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
WDR8	49856	broad.mit.edu	37	1	3553570	3553570	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3553570G>A	uc001ako.2	-	5	613	c.505C>T	c.(505-507)CAG>TAG	p.Q169*	WDR8_uc001akn.3_Nonsense_Mutation_p.Q169*|WDR8_uc010nzi.1_Nonsense_Mutation_p.Q169*	NM_017818	NP_060288	Q9P2S5	WRP73_HUMAN	WD repeat domain 8	169						centrosome	protein binding				0	all_cancers(77;0.0128)|all_epithelial(69;0.00526)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;4.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.16e-22)|GBM - Glioblastoma multiforme(42;1.05e-14)|Colorectal(212;1.19e-05)|BRCA - Breast invasive adenocarcinoma(365;2.67e-05)|COAD - Colon adenocarcinoma(227;5.82e-05)|Kidney(185;0.000364)|KIRC - Kidney renal clear cell carcinoma(229;0.00223)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		CGCAGGAGCTGCCAATCACTG	0.562													5	17	---	---	---	---	PASS
UTS2	10911	broad.mit.edu	37	1	7913479	7913479	+	5'Flank	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7913479C>G	uc001aor.2	-						UTS2_uc001aoq.2_5'UTR|UTS2_uc001aos.2_Missense_Mutation_p.V5L	NM_006786	NP_006777	O95399	UTS2_HUMAN	urotensin 2 isoform b preproprotein						muscle contraction|regulation of blood pressure|synaptic transmission	extracellular space	hormone activity				0	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)		AGATGAAATACGTTGGTTTCC	0.413													13	52	---	---	---	---	PASS
PLEKHM2	23207	broad.mit.edu	37	1	16054794	16054794	+	Silent	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16054794C>A	uc010obo.1	+	11	2090	c.1863C>A	c.(1861-1863)GGC>GGA	p.G621G		NM_015164	NP_055979	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M	621					Golgi organization	cytoplasm	kinesin binding			ovary(1)	1		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		ACATGGAGGGCAACCTGCAGC	0.672													8	9	---	---	---	---	PASS
PADI6	353238	broad.mit.edu	37	1	17720956	17720956	+	Intron	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17720956C>A	uc001bak.1	+							NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CCCAGGTGAGCCACAAAGCCA	0.587													4	14	---	---	---	---	PASS
USP48	84196	broad.mit.edu	37	1	22063027	22063027	+	Silent	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22063027T>C	uc001bfb.2	-	9	1321	c.1083A>G	c.(1081-1083)CCA>CCG	p.P361P	USP48_uc010odq.1_Silent_p.P361P|USP48_uc009vqc.2_Silent_p.P361P|USP48_uc001bfc.2_Silent_p.P361P|USP48_uc001bfe.1_Silent_p.P361P|USP48_uc001bff.2_Silent_p.P361P	NM_032236	NP_115612	Q86UV5	UBP48_HUMAN	ubiquitin specific protease 48 isoform a	361					ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CACCAGACTGTGGATCTTTCA	0.443													14	40	---	---	---	---	PASS
S100PBP	64766	broad.mit.edu	37	1	33321622	33321622	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33321622G>T	uc001bvz.2	+	7	1487	c.1210G>T	c.(1210-1212)GAC>TAC	p.D404Y	S100PBP_uc001bwc.2_Missense_Mutation_p.D404Y|S100PBP_uc001bwd.2_RNA	NM_022753	NP_073590	Q96BU1	S1PBP_HUMAN	S100P binding protein isoform a	404						nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				GCGTCTCCCAGACTTCTCGTA	0.493													7	33	---	---	---	---	PASS
GRIK3	2899	broad.mit.edu	37	1	37307519	37307519	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37307519G>A	uc001caz.2	-	10	1483	c.1348C>T	c.(1348-1350)CGG>TGG	p.R450W	GRIK3_uc001cba.1_Missense_Mutation_p.R450W	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	450	Extracellular (Potential).				negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)	TCTGATTTCCGAAACATGACG	0.567													22	79	---	---	---	---	PASS
DOCK7	85440	broad.mit.edu	37	1	62973692	62973692	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62973692C>T	uc001daq.2	-	35	4424	c.4390G>A	c.(4390-4392)GGA>AGA	p.G1464R	DOCK7_uc001dan.2_Missense_Mutation_p.G1325R|DOCK7_uc001dao.2_Missense_Mutation_p.G1325R|DOCK7_uc001dap.2_Missense_Mutation_p.G1442R|DOCK7_uc001dam.2_Missense_Mutation_p.G644R|DOCK7_uc010oov.1_Missense_Mutation_p.G203R	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1473					activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2						GCCAGGTTTCCATCAATCAGT	0.303													6	22	---	---	---	---	PASS
LEPR	3953	broad.mit.edu	37	1	66102541	66102541	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66102541G>A	uc001dci.2	+	20	3543	c.3341G>A	c.(3340-3342)AGA>AAA	p.R1114K	LEPR_uc009waq.2_3'UTR	NM_002303	NP_002294	P48357	LEPR_HUMAN	leptin receptor isoform 1	1114	Cytoplasmic (Potential).				energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		ACGGACATCAGAGTTCTCCAG	0.433													8	25	---	---	---	---	PASS
PDE4B	5142	broad.mit.edu	37	1	66713282	66713282	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66713282G>T	uc001dcn.2	+	4	612	c.421G>T	c.(421-423)GAC>TAC	p.D141Y	PDE4B_uc009war.2_Missense_Mutation_p.D49Y|PDE4B_uc001dco.2_Missense_Mutation_p.D141Y|PDE4B_uc001dcp.2_Missense_Mutation_p.D126Y	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1	141					signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)	ATCAGACAGCGACTATGACTT	0.522													20	48	---	---	---	---	PASS
DIRAS3	9077	broad.mit.edu	37	1	68512321	68512321	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68512321C>T	uc001ded.2	-	2	955	c.660G>A	c.(658-660)GAG>GAA	p.E220E	uc001deb.1_Intron|uc001dec.1_Intron	NM_004675	NP_004666	O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	220					regulation of cyclin-dependent protein kinase activity|regulation of gene expression by genetic imprinting|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			skin(1)	1						CAAGCAGCTTCTCAGTGGTGT	0.507													9	51	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70503937	70503937	+	Silent	SNP	G	C	C	rs12567778	byFrequency	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70503937G>C	uc001dep.2	+	19	2346	c.2316G>C	c.(2314-2316)TCG>TCC	p.S772S	LRRC7_uc009wbg.2_Silent_p.S56S|LRRC7_uc001deq.2_Silent_p.S13S	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	772						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						CTGATGGCTCGCATTATGACA	0.507													18	64	---	---	---	---	PASS
FPGT	8790	broad.mit.edu	37	1	74670749	74670749	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74670749C>T	uc001dgb.1	+	4	1055	c.1018C>T	c.(1018-1020)CTT>TTT	p.L340F	TNNI3K_uc001dgc.1_Intron|TNNI3K_uc001dgd.2_Intron|TNNI3K_uc001dge.1_Intron|FPGT_uc010oqt.1_Intron|FPGT_uc010oqu.1_Intron|FPGT_uc010oqv.1_Intron	NM_003838	NP_003829	O14772	FPGT_HUMAN	fucose-1-phosphate guanyltransferase	340					fucose metabolic process	cytoplasm	fucose-1-phosphate guanylyltransferase activity|GTP binding			skin(1)	1						AATATTTCATCTTCTTAAAGG	0.353													14	30	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103470046	103470046	+	Splice_Site	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103470046T>C	uc001dul.2	-	20	2218	c.1900_splice	c.e20-1	p.G634_splice	COL11A1_uc001duk.2_Splice_Site|COL11A1_uc001dum.2_Splice_Site_p.G646_splice|COL11A1_uc001dun.2_Splice_Site_p.G595_splice|COL11A1_uc009weh.2_Splice_Site_p.G518_splice	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		ATCTTCTCCCTGTCATTGACA	0.284													3	13	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152282314	152282314	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152282314G>A	uc001ezu.1	-	3	5084	c.5048C>T	c.(5047-5049)TCC>TTC	p.S1683F		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1683	Ser-rich.|Filaggrin 10.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGGTGGCGGGATCCATGTCT	0.562									Ichthyosis				232	287	---	---	---	---	PASS
ATP1A4	480	broad.mit.edu	37	1	160143362	160143362	+	Intron	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160143362C>G	uc001fve.3	+						ATP1A4_uc001fvf.3_Intron|ATP1A4_uc001fvg.2_Intron	NM_144699	NP_653300	Q13733	AT1A4_HUMAN	Na+/K+ -ATPase alpha 4 subunit isoform 1						ATP biosynthetic process|ATP hydrolysis coupled proton transport|regulation of cellular pH|sperm motility	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(2)|skin(2)	4	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CCTCTCCTTCCCAACCCAGGT	0.498													41	142	---	---	---	---	PASS
GPR161	23432	broad.mit.edu	37	1	168065986	168065986	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168065986T>C	uc001gfc.2	-	5	1173	c.859A>G	c.(859-861)ATG>GTG	p.M287V	GPR161_uc001gfb.2_Missense_Mutation_p.M155V|GPR161_uc010pll.1_Missense_Mutation_p.M197V|GPR161_uc010plm.1_Missense_Mutation_p.M173V|GPR161_uc009wvo.2_Missense_Mutation_p.M304V|GPR161_uc001gfd.2_Missense_Mutation_p.M287V|GPR161_uc010pln.1_Missense_Mutation_p.M307V|GPR161_uc001gfe.1_Missense_Mutation_p.M287V	NM_153832	NP_722561	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161 isoform 2	287	Helical; Name=6; (Potential).				multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)					ATGACAACCATGTAGGGGCCC	0.612													28	88	---	---	---	---	PASS
F5	2153	broad.mit.edu	37	1	169494157	169494157	+	Intron	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169494157C>T	uc001ggg.1	-							NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor						cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	CTATGAAAAACAGAAAAAAAA	0.323													12	37	---	---	---	---	PASS
DENND1B	163486	broad.mit.edu	37	1	197684152	197684152	+	Intron	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197684152G>T	uc001guf.3	-						DENND1B_uc010ppe.1_Intron|DENND1B_uc010ppf.1_Intron|DENND1B_uc001gue.3_Intron	NM_144977	NP_659414	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B isoform 2							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0						aaaattatGTGGTACCAACCT	0.328													5	23	---	---	---	---	PASS
ARID4B	51742	broad.mit.edu	37	1	235331905	235331905	+	Silent	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235331905A>G	uc001hwq.2	-	24	4372	c.3874T>C	c.(3874-3876)TTA>CTA	p.L1292L	ARID4B_uc001hwr.2_Silent_p.L1206L|ARID4B_uc001hwp.2_RNA	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	1292	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			GCTAAAGTTAACATAACAGCA	0.443													4	33	---	---	---	---	PASS
ARID4B	51742	broad.mit.edu	37	1	235331906	235331906	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235331906C>A	uc001hwq.2	-	24	4371	c.3873G>T	c.(3871-3873)ATG>ATT	p.M1291I	ARID4B_uc001hwr.2_Missense_Mutation_p.M1205I|ARID4B_uc001hwp.2_RNA	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	1291	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			CTAAAGTTAACATAACAGCAG	0.438													4	34	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237758806	237758806	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237758806G>C	uc001hyl.1	+	34	4565	c.4445G>C	c.(4444-4446)CGC>CCC	p.R1482P		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1482	Cytoplasmic (By similarity).|B30.2/SPRY 3.|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGCATCAAACGCAGCAACTGC	0.443													21	46	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237774129	237774129	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237774129C>T	uc001hyl.1	+	36	4871	c.4751C>T	c.(4750-4752)CCG>CTG	p.P1584L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1584	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CAGTGCCCCCCGCGCCTCCAC	0.542													9	22	---	---	---	---	PASS
CNST	163882	broad.mit.edu	37	1	246829021	246829021	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246829021C>T	uc001ibp.2	+	11	2370	c.1992C>T	c.(1990-1992)TCC>TCT	p.S664S		NM_152609	NP_689822	Q6PJW8	CNST_HUMAN	hypothetical protein LOC163882 isoform 1	664					positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0						GAGGTGGCTCCTGTATTTTGC	0.428													15	45	---	---	---	---	PASS
AHCTF1	25909	broad.mit.edu	37	1	247025278	247025278	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247025278G>A	uc001ibu.1	-	27	3725	c.3718C>T	c.(3718-3720)CCA>TCA	p.P1240S	AHCTF1_uc001ibv.1_Missense_Mutation_p.P1249S|AHCTF1_uc009xgs.1_Missense_Mutation_p.P101S|AHCTF1_uc001ibw.1_RNA	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	1240	Necessary for nuclear localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ATCCATTTTGGGTGGACATCT	0.358													23	30	---	---	---	---	PASS
OR2L3	391192	broad.mit.edu	37	1	248224555	248224555	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248224555C>A	uc001idx.1	+	1	572	c.572C>A	c.(571-573)ACC>AAC	p.T191N	OR2L13_uc001ids.2_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	191	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	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)			TGCATGGACACCTGGGTCTAT	0.478													23	125	---	---	---	---	PASS
WDR35	57539	broad.mit.edu	37	2	20153629	20153629	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20153629G>C	uc002rdi.2	-	13	1507	c.1399C>G	c.(1399-1401)CAG>GAG	p.Q467E	WDR35_uc002rdj.2_Missense_Mutation_p.Q456E|WDR35_uc010ext.2_RNA|WDR35_uc002rdh.2_Missense_Mutation_p.Q32E|WDR35_uc002rdk.3_Missense_Mutation_p.Q32E	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1	467										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CGTGTGATCTGATTAATTTCC	0.383													53	93	---	---	---	---	PASS
DHX57	90957	broad.mit.edu	37	2	39095469	39095469	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39095469T>C	uc002rrf.2	-	2	178	c.79A>G	c.(79-81)AGG>GGG	p.R27G	DHX57_uc002rre.2_5'Flank|DHX57_uc002rrg.2_Missense_Mutation_p.R27G	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	27	Gly-rich.						ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				GCGTGACTCCTGCCTCCTCTT	0.368													17	96	---	---	---	---	PASS
SRBD1	55133	broad.mit.edu	37	2	45778336	45778336	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45778336G>A	uc002rus.2	-	12	1679	c.1603C>T	c.(1603-1605)CCA>TCA	p.P535S	SRBD1_uc010yoc.1_Missense_Mutation_p.P54S	NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	535					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			GTGCGCCCTGGAACAGGGCTT	0.403													9	48	---	---	---	---	PASS
RTN4	57142	broad.mit.edu	37	2	55253647	55253647	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55253647C>G	uc002rye.2	-	3	1886	c.1588G>C	c.(1588-1590)GTC>CTC	p.V530L	RTN4_uc002ryd.2_Missense_Mutation_p.V324L|RTN4_uc002ryf.2_Intron|RTN4_uc002ryg.2_Intron	NM_020532	NP_065393	Q9NQC3	RTN4_HUMAN	reticulon 4 isoform A	530	Cytoplasmic (Potential).				apoptosis|axonal fasciculation|cerebral cortex radial glia guided migration|endoplasmic reticulum tubular network organization|negative regulation of anti-apoptosis|negative regulation of axon extension|nerve growth factor receptor signaling pathway|regulation of apoptosis|regulation of branching morphogenesis of a nerve|regulation of cell migration	integral to endoplasmic reticulum membrane|nuclear envelope|plasma membrane	protein binding			ovary(2)|large_intestine(1)	3						TCTGTTGTGACATAATCTGTC	0.398													28	66	---	---	---	---	PASS
C2orf78	388960	broad.mit.edu	37	2	74042819	74042819	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74042819G>T	uc002sjr.1	+	3	1590	c.1469G>T	c.(1468-1470)TGT>TTT	p.C490F		NM_001080474	NP_001073943	A6NCI8	CB078_HUMAN	hypothetical protein LOC388960	490										ovary(2)	2						GAAAAGTCATGTGTCATAAAG	0.463													20	62	---	---	---	---	PASS
ANAPC1	64682	broad.mit.edu	37	2	112638181	112638181	+	Intron	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112638181C>A	uc002thi.2	-						ANAPC1_uc002thj.2_Intron	NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2						ATGGGAAACTCAATGGAACCT	0.433													6	11	---	---	---	---	PASS
SLC20A1	6574	broad.mit.edu	37	2	113405026	113405026	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113405026G>C	uc002tib.2	+	3	906	c.460G>C	c.(460-462)GAA>CAA	p.E154Q	uc010fkq.1_5'Flank	NM_005415	NP_005406	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate	154	Extracellular (Potential).				phosphate metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to plasma membrane	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity			ovary(2)	2						CAAGTGGTCTGAACTGATAAA	0.418													47	121	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141457889	141457889	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141457889G>T	uc002tvj.1	-	41	7701	c.6729C>A	c.(6727-6729)TAC>TAA	p.Y2243*		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2243	Extracellular (Potential).|LDL-receptor class B 23.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GTGCATCACTGTAAAAGATTC	0.343										TSP Lung(27;0.18)			20	63	---	---	---	---	PASS
SCN2A	6326	broad.mit.edu	37	2	166165204	166165204	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166165204G>C	uc002udc.2	+	5	795	c.505G>C	c.(505-507)GAA>CAA	p.E169Q	SCN2A_uc002udd.2_Missense_Mutation_p.E169Q|SCN2A_uc002ude.2_Missense_Mutation_p.E169Q	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	169	I.|Helical; Name=S2 of repeat I; (Potential).				myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)	TTATACTTTTGAATCACTTAT	0.318													26	38	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178098953	178098953	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178098953C>G	uc002ulh.3	-	2	647	c.92G>C	c.(91-93)GGA>GCA	p.G31A	NFE2L2_uc002ulg.3_Missense_Mutation_p.G15A|NFE2L2_uc010zfa.1_Missense_Mutation_p.G15A|NFE2L2_uc002uli.3_Missense_Mutation_p.G15A|NFE2L2_uc010fra.2_Missense_Mutation_p.G15A|NFE2L2_uc010frb.2_Missense_Mutation_p.G15A	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	31					transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	p.G31R(1)		central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			TCGACTTACTCCAAGATCTAT	0.363			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			8	44	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179434029	179434029	+	Silent	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179434029G>T	uc010zfg.1	-	275	69350	c.69126C>A	c.(69124-69126)GTC>GTA	p.V23042V	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.V16737V|TTN_uc010zfi.1_Silent_p.V16670V|TTN_uc010zfj.1_Silent_p.V16545V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23969							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)			TGATTTCTGTGACTTTCAGGT	0.403													50	187	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179606435	179606435	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179606435G>A	uc010zfh.1	-	46	11236	c.11012C>T	c.(11011-11013)ACT>ATT	p.T3671I	TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Missense_Mutation_p.T3604I|TTN_uc010zfj.1_Missense_Mutation_p.T3479I|TTN_uc002umz.1_Intron	NM_133437	NP_597681	Q8WZ42	TITIN_HUMAN	titin isoform novex-2	3643							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)			GCCAATGACAGTTACAGACAG	0.403													8	42	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	186670267	186670267	+	Intron	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186670267C>A	uc002upm.2	+						uc010zfu.1_5'Flank					Homo sapiens cDNA FLJ44048 fis, clone TESTI4030669.																		ATTTCTAAATCCAGATAATAT	0.398													14	49	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	186671569	186671569	+	Intron	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186671569G>C	uc002upm.2	+						uc010zfu.1_Missense_Mutation_p.V344L					Homo sapiens cDNA FLJ44048 fis, clone TESTI4030669.																		TCAAATTAAGGTTTTCAGGCC	0.398													19	45	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196759756	196759756	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196759756C>T	uc002utj.3	-	30	4941	c.4840G>A	c.(4840-4842)GGA>AGA	p.G1614R		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1614	ATP (Potential).|AAA 2 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						CTAGTTTTTCCTCCAAATGGT	0.318													3	27	---	---	---	---	PASS
STK17B	9262	broad.mit.edu	37	2	197004392	197004392	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197004392G>A	uc002utk.2	-	7	1112	c.788C>T	c.(787-789)TCA>TTA	p.S263L	STK17B_uc010fsh.2_Missense_Mutation_p.S263L	NM_004226	NP_004217	O94768	ST17B_HUMAN	serine/threonine kinase 17B	263	Protein kinase.				apoptosis|induction of apoptosis|intracellular protein kinase cascade	nucleus	ATP binding|protein serine/threonine kinase activity			lung(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.141)			GGCCAGCTGTGAAACTGATGA	0.294													13	45	---	---	---	---	PASS
CPS1	1373	broad.mit.edu	37	2	211521310	211521310	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211521310C>A	uc002vee.3	+	30	3752	c.3620C>A	c.(3619-3621)ACT>AAT	p.T1207N	CPS1_uc010fur.2_Missense_Mutation_p.T1213N|CPS1_uc010fus.2_Missense_Mutation_p.T756N	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	1207	ATP-grasp 2.				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		GGAGATGCCACTCTGATGCTG	0.403													15	42	---	---	---	---	PASS
DNPEP	23549	broad.mit.edu	37	2	220246262	220246262	+	Intron	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220246262C>T	uc010zlg.1	-						DNPEP_uc010zlf.1_Intron|DNPEP_uc002vle.2_Intron|DNPEP_uc002vlf.1_Intron|DNPEP_uc002vlh.2_Intron|DNPEP_uc002vli.1_Intron	NM_012100	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase						peptide metabolic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	L-Glutamic Acid(DB00142)	AATGGCACGTCTCACCTTGTG	0.458													37	150	---	---	---	---	PASS
SEC13	6396	broad.mit.edu	37	3	10347307	10347307	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10347307G>A	uc003bvn.2	-	6	639	c.520C>T	c.(520-522)CAG>TAG	p.Q174*	SEC13_uc003bvl.2_Nonsense_Mutation_p.Q106*|SEC13_uc003bvm.2_Nonsense_Mutation_p.Q160*|SEC13_uc003bvp.2_Nonsense_Mutation_p.Q177*|SEC13_uc003bvo.2_Nonsense_Mutation_p.Q220*|SEC13_uc003bvq.1_Nonsense_Mutation_p.Q160*|SEC13_uc003bvr.1_Nonsense_Mutation_p.Q160*	NM_183352	NP_899195	P55735	SEC13_HUMAN	SEC13 protein isoform 1	174	WD 4.				COPII vesicle coating|intracellular protein transport|mitotic prometaphase|mRNA transport|post-translational protein modification|protein N-linked glycosylation via asparagine|transmembrane transport	cytosol|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Nup107-160 complex	protein binding			ovary(1)	1						TTGGGTTTCTGCCCCGATGGG	0.532													29	77	---	---	---	---	PASS
