream) : PHF8 (180357 downstream)																							TCTTGGCCATATTttttttaat	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	53870612	53870612	+	IGR	DEL	G	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53870612delG								HUWE1 (156939 upstream) : PHF8 (92502 downstream)																							CACCAACCCCGCACCCAACTC	0.318													4	2	---	---	---	---	
OPHN1	4983	broad.mit.edu	37	X	67585344	67585344	+	Intron	DEL	T	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67585344delT	uc004dww.3	-						OPHN1_uc011mpg.1_Intron|OPHN1_uc004dwx.2_Intron	NM_002547	NP_002538	O60890	OPHN1_HUMAN	oligophrenin 1						axon guidance|endocytosis|filopodium assembly|small GTPase mediated signal transduction|substrate-dependent cell migration, cell extension	axon|cell junction|cytosol|dendritic spine|synapse	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(2)	2						ATTTTGTTCATTTTCCACAAA	0.453													4	2	---	---	---	---	
TRPC5	7224	broad.mit.edu	37	X	111288175	111288176	+	Intron	DEL	CA	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111288175_111288176delCA	uc004epl.1	-						TRPC5_uc004epm.1_Intron	NM_012471	NP_036603	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel,						axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1						gccaatctctcacagcatgtaa	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	112008803	112008805	+	IGR	DEL	ACA	-	-	rs73630526	by1000genomes	TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112008803_112008805delACA								LHFPL1 (85428 upstream) : AMOT (9301 downstream)																							gcagatatagacaaGGTCATTTG	0.030													4	2	---	---	---	---	
CXorf56	63932	broad.mit.edu	37	X	118689922	118689922	+	Intron	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118689922delC	uc004erk.1	-						CXorf56_uc004erj.1_Intron|CXorf56_uc011mtu.1_Intron	NM_022101	NP_071384	Q9H5V9	CX056_HUMAN	hypothetical protein LOC63932								protein binding				0						gcaatggcttcaacaaaagag	0.000													4	2	---	---	---	---	
GPC3	2719	broad.mit.edu	37	X	132791851	132791851	+	Intron	DEL	A	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132791851delA	uc004exe.1	-						GPC3_uc004exd.1_Intron|GPC3_uc010nrn.1_Intron|GPC3_uc011mvh.1_Intron|GPC3_uc010nro.1_Intron	NM_004484	NP_004475	P51654	GPC3_HUMAN	glypican 3 isoform 2 precursor							extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)					AAACAAAGTGAAAAGCTATTT	0.378			T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	152053394	152053394	+	IGR	DEL	C	-	-			TCGA-CZ-4866-01A-01D-1501-10	TCGA-CZ-4866-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152053394delC								NSDHL (15487 upstream) : ZNF185 (29603 downstream)																							ATCAAAGTGGCCACAAGATGA	0.488													4	2	---	---	---	---	