PPARG	5468	broad.mit.edu	37	3	12475387	12475387	+	Intron	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12475387G>A	uc003bwx.2	+						PPARG_uc003bwr.2_Intron|PPARG_uc003bws.2_Intron|PPARG_uc003bwu.2_Intron|PPARG_uc003bwv.2_Intron	NM_015869	NP_056953	P37231	PPARG_HUMAN	peroxisome proliferative activated receptor						activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|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|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation	cytosol|nucleoplasm	activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|kidney(1)	2					Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197)	TTCCATATGTGCTTCCCCAGA	0.522			T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy|familial partial L;diabetes mellitus|insulin-resistantI|with acanthosis nigricans and hypertension						16	66	---	---	---	---	PASS
FGD5	152273	broad.mit.edu	37	3	14862234	14862234	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14862234C>T	uc003bzc.2	+	1	1766	c.1656C>T	c.(1654-1656)TCC>TCT	p.S552S	FGD5_uc011avk.1_Silent_p.S552S	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	552					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5						GGTCGTTCTCCGTGGAAGGCC	0.552													12	21	---	---	---	---	PASS
NGLY1	55768	broad.mit.edu	37	3	25777608	25777608	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25777608G>T	uc003cdl.2	-	7	1144	c.1036C>A	c.(1036-1038)CAG>AAG	p.Q346K	NGLY1_uc010hfg.2_Intron|NGLY1_uc003cdm.2_Missense_Mutation_p.Q346K|NGLY1_uc011awo.1_Missense_Mutation_p.Q304K|NGLY1_uc003cdk.2_RNA	NM_018297	NP_060767	Q96IV0	NGLY1_HUMAN	N-glycanase 1 isoform 1	346					glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1						CACCGCTGCTGAGAAGGAGAA	0.413													7	21	---	---	---	---	PASS
OSBPL10	114884	broad.mit.edu	37	3	31871555	31871555	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31871555C>T	uc003cev.2	-	5	1087	c.706G>A	c.(706-708)GGC>AGC	p.G236S	OSBPL10_uc003ceu.1_5'UTR|OSBPL10_uc011axf.1_Intron	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10	236					lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)		TGAAGCTGGCCGGAATACTGA	0.597													7	20	---	---	---	---	PASS
XIRP1	165904	broad.mit.edu	37	3	39227557	39227557	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39227557A>T	uc003cjk.1	-	2	3601	c.3380T>A	c.(3379-3381)CTA>CAA	p.L1127Q	XIRP1_uc003cji.2_Intron|XIRP1_uc003cjj.2_Intron	NM_194293	NP_919269	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1127							actin binding			ovary(4)|breast(2)|central_nervous_system(1)|pancreas(1)	8				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CCCTCTGGGTAGTGCTTGCTC	0.602													21	27	---	---	---	---	PASS
TRAK1	22906	broad.mit.edu	37	3	42133051	42133051	+	Nonsense_Mutation	SNP	T	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42133051T>A	uc003cky.2	+	1	306	c.90T>A	c.(88-90)TGT>TGA	p.C30*	TRAK1_uc011azh.1_Nonsense_Mutation_p.C30*|TRAK1_uc011azi.1_Nonsense_Mutation_p.C30*	NM_001042646	NP_001036111	Q9UPV9	TRAK1_HUMAN	OGT(O-Glc-NAc transferase)-interacting protein	30					endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1						CAAACGCCTGTGGTAAGTTTG	0.527													5	5	---	---	---	---	PASS
PDE12	201626	broad.mit.edu	37	3	57545540	57545540	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57545540C>A	uc003diw.3	+	3	1765	c.1639C>A	c.(1639-1641)CCT>ACT	p.P547T	PDE12_uc003div.2_3'UTR	NM_177966	NP_808881	Q6L8Q7	PDE12_HUMAN	phosphodiesterase 12	547							hydrolase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.011)|Kidney(284;0.0127)		TTGTGGTGAACCTGCTTACAC	0.403													46	45	---	---	---	---	PASS
FOXP1	27086	broad.mit.edu	37	3	71179753	71179753	+	Intron	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71179753C>G	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003doj.2_5'Flank|FOXP1_uc003dok.2_5'Flank	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GCGGGGGTTGCCGAGTGGTAA	0.483			T	PAX5	ALL								11	41	---	---	---	---	PASS
STXBP5L	9515	broad.mit.edu	37	3	121100357	121100357	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121100357G>T	uc003eec.3	+	23	2777	c.2637G>T	c.(2635-2637)GAG>GAT	p.E879D	STXBP5L_uc011bji.1_Missense_Mutation_p.E855D	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	879	WD 11.				exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		GGTTTACAGAGCCAGTCATGG	0.358													51	40	---	---	---	---	PASS
COPG	22820	broad.mit.edu	37	3	128996139	128996139	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128996139G>A	uc003els.2	+	24	2597	c.2497G>A	c.(2497-2499)GTG>ATG	p.V833M	COPG_uc010htb.2_Missense_Mutation_p.V739M|C3orf37_uc003elt.2_5'Flank|C3orf37_uc003elu.2_5'Flank|C3orf37_uc003elv.2_5'Flank|C3orf37_uc003elw.2_5'Flank	NM_016128	NP_057212	Q9Y678	COPG_HUMAN	coatomer protein complex, subunit gamma 1	833	Interaction with ZNF289/ARFGAP2.				COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(3)|breast(1)	4						CCTTCTAGGTGTGTTCCGGGG	0.502													5	102	---	---	---	---	PASS
GPR87	53836	broad.mit.edu	37	3	151012086	151012086	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151012086G>T	uc003eyt.2	-	3	1309	c.948C>A	c.(946-948)TTC>TTA	p.F316L	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_023915	NP_076404	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	316	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACCTACACATGAAAAAGTAAA	0.348													58	80	---	---	---	---	PASS
NMD3	51068	broad.mit.edu	37	3	160965101	160965101	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160965101G>A	uc003feb.1	+	13	1305	c.1186G>A	c.(1186-1188)GAT>AAT	p.D396N	NMD3_uc003fec.2_Missense_Mutation_p.D396N|NMD3_uc003fed.1_Missense_Mutation_p.D396N|NMD3_uc010hwh.2_Missense_Mutation_p.D216N	NM_015938	NP_057022	Q96D46	NMD3_HUMAN	NMD3 homolog	396					protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			AATGAACTCAGATAGAGTTCC	0.363													4	61	---	---	---	---	PASS
C3orf59	151963	broad.mit.edu	37	3	192516538	192516538	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192516538G>T	uc011bsp.1	-	2	1434	c.1113C>A	c.(1111-1113)AAC>AAA	p.N371K		NM_178496	NP_848591	Q8IYB1	M21D2_HUMAN	hypothetical protein LOC151963	371											0	all_cancers(143;1.56e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.8e-18)|LUSC - Lung squamous cell carcinoma(58;8.04e-06)|Lung(62;8.62e-06)	GBM - Glioblastoma multiforme(46;3.86e-05)		GGCACATCTTGTTGACCAGAC	0.532													7	52	---	---	---	---	PASS
ACAP2	23527	broad.mit.edu	37	3	195027347	195027347	+	Splice_Site	SNP	T	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195027347T>A	uc003fun.3	-	13	1252	c.1011_splice	c.e13-1	p.K337_splice		NM_012287	NP_036419	Q15057	ACAP2_HUMAN	centaurin, beta 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2						ATGCAACTTCTAAAAGGAAAT	0.373													79	90	---	---	---	---	PASS
ABLIM2	84448	broad.mit.edu	37	4	8046942	8046942	+	Silent	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8046942G>T	uc003gko.2	-	9	992	c.849C>A	c.(847-849)ATC>ATA	p.I283I	ABLIM2_uc003gkl.2_Silent_p.I33I|ABLIM2_uc003gkj.3_Silent_p.I283I|ABLIM2_uc003gkm.3_Silent_p.I283I|ABLIM2_uc003gkp.2_Silent_p.I283I|ABLIM2_uc003gkq.2_Silent_p.I283I|ABLIM2_uc003gkr.2_Silent_p.I283I|ABLIM2_uc003gks.3_Silent_p.I283I|ABLIM2_uc011bwl.1_Silent_p.I288I	NM_001130084	NP_001123556	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	283					axon guidance|cytoskeleton organization	actin cytoskeleton|cytoplasm|intermediate filament cytoskeleton|nucleus	actin binding|zinc ion binding			pancreas(3)	3						GGACAGAAATGATGCTCTCTG	0.537													16	49	---	---	---	---	PASS
RELL1	768211	broad.mit.edu	37	4	37633048	37633048	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37633048C>G	uc003gsz.2	-	6	868	c.778G>C	c.(778-780)GCA>CCA	p.A260P	RELL1_uc010ifc.2_Missense_Mutation_p.A260P	NM_001085399	NP_001078868	Q8IUW5	RELL1_HUMAN	receptor expressed in lymphoid tissues like 1	260	Cytoplasmic (Potential).					cytoplasm|integral to membrane|microtubule cytoskeleton|plasma membrane					0						ACAGGTGTTGCCGGCACCTCC	0.532													22	58	---	---	---	---	PASS
REST	5978	broad.mit.edu	37	4	57797830	57797830	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57797830G>T	uc003hch.2	+	4	3153	c.2806G>T	c.(2806-2808)GGT>TGT	p.G936C	REST_uc003hci.2_Missense_Mutation_p.G936C|REST_uc010ihf.2_Missense_Mutation_p.G610C	NM_005612	NP_005603	Q13127	REST_HUMAN	RE1-silencing transcription factor	936					cardiac muscle cell myoblast differentiation|cellular response to drug|cellular response to electrical stimulus|cellular response to glucocorticoid stimulus|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of aldosterone biosynthetic process|negative regulation of calcium ion-dependent exocytosis|negative regulation of cell proliferation|negative regulation of cortisol biosynthetic process|negative regulation of dense core granule biogenesis|negative regulation of insulin secretion|negative regulation of mesenchymal stem cell differentiation|negative regulation of neurogenesis|negative regulation of neuron differentiation|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of transcription, DNA-dependent	cytoplasm|transcriptional repressor complex	calcium channel activity|chromatin binding|core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|outward rectifier potassium channel activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|zinc ion binding			skin(5)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	9	Glioma(25;0.08)|all_neural(26;0.181)					AACTTTAAATGGTAAACATCA	0.388													4	37	---	---	---	---	PASS
ANKRD56	345079	broad.mit.edu	37	4	77816829	77816829	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77816829G>T	uc003hki.2	-	1	2174	c.2174C>A	c.(2173-2175)GCT>GAT	p.A725D		NM_001029870	NP_001025041	A6NEL2	ANR56_HUMAN	ankyrin repeat domain 56	725											0						GCCCCGAGGAGCTCCCAACAG	0.507													42	142	---	---	---	---	PASS
NEUROG2	63973	broad.mit.edu	37	4	113436154	113436154	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113436154A>G	uc003ias.2	-	2	805	c.478T>C	c.(478-480)TAC>CAC	p.Y160H		NM_024019	NP_076924	Q9H2A3	NGN2_HUMAN	neurogenin 2	160	Helix-loop-helix motif.				positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent	nucleus	E-box binding			skin(2)|central_nervous_system(1)	3		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.00168)		GCCCAGATGTAGTTGTGGGCG	0.537													11	22	---	---	---	---	PASS
NDST4	64579	broad.mit.edu	37	4	115773882	115773882	+	Silent	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115773882T>C	uc003ibu.2	-	8	2494	c.1815A>G	c.(1813-1815)ACA>ACG	p.T605T	NDST4_uc010imw.2_RNA	NM_022569	NP_072091	Q9H3R1	NDST4_HUMAN	heparan sulfate N-deacetylase/N-sulfotransferase	605	Lumenal (Potential).|Heparan sulfate N-sulfotransferase 4.|PAPS (By similarity).					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		TATTTTTACCTGTTTTTTGTG	0.303													5	8	---	---	---	---	PASS
NDST4	64579	broad.mit.edu	37	4	115997337	115997337	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115997337C>G	uc003ibu.2	-	2	1535	c.856G>C	c.(856-858)GAT>CAT	p.D286H	NDST4_uc010imw.2_Intron	NM_022569	NP_072091	Q9H3R1	NDST4_HUMAN	heparan sulfate N-deacetylase/N-sulfotransferase	286	Lumenal (Potential).|Heparan sulfate N-deacetylase 4.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		GAGATGGCATCTATGAAGATG	0.443													47	49	---	---	---	---	PASS
PLRG1	5356	broad.mit.edu	37	4	155458514	155458514	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155458514A>G	uc003iny.2	-	14	1472	c.1409T>C	c.(1408-1410)TTT>TCT	p.F470S	PLRG1_uc003inz.2_Missense_Mutation_p.F461S	NM_002669	NP_002660	O43660	PLRG1_HUMAN	pleiotropic regulator 1 (PRL1 homolog,	470	WD 7.					catalytic step 2 spliceosome|nuclear speck	protein binding|signal transducer activity|transcription corepressor activity				0	all_hematologic(180;0.215)	Renal(120;0.0854)				AGACTGATCAAAAGCACAAGC	0.423													10	34	---	---	---	---	PASS
TMEM144	55314	broad.mit.edu	37	4	159140530	159140530	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159140530T>A	uc003ipx.2	+	6	921	c.401T>A	c.(400-402)CTA>CAA	p.L134Q	TMEM144_uc010iqi.2_RNA	NM_018342	NP_060812	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	134	Helical; (Potential).					integral to membrane					0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)		GGAGCTGGGCTATCAGTAGTA	0.363													20	35	---	---	---	---	PASS
ADAMTS16	170690	broad.mit.edu	37	5	5182171	5182171	+	Silent	SNP	A	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5182171A>T	uc003jdl.2	+	4	654	c.516A>T	c.(514-516)CGA>CGT	p.R172R	ADAMTS16_uc003jdk.1_Silent_p.R172R|ADAMTS16_uc003jdj.1_Silent_p.R172R	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	172					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						GCATGATACGAACAGAAGAGG	0.463													14	120	---	---	---	---	PASS
RNASEN	29102	broad.mit.edu	37	5	31526873	31526873	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31526873G>T	uc003jhg.2	-	4	526	c.167C>A	c.(166-168)CCA>CAA	p.P56Q	RNASEN_uc003jhh.2_Missense_Mutation_p.P56Q|RNASEN_uc003jhi.2_Missense_Mutation_p.P56Q|RNASEN_uc010iui.1_Missense_Mutation_p.P47Q	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1	56	Pro-rich.				gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0						AGGGGCACTTGGAGGTTCATA	0.562													3	14	---	---	---	---	PASS
ADAMTS12	81792	broad.mit.edu	37	5	33534964	33534964	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33534964T>A	uc003jia.1	-	23	4743	c.4580A>T	c.(4579-4581)AAC>ATC	p.N1527I	ADAMTS12_uc010iuq.1_Missense_Mutation_p.N1442I	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1527	TSP type-1 8.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						GGCCTGCTGGTTGCATTTTTT	0.463										HNSCC(64;0.19)			13	90	---	---	---	---	PASS
LMBRD2	92255	broad.mit.edu	37	5	36143415	36143415	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36143415C>A	uc003jkb.1	-	2	452	c.37G>T	c.(37-39)GTC>TTC	p.V13F		NM_001007527	NP_001007528	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	13	Helical; (Potential).					integral to membrane					0	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AGAAAAAAGACAAAAACAATC	0.363													12	64	---	---	---	---	PASS
SKP2	6502	broad.mit.edu	37	5	36184122	36184122	+	3'UTR	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36184122T>C	uc003jkd.2	+	10						NM_032637	NP_116026	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2 isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G1/S transition of mitotic cell cycle|S phase of mitotic cell cycle	nucleoplasm|SCF ubiquitin ligase complex	protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AAAACACATTTTTATAAAAAT	0.284													8	26	---	---	---	---	PASS
CARD6	84674	broad.mit.edu	37	5	40852859	40852859	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40852859C>T	uc003jmg.2	+	3	1500	c.1425C>T	c.(1423-1425)CTC>CTT	p.L475L		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	475					apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5						ACACACTTCTCAGCCCTGCCC	0.428													11	45	---	---	---	---	PASS
PLCXD3	345557	broad.mit.edu	37	5	41382440	41382440	+	Silent	SNP	G	T	T	rs146343766		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41382440G>T	uc003jmm.1	-	2	402	c.300C>A	c.(298-300)TCC>TCA	p.S100S		NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X	100	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity	p.S100S(1)		skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						TGGGCTTGGTGGAAATTCGAA	0.453													7	53	---	---	---	---	PASS
NNT	23530	broad.mit.edu	37	5	43650653	43650653	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43650653G>T	uc003joe.2	+	12	1936	c.1681G>T	c.(1681-1683)GCT>TCT	p.A561S	NNT_uc003jof.2_Missense_Mutation_p.A561S	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	561	Helical; (Potential).				tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)	GGGCCTTGCTGCTCTTGCTGC	0.428													8	42	---	---	---	---	PASS
DMXL1	1657	broad.mit.edu	37	5	118529647	118529647	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118529647C>G	uc003ksd.2	+	30	7620	c.7439C>G	c.(7438-7440)TCT>TGT	p.S2480C	DMXL1_uc010jcl.1_Missense_Mutation_p.S2480C	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2480										ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CAGGAACATTCTAATTCAAAT	0.194													6	17	---	---	---	---	PASS
PHAX	51808	broad.mit.edu	37	5	125960471	125960471	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125960471G>A	uc003kua.1	+	5	1142	c.1120G>A	c.(1120-1122)GAA>AAA	p.E374K		NM_032177	NP_115553	Q9H814	PHAX_HUMAN	RNA U, small nuclear RNA export adaptor	374					ncRNA metabolic process|protein transport|snRNA export from nucleus|spliceosomal snRNP assembly	Cajal body|cytosol	RNA binding				0						AGGACATGCAGAAGCCAAGTT	0.408													11	63	---	---	---	---	PASS
ADAMTS19	171019	broad.mit.edu	37	5	128977660	128977660	+	Intron	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128977660C>T	uc003kvb.1	+						ADAMTS19_uc010jdh.1_Intron	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		TAAGGTAAGTCATTTGTGTTG	0.398													13	49	---	---	---	---	PASS
CDC23	8697	broad.mit.edu	37	5	137527989	137527989	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137527989G>T	uc003lcl.2	-	11	1286	c.1255C>A	c.(1255-1257)CTT>ATT	p.L419I		NM_004661	NP_004652	Q9UJX2	CDC23_HUMAN	cell division cycle protein 23	419	TPR 7.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1 phase of mitotic cell cycle|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase plate congression|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|regulation of exit from mitosis	anaphase-promoting complex|cytosol|nucleoplasm	binding|ubiquitin-protein ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TAATAATAAAGGCAGTAAAAT	0.438													4	45	---	---	---	---	PASS
SH3RF2	153769	broad.mit.edu	37	5	145393529	145393529	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145393529G>A	uc003lnt.2	+	5	1202	c.964G>A	c.(964-966)GAG>AAG	p.E322K	SH3RF2_uc011dbl.1_Missense_Mutation_p.E322K	NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	322							ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCATATGGTAGAGATCAGCAC	0.572													21	88	---	---	---	---	PASS
CLK4	57396	broad.mit.edu	37	5	178035369	178035369	+	Intron	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178035369C>T	uc003mjf.1	-						CLK4_uc003mjg.1_Intron|CLK4_uc010jku.1_Intron|CLK4_uc003mjh.1_Intron|CLK4_uc010jkv.1_Intron|CLK4_uc011dgg.1_Intron|CLK4_uc011dgh.1_Intron	NM_020666	NP_065717	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4							nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(1)	1	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		AATTTACTAGCCACGTACCTG	0.323													5	30	---	---	---	---	PASS
CLK4	57396	broad.mit.edu	37	5	178043908	178043908	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178043908C>G	uc003mjf.1	-	5	625	c.517G>C	c.(517-519)GTT>CTT	p.V173L	CLK4_uc003mjg.1_Missense_Mutation_p.V137L|CLK4_uc010jku.1_5'UTR|CLK4_uc003mjh.1_5'UTR|CLK4_uc010jkv.1_RNA|CLK4_uc011dgg.1_Missense_Mutation_p.V173L|CLK4_uc011dgh.1_5'UTR	NM_020666	NP_065717	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	173	ATP (By similarity).|Protein kinase.					nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(1)	1	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		CACTCTACAACTTTGCCAAAG	0.378													12	21	---	---	---	---	PASS
CLK4	57396	broad.mit.edu	37	5	178043926	178043926	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178043926C>T	uc003mjf.1	-	5	607	c.499G>A	c.(499-501)GAA>AAA	p.E167K	CLK4_uc003mjg.1_Missense_Mutation_p.E131K|CLK4_uc010jku.1_5'UTR|CLK4_uc003mjh.1_5'UTR|CLK4_uc010jkv.1_RNA|CLK4_uc011dgg.1_Missense_Mutation_p.E167K|CLK4_uc011dgh.1_5'UTR	NM_020666	NP_065717	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	167	ATP (By similarity).|Protein kinase.					nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(1)	1	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		AAGGCTCCTTCACCCAAAGTG	0.388													12	23	---	---	---	---	PASS
HIST1H3B	8358	broad.mit.edu	37	6	26032069	26032069	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26032069C>T	uc003nfs.1	-	1	220	c.220G>A	c.(220-222)GAA>AAA	p.E74K		NM_003537	NP_003528	P68431	H31_HUMAN	histone cluster 1, H3b	74					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(2)	2						TGGGCGATTTCTCGCACCAGG	0.607													24	61	---	---	---	---	PASS
BTN3A3	10384	broad.mit.edu	37	6	26452620	26452620	+	Missense_Mutation	SNP	G	A	A	rs144256388		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26452620G>A	uc003nhz.2	+	11	1916	c.1736G>A	c.(1735-1737)CGC>CAC	p.R579H	BTN3A3_uc003nia.2_Missense_Mutation_p.R537H|BTN3A3_uc011dkn.1_Missense_Mutation_p.R530H	NM_006994	NP_008925	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3 isoform a	579	Cytoplasmic (Potential).					integral to membrane					0						CTACAGGcacgcactgaagca	0.264													4	19	---	---	---	---	PASS
RNF8	9025	broad.mit.edu	37	6	37328291	37328291	+	Silent	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37328291C>A	uc003onq.3	+	2	374	c.181C>A	c.(181-183)CGA>AGA	p.R61R	RNF8_uc003onr.3_Silent_p.R61R|RNF8_uc011dtx.1_5'UTR	NM_003958	NP_003949	O76064	RNF8_HUMAN	ring finger protein 8 isoform 1	61	FHA.				cell division|double-strand break repair|histone H2A ubiquitination|histone H2B ubiquitination|mitosis|positive regulation of DNA repair|response to ionizing radiation	midbody|nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1						GATGATTTCTCGAAACCACTG	0.413													4	69	---	---	---	---	PASS
KIAA0240	23506	broad.mit.edu	37	6	42823596	42823596	+	Silent	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42823596G>T	uc003osn.1	+	9	2200	c.2049G>T	c.(2047-2049)GTG>GTT	p.V683V	KIAA0240_uc011duw.1_Silent_p.V683V|KIAA0240_uc003osp.1_Silent_p.V683V	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506	683										ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)			GTCTTTAGGTGGAGAGTCATT	0.358													5	190	---	---	---	---	PASS
PHF3	23469	broad.mit.edu	37	6	64395298	64395298	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64395298C>T	uc003pep.1	+	3	1701	c.1675C>T	c.(1675-1677)CAG>TAG	p.Q559*	PHF3_uc010kaf.1_Nonsense_Mutation_p.Q559*|PHF3_uc003pem.2_Nonsense_Mutation_p.Q512*|PHF3_uc010kag.1_Nonsense_Mutation_p.Q471*|PHF3_uc010kah.1_Nonsense_Mutation_p.Q373*|PHF3_uc003pen.2_Nonsense_Mutation_p.Q471*|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_Nonsense_Mutation_p.Q559*	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	559					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GCCAAAGATTCAGAGTTGCAA	0.343													8	38	---	---	---	---	PASS
ROS1	6098	broad.mit.edu	37	6	117708041	117708041	+	Intron	SNP	T	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117708041T>G	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)		AACAGAGGACTTGGGGTTTAC	0.383			T	GOPC|ROS1	glioblastoma|NSCLC								8	41	---	---	---	---	PASS
MED23	9439	broad.mit.edu	37	6	131917168	131917168	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131917168G>T	uc003qcs.1	-	22	3088	c.2914C>A	c.(2914-2916)CAC>AAC	p.H972N	MED23_uc003qcq.2_Missense_Mutation_p.H978N|MED23_uc003qcr.1_5'Flank|MED23_uc011eca.1_Missense_Mutation_p.H613N	NM_004830	NP_004821	Q9ULK4	MED23_HUMAN	mediator complex subunit 23 isoform a	972					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		AAAAATCTGTGGATTACTATA	0.408													5	115	---	---	---	---	PASS
SYNJ2	8871	broad.mit.edu	37	6	158483013	158483013	+	Intron	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158483013C>A	uc003qqx.1	+						SYNJ2_uc011efm.1_Intron|SYNJ2_uc003qqw.1_Intron|SYNJ2_uc003qqy.1_Intron|SYNJ2_uc011efn.1_Intron|SYNJ2_uc010kjo.1_Intron|SYNJ2_uc003qqz.1_Intron	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2								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)		gccctcccctcctctTTTCAG	0.408													6	139	---	---	---	---	PASS
C7orf31	136895	broad.mit.edu	37	7	25176259	25176259	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25176259T>C	uc003sxn.1	-	10	1666	c.1105A>G	c.(1105-1107)ACC>GCC	p.T369A	C7orf31_uc003sxm.1_Missense_Mutation_p.T211A	NM_138811	NP_620166	Q8N865	CG031_HUMAN	hypothetical protein LOC136895	369											0						GGTACAAAGGTATGAAAATTA	0.423													38	54	---	---	---	---	PASS
GARS	2617	broad.mit.edu	37	7	30661928	30661928	+	Intron	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30661928C>T	uc003tbm.2	+							NM_002047	NP_002038	P41250	SYG_HUMAN	glycyl-tRNA synthetase						cell death|diadenosine tetraphosphate biosynthetic process|glycyl-tRNA aminoacylation	cytosol|mitochondrial matrix|soluble fraction	ATP binding|glycine-tRNA ligase activity|protein dimerization activity			ovary(1)	1					Glycine(DB00145)	TTGACTACTTCATACAAAACA	0.393													16	59	---	---	---	---	PASS
CCDC129	223075	broad.mit.edu	37	7	31682731	31682731	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31682731C>A	uc003tcj.1	+	11	2740	c.1747C>A	c.(1747-1749)CCT>ACT	p.P583T	CCDC129_uc011kad.1_Missense_Mutation_p.P593T|CCDC129_uc003tci.1_Missense_Mutation_p.P434T|CCDC129_uc011kae.1_Missense_Mutation_p.P609T|CCDC129_uc003tck.1_Missense_Mutation_p.P491T	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	583											0						TTTTGTGAGGCCTGAGGGAGC	0.483													30	215	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48315064	48315064	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48315064A>T	uc003toq.2	+	17	5826	c.5801A>T	c.(5800-5802)CAA>CTA	p.Q1934L	ABCA13_uc010kyr.2_Missense_Mutation_p.Q1437L	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	1934					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						TCAATAAATCAAACTAGGGAT	0.358													26	103	---	---	---	---	PASS
POM121L12	285877	broad.mit.edu	37	7	53104213	53104213	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53104213C>G	uc003tpz.2	+	1	865	c.849C>G	c.(847-849)TTC>TTG	p.F283L		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	POM121 membrane glycoprotein-like 12	283											0						GGGTCTCCTTCGCCCTCGAGG	0.617													10	22	---	---	---	---	PASS
ADAM22	53616	broad.mit.edu	37	7	87800867	87800867	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87800867G>A	uc003ujn.2	+	26	2370	c.2291G>A	c.(2290-2292)CGA>CAA	p.R764Q	ADAM22_uc003ujk.1_Missense_Mutation_p.R764Q|ADAM22_uc003ujl.1_Missense_Mutation_p.R764Q|ADAM22_uc003ujm.2_Missense_Mutation_p.R764Q|ADAM22_uc003ujo.2_Missense_Mutation_p.R764Q|ADAM22_uc003ujp.1_Missense_Mutation_p.R816Q	NM_021723	NP_068369	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 1	764	Cytoplasmic (Potential).				cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			AGAAACTATCGAGAACAGAGG	0.333													7	42	---	---	---	---	PASS
PPP1R9A	55607	broad.mit.edu	37	7	94898580	94898580	+	Intron	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94898580G>T	uc003unp.2	+						PPP1R9A_uc010lfj.2_Missense_Mutation_p.R962I|PPP1R9A_uc011kif.1_Missense_Mutation_p.R922I|PPP1R9A_uc003unq.2_Missense_Mutation_p.R940I|PPP1R9A_uc011kig.1_Intron|PPP1R9A_uc003unr.2_Missense_Mutation_p.R13I	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)							cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			AAGGGTTTGAGAACGTCTTCT	0.433										HNSCC(28;0.073)			11	53	---	---	---	---	PASS
NRCAM	4897	broad.mit.edu	37	7	107824715	107824715	+	Silent	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107824715T>C	uc003vfb.2	-	22	2745	c.2274A>G	c.(2272-2274)TCA>TCG	p.S758S	NRCAM_uc003vfc.2_Silent_p.S742S|NRCAM_uc011kmk.1_Silent_p.S753S|NRCAM_uc003vfd.2_Silent_p.S734S|NRCAM_uc003vfe.2_Silent_p.S734S	NM_001037132	NP_001032209	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule isoform A	758	Fibronectin type-III 2.|Extracellular (Potential).				angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5						TATCAGGCTCTGATCCCAGTC	0.388													4	32	---	---	---	---	PASS
CFTR	1080	broad.mit.edu	37	7	117180378	117180378	+	Missense_Mutation	SNP	T	C	C	rs76727851		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117180378T>C	uc003vjd.2	+	8	1226	c.1094T>C	c.(1093-1095)CTT>CCT	p.L365P	CFTR_uc011knq.1_5'UTR	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	365	Cytoplasmic (Potential).|ABC transmembrane type-1 1.				respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)	TATGACTCTCTTGGAGCAATA	0.383									Cystic_Fibrosis				13	62	---	---	---	---	PASS
CADPS2	93664	broad.mit.edu	37	7	121985692	121985692	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121985692C>G	uc010lkp.2	-	27	3711	c.3548G>C	c.(3547-3549)CGG>CCG	p.R1183P	CADPS2_uc011knx.1_Missense_Mutation_p.R558P|CADPS2_uc003vkg.3_Missense_Mutation_p.R837P|CADPS2_uc010lkq.2_Missense_Mutation_p.R1142P	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2	1183					exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						TTGGTTTTGCCGAACAAACAT	0.373													12	81	---	---	---	---	PASS
SLC13A1	6561	broad.mit.edu	37	7	122755644	122755644	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122755644C>T	uc003vkm.2	-	15	1741	c.1716G>A	c.(1714-1716)TGG>TGA	p.W572*	SLC13A1_uc010lks.2_Nonsense_Mutation_p.W448*	NM_022444	NP_071889	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate	572	Helical; (Potential).					integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)	TGGGTACAATCCAAGTACATA	0.433													15	56	---	---	---	---	PASS
SND1	27044	broad.mit.edu	37	7	127544839	127544839	+	Silent	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127544839A>G	uc003vmi.2	+	14	1720	c.1494A>G	c.(1492-1494)GAA>GAG	p.E498E	SND1_uc010lle.2_Silent_p.E151E	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1	498					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						GCAAGAAGGAAGTGCCTATCC	0.458													8	65	---	---	---	---	PASS
DENND2A	27147	broad.mit.edu	37	7	140255464	140255464	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140255464C>A	uc010lnj.2	-	10	2154	c.2009G>T	c.(2008-2010)CGC>CTC	p.R670L	DENND2A_uc011kre.1_RNA|DENND2A_uc010lnk.2_Missense_Mutation_p.R670L|DENND2A_uc003vvw.2_Missense_Mutation_p.R670L|DENND2A_uc003vvx.2_Missense_Mutation_p.R670L	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	670	DENN.									ovary(3)|breast(1)	4	Melanoma(164;0.00956)					GCATCCCAGGCGGCTCACAAT	0.527													48	79	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142197744	142197744	+	Intron	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142197744A>G	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc011krx.1_Intron|uc011ksa.1_Intron|uc011ksb.1_RNA					SubName: Full=V_segment translation product; Flags: Fragment;																		GCCCTGTCCCAGGATCTGCTG	0.463													39	48	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142250944	142250944	+	Intron	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142250944C>T	uc011krp.1	+						uc011krr.1_Intron|uc011krx.1_Intron|uc011ksa.1_Intron|uc011kse.1_Intron|uc011ksf.1_RNA					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																		ATGCTCCGTCCTGCTGCCAGG	0.507													23	35	---	---	---	---	PASS
OR9A2	135924	broad.mit.edu	37	7	142723325	142723325	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142723325C>A	uc003wcc.1	-	1	895	c.895G>T	c.(895-897)GAT>TAT	p.D299Y		NM_001001658	NP_001001658	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A,	299	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	Melanoma(164;0.059)					TTCATCCCATCTCGGAGGGCC	0.428													28	51	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	3257006	3257006	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3257006G>T	uc011kwk.1	-	16	2705	c.2315C>A	c.(2314-2316)CCT>CAT	p.P772H	CSMD1_uc011kwj.1_Missense_Mutation_p.P164H	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	772	Extracellular (Potential).|CUB 5.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CCATCCAGGAGGCAAAATGAC	0.403													7	39	---	---	---	---	PASS
MSR1	4481	broad.mit.edu	37	8	15978098	15978098	+	Silent	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15978098G>T	uc003wwz.2	-	9	1249	c.1051C>A	c.(1051-1053)CGA>AGA	p.R351R	MSR1_uc010lsu.2_Silent_p.R369R|MSR1_uc003wxa.2_Intron	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1	351	SRCR.|Extracellular (Potential).				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)		CCGACCAGTCGAACTTTCGTA	0.453													16	26	---	---	---	---	PASS
UNC5D	137970	broad.mit.edu	37	8	35608158	35608158	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35608158C>A	uc003xjr.1	+	13	2322	c.1994C>A	c.(1993-1995)GCG>GAG	p.A665E	UNC5D_uc003xjs.1_Missense_Mutation_p.A660E|UNC5D_uc003xju.1_Missense_Mutation_p.A241E	NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor	665	Cytoplasmic (Potential).				apoptosis|axon guidance	integral to membrane	receptor activity			upper_aerodigestive_tract(2)|ovary(2)|pancreas(1)|skin(1)	6				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		GACCCCTTTGCGTGTCATGTG	0.488													14	57	---	---	---	---	PASS
CHRNA6	8973	broad.mit.edu	37	8	42611507	42611507	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42611507G>T	uc003xpj.2	-	5	881	c.835C>A	c.(835-837)CTG>ATG	p.L279M	CHRNA6_uc011lcw.1_Missense_Mutation_p.L264M	NM_004198	NP_004189	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6	279	Helical; (Potential).					cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)			AGAGAAAGCAGGACTGAAATA	0.448													5	89	---	---	---	---	PASS
PRKDC	5591	broad.mit.edu	37	8	48824970	48824970	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48824970C>A	uc003xqi.2	-	25	2991	c.2934G>T	c.(2932-2934)CAG>CAT	p.Q978H	PRKDC_uc003xqj.2_Missense_Mutation_p.Q978H|PRKDC_uc011ldh.1_Missense_Mutation_p.Q978H	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	978					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				AAGCCCTTACCTGATCAACAT	0.413								NHEJ					6	166	---	---	---	---	PASS
CHD7	55636	broad.mit.edu	37	8	61735123	61735123	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61735123C>T	uc003xue.2	+	12	3496	c.3019C>T	c.(3019-3021)CTC>TTC	p.L1007F	CHD7_uc003xuf.2_Missense_Mutation_p.L120F	NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1007	Helicase ATP-binding.				central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CATTACATTTCTCTATGAGAT	0.388													30	100	---	---	---	---	PASS
NCOA2	10499	broad.mit.edu	37	8	71078966	71078966	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71078966C>A	uc003xyn.1	-	7	727	c.565G>T	c.(565-567)GAA>TAA	p.E189*		NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	189					cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CTCGGAGGTTCGCCAGACCAA	0.428			T	RUNXBP2	AML								33	179	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77763355	77763355	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77763355A>G	uc003yav.2	+	10	4450	c.4063A>G	c.(4063-4065)AAC>GAC	p.N1355D	ZFHX4_uc003yau.1_Missense_Mutation_p.N1400D|ZFHX4_uc003yaw.1_Missense_Mutation_p.N1355D	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1355	C2H2-type 10.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GTATCGCTGTAACCATTGTAG	0.453										HNSCC(33;0.089)			9	41	---	---	---	---	PASS
RALYL	138046	broad.mit.edu	37	8	85785583	85785583	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85785583C>T	uc003ycq.3	+	8	1052	c.636C>T	c.(634-636)TCC>TCT	p.S212S	RALYL_uc003ycr.3_Silent_p.S212S|RALYL_uc003ycs.3_Silent_p.S212S|RALYL_uc010lzy.2_Silent_p.S201S|RALYL_uc003yct.3_Silent_p.S225S|RALYL_uc003ycu.3_Silent_p.S139S|RALYL_uc003ycv.3_Silent_p.S124S	NM_001100392	NP_001093862	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like isoform 2	212	Potential.						identical protein binding|nucleotide binding|RNA binding			ovary(1)	1						AAATTGACTCCTTGCTAGGGC	0.428													7	21	---	---	---	---	PASS
SLC7A13	157724	broad.mit.edu	37	8	87235284	87235284	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87235284G>A	uc003ydq.1	-	2	832	c.734C>T	c.(733-735)GCG>GTG	p.A245V	SLC7A13_uc003ydr.1_Missense_Mutation_p.A236V	NM_138817	NP_620172	Q8TCU3	S7A13_HUMAN	solute carrier family 7, (cationic amino acid	245	Helical; Name=7; (Potential).					integral to membrane	amino acid transmembrane transporter activity			central_nervous_system(1)	1						CAGAGGTAACGCAGTAAATAT	0.383													26	110	---	---	---	---	PASS
SLC26A7	115111	broad.mit.edu	37	8	92307881	92307881	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92307881C>T	uc003yex.2	+	5	705	c.427C>T	c.(427-429)CAA>TAA	p.Q143*	SLC26A7_uc003yey.2_RNA|SLC26A7_uc003yez.2_Nonsense_Mutation_p.Q143*|SLC26A7_uc003yfa.2_Nonsense_Mutation_p.Q143*	NM_052832	NP_439897	Q8TE54	S26A7_HUMAN	solute carrier family 26, member 7 isoform a	143	Extracellular (Potential).					basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)			CTTTGAAATGCAAAGGATCCA	0.498													16	45	---	---	---	---	PASS
GLDC	2731	broad.mit.edu	37	9	6540093	6540093	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6540093T>A	uc003zkc.2	-	22	2816	c.2623A>T	c.(2623-2625)AAT>TAT	p.N875Y		NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	875					glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	GCCTCAATATTTGCAGACTTT	0.453													12	59	---	---	---	---	PASS
ACER2	340485	broad.mit.edu	37	9	19424709	19424709	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19424709G>A	uc003zny.1	+	3	393	c.235G>A	c.(235-237)GTC>ATC	p.V79I	ACER2_uc003znx.1_RNA|ACER2_uc003znz.1_Missense_Mutation_p.V30I	NM_001010887	NP_001010887	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	79	Helical; (Potential).				ceramide metabolic process|negative regulation of cell adhesion mediated by integrin|negative regulation of cell-matrix adhesion|negative regulation of protein glycosylation in Golgi|positive regulation of cell proliferation|response to retinoic acid|sphingosine biosynthetic process	integral to Golgi membrane	ceramidase activity			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2						AATTGGATCCGTCTACTTCCA	0.428													13	53	---	---	---	---	PASS
SLC24A2	25769	broad.mit.edu	37	9	19576937	19576937	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19576937C>A	uc003zoa.1	-	5	1275	c.1213G>T	c.(1213-1215)GCT>TCT	p.A405S	SLC24A2_uc003zob.1_Missense_Mutation_p.A388S	NM_020344	NP_065077	Q9UI40	NCKX2_HUMAN	solute carrier family 24	405	Cytoplasmic (Potential).				visual perception	integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(3)	3				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		TGGTTGGCAGCCCCATTCTGC	0.537													11	46	---	---	---	---	PASS
PRSS3	5646	broad.mit.edu	37	9	33795597	33795597	+	Intron	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33795597T>C	uc003ztj.3	+						uc003ztk.1_Intron|PRSS3_uc003zti.3_Intron|PRSS3_uc003ztl.3_Missense_Mutation_p.F9S	NM_007343	NP_031369	P35030	TRY3_HUMAN	mesotrypsin isoform 1 preproprotein						digestion|endothelial cell migration|zymogen activation	extracellular space	calcium ion binding|protein binding|serine-type endopeptidase activity|serine-type peptidase activity				0			LUSC - Lung squamous cell carcinoma(29;0.0176)			ATCCTTGCCTTTGTGGGAGCT	0.557													4	64	---	---	---	---	PASS
C9orf79	286234	broad.mit.edu	37	9	90499950	90499950	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90499950A>T	uc004app.3	+	4	583	c.548A>T	c.(547-549)GAT>GTT	p.D183V	C9orf79_uc004apo.1_Intron	NM_178828	NP_849150	Q6ZUB1	CI079_HUMAN	chromosome 9 open reading frame 79	183	Pro-rich.					integral to membrane				ovary(3)	3						TGCATGCAAGATCCGTCTCCT	0.627													39	31	---	---	---	---	PASS
SEMA4D	10507	broad.mit.edu	37	9	92006320	92006320	+	Silent	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92006320G>A	uc004aqo.1	-	11	1205	c.633C>T	c.(631-633)TTC>TTT	p.F211F	SEMA4D_uc011ltm.1_Silent_p.F211F|SEMA4D_uc011ltn.1_RNA|SEMA4D_uc011lto.1_RNA|SEMA4D_uc004aqp.1_Silent_p.F209F	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1	211	Sema.|Extracellular (Potential).				anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2						CAGCAAACACGAAACTAGGCT	0.557													16	58	---	---	---	---	PASS
KIAA1958	158405	broad.mit.edu	37	9	115337436	115337436	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115337436C>A	uc004bgf.1	+	2	1251	c.1076C>A	c.(1075-1077)CCC>CAC	p.P359H	KIAA1958_uc011lwx.1_Missense_Mutation_p.P359H	NM_133465	NP_597722	Q8N8K9	K1958_HUMAN	hypothetical protein LOC158405	359										skin(1)	1						GCCCTTTCTCCCTCAGTTAAC	0.582													5	102	---	---	---	---	PASS
KIF12	113220	broad.mit.edu	37	9	116857503	116857503	+	Silent	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116857503G>T	uc004bif.2	-	7	829	c.591C>A	c.(589-591)GTC>GTA	p.V197V	KIF12_uc004big.2_RNA	NM_138424	NP_612433	Q96FN5	KIF12_HUMAN	kinesin family member 12	330					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						CCATGAGGGTGACCCCGCGCC	0.647													11	51	---	---	---	---	PASS
PHF19	26147	broad.mit.edu	37	9	123629244	123629244	+	Splice_Site	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123629244C>T	uc004bks.1	-	7	868	c.615_splice	c.e7-1	p.E205_splice	PHF19_uc011lyf.1_Splice_Site|PHF19_uc004bkr.2_Splice_Site	NM_015651	NP_056466	Q5T6S3	PHF19_HUMAN	PHD finger protein 19 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|breast(1)	2						CAGGTACCATCTGGAGAGACA	0.567													12	25	---	---	---	---	PASS
DBH	1621	broad.mit.edu	37	9	136508547	136508547	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136508547G>A	uc004cel.2	+	4	766	c.757G>A	c.(757-759)GTC>ATC	p.V253I		NM_000787	NP_000778	P09172	DOPO_HUMAN	dopamine beta hydroxylase precursor	253	Intragranular (Potential).				hormone biosynthetic process	chromaffin granule lumen|chromaffin granule membrane|extracellular region|integral to membrane|membrane fraction|soluble fraction|transport vesicle membrane	dopamine beta-monooxygenase activity|L-ascorbic acid binding			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Dopamine(DB00988)|Vitamin C(DB00126)	CGAGCCCATCGTCACCAAGGG	0.592													15	34	---	---	---	---	PASS
UPF2	26019	broad.mit.edu	37	10	11997500	11997500	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11997500G>C	uc001ila.2	-	13	3055	c.2581C>G	c.(2581-2583)CAA>GAA	p.Q861E	UPF2_uc001ilb.2_Missense_Mutation_p.Q861E|UPF2_uc001ilc.2_Missense_Mutation_p.Q861E|UPF2_uc009xiz.1_Missense_Mutation_p.Q861E	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	861	Sufficient for interaction with UPF3A and UPF3B.|MIF4G 3.|Sufficient for interaction with EIF4A1 and EIF1.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				AATTTAGGTTGATTAACCTAA	0.343													19	26	---	---	---	---	PASS
C1QL3	389941	broad.mit.edu	37	10	16562655	16562655	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16562655T>A	uc001ioj.1	-	1	1350	c.410A>T	c.(409-411)CAT>CTT	p.H137L		NM_001010908	NP_001010908	Q5VWW1	C1QL3_HUMAN	complement component 1, q subcomponent-like 3	137	C1q.					collagen				ovary(1)	1						GTAGCCTTCATGCTGCCGCTT	0.582													6	44	---	---	---	---	PASS
MRC1	4360	broad.mit.edu	37	10	18112280	18112280	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18112280T>C	uc001ipm.2	+	2	401	c.298T>C	c.(298-300)TGG>CGG	p.W100R		NM_002438	NP_002429	P22897	MRC1_HUMAN	mannose receptor C type 1 precursor	100	Extracellular (Potential).|Ricin B-type lectin.				receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0						ATTTCAGAAATGGGAGTGCAA	0.378													47	34	---	---	---	---	PASS
SEC23IP	11196	broad.mit.edu	37	10	121663646	121663646	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121663646G>T	uc001leu.1	+	4	1030	c.958G>T	c.(958-960)GAT>TAT	p.D320Y	SEC23IP_uc010qtc.1_Missense_Mutation_p.D109Y	NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125	320	Interaction with SEC23A.				Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		AGGGCGCTACGATGTTTACCT	0.493													3	42	---	---	---	---	PASS
ART1	417	broad.mit.edu	37	11	3680845	3680845	+	Silent	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3680845C>G	uc001lye.1	+	3	197	c.96C>G	c.(94-96)CTC>CTG	p.L32L	ART1_uc009yeb.1_Silent_p.L32L	NM_004314	NP_004305	P52961	NAR1_HUMAN	ADP-ribosyltransferase 1 precursor	32					protein ADP-ribosylation	anchored to membrane|integral to plasma membrane|sarcoplasmic reticulum membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity				0		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)	Becaplermin(DB00102)	GACGAGACCTCTTCTCTCAAG	0.602													4	42	---	---	---	---	PASS
OR52R1	119695	broad.mit.edu	37	11	4825066	4825066	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4825066C>A	uc010qym.1	-	1	782	c.782G>T	c.(781-783)TGT>TTT	p.C261F		NM_001005177	NP_001005177	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R,	182	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		CATGTGCTCACAGTATGACTG	0.527													14	75	---	---	---	---	PASS
TRIM3	10612	broad.mit.edu	37	11	6471848	6471848	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6471848G>A	uc001mdh.2	-	11	2261	c.1874C>T	c.(1873-1875)CCC>CTC	p.P625L	TRIM3_uc001mdi.2_Missense_Mutation_p.P625L|TRIM3_uc010raj.1_Missense_Mutation_p.P506L|TRIM3_uc009yfd.2_Missense_Mutation_p.P625L|TRIM3_uc010rak.1_Missense_Mutation_p.P625L	NM_006458	NP_006449	O75382	TRIM3_HUMAN	tripartite motif-containing 3	625	NHL 4.				nervous system development|protein transport	early endosome	protein C-terminus binding|zinc ion binding			central_nervous_system(2)|large_intestine(1)|ovary(1)|skin(1)	5		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACAAAATGGGGCCCTGAAAA	0.483													21	23	---	---	---	---	PASS
WEE1	7465	broad.mit.edu	37	11	9608356	9608356	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9608356A>T	uc001mhs.2	+	10	1993	c.1740A>T	c.(1738-1740)TTA>TTT	p.L580F	WEE1_uc001mht.2_Missense_Mutation_p.L366F	NM_003390	NP_003381	P30291	WEE1_HUMAN	WEE1 tyrosine kinase isoform 1	580					blood coagulation|cell cycle checkpoint|cell division|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|S phase of mitotic cell cycle	nucleoplasm	ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	5				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		CAGAACAATTACGAATAGAAT	0.353													22	23	---	---	---	---	PASS
COPB1	1315	broad.mit.edu	37	11	14490962	14490962	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14490962C>T	uc001mli.2	-	15	2192	c.1885G>A	c.(1885-1887)GAC>AAC	p.D629N	COPB1_uc001mlg.2_Missense_Mutation_p.D629N|COPB1_uc001mlh.2_Missense_Mutation_p.D629N	NM_016451	NP_057535	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	629					COPI coating of Golgi vesicle|interspecies interaction between organisms|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|ER-Golgi intermediate compartment|plasma membrane	protein binding|structural molecule activity			ovary(1)|central_nervous_system(1)	2						TTGAAAATGTCATTCATTAAA	0.383													57	100	---	---	---	---	PASS
SAAL1	113174	broad.mit.edu	37	11	18111715	18111715	+	Intron	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18111715G>A	uc001mnq.2	-						SAAL1_uc001mnr.2_Intron|SAAL1_uc001mns.2_Intron|SAAL1_uc009yhf.2_Intron	NM_138421	NP_612430	Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1						acute-phase response	extracellular region	binding				0						AGTACATGATGACTTACCATT	0.338													4	39	---	---	---	---	PASS
LGR4	55366	broad.mit.edu	37	11	27390143	27390143	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27390143C>T	uc001mrj.3	-	18	2612	c.2127G>A	c.(2125-2127)ACG>ACA	p.T709T	LGR4_uc001mrk.3_Silent_p.T685T	NM_018490	NP_060960	Q9BXB1	LGR4_HUMAN	leucine-rich repeat-containing G protein-coupled	709	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1						ATAGCACTAACGTTACAGTGA	0.398													22	87	---	---	---	---	PASS
TTC17	55761	broad.mit.edu	37	11	43419670	43419670	+	Intron	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43419670G>C	uc001mxi.2	+						TTC17_uc001mxh.2_Intron|TTC17_uc010rfj.1_Intron|TTC17_uc001mxj.2_Intron	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17								binding			ovary(5)	5						ATAGGTAATTGAGAGGAAAAA	0.408													5	30	---	---	---	---	PASS
OR4C3	256144	broad.mit.edu	37	11	48346985	48346985	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48346985C>G	uc010rhv.1	+	1	493	c.493C>G	c.(493-495)CTC>GTC	p.L165V		NM_001004702	NP_001004702	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C,	138	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						GACCAGGCATCTCTGTGCCAT	0.532													16	79	---	---	---	---	PASS
OR4C46	119749	broad.mit.edu	37	11	51515731	51515731	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51515731C>T	uc010ric.1	+	1	450	c.450C>T	c.(448-450)GGC>GGT	p.G150G		NM_001004703	NP_001004703	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C,	150	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						GGATGGGAGGCTTTCTTCATG	0.458													27	47	---	---	---	---	PASS
OR4C16	219428	broad.mit.edu	37	11	55340086	55340086	+	Silent	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55340086C>A	uc010rih.1	+	1	483	c.483C>A	c.(481-483)GCC>GCA	p.A161A		NM_001004701	NP_001004701	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C,	161	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)				TTTTTCTTGCCCTGAGTTTGC	0.473													12	74	---	---	---	---	PASS
OR5D18	219438	broad.mit.edu	37	11	55587702	55587702	+	Silent	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55587702G>T	uc010rin.1	+	1	597	c.597G>T	c.(595-597)CTG>CTT	p.L199L		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	199	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.208)				ACCAGTGGCTGCTATTCTTTC	0.403													4	73	---	---	---	---	PASS
OR8H3	390152	broad.mit.edu	37	11	55890545	55890545	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55890545G>A	uc001nii.1	+	1	697	c.697G>A	c.(697-699)GGA>AGA	p.G233R		NM_001005201	NP_001005201	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H,	233	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00693)					TTCCACTTCAGGAAAGCAGAA	0.398													19	64	---	---	---	---	PASS
OR5B2	390190	broad.mit.edu	37	11	58190360	58190360	+	Silent	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58190360G>A	uc010rkg.1	-	1	375	c.375C>T	c.(373-375)TGC>TGT	p.C125C		NM_001005566	NP_001005566	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B,	125	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GTAGGGGTTTGCACACTGCTG	0.507													28	38	---	---	---	---	PASS
MS4A14	84689	broad.mit.edu	37	11	60183423	60183423	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60183423G>A	uc001npj.2	+	5	1547	c.982G>A	c.(982-984)GAA>AAA	p.E328K	MS4A14_uc001npi.2_Missense_Mutation_p.E216K|MS4A14_uc001npn.2_Missense_Mutation_p.E66K|MS4A14_uc001npk.2_Missense_Mutation_p.E311K|MS4A14_uc001npl.2_Missense_Mutation_p.E66K|MS4A14_uc001npm.2_Missense_Mutation_p.E66K	NM_032597	NP_115986	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member	328						integral to membrane	receptor activity			breast(1)	1						TCTACCAGTAGAAGGCCTGTC	0.458													12	73	---	---	---	---	PASS
RCOR2	283248	broad.mit.edu	37	11	63682017	63682017	+	Intron	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63682017G>A	uc001nyc.2	-							NM_173587	NP_775858	Q8IZ40	RCOR2_HUMAN	REST corepressor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)|skin(1)	2						CAGGCAGCTGGAGGAGGCAAC	0.602													14	63	---	---	---	---	PASS
RCOR2	283248	broad.mit.edu	37	11	63682020	63682020	+	Intron	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63682020G>A	uc001nyc.2	-							NM_173587	NP_775858	Q8IZ40	RCOR2_HUMAN	REST corepressor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)|skin(1)	2						GCAGCTGGAGGAGGCAACGCC	0.602													14	64	---	---	---	---	PASS
CCDC87	55231	broad.mit.edu	37	11	66359641	66359641	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66359641C>A	uc001oiq.3	-	1	914	c.846G>T	c.(844-846)CAG>CAT	p.Q282H	CCS_uc001oir.2_5'Flank	NM_018219	NP_060689	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	282										ovary(1)|skin(1)	2						GCGACACCATCTGTGAGGAAC	0.572													14	24	---	---	---	---	PASS
SPTBN2	6712	broad.mit.edu	37	11	66460763	66460763	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66460763C>T	uc001ojd.2	-	23	4820	c.4748G>A	c.(4747-4749)CGA>CAA	p.R1583Q		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1583	Spectrin 12.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						ATCCTCCAGTCGCTTCCCTCG	0.637													11	43	---	---	---	---	PASS
LRRC32	2615	broad.mit.edu	37	11	76372514	76372514	+	Silent	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76372514G>C	uc001oxq.3	-	3	366	c.123C>G	c.(121-123)CTC>CTG	p.L41L	LRRC32_uc001oxr.3_Silent_p.L41L|LRRC32_uc010rsf.1_Silent_p.L41L	NM_005512	NP_005503	Q14392	LRC32_HUMAN	leucine rich repeat containing 32 precursor	41	Extracellular (Potential).					integral to plasma membrane					0						AGGGGACCTGGAGCAGGCCCA	0.622													5	10	---	---	---	---	PASS
CCDC81	60494	broad.mit.edu	37	11	86125862	86125862	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86125862G>C	uc001pbx.1	+	12	1851	c.1423G>C	c.(1423-1425)GAT>CAT	p.D475H	CCDC81_uc001pbw.1_Missense_Mutation_p.D385H|CCDC81_uc010rtq.1_Missense_Mutation_p.D258H|CCDC81_uc001pby.1_Missense_Mutation_p.D210H	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81 isoform 1	475	Potential.									skin(1)	1		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				ATTTTTAAAAGATAAGATGGA	0.353													9	24	---	---	---	---	PASS
KIAA1731	85459	broad.mit.edu	37	11	93454723	93454723	+	Intron	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93454723T>C	uc009ywb.1	+						KIAA1731_uc001pdu.1_Intron|SCARNA9_uc001pdv.2_RNA|KIAA1731_uc001pdw.1_5'Flank	NM_033395	NP_203753	Q9C0D2	K1731_HUMAN	hypothetical protein LOC85459							centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ATGATGAAACTAGCCAAATCT	0.353													31	54	---	---	---	---	PASS
OR8B4	283162	broad.mit.edu	37	11	124294666	124294666	+	Silent	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124294666G>T	uc010sak.1	-	1	102	c.102C>A	c.(100-102)ATC>ATA	p.I34I		NM_001005196	NP_001005196	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B,	34	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		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;0.0279)		TGAACACATAGATCCCTAAGA	0.458													17	57	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2602441	2602441	+	Silent	SNP	C	T	T	rs112002520		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2602441C>T	uc009zdu.1	+	7	1315	c.1002C>T	c.(1000-1002)CCC>CCT	p.P334P	CACNA1C_uc009zdv.1_Silent_p.P331P|CACNA1C_uc001qkb.2_Silent_p.P334P|CACNA1C_uc001qkc.2_Silent_p.P334P|CACNA1C_uc001qke.2_Silent_p.P334P|CACNA1C_uc001qkf.2_Silent_p.P334P|CACNA1C_uc001qjz.2_Silent_p.P334P|CACNA1C_uc001qkd.2_Silent_p.P334P|CACNA1C_uc001qkg.2_Silent_p.P334P|CACNA1C_uc009zdw.1_Silent_p.P334P|CACNA1C_uc001qkh.2_Silent_p.P334P|CACNA1C_uc001qkl.2_Silent_p.P334P|CACNA1C_uc001qkn.2_Silent_p.P334P|CACNA1C_uc001qko.2_Silent_p.P334P|CACNA1C_uc001qkp.2_Silent_p.P334P|CACNA1C_uc001qkr.2_Silent_p.P334P|CACNA1C_uc001qku.2_Silent_p.P334P|CACNA1C_uc001qkq.2_Silent_p.P334P|CACNA1C_uc001qks.2_Silent_p.P334P|CACNA1C_uc001qkt.2_Silent_p.P334P|CACNA1C_uc001qka.1_5'UTR|CACNA1C_uc001qki.1_Silent_p.P70P|CACNA1C_uc001qkj.1_Silent_p.P70P|CACNA1C_uc001qkk.1_Silent_p.P70P|CACNA1C_uc001qkm.1_Silent_p.P70P	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	334	I.|Extracellular (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	TGTGCAAGCCCGGCTGGGATG	0.602													23	106	---	---	---	---	PASS
KIAA0528	9847	broad.mit.edu	37	12	22623791	22623791	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22623791T>A	uc001rfq.2	-	21	2641	c.2413A>T	c.(2413-2415)ACA>TCA	p.T805S	KIAA0528_uc010sir.1_Missense_Mutation_p.T620S|KIAA0528_uc010sis.1_Missense_Mutation_p.T805S|KIAA0528_uc010sit.1_Missense_Mutation_p.T807S|KIAA0528_uc010siu.1_Missense_Mutation_p.T805S|KIAA0528_uc001rfr.2_Missense_Mutation_p.T796S	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847	805							protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						GGGGTTTTTGTGGTTTGTAAA	0.338													8	26	---	---	---	---	PASS
ABCD2	225	broad.mit.edu	37	12	40013001	40013001	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40013001C>A	uc001rmb.2	-	1	843	c.417G>T	c.(415-417)AAG>AAT	p.K139N		NM_005164	NP_005155	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D, member 2	139	ABC transmembrane type-1.|Interaction with PEX19.				fatty acid metabolic process|transport	ATP-binding cassette (ABC) transporter complex|integral to plasma membrane|peroxisomal membrane	ATP binding|ATPase activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)|skin(1)	6						AAGTCCGAGGCTTCTTTTCCA	0.438													11	70	---	---	---	---	PASS
FMNL3	91010	broad.mit.edu	37	12	50037879	50037879	+	3'UTR	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50037879A>G	uc001ruv.1	-	26					FMNL3_uc001ruw.1_3'UTR|PRPF40B_uc001ruq.1_Intron|PRPF40B_uc001rur.1_Intron|PRPF40B_uc001rus.1_Intron|FMNL3_uc001rut.1_3'UTR|FMNL3_uc001ruu.1_3'UTR	NM_175736	NP_783863	Q8IVF7	FMNL3_HUMAN	formin-like 3 isoform 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4						CTTTGCTCCAACAGACAGGCT	0.607											OREG0021798	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	34	---	---	---	---	PASS
AMHR2	269	broad.mit.edu	37	12	53819613	53819613	+	Silent	SNP	C	T	T	rs115267458	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53819613C>T	uc001scx.1	+	6	840	c.762C>T	c.(760-762)CAC>CAT	p.H254H	AMHR2_uc009zmy.1_Silent_p.H254H	NM_020547	NP_065434	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II isoform	254	Cytoplasmic (Potential).|Protein kinase.				Mullerian duct regression		ATP binding|hormone binding|metal ion binding			ovary(1)|skin(1)	2					Adenosine triphosphate(DB00171)	GCCTACAGCACGACCACATTG	0.587									Persistant_Mullerian_Duct_Syndrome_(type_I_and_II)				5	24	---	---	---	---	PASS
SHMT2	6472	broad.mit.edu	37	12	57626301	57626301	+	Silent	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57626301C>G	uc001snf.1	+	6	670	c.660C>G	c.(658-660)CTC>CTG	p.L220L	SHMT2_uc001sng.1_Silent_p.L116L|SHMT2_uc001snh.1_Silent_p.L59L|SHMT2_uc009zpk.1_Silent_p.L210L|SHMT2_uc001sni.1_Silent_p.L199L|SHMT2_uc010srg.1_Silent_p.L229L|SHMT2_uc001snj.1_Silent_p.L124L|SHMT2_uc010srh.1_Silent_p.L199L|SHMT2_uc001snk.1_Silent_p.L124L|SHMT2_uc010sri.1_Silent_p.L199L|SHMT2_uc001snl.2_Silent_p.L124L|SHMT2_uc010srj.1_5'Flank	NM_005412	NP_005403	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2	220						microtubule cytoskeleton|mitochondrial nucleoid	glycine hydroxymethyltransferase activity|methyltransferase activity			ovary(1)|central_nervous_system(1)	2					Glycine(DB00145)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)	GGCCACGGCTCATCATAGCTG	0.597													18	87	---	---	---	---	PASS
AGAP2	116986	broad.mit.edu	37	12	58135755	58135755	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58135755C>G	uc001spr.2	-	1	186	c.100G>C	c.(100-102)GAG>CAG	p.E34Q		NM_014770	NP_055585	Q99490	AGAP2_HUMAN	centaurin, gamma 1 isoform PIKE-S	Error:Variant_position_missing_in_Q99490_after_alignment					axon guidance|negative regulation of neuron apoptosis|negative regulation of protein catabolic process|protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	mitochondrion|nucleolus	ARF GTPase activator activity|GTP binding|zinc ion binding			central_nervous_system(3)|breast(2)	5						TCCACCCTCTCTGCCAGCTTC	0.567													15	77	---	---	---	---	PASS
HELB	92797	broad.mit.edu	37	12	66700160	66700160	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66700160C>T	uc001sti.2	+	3	671	c.643C>T	c.(643-645)CCG>TCG	p.P215S	HELB_uc010ssz.1_RNA|HELB_uc009zqt.1_RNA	NM_033647	NP_387467	Q8NG08	HELB_HUMAN	helicase (DNA) B	215					DNA replication, synthesis of RNA primer		ATP binding|ATP-dependent 5'-3' DNA helicase activity|single-stranded DNA-dependent ATP-dependent DNA helicase activity			central_nervous_system(1)|pancreas(1)	2			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		TTTGCAGTTTCCGAAGATAAT	0.348													13	45	---	---	---	---	PASS
PPFIA2	8499	broad.mit.edu	37	12	82147871	82147871	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82147871G>T	uc001szo.1	-	3	291	c.130C>A	c.(130-132)CGT>AGT	p.R44S	PPFIA2_uc010suj.1_RNA|PPFIA2_uc009zsi.1_RNA	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment										ovary(3)|lung(2)|pancreas(1)	6						TCTAGAAGACGATCCCTTTCA	0.527													9	35	---	---	---	---	PASS
SOCS2	8835	broad.mit.edu	37	12	93968716	93968716	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93968716G>C	uc001tcw.1	+	3	948	c.358G>C	c.(358-360)GAC>CAC	p.D120H	SOCS2_uc001tcx.1_Missense_Mutation_p.D120H|SOCS2_uc009zsu.2_3'UTR|SOCS2_uc001tcy.1_Missense_Mutation_p.D120H|SOCS2_uc001tcz.2_3'UTR	NM_003877	NP_003868	O14508	SOCS2_HUMAN	suppressor of cytokine signaling-2	120	SH2.				anti-apoptosis|growth hormone receptor signaling pathway|JAK-STAT cascade|negative regulation of signal transduction|regulation of cell growth|response to estradiol stimulus	cytoplasm	growth hormone receptor binding|insulin-like growth factor receptor binding|JAK pathway signal transduction adaptor activity|prolactin receptor binding|SH3/SH2 adaptor activity			lung(1)	1						TAAACAATTTGACAGTGTGGT	0.433													4	38	---	---	---	---	PASS
C12orf63	374467	broad.mit.edu	37	12	97087548	97087548	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97087548C>T	uc001tet.1	+	12	1666	c.1588C>T	c.(1588-1590)CAA>TAA	p.Q530*		NM_198520	NP_940922	Q6ZTY8	CL063_HUMAN	hypothetical protein LOC374467	530										skin(6)|ovary(1)	7						TGGAATTTGTCAAGACATAAC	0.294													8	44	---	---	---	---	PASS
ANKS1B	56899	broad.mit.edu	37	12	99478771	99478771	+	Silent	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99478771A>G	uc001tge.1	-	16	2974	c.2557T>C	c.(2557-2559)TTG>CTG	p.L853L	ANKS1B_uc001tgf.1_Silent_p.L429L|ANKS1B_uc001tgk.2_Silent_p.L150L|ANKS1B_uc001tgd.1_Silent_p.L79L|ANKS1B_uc001tgi.2_Silent_p.L79L|ANKS1B_uc009ztr.2_Silent_p.L79L|ANKS1B_uc001tgj.2_Silent_p.L79L|ANKS1B_uc001tgg.3_Silent_p.L22L|ANKS1B_uc010svg.1_Silent_p.L48L|ANKS1B_uc009zts.1_Silent_p.L79L|ANKS1B_uc001tgm.1_Silent_p.L79L	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a	853	SAM 1.					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)		CCAATTTCCAACAAATCCTGA	0.363													3	12	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112632695	112632695	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112632695G>A	uc009zwc.2	-	49	7495	c.7477C>T	c.(7477-7479)CTC>TTC	p.L2493F		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						TTACCTGGGAGAGGAGGTGCG	0.567													4	12	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112632708	112632708	+	Silent	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112632708G>A	uc009zwc.2	-	49	7482	c.7464C>T	c.(7462-7464)CTC>CTT	p.L2488L		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						GAGGTGCGAGGAGCTGATTGG	0.567													6	12	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117665253	117665253	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117665253A>C	uc001twm.1	-	23	4285	c.3599T>G	c.(3598-3600)GTT>GGT	p.V1200G		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	1200	FAD-binding FR-type.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	GCGGTAGGAAACGATGGCCAC	0.612													7	18	---	---	---	---	PASS
RFC5	5985	broad.mit.edu	37	12	118457434	118457434	+	Intron	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118457434C>T	uc001twq.2	+						RFC5_uc010syx.1_Intron|RFC5_uc010syy.1_Intron|RFC5_uc010syz.1_Intron|RFC5_uc009zwr.2_Intron	NM_007370	NP_031396	P40937	RFC5_HUMAN	replication factor C 5 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|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	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|enzyme binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCCTGATCCTCAGTTCAGAAG	0.517													26	90	---	---	---	---	PASS
PIWIL1	9271	broad.mit.edu	37	12	130839091	130839091	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130839091C>A	uc001uik.2	+	10	1144	c.1054C>A	c.(1054-1056)CAA>AAA	p.Q352K	PIWIL1_uc001uij.1_Missense_Mutation_p.Q352K	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	352	PAZ.				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)		GCAATACAACCAAGAGATCAC	0.522													5	108	---	---	---	---	PASS
RIMBP2	23504	broad.mit.edu	37	12	130935867	130935867	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130935867C>T	uc001uil.2	-	5	490	c.326G>A	c.(325-327)GGA>GAA	p.G109E	RIMBP2_uc001uim.2_Missense_Mutation_p.G17E	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2	109						cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		AGAGCTGCCTCCAATAGCGCT	0.562													10	9	---	---	---	---	PASS
PARP4	143	broad.mit.edu	37	13	25043157	25043157	+	Intron	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25043157C>G	uc001upl.2	-						PARP4_uc010tdc.1_Intron	NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4						cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CACACCAAGCCATACCGGAGC	0.473													3	74	---	---	---	---	PASS
MTRF1	9617	broad.mit.edu	37	13	41828703	41828703	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41828703G>T	uc001uxx.2	-	5	939	c.469C>A	c.(469-471)CAA>AAA	p.Q157K	MTRF1_uc001uxy.2_Missense_Mutation_p.Q157K|MTRF1_uc001uxz.2_5'UTR|MTRF1_uc010tff.1_Missense_Mutation_p.Q170K|MTRF1_uc001uyc.1_Missense_Mutation_p.Q157K	NM_004294	NP_004285	O75570	RF1M_HUMAN	mitochondrial translational release factor 1	157					regulation of translational termination	mitochondrion	translation release factor activity, codon specific				0		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)		TCAATGGTTTGCCTTTCTTCC	0.333													4	23	---	---	---	---	PASS
TSC22D1	8848	broad.mit.edu	37	13	45147368	45147368	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45147368G>T	uc001uzn.3	-	1	3334	c.2843C>A	c.(2842-2844)GCC>GAC	p.A948D	TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358	Q15714	T22D1_HUMAN	TSC22 domain family, member 1 isoform 1	948					transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		AGAAGCAGAGGCTGCTAGGCT	0.537													9	25	---	---	---	---	PASS
LRCH1	23143	broad.mit.edu	37	13	47275295	47275295	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47275295G>C	uc001vbj.2	+	11	1589	c.1353G>C	c.(1351-1353)ATG>ATC	p.M451I	LRCH1_uc010acp.2_Missense_Mutation_p.M451I|LRCH1_uc001vbk.2_Missense_Mutation_p.M451I|LRCH1_uc001vbl.3_Missense_Mutation_p.M451I	NM_015116	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH)	451										ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		ATATAGCAATGATCGAGCAGC	0.378													8	39	---	---	---	---	PASS
KCNRG	283518	broad.mit.edu	37	13	50590025	50590025	+	Silent	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50590025A>G	uc001vdu.2	+	1	636	c.396A>G	c.(394-396)ACA>ACG	p.T132T	DLEU2_uc001vdn.1_Intron|DLEU2_uc001vdo.1_Intron|KCNRG_uc001vdt.2_Silent_p.T132T|TRIM13_uc001vdp.1_3'UTR|TRIM13_uc001vdq.1_3'UTR|TRIM13_uc001vdr.1_3'UTR|TRIM13_uc001vds.1_3'UTR	NM_173605	NP_775876	Q8N5I3	KCNRG_HUMAN	potassium channel regulator isoform 1	132						voltage-gated potassium channel complex	identical protein binding|voltage-gated potassium channel activity				0		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.48e-10)|COAD - Colon adenocarcinoma(199;0.204)		GCAGCAAAACAATTGAGATGC	0.473													47	82	---	---	---	---	PASS
RNASEH2B	79621	broad.mit.edu	37	13	51501612	51501612	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51501612C>T	uc001vfa.3	+	2	455	c.134C>T	c.(133-135)TCA>TTA	p.S45L	RNASEH2B_uc001vfb.3_Missense_Mutation_p.S45L	NM_024570	NP_078846	Q5TBB1	RNH2B_HUMAN	ribonuclease H2, subunit B isoform 1	45					RNA catabolic process	nucleus|ribonuclease H2 complex					0		Acute lymphoblastic leukemia(7;1.03e-07)|Breast(56;0.00122)|Lung NSC(96;0.00143)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;9e-08)		AACCCCTGTTCAGGTAAGTTC	0.308													10	49	---	---	---	---	PASS
KLHL1	57626	broad.mit.edu	37	13	70456529	70456529	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70456529A>T	uc001vip.2	-	5	1907	c.1113T>A	c.(1111-1113)GAT>GAA	p.D371E	KLHL1_uc010thm.1_Missense_Mutation_p.D310E	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein	371					actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TGGTTTCTTCATCAGGAACAT	0.418													30	35	---	---	---	---	PASS
TBC1D4	9882	broad.mit.edu	37	13	75936518	75936518	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75936518C>T	uc001vjl.1	-	2	1071	c.724G>A	c.(724-726)GAG>AAG	p.E242K	TBC1D4_uc010aer.2_Missense_Mutation_p.E242K|TBC1D4_uc010aes.2_Missense_Mutation_p.E242K	NM_014832	NP_055647	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	242						cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		CCGCGCTGCTCCCCTTGGATC	0.647													9	42	---	---	---	---	PASS
GPC5	2262	broad.mit.edu	37	13	93518526	93518526	+	Intron	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93518526C>T	uc010tif.1	+							NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				TTCTTATTTGCCTCTACAGGG	0.423													6	35	---	---	---	---	PASS
NALCN	259232	broad.mit.edu	37	13	101763536	101763536	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101763536C>T	uc001vox.1	-	19	2423	c.2234G>A	c.(2233-2235)GGG>GAG	p.G745E		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	745	Cytoplasmic (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGCGGGCTGCCCCTCAAATGA	0.488													45	48	---	---	---	---	PASS
OR4K15	81127	broad.mit.edu	37	14	20443959	20443959	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20443959C>T	uc010tkx.1	+	1	282	c.282C>T	c.(280-282)GAC>GAT	p.D94D		NM_001005486	NP_001005486	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K,	94	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CATTTATAGACGTATGTGTTG	0.453													44	42	---	---	---	---	PASS
OR4K13	390433	broad.mit.edu	37	14	20502611	20502611	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20502611A>T	uc010tkz.1	-	1	307	c.307T>A	c.(307-309)TTT>ATT	p.F103I		NM_001004714	NP_001004714	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K,	103	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		AGGTGCATAAAGAACATCTGG	0.453													49	54	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22521061	22521061	+	Intron	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22521061G>C	uc001wbw.2	+						uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_RNA					SubName: Full=Alpha-chain C region; Flags: Fragment;																		GCAGATTCCTGCAGCTCTGAG	0.453													34	67	---	---	---	---	PASS
FANCM	57697	broad.mit.edu	37	14	45668130	45668130	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45668130G>T	uc001wwd.3	+	22	6099	c.6000G>T	c.(5998-6000)ATG>ATT	p.M2000I	FANCM_uc010anf.2_Missense_Mutation_p.M1974I|FANCM_uc001wwe.3_Missense_Mutation_p.M1536I|FANCM_uc010ang.2_Missense_Mutation_p.M1249I	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	2000	Interaction with FAAP24 and EME1.				DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7						TGAAAAGGATGGCTAACAGGT	0.284								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				11	8	---	---	---	---	PASS
RPL10L	140801	broad.mit.edu	37	14	47120363	47120363	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47120363C>T	uc001wwg.2	-	1	666	c.577G>A	c.(577-579)GAT>AAT	p.D193N		NM_080746	NP_542784	Q96L21	RL10L_HUMAN	ribosomal protein L10-like protein	193					spermatogenesis|translation	cytosolic large ribosomal subunit|nucleus	structural constituent of ribosome			ovary(1)	1						CCACAACCATCAGGGATGAGG	0.517													57	38	---	---	---	---	PASS
SDCCAG1	9147	broad.mit.edu	37	14	50280773	50280773	+	Intron	SNP	A	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50280773A>T	uc001wxc.2	-						SDCCAG1_uc010anj.1_Intron|SDCCAG1_uc010tqi.1_Intron|SDCCAG1_uc001wxe.2_Intron|SDCCAG1_uc001wxd.1_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		TGTCTCCTTAAATACAGACAA	0.209													4	43	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102460520	102460520	+	Splice_Site	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102460520G>C	uc001yks.2	+	12	3180	c.3016_splice	c.e12-1	p.V1006_splice		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1						cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						TGGTTGGCTAGGTGGGTGTAC	0.403													39	92	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102460647	102460647	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102460647G>C	uc001yks.2	+	12	3306	c.3142G>C	c.(3142-3144)GAA>CAA	p.E1048Q		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	1048	Stem (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						ATCTGAAGTTGAACAGTATGT	0.398													36	63	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106829997	106829997	+	RNA	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106829997G>T	uc010tyt.1	-	323		c.12508C>A			uc001ysx.1_Intron					Parts of antibodies, mostly variable regions.												0						GCTGCCACCAGGAGGAGGAAG	0.502													5	65	---	---	---	---	PASS
NDN	4692	broad.mit.edu	37	15	23931855	23931855	+	Silent	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23931855C>G	uc001ywk.2	-	1	596	c.510G>C	c.(508-510)GCG>GCC	p.A170A		NM_002487	NP_002478	Q99608	NECD_HUMAN	necdin	170	MAGE.				negative regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perikaryon	DNA binding				0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		CGGGCTCCAGCGCTTTGACCA	0.652									Prader-Willi_syndrome				7	16	---	---	---	---	PASS
RNF111	54778	broad.mit.edu	37	15	59323210	59323210	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59323210A>C	uc002afv.2	+	2	468	c.189A>C	c.(187-189)GAA>GAC	p.E63D	RNF111_uc002afs.2_Missense_Mutation_p.E63D|RNF111_uc002aft.2_Missense_Mutation_p.E63D|RNF111_uc002afu.2_Missense_Mutation_p.E63D|RNF111_uc002afw.2_Missense_Mutation_p.E63D	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	63					multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)		TGGGGAATGAATTCTCTCACC	0.418													5	48	---	---	---	---	PASS
KIF23	9493	broad.mit.edu	37	15	69715541	69715541	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69715541G>C	uc002asb.2	+	7	724	c.607G>C	c.(607-609)GAA>CAA	p.E203Q	KIF23_uc002asc.2_Missense_Mutation_p.E203Q|KIF23_uc010bii.2_Missense_Mutation_p.E93Q|KIF23_uc010ukc.1_Missense_Mutation_p.E6Q|KIF23_uc010bih.1_RNA	NM_138555	NP_612565	Q02241	KIF23_HUMAN	kinesin family member 23 isoform 1	203	Kinesin-motor.				blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0						AACTGTACAAGAATTCTGCAA	0.284													29	60	---	---	---	---	PASS
BBS4	585	broad.mit.edu	37	15	73028217	73028217	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73028217C>T	uc002avb.2	+	14	1201	c.1158C>T	c.(1156-1158)GGC>GGT	p.G386G	BBS4_uc010ukv.1_Silent_p.G374G|BBS4_uc002avc.2_Silent_p.G214G|BBS4_uc002avd.2_Silent_p.G394G	NM_033028	NP_149017	Q96RK4	BBS4_HUMAN	Bardet-Biedl syndrome 4	386	TPR 10.|Required for localization to centrosomes.				adult behavior|brain morphogenesis|cell cycle cytokinesis|centrosome organization|cerebral cortex development|convergent extension involved in gastrulation|dendrite development|fat cell differentiation|heart looping|hippocampus development|intracellular transport|maintenance of protein location in nucleus|melanosome transport|microtubule anchoring at centrosome|neural tube closure|nonmotile primary cilium assembly|photoreceptor cell maintenance|pigment granule aggregation in cell center|positive regulation of flagellum assembly|regulation of cilium beat frequency involved in ciliary motility|regulation of cytokinesis|regulation of lipid metabolic process|retina homeostasis|retinal rod cell development|sensory perception of smell|sensory processing|spermatid development|striatum development	BBSome|centriolar satellite|centriole|cilium membrane|microtubule basal body|motile cilium|nonmotile primary cilium|nucleus|pericentriolar material	alpha-tubulin binding|beta-tubulin binding|dynactin binding|microtubule motor activity				0						ACAACCAGGGCGAGAAGAAGA	0.483									Bardet-Biedl_syndrome				11	129	---	---	---	---	PASS
KIAA0430	9665	broad.mit.edu	37	16	15730188	15730188	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15730188C>A	uc002ddr.2	-	3	349	c.156G>T	c.(154-156)ATG>ATT	p.M52I	KIAA0430_uc002ddq.2_Missense_Mutation_p.M51I|KIAA0430_uc010uzv.1_Missense_Mutation_p.M51I|KIAA0430_uc010uzw.1_Missense_Mutation_p.M51I|KIAA0430_uc010uzx.1_Missense_Mutation_p.M51I	NM_014647	NP_055462	Q9Y4F3	LKAP_HUMAN	limkain b1	51						peroxisome	nucleotide binding|RNA binding				0						TCTTGTTCTCCATGTACTCTT	0.388													4	64	---	---	---	---	PASS
GTF3C1	2975	broad.mit.edu	37	16	27495561	27495561	+	Silent	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27495561G>A	uc002dov.1	-	25	4012	c.3972C>T	c.(3970-3972)GTC>GTT	p.V1324V	GTF3C1_uc002dou.2_Silent_p.V1324V	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	1324						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5						GTGGGTTTTTGACTATGTAGC	0.488													22	67	---	---	---	---	PASS
RNF40	9810	broad.mit.edu	37	16	30773931	30773931	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30773931T>C	uc002dzq.2	+	2	188	c.65T>C	c.(64-66)CTG>CCG	p.L22P	C16orf93_uc002dzm.2_5'Flank|C16orf93_uc002dzn.2_5'Flank|C16orf93_uc002dzo.2_5'Flank|C16orf93_uc002dzp.2_5'Flank|RNF40_uc010caa.2_Missense_Mutation_p.L22P|RNF40_uc010cab.2_Missense_Mutation_p.L22P|RNF40_uc010vfa.1_Intron|RNF40_uc002dzr.2_Missense_Mutation_p.L22P|RNF40_uc010vfb.1_Missense_Mutation_p.L22P	NM_014771	NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40	22					histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding			central_nervous_system(1)	1			Colorectal(24;0.198)			GAAAAGAAGCTGAGTCGTGAG	0.632													3	25	---	---	---	---	PASS
ATP2C2	9914	broad.mit.edu	37	16	84492924	84492924	+	Silent	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84492924G>T	uc002fhx.2	+	23	2354	c.2265G>T	c.(2263-2265)CTG>CTT	p.L755L	ATP2C2_uc010chj.2_Silent_p.L755L|ATP2C2_uc002fhy.2_Silent_p.L772L|ATP2C2_uc002fhz.2_Silent_p.L604L|ATP2C2_uc002fia.2_5'Flank	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	755	Helical; Name=6; (Potential).				ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						TGTTCAACCTGCCCAGCCCCC	0.647													15	35	---	---	---	---	PASS
IL17C	27189	broad.mit.edu	37	16	88705514	88705514	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88705514C>T	uc002fla.2	+	2	181	c.132C>T	c.(130-132)CTC>CTT	p.L44L		NM_013278	NP_037410	Q9P0M4	IL17C_HUMAN	interleukin 17C precursor	44					cell surface receptor linked signaling pathway|cell-cell signaling|inflammatory response	extracellular space|soluble fraction	cytokine activity				0				BRCA - Breast invasive adenocarcinoma(80;0.0477)		AACTGCCCCTCGGCCAGGCCC	0.687													23	17	---	---	---	---	PASS
RPL13	6137	broad.mit.edu	37	16	89628749	89628749	+	Missense_Mutation	SNP	G	A	A	rs140485395		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89628749G>A	uc002fnm.1	+	5	478	c.427G>A	c.(427-429)GAA>AAA	p.E143K	RPL13_uc010vpj.1_Missense_Mutation_p.E96K|RPL13_uc002fnn.1_Missense_Mutation_p.E143K|RPL13_uc002fno.1_3'UTR	NM_000977	NP_000968	P26373	RL13_HUMAN	ribosomal protein L13	143					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic ribosome	protein binding|RNA binding|structural constituent of ribosome				0		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)		ACAGGCTGAAGAACTGAAACT	0.562													22	14	---	---	---	---	PASS
USP6	9098	broad.mit.edu	37	17	5048769	5048769	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5048769C>G	uc002gau.1	+	27	4292	c.2062C>G	c.(2062-2064)CAA>GAA	p.Q688E	USP6_uc002gav.1_Missense_Mutation_p.Q688E|USP6_uc010ckz.1_Missense_Mutation_p.Q371E	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6	688					protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5						GCTAAGATCTCAAGTCAAATG	0.378			T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								28	35	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577092	7577092	+	Silent	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577092C>G	uc002gim.2	-	8	1040	c.846G>C	c.(844-846)CGG>CGC	p.R282R	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Silent_p.R282R|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Silent_p.R150R|TP53_uc010cng.1_Silent_p.R150R|TP53_uc002gii.1_Silent_p.R150R|TP53_uc010cnh.1_Silent_p.R282R|TP53_uc010cni.1_Silent_p.R282R|TP53_uc002gij.2_Silent_p.R282R	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	282	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|DR -> EW (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R282W(365)|p.R282G(26)|p.R282Q(20)|p.R282P(14)|p.R282R(8)|p.0?(7)|p.R282L(3)|p.R283fs*63(2)|p.D281fs*63(2)|p.?(2)|p.R282fs*24(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.R283del(1)|p.R282_E287delRRTEEE(1)|p.G279fs*59(1)|p.S269fs*21(1)|p.C275_R283delCACPGRDRR(1)|p.D281_R282insXX(1)|p.L265_K305del41(1)|p.R282H(1)|p.R283_T284>T(1)|p.V272_K292del21(1)|p.R282fs*63(1)|p.C275fs*20(1)|p.D281_R282delDR(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CCTCTGTGCGCCGGTCTCTCC	0.557		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			8	14	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577093	7577093	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577093C>T	uc002gim.2	-	8	1039	c.845G>A	c.(844-846)CGG>CAG	p.R282Q	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.R282Q|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R150Q|TP53_uc010cng.1_Missense_Mutation_p.R150Q|TP53_uc002gii.1_Missense_Mutation_p.R150Q|TP53_uc010cnh.1_Missense_Mutation_p.R282Q|TP53_uc010cni.1_Missense_Mutation_p.R282Q|TP53_uc002gij.2_Missense_Mutation_p.R282Q	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	282	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|DR -> EW (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R282W(365)|p.R282G(26)|p.R282Q(21)|p.R282P(14)|p.R282R(8)|p.0?(7)|p.R282L(3)|p.D281fs*63(2)|p.?(2)|p.R282fs*24(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.R283fs*62(1)|p.R282_E287delRRTEEE(1)|p.G279fs*59(1)|p.S269fs*21(1)|p.C275_R283delCACPGRDRR(1)|p.D281_R282insXX(1)|p.L265_K305del41(1)|p.R282H(1)|p.R283_T284>T(1)|p.V272_K292del21(1)|p.R282fs*63(1)|p.C275fs*20(1)|p.D281_R282delDR(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CTCTGTGCGCCGGTCTCTCCC	0.557		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			7	14	---	---	---	---	PASS
KDM6B	23135	broad.mit.edu	37	17	7750890	7750890	+	Silent	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7750890C>A	uc002giw.1	+	11	1660	c.1284C>A	c.(1282-1284)CCC>CCA	p.P428P	KDM6B_uc002gix.2_5'UTR	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	428	Pro-rich.				inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|pancreas(1)	2						ACCAAACTCCCGCGCTGGAGG	0.547													3	15	---	---	---	---	PASS
MYOCD	93649	broad.mit.edu	37	17	12655725	12655725	+	Intron	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12655725C>A	uc002gnn.2	+						MYOCD_uc002gno.2_Intron|MYOCD_uc002gnp.1_Intron|MYOCD_uc002gnq.2_Intron	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin isoform 2						cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		ATTCTGATTTCTTTAGGTCTC	0.403													17	18	---	---	---	---	PASS
PIGS	94005	broad.mit.edu	37	17	26885558	26885558	+	Silent	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26885558G>A	uc002hbo.2	-	8	1243	c.870C>T	c.(868-870)TCC>TCT	p.S290S	PIGS_uc002hbn.2_Silent_p.S282S|PIGS_uc010wap.1_Silent_p.S229S	NM_033198	NP_149975	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	290	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			breast(2)|urinary_tract(1)|kidney(1)	4	Lung NSC(42;0.00431)					AGTAGCTGGAGGAAGCTGAGT	0.458													5	24	---	---	---	---	PASS
RASL10B	91608	broad.mit.edu	37	17	34068269	34068269	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34068269A>G	uc002hju.2	+	4	923	c.557A>G	c.(556-558)CAC>CGC	p.H186R		NM_033315	NP_201572	Q96S79	RSLAB_HUMAN	RAS-like, family 10, member B precursor	186	Small GTPase-like.				small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			lung(2)|breast(2)	4				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AAGCACGTGCACGCTGCCCTG	0.692													5	10	---	---	---	---	PASS
DUSP14	11072	broad.mit.edu	37	17	35872857	35872857	+	Silent	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35872857C>T	uc002hnx.2	+	3	777	c.483C>T	c.(481-483)TAC>TAT	p.Y161Y	DUSP14_uc002hny.2_Silent_p.Y148Y|DUSP14_uc002hnz.2_Silent_p.Y148Y	NM_007026	NP_008957	O95147	DUS14_HUMAN	dual specificity phosphatase 14	161							MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Breast(25;0.00637)|Ovarian(249;0.15)				TGATAGACTACGAGCGCCAGC	0.537													15	44	---	---	---	---	PASS
WNK4	65266	broad.mit.edu	37	17	40948204	40948204	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40948204C>A	uc002ibj.2	+	17	3516	c.3495C>A	c.(3493-3495)AGC>AGA	p.S1165R	WNK4_uc010wgx.1_Missense_Mutation_p.S829R|CCDC56_uc010wgz.1_Intron|CNTD1_uc002ibm.3_5'Flank|CNTD1_uc010wha.1_5'Flank	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	1165					intracellular protein kinase cascade	tight junction	ATP binding|protein serine/threonine kinase activity			ovary(3)|skin(3)|stomach(1)	7		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		ATTTGTACAGCCGGCTGGGGA	0.592													11	50	---	---	---	---	PASS
HDAC5	10014	broad.mit.edu	37	17	42162413	42162413	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42162413T>C	uc002ifd.1	-	15	2372	c.2161A>G	c.(2161-2163)ACA>GCA	p.T721A	HDAC5_uc002ife.1_Missense_Mutation_p.T721A|HDAC5_uc002iff.1_Missense_Mutation_p.T722A|HDAC5_uc010czp.1_Intron|HDAC5_uc002ifg.1_Missense_Mutation_p.T31A|HDAC5_uc002ifh.2_Missense_Mutation_p.T721A	NM_005474	NP_005465	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 1	721	Histone deacetylase.				B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		AGCAGGCCTGTCTCCTGCAGC	0.552													14	40	---	---	---	---	PASS
MRPL10	124995	broad.mit.edu	37	17	45901685	45901685	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45901685G>T	uc002ilz.2	-	5	698	c.672C>A	c.(670-672)CAC>CAA	p.H224Q	OSBPL7_uc002ilx.1_5'Flank|MRPL10_uc010wky.1_Missense_Mutation_p.H185Q|MRPL10_uc002ily.2_Missense_Mutation_p.H234Q	NM_145255	NP_660298	Q7Z7H8	RM10_HUMAN	mitochondrial ribosomal protein L10 precursor	224					ribosome biogenesis|translation	mitochondrial large ribosomal subunit	structural constituent of ribosome			ovary(1)	1						GGAGGGGCTGGTGCTGGAGCA	0.602													5	32	---	---	---	---	PASS
CDK5RAP3	80279	broad.mit.edu	37	17	46056209	46056209	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46056209G>T	uc002imr.2	+	11	1087	c.1003G>T	c.(1003-1005)GCC>TCC	p.A335S	CDK5RAP3_uc010wlc.1_Missense_Mutation_p.A355S|CDK5RAP3_uc002imq.1_Missense_Mutation_p.A110S|CDK5RAP3_uc002imu.2_Missense_Mutation_p.A179S|CDK5RAP3_uc002ims.2_Missense_Mutation_p.A248S|CDK5RAP3_uc002imv.2_Missense_Mutation_p.A179S|CDK5RAP3_uc002imw.2_Missense_Mutation_p.A177S|CDK5RAP3_uc002imx.2_Missense_Mutation_p.A110S	NM_176096	NP_788276	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	335					brain development|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation		neuronal Cdc2-like kinase binding				0						AGAAGGTGTTGCCAGGGGCCC	0.517											OREG0024508	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	46	---	---	---	---	PASS
UBE2Z	65264	broad.mit.edu	37	17	47004450	47004450	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47004450G>T	uc002ioi.2	+	7	1118	c.1019G>T	c.(1018-1020)AGT>ATT	p.S340I		NM_023079	NP_075567	Q9H832	UBE2Z_HUMAN	ubiquitin-conjugating enzyme E2Z	340					apoptosis	cytoplasm|nucleus	ATP binding|ubiquitin-protein ligase activity				0						TCTGATAGCAGTTCATCTGGG	0.532													23	28	---	---	---	---	PASS
MPO	4353	broad.mit.edu	37	17	56348128	56348128	+	Silent	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56348128G>A	uc002ivu.1	-	12	2304	c.2127C>T	c.(2125-2127)ATC>ATT	p.I709I		NM_000250	NP_000241	P05164	PERM_HUMAN	myeloperoxidase	709					anti-apoptosis|hydrogen peroxide catabolic process|low-density lipoprotein particle remodeling	extracellular space|lysosome|nucleus|stored secretory granule	chromatin binding|heme binding|heparin binding|peroxidase activity			ovary(2)|large_intestine(1)|pancreas(1)	4					Cefdinir(DB00535)	ACACGGTGGTGATGCCTGTGT	0.547													13	22	---	---	---	---	PASS
NOL11	25926	broad.mit.edu	37	17	65720260	65720260	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65720260G>C	uc002jgd.1	+	6	618	c.615G>C	c.(613-615)AAG>AAC	p.K205N	NOL11_uc010wql.1_Missense_Mutation_p.K23N|NOL11_uc010deu.1_5'UTR	NM_015462	NP_056277	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	205						nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			CTGTTATAAAGAGTTTTACTG	0.313													13	43	---	---	---	---	PASS
NARF	26502	broad.mit.edu	37	17	80442724	80442724	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80442724A>G	uc002kfg.3	+	9	1009	c.869A>G	c.(868-870)CAT>CGT	p.H290R	NARF_uc002kff.3_Missense_Mutation_p.H231R|NARF_uc010wvp.1_3'UTR|NARF_uc010dit.2_Missense_Mutation_p.H336R|NARF_uc002kfj.3_Missense_Mutation_p.H242R|NARF_uc002kfi.3_RNA|NARF_uc002kfh.3_Missense_Mutation_p.H336R|NARF_uc002kfk.2_RNA	NM_012336	NP_036468	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor isoform a	290						lamin filament	lamin binding			skin(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GTGACGCGTCATGATGGAGCC	0.517													25	23	---	---	---	---	PASS
ASXL3	80816	broad.mit.edu	37	18	31324466	31324466	+	Silent	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31324466T>C	uc010dmg.1	+	12	4709	c.4654T>C	c.(4654-4656)TTG>CTG	p.L1552L	ASXL3_uc002kxq.2_Silent_p.L1259L	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1552					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						CAGTAAAACATTGCCGGCCAC	0.493											OREG0024911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	24	---	---	---	---	PASS
SLC14A2	8170	broad.mit.edu	37	18	43219767	43219767	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43219767G>T	uc010dnj.2	+	8	1221	c.900G>T	c.(898-900)TGG>TGT	p.W300C	SLC14A2_uc002lbb.2_Missense_Mutation_p.W300C|SLC14A2_uc002lbe.2_Missense_Mutation_p.W300C	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),	300						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						ACAATCCCTGGACAGGCGGCG	0.547													10	65	---	---	---	---	PASS
PIAS2	9063	broad.mit.edu	37	18	44470757	44470757	+	Silent	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44470757G>A	uc002lck.2	-	2	443	c.285C>T	c.(283-285)GAC>GAT	p.D95D	PIAS2_uc010dnp.2_5'UTR|PIAS2_uc002lcl.2_Silent_p.D95D|PIAS2_uc010xda.1_Intron|PIAS2_uc002lcm.2_Silent_p.D95D|PIAS2_uc002lcn.1_Silent_p.D99D	NM_004671	NP_004662	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT X isoform	95					androgen receptor signaling pathway|negative regulation of androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|PML body	androgen receptor binding|DNA binding|protein binding|SUMO ligase activity|transcription coactivator activity|zinc ion binding			ovary(2)|breast(1)|skin(1)	4						CCACGGCCAAGTCAGGTTCTA	0.483													14	25	---	---	---	---	PASS
CCBE1	147372	broad.mit.edu	37	18	57103325	57103325	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57103325G>A	uc002lib.2	-	11	1106	c.1036C>T	c.(1036-1038)CGC>TGC	p.R346C	CCBE1_uc010dpq.2_Missense_Mutation_p.R75C|CCBE1_uc002lia.2_Missense_Mutation_p.R199C	NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	346					lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)				ATGTCATTGCGGATGTCAGCC	0.522													32	103	---	---	---	---	PASS
ZNF554	115196	broad.mit.edu	37	19	2834406	2834406	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2834406G>C	uc002lwm.2	+	5	1371	c.1173G>C	c.(1171-1173)AGG>AGC	p.R391S	ZNF554_uc002lwl.2_Missense_Mutation_p.R340S	NM_001102651	NP_001096121	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	391	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		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)		CCTTCAACAGGATCTCATCGC	0.542													11	44	---	---	---	---	PASS
LRG1	116844	broad.mit.edu	37	19	4538952	4538952	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4538952A>G	uc002mau.2	-	2	55	c.44T>C	c.(43-45)ATT>ACT	p.I15T	PLIN5_uc002mat.1_Intron	NM_052972	NP_443204	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1 precursor	15						extracellular region|membrane				ovary(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGGGGTTGAATGCCCCCTGG	0.468													21	42	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9091636	9091636	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9091636G>A	uc002mkp.2	-	1	383	c.179C>T	c.(178-180)CCA>CTA	p.P60L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	60	Thr-rich.|Extracellular (Potential).				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						GGTCTTATCTGGGGAAGTAAA	0.512													48	38	---	---	---	---	PASS
ZNF562	54811	broad.mit.edu	37	19	9763810	9763810	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9763810G>C	uc010xks.1	-	6	1259	c.1096C>G	c.(1096-1098)CAC>GAC	p.H366D	ZNF562_uc002mly.2_Missense_Mutation_p.H366D|ZNF562_uc002mlx.2_Missense_Mutation_p.H294D|ZNF562_uc010xkt.1_Missense_Mutation_p.H329D|ZNF562_uc010xku.1_Missense_Mutation_p.H297D|ZNF562_uc010xkv.1_Missense_Mutation_p.H365D|ZNF562_uc010xkw.1_Missense_Mutation_p.H250D	NM_001130032	NP_001123504	Q6V9R5	ZN562_HUMAN	zinc finger protein 562 isoform a	366	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TCTCCAGTGTGATTTCGTATG	0.428													16	73	---	---	---	---	PASS
ZNF562	54811	broad.mit.edu	37	19	9763923	9763923	+	Nonsense_Mutation	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9763923G>C	uc010xks.1	-	6	1146	c.983C>G	c.(982-984)TCA>TGA	p.S328*	ZNF562_uc002mly.2_Nonsense_Mutation_p.S328*|ZNF562_uc002mlx.2_Nonsense_Mutation_p.S256*|ZNF562_uc010xkt.1_Nonsense_Mutation_p.S291*|ZNF562_uc010xku.1_Nonsense_Mutation_p.S259*|ZNF562_uc010xkv.1_Nonsense_Mutation_p.S327*|ZNF562_uc010xkw.1_Nonsense_Mutation_p.S212*	NM_001130032	NP_001123504	Q6V9R5	ZN562_HUMAN	zinc finger protein 562 isoform a	328	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AAGGTGAGTTGATCTAGTGAA	0.398													18	74	---	---	---	---	PASS
ZNF20	7568	broad.mit.edu	37	19	12243726	12243726	+	Silent	SNP	A	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12243726A>G	uc002mtf.1	-	4	1418	c.1275T>C	c.(1273-1275)TGT>TGC	p.C425C	ZNF20_uc002mte.1_Silent_p.C390C|ZNF20_uc002mtg.1_Silent_p.C425C	NM_021143	NP_066966	P17024	ZNF20_HUMAN	zinc finger protein 20	425	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CACATTGCTTACATTCATGGG	0.403													24	43	---	---	---	---	PASS
ZNF563	147837	broad.mit.edu	37	19	12429407	12429407	+	3'UTR	SNP	T	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12429407T>G	uc002mtp.2	-	4						NM_145276	NP_660319	Q8TA94	ZN563_HUMAN	zinc finger protein 563						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ATAGTTTACATTCATATTGTT	0.373													31	20	---	---	---	---	PASS
RASAL3	64926	broad.mit.edu	37	19	15562928	15562928	+	Intron	SNP	G	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15562928G>C	uc002nbe.2	-						WIZ_uc002nbb.3_5'Flank|RASAL3_uc002nbd.2_3'UTR|RASAL3_uc010eaa.1_Intron	NM_022904	NP_075055	Q86YV0	RASL3_HUMAN	RAS protein activator like 3						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity				0						TCCTGTGGGGGTCGGGGGATT	0.602													17	53	---	---	---	---	PASS
ZNF100	163227	broad.mit.edu	37	19	21910559	21910559	+	Silent	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21910559G>T	uc002nqi.2	-	5	754	c.555C>A	c.(553-555)GTC>GTA	p.V185V	ZNF100_uc002nqh.2_Silent_p.V121V	NM_173531	NP_775802	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	185	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ATGTATGAAAGACTTTTGCAG	0.303													8	95	---	---	---	---	PASS
LSR	51599	broad.mit.edu	37	19	35757275	35757275	+	Silent	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35757275C>A	uc002nyl.2	+	6	1159	c.936C>A	c.(934-936)GGC>GGA	p.G312G	LSR_uc002nym.2_Silent_p.G293G|LSR_uc002nyn.2_Silent_p.G244G|LSR_uc002nyo.2_Silent_p.G293G|LSR_uc010xsr.1_Silent_p.G204G|LSR_uc002nyp.2_Silent_p.G275G|USF2_uc010xss.1_5'Flank|USF2_uc002nyq.1_5'Flank|USF2_uc002nyr.1_5'Flank|USF2_uc002nys.1_5'Flank|USF2_uc002nyt.1_5'Flank	NM_205834	NP_991403	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	312	Cytoplasmic (Potential).				embryo development|liver development	chylomicron|integral to membrane|low-density lipoprotein particle|plasma membrane|very-low-density lipoprotein particle	receptor activity				0	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			ATGCCGCCGGCAAAGCAGCCA	0.617													4	73	---	---	---	---	PASS
ZNF473	25888	broad.mit.edu	37	19	50550136	50550136	+	Silent	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50550136G>A	uc002prn.2	+	5	2673	c.2436G>A	c.(2434-2436)AAG>AAA	p.K812K	ZNF473_uc002prm.2_Silent_p.K812K|ZNF473_uc010ybo.1_Silent_p.K800K	NM_001006656	NP_001006657	Q8WTR7	ZN473_HUMAN	zinc finger protein 473	812					histone mRNA 3'-end processing|regulation of transcription, DNA-dependent|termination of RNA polymerase II transcription	Cajal body	DNA binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		CAGGGGAGAAGCCTTACTCCT	0.493											OREG0025632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	21	46	---	---	---	---	PASS
LILRA2	11027	broad.mit.edu	37	19	55086982	55086982	+	Missense_Mutation	SNP	G	T	T	rs143337690		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55086982G>T	uc002qgg.3	+	5	1004	c.915G>T	c.(913-915)TGG>TGT	p.W305C	LILRA2_uc010ern.2_Missense_Mutation_p.W305C|LILRA2_uc002qgf.2_Missense_Mutation_p.W305C|LILRA2_uc010yfe.1_Missense_Mutation_p.W305C|LILRA2_uc010yff.1_Missense_Mutation_p.W293C|LILRA2_uc010ero.2_Missense_Mutation_p.W293C|LILRA2_uc010yfg.1_Intron	NM_001130917	NP_001124389	Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor,	305	Ig-like C2-type 3.|Extracellular (Potential).				defense response	integral to membrane	antigen binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0963)		CCTCCGAGTGGTCGGCCCCCA	0.672													4	55	---	---	---	---	PASS
KIR2DL3	3804	broad.mit.edu	37	19	55255266	55255266	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55255266T>G	uc002qgv.2	+	4	412	c.394T>G	c.(394-396)TCA>GCA	p.S132A	KIR2DL3_uc002qgx.2_Missense_Mutation_p.S132A|KIR2DL3_uc002qgy.2_Intron|KIR2DL3_uc010erw.1_Missense_Mutation_p.S132A|KIR2DL1_uc002qgz.1_Missense_Mutation_p.S42A|KIR2DL3_uc002qha.1_Intron	NM_015868	NP_056952	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two	132	Extracellular (Potential).				immune response|regulation of immune response	integral to plasma membrane	antigen binding|protein binding|receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(193;0.0192)		ACCTTCTCTCTCAGCCCAGCC	0.562													41	21	---	---	---	---	PASS
PLCB1	23236	broad.mit.edu	37	20	8707972	8707972	+	Silent	SNP	T	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8707972T>C	uc002wnb.2	+	17	1698	c.1695T>C	c.(1693-1695)TTT>TTC	p.F565F	PLCB1_uc010zrb.1_Silent_p.F464F|PLCB1_uc002wna.2_Silent_p.F565F|PLCB1_uc002wnc.1_Silent_p.F464F|PLCB1_uc002wnd.1_Silent_p.F142F	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	565	PI-PLC Y-box.				activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						ATAAAAGTTTTGAAATGTCTT	0.328													5	37	---	---	---	---	PASS
MYH7B	57644	broad.mit.edu	37	20	33572514	33572514	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33572514C>T	uc002xbi.1	+	9	862	c.770C>T	c.(769-771)ACG>ATG	p.T257M		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	215	Myosin head-like.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GCAACAAAGACGGGGGTGAGT	0.647													6	33	---	---	---	---	PASS
UQCC	55245	broad.mit.edu	37	20	33894581	33894581	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33894581C>A	uc002xcd.2	-	9	720	c.653G>T	c.(652-654)GGG>GTG	p.G218V	UQCC_uc010zuy.1_Missense_Mutation_p.G119V|UQCC_uc010zuz.1_Missense_Mutation_p.G63V|UQCC_uc010zva.1_Missense_Mutation_p.G81V|UQCC_uc002xce.2_Missense_Mutation_p.G191V|UQCC_uc002xcg.2_Missense_Mutation_p.G84V|UQCC_uc010gfb.2_Missense_Mutation_p.G192V|UQCC_uc010zvb.1_Missense_Mutation_p.G150V|UQCC_uc002xcf.2_Missense_Mutation_p.G106V|UQCC_uc002xch.2_5'Flank|UQCC_uc002xcc.2_Missense_Mutation_p.G31V	NM_018244	NP_060714	Q9NVA1	UQCC_HUMAN	basic FGF-repressed Zic binding protein isoform	218						cytoplasmic membrane-bounded vesicle				breast(1)	1			BRCA - Breast invasive adenocarcinoma(18;0.00252)			TGAAAGGATCCCCTGGAACAT	0.522											OREG0025889	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	28	---	---	---	---	PASS
SERINC3	10955	broad.mit.edu	37	20	43129878	43129878	+	Silent	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43129878G>A	uc002xme.2	-	9	1253	c.1119C>T	c.(1117-1119)ATC>ATT	p.I373I	SERINC3_uc002xmf.1_Silent_p.I373I|SERINC3_uc010ggs.1_Silent_p.I366I|SERINC3_uc010zwp.1_Silent_p.I318I	NM_198941	NP_945179	Q13530	SERC3_HUMAN	tumor differentially expressed protein 1	373	Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			skin(3)	3		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)			TATCACCAAGGATGACGCTGT	0.517													15	35	---	---	---	---	PASS
SON	6651	broad.mit.edu	37	21	34927341	34927341	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34927341G>A	uc002yse.1	+	3	5853	c.5804G>A	c.(5803-5805)AGT>AAT	p.S1935N	SON_uc002ysb.1_Missense_Mutation_p.S1935N|SON_uc002ysc.2_Missense_Mutation_p.S1935N|SON_uc002ysd.2_Missense_Mutation_p.S926N|SON_uc002ysf.1_Intron|SON_uc002ysg.2_Missense_Mutation_p.S926N	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	1935	2 X 19 AA repeats of P-S-R-R-R-R-S-R-S-V- V-R-R-R-S-F-S-I-S.|3-1.|7 X 7 AA repeats of P-S-R-R-S-R-[TS].				anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6						CATACTCCAAGTCGTCGACGA	0.373													7	51	---	---	---	---	PASS
SETD4	54093	broad.mit.edu	37	21	37408483	37408483	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37408483T>A	uc002yuw.1	-	10	2628	c.1255A>T	c.(1255-1257)ACG>TCG	p.T419S	SETD4_uc002yux.1_Missense_Mutation_p.T395S|SETD4_uc002yuu.2_RNA|SETD4_uc002yuv.2_Missense_Mutation_p.T419S	NM_017438	NP_059134	Q9NVD3	SETD4_HUMAN	SET domain containing 4 isoform a	419				EILVKYLPSTDKQMDKKISILKDHGYIENLTFGWDGPSWRL LTALKLLCLEAEKFTCWKKVLLGEVISDTNEKTSLDIAQKI CYYFIEETNAVLQKVSHMKDEKEALINQLTLVESLWTEELK ILRASAETLHSLQTAFT -> GWNQLCS (in Ref. 5; AAH02898).						large_intestine(1)|ovary(1)	2						AGCTCTTCCGTCCACAAGGAT	0.408													41	63	---	---	---	---	PASS
FAM3B	54097	broad.mit.edu	37	21	42720533	42720533	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42720533C>G	uc002yzb.1	+	7	646	c.500C>G	c.(499-501)GCC>GGC	p.A167G	FAM3B_uc002yza.2_RNA|FAM3B_uc002yzc.1_Missense_Mutation_p.A119G|FAM3B_uc002yzd.1_Missense_Mutation_p.A190G	NM_058186	NP_478066	P58499	FAM3B_HUMAN	family with sequence similarity 3, member B	167					apoptosis|insulin secretion	extracellular space	cytokine activity				0		Prostate(19;1.57e-07)|all_epithelial(19;0.0404)				AATAACGATGCCAAGAATGCC	0.468													8	36	---	---	---	---	PASS
XRCC6	2547	broad.mit.edu	37	22	42032651	42032651	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42032651G>A	uc003bao.1	+	5	536	c.466G>A	c.(466-468)GAT>AAT	p.D156N	XRCC6_uc003bap.1_Missense_Mutation_p.D115N|XRCC6_uc011apc.1_Missense_Mutation_p.D106N|XRCC6_uc003baq.1_Missense_Mutation_p.D156N|XRCC6_uc003bar.1_Missense_Mutation_p.D156N|XRCC6_uc003bas.1_Missense_Mutation_p.D106N	NM_001469	NP_001460	P12956	XRCC6_HUMAN	ATP-dependent DNA helicase II, 70 kDa subunit	156					DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding			skin(2)|ovary(1)|lung(1)|kidney(1)	5						CCTCTTTAGTGATGTCCAATT	0.507								Direct_reversal_of_damage|NHEJ					7	64	---	---	---	---	PASS
MXRA5	25878	broad.mit.edu	37	X	3248704	3248704	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3248704C>A	uc004crg.3	-	3	456	c.299G>T	c.(298-300)AGA>ATA	p.R100I		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	100	LRR 2.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GCTGAGGTCTCTTAAAGCTCC	0.438													4	45	---	---	---	---	PASS
ZNF711	7552	broad.mit.edu	37	X	84526736	84526736	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84526736G>A	uc004eeo.2	+	9	2535	c.2188G>A	c.(2188-2190)GAC>AAC	p.D730N	ZNF711_uc004eep.2_Missense_Mutation_p.D730N|ZNF711_uc004eeq.2_Missense_Mutation_p.D776N|ZNF711_uc011mqy.1_Missense_Mutation_p.D329N	NM_021998	NP_068838	Q9Y462	ZN711_HUMAN	zinc finger protein 711	730					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			ovary(3)|skin(1)	4						ACATACAAAAGACTATCCACA	0.388													5	56	---	---	---	---	PASS
ALG13	79868	broad.mit.edu	37	X	110970887	110970887	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110970887G>T	uc011msy.1	+	18	2170	c.2136G>T	c.(2134-2136)GAG>GAT	p.E712D	ALG13_uc011msx.1_Missense_Mutation_p.E608D|ALG13_uc011msz.1_Missense_Mutation_p.E634D|ALG13_uc011mta.1_Missense_Mutation_p.E608D|ALG13_uc011mtb.1_Missense_Mutation_p.E608D			Q9NP73	ALG13_HUMAN	SubName: Full=Asparagine-linked glycosylation 13 homolog (S. cerevisiae);	712					dolichol-linked oligosaccharide biosynthetic process|lipid glycosylation|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane	carbohydrate binding|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity			lung(1)	1						TGAATAAGGAGTCCCAGTATG	0.383													22	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	2776000	2776001	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2776000_2776001insA								MMEL1 (211519 upstream) : ACTRT2 (162045 downstream)																							gaaggaaggagaaagaaggagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5730763	5730764	+	5'Flank	DEL	CA	-	-	rs113891886		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5730763_5730764delCA	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																		GCATCACAAGCACACACCATGC	0.465													6	3	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7530274	7530274	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7530274delC	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)		GGTTCCTGCTCCCCCAGGTCT	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	10264695	10264695	+	IGR	DEL	T	-	-	rs35249042		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10264695delT								UBE4B (23401 upstream) : KIF1B (6069 downstream)																							GACAAATATCttttttttttt	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	11388745	11388745	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11388745delT								UBIAD1 (40255 upstream) : PTCHD2 (150550 downstream)																							TTCCGCTCCCTTAATGGCCTT	0.438													4	2	---	---	---	---	
C1orf187	374946	broad.mit.edu	37	1	11762477	11762478	+	Intron	DEL	CA	-	-	rs151236280		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11762477_11762478delCA	uc001asr.1	+							NM_198545	NP_940947	Q8NBI3	DRAXI_HUMAN	chromosome 1 open reading frame 187 precursor						axon guidance|commissural neuron differentiation in spinal cord|dorsal spinal cord development|forebrain development|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular region					0	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.48e-06)|COAD - Colon adenocarcinoma(227;0.000283)|BRCA - Breast invasive adenocarcinoma(304;0.000316)|Kidney(185;0.000841)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|STAD - Stomach adenocarcinoma(313;0.00754)|READ - Rectum adenocarcinoma(331;0.0651)		cacacatgttcacacacacatg	0.069													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	12866359	12866359	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12866359delG								PRAMEF1 (10136 upstream) : PRAMEF11 (18109 downstream)																							ATCTGATGTTGACCTTAGTTG	0.473													4	2	---	---	---	---	
SPATA21	374955	broad.mit.edu	37	1	16729986	16729987	+	Intron	DEL	TC	-	-	rs57948110		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16729986_16729987delTC	uc001ayn.2	-						SPATA21_uc001ayl.1_Intron|SPATA21_uc010occ.1_Intron	NM_198546	NP_940948	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21								calcium ion binding			ovary(2)|breast(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		ttcttttttttctttttttttt	0.010													4	3	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17197242	17197245	+	Intron	DEL	TATG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17197242_17197245delTATG	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		ccacccagtttatgtatggtacag	0.157													2	4	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17229404	17229404	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17229404delT	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GGGCAGTGTCTTTTAGGATAT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17511953	17511953	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17511953delG								PADI2 (66005 upstream) : PADI1 (19668 downstream)																							CTTACCCTCTGGagataaact	0.323													4	2	---	---	---	---	
ALPL	249	broad.mit.edu	37	1	21869792	21869792	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21869792delT	uc001bet.2	+						ALPL_uc010odn.1_Intron|ALPL_uc010odo.1_Intron|ALPL_uc010odp.1_Intron	NM_000478	NP_000469	P05186	PPBT_HUMAN	tissue-nonspecific alkaline phosphatase						response to vitamin D|skeletal system development	anchored to membrane|cytoplasm|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)	CACTAAACCCTTTTTTTCCCC	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	22591868	22591873	+	IGR	DEL	GTGTGC	-	-	rs148406788	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22591868_22591873delGTGTGC								WNT4 (121483 upstream) : ZBTB40 (186471 downstream)																							gtgtgtgtgtgtgtgcgcgccagggt	0.184													3	3	---	---	---	---	
ASAP3	55616	broad.mit.edu	37	1	23762668	23762668	+	Intron	DEL	T	-	-	rs77206819		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23762668delT	uc001bha.2	-						ASAP3_uc001bgy.1_Intron|ASAP3_uc001bgz.1_Intron|ASAP3_uc010odz.1_Intron|ASAP3_uc010oea.1_Intron|ASAP3_uc001bhb.2_Intron	NM_017707	NP_060177	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	cytoplasm	ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3						CTCCCCAGGCtttttttttag	0.289													5	3	---	---	---	---	
AHDC1	27245	broad.mit.edu	37	1	27931131	27931131	+	5'Flank	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27931131delA	uc009vsy.2	-						AHDC1_uc009vsz.1_5'Flank|AHDC1_uc001boh.1_5'Flank	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1								DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CTTATTGAGTAAAGCTCAAGT	0.577													4	2	---	---	---	---	
PHC2	1912	broad.mit.edu	37	1	33836943	33836948	+	Intron	DEL	GCACTC	-	-	rs72427573		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33836943_33836948delGCACTC	uc001bxg.1	-						PHC2_uc001bxh.1_Intron|PHC2_uc009vuh.1_Intron|PHC2_uc001bxi.1_Intron	NM_198040	NP_932157	Q8IXK0	PHC2_HUMAN	polyhomeotic-like 2 isoform a						multicellular organismal development	PcG protein complex	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				tTGCCACTGAGCACTCCAACTATTAG	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	34903076	34903077	+	IGR	DEL	AC	-	-	rs111621580		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34903076_34903077delAC								C1orf94 (218347 upstream) : MIR552 (232123 downstream)																							tcCCCCCAAGacacacacacac	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37551780	37551780	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37551780delT								GRIK3 (51936 upstream) : ZC3H12A (388339 downstream)																							tagtttccactttttggctgt	0.005													4	2	---	---	---	---	
SLC6A9	6536	broad.mit.edu	37	1	44496839	44496844	+	Intron	DEL	CACACA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44496839_44496844delCACACA	uc001cln.2	-						SLC6A9_uc010okm.1_Intron|SLC6A9_uc010oko.1_Intron|SLC6A9_uc010okp.1_Intron	NM_001024845	NP_001020016	P48067	SC6A9_HUMAN	solute carrier family 6 member 9 isoform 3							integral to plasma membrane|membrane fraction	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity				0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	CATGCGCGATcacacacacacacaca	0.553													3	3	---	---	---	---	
CYP4Z2P	163720	broad.mit.edu	37	1	47337449	47337450	+	Intron	DEL	TG	-	-	rs72322734		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47337449_47337450delTG	uc001cqo.1	-						CYP4Z2P_uc009vyn.1_Intron	NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0						GAAAATTAAATGTGTGTGTGTG	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	53967836	53967858	+	IGR	DEL	AGGAGAAGAGGGACAGGGGAGAG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53967836_53967858delAGGAGAAGAGGGACAGGGGAGAG								DMRTB1 (34678 upstream) : GLIS1 (4048 downstream)																							agaggagagaaggagaagagggacaggggagagaggagaagag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	55435609	55435609	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55435609delG								DHCR24 (82688 upstream) : TMEM61 (10856 downstream)																							ggtgGGTGCTGGAACCACAAG	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56289722	56289724	+	IGR	DEL	GCT	-	-	rs10568118		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56289722_56289724delGCT								USP24 (608960 upstream) : PPAP2B (670709 downstream)																							CTCCAAACTAGCTTTAGAATGTT	0.443													3	4	---	---	---	---	
NFIA	4774	broad.mit.edu	37	1	61850283	61850283	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61850283delT	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145	Q12857	NFIA_HUMAN	nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2						TATTAAGATATTATCCTCATA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	65183946	65183946	+	IGR	DEL	G	-	-	rs112978881		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65183946delG								CACHD1 (25205 upstream) : RAVER2 (26832 downstream)																							gaccccccccgcatccatgaa	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	73350864	73350865	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73350864_73350865insA								NEGR1 (602459 upstream) : None (None downstream)																							ttccaggcaggaaaaaaaaaca	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	80154817	80154819	+	IGR	DEL	CTG	-	-	rs67900456		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80154817_80154819delCTG								ELTD1 (682322 upstream) : None (None downstream)																							ACGACAGACTCTGCTTAGTTTAA	0.305													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	82938092	82938095	+	IGR	DEL	TGTG	-	-	rs112816589		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82938092_82938095delTGTG								LPHN2 (479986 upstream) : None (None downstream)																							gccccatcaatgtgtgtgtgtgtg	0.000													5	3	---	---	---	---	
WDR63	126820	broad.mit.edu	37	1	85589230	85589230	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85589230delA	uc001dkt.2	+						WDR63_uc009wcl.2_Intron	NM_145172	NP_660155	Q8IWG1	WDR63_HUMAN	WD repeat domain 63											upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		ccttcacaccaaaatcttccc	0.000													4	2	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	85984427	85984428	+	Intron	INS	-	AAC	AAC	rs146066636	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85984427_85984428insAAC	uc001dlc.2	-							NM_001134445	NP_001127917	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	ccatgtaagataaactcacagg	0.000													6	3	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	85999311	85999312	+	Intron	INS	-	A	A	rs148995837	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85999311_85999312insA	uc001dlc.2	-							NM_001134445	NP_001127917	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	AAGACAAGCTTAAAAAAAACAG	0.307													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	90079594	90079594	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90079594delC								LRRC8B (16176 upstream) : LRRC8C (19050 downstream)																							aggtgattctcccacctcagc	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	95544292	95544293	+	IGR	INS	-	AA	AA	rs139120180	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95544292_95544293insAA								ALG14 (5785 upstream) : TMEM56 (38601 downstream)																							acatgaaaaagaaaaaaaaaac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96435566	96435566	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96435566delT								RWDD3 (722793 upstream) : PTBP2 (751609 downstream)																							ctgcaattgcttttggcatta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98594773	98594774	+	IGR	INS	-	ACAC	ACAC	rs147864122	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98594773_98594774insACAC								MIR137 (83046 upstream) : SNX7 (532462 downstream)																							CTTTTGGTAATacacacacaca	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	104737170	104737170	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104737170delA								AMY1A (529998 upstream) : None (None downstream)																							gaggaaaaggaaaaaaaaaat	0.035													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	112854466	112854469	+	IGR	DEL	CACA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112854466_112854469delCACA								KCND3 (322689 upstream) : CTTNBP2NL (84331 downstream)																							cacatgcacgcacacacacacaca	0.235													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142640077	142640078	+	Intron	DEL	TG	-	-	rs71582729		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142640077_142640078delTG	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		gttgaggctctgtgtgtgtgtg	0.000													14	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142687897	142687899	+	Intron	DEL	TAT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142687897_142687899delTAT	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		AATAAAGTGGTATTATCATTTTT	0.315													4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145267664	145267664	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145267664delT	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_Intron|NOTCH2NL_uc001emm.3_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)		tctatttccctttctttacag	0.000													6	4	---	---	---	---	
NOTCH2NL	388677	broad.mit.edu	37	1	145291063	145291063	+	3'UTR	DEL	A	-	-	rs11322524		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145291063delA	uc001emo.2	+	6					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Intron|NOTCH2NL_uc010oyh.1_Intron|NBPF10_uc001end.3_5'Flank|NBPF10_uc001emq.1_5'Flank	NM_203458	NP_982283	Q7Z3S9	NT2NL_HUMAN	Notch homolog 2 N-terminal like protein						cell differentiation|multicellular organismal development|Notch signaling pathway	cytoplasm|extracellular region	calcium ion binding			ovary(1)	1						CATAAAACCTAAAACTATTGC	0.289													9	5	---	---	---	---	
FMO5	2330	broad.mit.edu	37	1	146660851	146660852	+	Intron	INS	-	A	A	rs149129480		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146660851_146660852insA	uc001epi.2	-						FMO5_uc001eph.3_Intron|FMO5_uc001epj.2_Intron	NM_001461	NP_001452	P49326	FMO5_HUMAN	flavin containing monooxygenase 5 isoform 1							integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			ovary(3)	3	all_hematologic(923;0.0487)					agactccgtctaaaaaaaaaaa	0.183													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	147302065	147302065	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147302065delT								GJA5 (56581 upstream) : GJA8 (72871 downstream)																							tctttcagtcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	147390832	147390833	+	IGR	INS	-	AC	AC	rs141918645	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147390832_147390833insAC								GJA8 (9439 upstream) : GPR89B (9673 downstream)																							CAATACATGAAACAAGATAATA	0.203													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148849954	148849955	+	IGR	INS	-	TTCAT	TTCAT	rs149858916		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148849954_148849955insTTCAT								NBPF16 (91643 upstream) : LOC645166 (78331 downstream)																							catcatttcacttcatttcatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148850655	148850657	+	IGR	DEL	TCA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148850655_148850657delTCA								NBPF16 (92344 upstream) : LOC645166 (77629 downstream)																							tcacttcatctcatcatttcatc	0.000													4	2	---	---	---	---	
LOC645166	645166	broad.mit.edu	37	1	148946694	148946695	+	Intron	INS	-	A	A	rs149264561		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148946694_148946695insA	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0						AGAACTCTGTCAAAAAAAAAAA	0.431													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149224579	149224579	+	IGR	DEL	T	-	-	rs67263328		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149224579delT								LOC645166 (271525 upstream) : LOC388692 (54897 downstream)																							TGTCTCTCCCTTTTTTCCCTC	0.642													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149299254	149299254	+	IGR	DEL	T	-	-	rs142718750		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149299254delT								LOC388692 (7512 upstream) : FCGR1C (70040 downstream)																							CCCCACATACTTGCGCCCTGC	0.532													4	5	---	---	---	---	
LOC728855	728855	broad.mit.edu	37	1	149655274	149655275	+	Intron	INS	-	T	T	rs145548002	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149655274_149655275insT	uc009wlc.2	+						LOC728855_uc009wld.2_Intron					Homo sapiens mRNA, chromosome 1 specific transcript KIAA0493.												0						ttaaaaggatattttttttccc	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	150007924	150007924	+	IGR	DEL	T	-	-	rs66518005		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150007924delT								OTUD7B (25238 upstream) : VPS45 (31418 downstream)																							ATTGTAACTGttttttttttt	0.164													4	3	---	---	---	---	
RPRD2	23248	broad.mit.edu	37	1	150335024	150335024	+	5'Flank	DEL	A	-	-	rs71578486		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150335024delA	uc009wlr.2	+						RPRD2_uc010pcc.1_5'Flank|RPRD2_uc001eup.3_5'Flank	NM_015203	NP_056018	Q5VT52	RPRD2_HUMAN	Regulation of nuclear pre-mRNA domain containing								protein binding			ovary(1)	1						AGAGTTACAGAAAAAAAAAAA	0.095													4	4	---	---	---	---	
SELENBP1	8991	broad.mit.edu	37	1	151343887	151343888	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151343887_151343888insA	uc001exx.2	-						SELENBP1_uc010pcy.1_Intron|SELENBP1_uc001exy.2_Intron|SELENBP1_uc001exz.2_Intron|SELENBP1_uc010pcz.1_Intron|SELENBP1_uc009wms.2_Intron|SELENBP1_uc009wmt.2_Intron|SELENBP1_uc001eya.2_Intron|SELENBP1_uc009wmu.2_Intron	NM_003944	NP_003935	Q13228	SBP1_HUMAN	selenium binding protein 1						protein transport	cytosol|membrane|nucleolus	protein binding|selenium binding				0	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			aaattctgactaaaaaaaaaaa	0.178													4	2	---	---	---	---	
POGZ	23126	broad.mit.edu	37	1	151387266	151387266	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151387266delA	uc001eyd.1	-						POGZ_uc001eye.1_Intron|POGZ_uc010pdb.1_Intron|POGZ_uc001eyf.1_Intron|POGZ_uc010pdc.1_Intron|POGZ_uc009wmv.1_Intron|POGZ_uc010pdd.1_Intron	NM_015100	NP_055915	Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain						cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			caaaaaaaagaaaaaaaagat	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152440269	152440269	+	IGR	DEL	T	-	-	rs113807999		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152440269delT								CRNN (53519 upstream) : LCE5A (43051 downstream)																							ctgtgactaattttttttttt	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	153119532	153119533	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153119532_153119533insA								SPRR2D (5563 upstream) : SPRR2G (2526 downstream)																							atttaatgggcaaaaaaaagaa	0.000													4	2	---	---	---	---	
PGLYRP3	114771	broad.mit.edu	37	1	153280476	153280477	+	Intron	INS	-	TT	TT	rs71582302		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153280476_153280477insTT	uc001fbn.1	-							NM_052891	NP_443123	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3 precursor						defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ttctctctctcttttttttttt	0.233													3	7	---	---	---	---	
NUP210L	91181	broad.mit.edu	37	1	153981391	153981391	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153981391delT	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			ATACCTTACAttttttttttt	0.214													6	3	---	---	---	---	
TPM3	7170	broad.mit.edu	37	1	154152010	154152010	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154152010delT	uc001fec.1	-						TPM3_uc010pei.1_Intron|TPM3_uc001fdy.1_Intron|TPM3_uc001fdz.1_Intron|TPM3_uc001fea.1_Intron|TPM3_uc001feb.1_Intron|TPM3_uc010pej.1_Intron|TPM3_uc009wor.2_Intron|TPM3_uc001fed.1_Intron	NM_152263	NP_689476	P06753	TPM3_HUMAN	tropomyosin 3 isoform 1						cellular component movement|muscle filament sliding|regulation of muscle contraction	cytosol|muscle thin filament tropomyosin|stress fiber	actin binding		TPM3/ALK(33)	haematopoietic_and_lymphoid_tissue(22)|soft_tissue(11)|skin(1)	34	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					TTGTTATTACTTTTTTTTTTC	0.413			T	NTRK1|ALK	papillary thyroid|ALCL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	155915071	155915072	+	IGR	INS	-	GTGT	GTGT	rs10634636		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155915071_155915072insGTGT								RXFP4 (2447 upstream) : ARHGEF2 (1558 downstream)																							TGGGGCTGAAGgtgtgtgtgtg	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	156668469	156668470	+	IGR	INS	-	A	A	rs150222180		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156668469_156668470insA								NES (21280 upstream) : CRABP2 (940 downstream)																							gactccatttcaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157053226	157053227	+	IGR	INS	-	TT	TT	rs72121586		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157053226_157053227insTT								ARHGEF11 (38064 upstream) : ETV3L (8609 downstream)																							taatttttgtattttttagtag	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157060418	157060418	+	IGR	DEL	G	-	-	rs10714376		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157060418delG								ARHGEF11 (45256 upstream) : ETV3L (1418 downstream)																							acagtgccaaggttgaaaaag	0.219											OREG0013895	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157196204	157196205	+	IGR	INS	-	TAATT	TAATT	rs144945059	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157196204_157196205insTAATT								ETV3 (87821 upstream) : FCRL5 (286963 downstream)																							ACCAAGACCGATAGAGACCCCT	0.416													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157635488	157635489	+	IGR	INS	-	CCTT	CCTT	rs141002242	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157635488_157635489insCCTT								FCRL4 (67618 upstream) : FCRL3 (10789 downstream)																							ttttcttttccccttccttcct	0.000													1	5	---	---	---	---	
IFI16	3428	broad.mit.edu	37	1	158984187	158984188	+	Intron	INS	-	AGGC	AGGC	rs140294698	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158984187_158984188insAGGC	uc001ftf.1	+						IFI16_uc001ftg.2_Intron|IFI16_uc010pis.1_Intron	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16						cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)					TCTTAACACTGAGGCAATTGCT	0.446													4	2	---	---	---	---	
CCDC19	25790	broad.mit.edu	37	1	159891161	159891163	+	Intron	DEL	AAC	-	-	rs72007288		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159891161_159891163delAAC	uc001ful.2	-						TAGLN2_uc001fum.1_5'Flank|TAGLN2_uc001fun.1_Intron|TAGLN2_uc001fuo.1_Intron|TAGLN2_uc010piy.1_Intron	NM_012337	NP_036469	Q9UL16	CCD19_HUMAN	nasopharyngeal epithelium specific protein 1							mitochondrion|soluble fraction				ovary(1)	1	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.151)			tgggagaagtaacaacaacaaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	162855971	162855972	+	IGR	DEL	GG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162855971_162855972delGG								C1orf110 (17366 upstream) : RGS4 (182424 downstream)																							ATTTGTGTTTGGGAAAAAAAGC	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163732004	163732004	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163732004delT								NUF2 (406451 upstream) : PBX1 (796798 downstream)																							ttaaggttaattacaaatcgc	0.000													4	2	---	---	---	---	
PBX1	5087	broad.mit.edu	37	1	164850800	164850801	+	Intron	DEL	GA	-	-	rs140679561	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164850800_164850801delGA	uc010pkw.1	+							NM_002585	NP_002576	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5						TAGCGGTGGTGAGAGAGAGAGA	0.322			T	TCF3|EWSR1	pre B-ALL|myoepithelioma								6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166307949	166307958	+	IGR	DEL	ACACAGATTC	-	-	rs141927512		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166307949_166307958delACACAGATTC								FAM78B (171743 upstream) : FMO9P (265195 downstream)																							CAGTTCTCAGACACAGATTCACACAGAGAG	0.433													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166526519	166526519	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166526519delT								FAM78B (390313 upstream) : FMO9P (46634 downstream)																							taggtcaccctttgatctatt	0.000													4	2	---	---	---	---	
NME7	29922	broad.mit.edu	37	1	169333575	169333576	+	Intron	INS	-	TCTT	TCTT	rs142386900	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169333575_169333576insTCTT	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron|NME7_uc001gfv.1_Intron	NM_013330	NP_037462	Q9Y5B8	NDK7_HUMAN	nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)					AACAATCAACCTCTTTTTCTTT	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	171390748	171390749	+	IGR	INS	-	A	A	rs149945213	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171390748_171390749insA								FMO4 (79526 upstream) : BAT2L2 (63917 downstream)																							TACTGATGTAGAAAAaaaaaca	0.069													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172469164	172469165	+	IGR	DEL	TC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172469164_172469165delTC								C1orf105 (31199 upstream) : C1orf9 (33095 downstream)																							CTGCCTCTCTTCTCAATGGGAA	0.540													4	2	---	---	---	---	
C1orf9	51430	broad.mit.edu	37	1	172563929	172563929	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172563929delA	uc001giq.3	+						C1orf9_uc010pmm.1_Intron|C1orf9_uc009wwd.2_Intron|C1orf9_uc010pmn.1_Intron|C1orf9_uc010pmo.1_Intron	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein						multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)		gatgtctattaagttggctca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172757035	172757035	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172757035delC								FASLG (121025 upstream) : TNFSF18 (253325 downstream)																							acctctgtggccaccaccacc	0.000													4	2	---	---	---	---	
KLHL20	27252	broad.mit.edu	37	1	173739840	173739840	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173739840delA	uc001gjc.2	+						KLHL20_uc010pmr.1_Intron|KLHL20_uc009wwf.2_Intron	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20						cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1						aagagagaggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175344314	175344314	+	Intron	DEL	T	-	-	rs71673529		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175344314delT	uc001gkp.1	-						TNR_uc009wwu.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					TGATTTGTTGTTTTTTTTTTT	0.299													3	3	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175677155	175677156	+	Intron	DEL	TG	-	-	rs141269566		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175677155_175677156delTG	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					tgtgtgtgtttgtgtgtgtgtg	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	175767912	175767913	+	IGR	INS	-	A	A	rs138645056		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175767912_175767913insA								TNR (55160 upstream) : RFWD2 (146054 downstream)																							gattccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	175841816	175841817	+	IGR	DEL	AC	-	-	rs72158180		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175841816_175841817delAC								TNR (129064 upstream) : RFWD2 (72150 downstream)																							ATGCCTGTAGacacacacacac	0.406													3	3	---	---	---	---	
PAPPA2	60676	broad.mit.edu	37	1	176756891	176756892	+	Intron	INS	-	G	G	rs138743979	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176756891_176756892insG	uc001gkz.2	+						PAPPA2_uc009www.2_Intron	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						TTCTGTGAGGTGGGATTAAAGA	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177616445	177616449	+	IGR	DEL	CCTTT	-	-	rs149849186		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177616445_177616449delCCTTT								FAM5B (364888 upstream) : SEC16B (281040 downstream)																							CCAGCTGGGCCCTTTCCTTGAAGTC	0.468													4	2	---	---	---	---	
NPL	80896	broad.mit.edu	37	1	182771602	182771602	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182771602delT	uc009wyb.2	+						NPL_uc010pnx.1_Intron|NPL_uc010pny.1_Intron|NPL_uc001gpo.1_Intron|NPL_uc009wyc.2_Intron|NPL_uc001gpp.3_Intron|NPL_uc001gpq.1_Intron	NM_030769	NP_110396	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase						carbohydrate metabolic process	cytoplasm	N-acetylneuraminate lyase activity			ovary(1)|central_nervous_system(1)|skin(1)	3						ATGCATCAGATTTTTTTTTTT	0.338													4	2	---	---	---	---	
PLA2G4A	5321	broad.mit.edu	37	1	186951803	186951804	+	Intron	INS	-	TG	TG	rs145784457	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186951803_186951804insTG	uc001gsc.2	+						PLA2G4A_uc010pos.1_Intron	NM_024420	NP_077734	P47712	PA24A_HUMAN	cytosolic phospholipase A2, group IVA						phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			lung(2)|breast(1)	3					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)	TAACTCCTCTTtgtgtgtgtgt	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	188097040	188097041	+	IGR	INS	-	T	T	rs142266146	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188097040_188097041insT								None (None upstream) : None (None downstream)																							ccatgcacggattttttctcag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192575173	192575174	+	IGR	INS	-	AGAA	AGAA	rs143027439	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192575173_192575174insAGAA								RGS1 (26014 upstream) : RGS13 (30108 downstream)																							aagagagagagagaaagaaaga	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192864670	192864671	+	IGR	DEL	AA	-	-	rs72513790		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192864670_192864671delAA								RGS2 (83264 upstream) : UCHL5 (120229 downstream)																							gcgcagacccaaagagtgagca	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	194192455	194192455	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194192455delG								CDC73 (968515 upstream) : None (None downstream)																							ccaggacactggtcttggcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	196728992	196728993	+	IGR	DEL	TA	-	-	rs75751943		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196728992_196728993delTA								CFH (12361 upstream) : CFHR3 (14937 downstream)																							atatcttttttatttttggtgt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199130171	199130172	+	IGR	INS	-	G	G	rs145131094	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199130171_199130172insG								MIR181A1 (301889 upstream) : NR5A2 (866598 downstream)																							gaaggaaggaagaaggaaggaa	0.084													7	7	---	---	---	---	
TMEM183A	92703	broad.mit.edu	37	1	202981277	202981278	+	Intron	DEL	CA	-	-	rs60471086	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202981277_202981278delCA	uc001gyu.1	+						TMEM183A_uc009xai.1_Intron|TMEM183A_uc001gyv.1_Intron|TMEM183A_uc001gyw.1_Intron|TMEM183A_uc001gyx.1_Intron	NM_001079809	NP_001073277	Q8IXX5	T183A_HUMAN	transmembrane protein 183B							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.18)			CCCACTCCATcacacacacaca	0.163													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	203366870	203366871	+	IGR	DEL	CA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203366870_203366871delCA								FMOD (46581 upstream) : PRELP (78012 downstream)																							gcatttcactcagcatagtgtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213918764	213918764	+	IGR	DEL	A	-	-	rs72186964		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213918764delA								RPS6KC1 (471957 upstream) : PROX1 (242522 downstream)																							ACTGTGACTTAAAAAAAAAAA	0.443													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	214213144	214213145	+	IGR	DEL	AC	-	-	rs66667661		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214213144_214213145delAC								PROX1 (3384 upstream) : SMYD2 (241420 downstream)																							ATGTGCGcatacacacacacac	0.292													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	215477888	215477889	+	IGR	DEL	GA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215477888_215477889delGA								KCNK2 (67453 upstream) : KCTD3 (262846 downstream)																							CACATTCTCTgagagagagaga	0.287													4	2	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	215864074	215864075	+	Intron	INS	-	T	T	rs146098732	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215864074_215864075insT	uc001hku.1	-							NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ttcattttctcttttttttcac	0.015										HNSCC(13;0.011)			5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	218147694	218147695	+	IGR	INS	-	GT	GT			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218147694_218147695insGT								SPATA17 (107192 upstream) : RRP15 (310934 downstream)																							GAGAAGTAGAAgtgtgtgtgtg	0.351													2	4	---	---	---	---	
TGFB2	7042	broad.mit.edu	37	1	218551301	218551304	+	Intron	DEL	TGTT	-	-	rs67890412		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218551301_218551304delTGTT	uc001hlm.2	+						TGFB2_uc001hll.2_Intron|TGFB2_uc001hln.2_Intron|TGFB2_uc010pue.1_Intron|TGFB2_uc001hlo.2_Intron	NM_003238	NP_003229	P61812	TGFB2_HUMAN	transforming growth factor, beta 2 isoform 2						activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway	axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen	beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding				0				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		TATTATAGTGtgtttgtttgtttg	0.191													4	2	---	---	---	---	
MOSC1	64757	broad.mit.edu	37	1	220967611	220967612	+	Intron	INS	-	T	T	rs33955560		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220967611_220967612insT	uc001hms.2	+						MOSC1_uc001hmt.2_Intron	NM_022746	NP_073583	Q5VT66	MOSC1_HUMAN	MOCO sulphurase C-terminal domain containing 1								molybdenum ion binding|oxidoreductase activity|pyridoxal phosphate binding				0				GBM - Glioblastoma multiforme(131;0.0358)		AAGGAGGGTGATTTTTTTTTTT	0.450													2	4	---	---	---	---	
LEFTY1	10637	broad.mit.edu	37	1	226075411	226075411	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226075411delC	uc001hpo.2	-						LEFTY1_uc010pvj.1_Intron|LEFTY1_uc009xej.1_3'UTR	NM_020997	NP_066277	O75610	LFTY1_HUMAN	left-right determination, factor B						cell growth|multicellular organismal development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity|transforming growth factor beta receptor binding				0	Breast(184;0.197)					CCCCGCACCGCCCCCCCGCGT	0.751													4	4	---	---	---	---	
CDC42BPA	8476	broad.mit.edu	37	1	227448257	227448260	+	Intron	DEL	AGAA	-	-	rs5781478		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227448257_227448260delAGAA	uc001hqr.2	-						CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				CCATGGTGTCAGAAAGAAAGTGTC	0.451													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	230107739	230107740	+	IGR	INS	-	AA	AA			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230107739_230107740insAA								URB2 (311793 upstream) : GALNT2 (85796 downstream)																							caaacatacacacaccccatcc	0.030													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	230439453	230439453	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230439453delG								GALNT2 (21578 upstream) : PGBD5 (17940 downstream)																							TCTCATGCCTGGTGGGGGCAG	0.428													4	2	---	---	---	---	
EGLN1	54583	broad.mit.edu	37	1	231541912	231541912	+	Intron	DEL	A	-	-	rs66466464		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231541912delA	uc001huv.2	-						EGLN1_uc001huu.3_Intron	NM_022051	NP_071334	Q9GZT9	EGLN1_HUMAN	egl nine homolog 1						negative regulation of sequence-specific DNA binding transcription factor activity|oxygen homeostasis|response to hypoxia	cytosol	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptidyl-proline dioxygenase activity|protein binding|zinc ion binding				0		Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244)			Vitamin C(DB00126)	actccgtctcaaaaaaaaaaa	0.179													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	233643245	233643246	+	IGR	INS	-	G	G	rs141916646	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233643245_233643246insG								KIAA1804 (122352 upstream) : KCNK1 (106504 downstream)																							CCTCTGCTGAAGTGCCTCCTAA	0.545													4	2	---	---	---	---	
ERO1LB	56605	broad.mit.edu	37	1	236426544	236426546	+	Intron	DEL	TTG	-	-	rs143552863		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236426544_236426546delTTG	uc001hxt.2	-						ERO1LB_uc010pxt.1_Intron	NM_019891	NP_063944	Q86YB8	ERO1B_HUMAN	endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			AACTTCAGTTttgttgttgttgt	0.064													4	2	---	---	---	---	
WDR64	128025	broad.mit.edu	37	1	241820184	241820185	+	Intron	INS	-	TA	TA	rs150831442	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241820184_241820185insTA	uc001hze.1	+									B1ANS9	WDR64_HUMAN	RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			gtgtgtgtgtgtgtgtgtgtgt	0.000													2	4	---	---	---	---	
C1orf101	257044	broad.mit.edu	37	1	244774057	244774057	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244774057delT	uc001iam.2	+						C1orf101_uc001ial.2_Intron|C1orf101_uc010pym.1_Intron|C1orf101_uc010pyn.1_Intron	NM_001130957	NP_001124429	Q5SY80	CA101_HUMAN	hypothetical protein LOC257044 isoform 1							integral to membrane				ovary(1)|breast(1)	2	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			ttttctttccttttttttttt	0.000													4	2	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245422036	245422036	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245422036delG	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GGCAGCTACAGGAGCACAGCA	0.592													4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246594438	246594438	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246594438delA	uc001ibl.2	-							NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		GATAAACAGGAAAAATCACCA	0.294													4	2	---	---	---	---	
AHCTF1	25909	broad.mit.edu	37	1	247018264	247018265	+	Intron	INS	-	TTTAC	TTTAC	rs140145476	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247018264_247018265insTTTAC	uc001ibu.1	-						AHCTF1_uc001ibv.1_Intron|AHCTF1_uc009xgs.1_Intron|AHCTF1_uc001ibw.1_Intron	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS						cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GTGATCGGCTTTTTACATGTTA	0.386													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	248593686	248593687	+	IGR	INS	-	T	T	rs138384377	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248593686_248593687insT								OR2T1 (23282 upstream) : OR2T2 (22412 downstream)																							gttttgttttgtttttttttct	0.000													4	2	---	---	---	---	
SNTG2	54221	broad.mit.edu	37	2	978737	978738	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:978737_978738insA	uc002qwq.2	+						SNTG2_uc002qwp.2_Intron|SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		TGCAGAGGTGGTGTCAGGATGA	0.540													4	2	---	---	---	---	
SNTG2	54221	broad.mit.edu	37	2	1217296	1217297	+	Intron	INS	-	CT	CT			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1217296_1217297insCT	uc002qwq.2	+						SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		tctgtctctgcctctctgtgtc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	1599527	1599528	+	IGR	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1599527_1599528delAC								TPO (53029 upstream) : PXDN (36132 downstream)																							cacagatcagacacacacacgc	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2591430	2591431	+	IGR	DEL	TG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2591430_2591431delTG								MYT1L (256385 upstream) : TSSC1 (601310 downstream)																							tgtgtgtgtctgtgtgtgtgtg	0.223													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2754254	2754255	+	IGR	DEL	GT	-	-	rs148194828		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2754254_2754255delGT								MYT1L (419209 upstream) : TSSC1 (438486 downstream)																							TATAtgtgtggtgtgtgtgtgt	0.243													2	5	---	---	---	---	
TTC15	51112	broad.mit.edu	37	2	3451222	3451222	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3451222delT	uc002qxm.1	+						TTC15_uc002qxn.1_Intron|TTC15_uc010ewm.1_Intron	NM_016030	NP_057114	Q8WVT3	TTC15_HUMAN	tetratricopeptide repeat domain 15								binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)		tgtcacatggtgagaaagaca	0.000													4	2	---	---	---	---	
ALLC	55821	broad.mit.edu	37	2	3711175	3711175	+	Intron	DEL	A	-	-	rs112720848		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3711175delA	uc010ewt.2	+							NM_018436	NP_060906	Q8N6M5	ALLC_HUMAN	allantoicase isoform a								allantoicase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		taaaagttggaaaaaaaaaaa	0.199										HNSCC(21;0.051)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4520398	4520400	+	IGR	DEL	CTG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4520398_4520400delCTG								ALLC (770140 upstream) : None (None downstream)																							GTTAGAAATTCTGTGAGTTCCTG	0.320													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4711400	4711400	+	IGR	DEL	C	-	-	rs699551	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4711400delC								ALLC (961142 upstream) : None (None downstream)																							TGAAGACTAACCTTTTCAAAT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6551955	6551956	+	IGR	INS	-	TCTC	TCTC	rs146914337	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6551955_6551956insTCTC								LOC400940 (423591 upstream) : CMPK2 (428547 downstream)																							AACTGGTCAGGTTGCTTGTAAC	0.485													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10224723	10224723	+	IGR	DEL	G	-	-	rs112044382		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10224723delG								CYS1 (4185 upstream) : RRM2 (38012 downstream)																							GTTGTAAGAAGGAGGGAAATC	0.443													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12196289	12196289	+	Intron	DEL	T	-	-	rs70955825		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12196289delT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		cccaccctaattgactttatc	0.000													3	6	---	---	---	---	
C2orf43	60526	broad.mit.edu	37	2	20935164	20935164	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20935164delG	uc002rec.2	-						C2orf43_uc002rea.1_Intron|C2orf43_uc002reb.1_Intron|C2orf43_uc010yka.1_Intron|C2orf43_uc010ykb.1_Intron|C2orf43_uc010ykc.1_Intron|C2orf43_uc010ykd.1_Intron|C2orf43_uc010yke.1_Intron|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744	Q9H6V9	CB043_HUMAN	hypothetical protein LOC60526												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ttttattgttggttccatcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	22133585	22133585	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22133585delA								APOB (866640 upstream) : None (None downstream)																							CAAGACTGTCAAATCTTCCCC	0.343													4	2	---	---	---	---	
GTF3C2	2976	broad.mit.edu	37	2	27563759	27563760	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27563759_27563760insT	uc002rjv.1	-						GTF3C2_uc002rju.1_Intron|GTF3C2_uc002rjw.1_Intron|GTF3C2_uc010eyz.1_Intron	NM_001521	NP_001512	Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide							transcription factor TFIIIC complex				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tcccaaagtgctgggattacag	0.104													0	7	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28261801	28261801	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28261801delT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					ggtagttctatttttagttct	0.000													4	2	---	---	---	---	
LCLAT1	253558	broad.mit.edu	37	2	30674938	30674940	+	Intron	DEL	TGG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30674938_30674940delTGG	uc002rnj.2	+						LCLAT1_uc010ymp.1_Intron|LCLAT1_uc002rnk.1_Intron|LCLAT1_uc002rnl.2_Intron|LCLAT1_uc010ymq.1_Intron	NM_182551	NP_872357	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1 isoform 1						multicellular organismal development|phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity			ovary(2)	2						tactctgggttggtggtggtggt	0.000													4	2	---	---	---	---	
LCLAT1	253558	broad.mit.edu	37	2	30764706	30764707	+	Intron	INS	-	T	T	rs142665752	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30764706_30764707insT	uc002rnj.2	+						LCLAT1_uc010ymp.1_Intron|LCLAT1_uc002rnk.1_Intron|LCLAT1_uc002rnl.2_Intron|LCLAT1_uc010ymq.1_Intron	NM_182551	NP_872357	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1 isoform 1						multicellular organismal development|phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity			ovary(2)	2						taccagtagtgtaagagagagt	0.064													4	3	---	---	---	---	
CRIM1	51232	broad.mit.edu	37	2	36679077	36679077	+	Intron	DEL	T	-	-	rs11340248		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36679077delT	uc002rpd.2	+							NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1 precursor						nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				ATCCATGTGCTTTTTACCATT	0.358													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37983016	37983020	+	IGR	DEL	TTGAG	-	-	rs146470126		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37983016_37983020delTTGAG								CDC42EP3 (83690 upstream) : FAM82A1 (169442 downstream)																							atgattcactttgagttaagttttg	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38608607	38608609	+	IGR	DEL	AAA	-	-	rs6146721		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38608607_38608609delAAA								ATL2 (4175 upstream) : HNRPLL (181719 downstream)																							tccatctcggaaaaaaaaaaaaa	0.177													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38623545	38623546	+	IGR	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38623545_38623546delAC								ATL2 (19113 upstream) : HNRPLL (166782 downstream)																							CTACCCACAGACACACACACAT	0.376													4	2	---	---	---	---	
GALM	130589	broad.mit.edu	37	2	38956002	38956003	+	Intron	INS	-	T	T	rs146925813	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38956002_38956003insT	uc002rqy.2	+							NM_138801	NP_620156	Q96C23	GALM_HUMAN	galactose mutarotase						hexose metabolic process	cytoplasm	aldose 1-epimerase activity|carbohydrate binding				0		all_hematologic(82;0.248)				CTGGCTGTTACTACTCCTGGGT	0.470													1	8	---	---	---	---	
CDKL4	344387	broad.mit.edu	37	2	39450754	39450754	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39450754delA	uc002rrm.2	-						CDKL4_uc010fal.1_Intron	NM_001009565	NP_001009565	Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4							cytoplasm	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1		all_hematologic(82;0.248)				TTCTGTCTTCAAAAAAAAAAA	0.040													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42339276	42339277	+	IGR	INS	-	CA	CA	rs67451952		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42339276_42339277insCA								PKDCC (53610 upstream) : EML4 (57213 downstream)																							acatatgcgcgcacacacacac	0.292													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	42617810	42617810	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42617810delT								COX7A2L (21660 upstream) : KCNG3 (51349 downstream)																							ATTCCTCACCTTTCTCAGAAC	0.373													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46190973	46190975	+	Intron	DEL	TGC	-	-	rs60644906		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46190973_46190975delTGC	uc002rut.2	+							NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			AATTAGCAAGTGCTCAAAACTGC	0.448													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	48234415	48234416	+	IGR	DEL	TT	-	-	rs144418174		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48234415_48234416delTT								FBXO11 (101601 upstream) : FOXN2 (307379 downstream)																							ttccccctcattttttttttac	0.109													0	6	---	---	---	---	
LHCGR	3973	broad.mit.edu	37	2	48979669	48979669	+	Intron	DEL	T	-	-	rs11327396		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48979669delT	uc002rwu.3	-						LHCGR_uc002rwv.2_Intron	NM_000233	NP_000224	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor						male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|lung(2)|breast(2)|skin(1)	8		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	TTAAGCTTTCTTTTTTTTTTT	0.368									Familial_Male-Limited_Precocious_Puberty				3	4	---	---	---	---	
SPTBN1	6711	broad.mit.edu	37	2	54895818	54895818	+	3'UTR	DEL	T	-	-	rs78796985		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54895818delT	uc002rxu.2	+	36					SPTBN1_uc010you.1_3'UTR	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			ATGTGGTTGattttttttttt	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57789331	57789331	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57789331delT								None (None upstream) : VRK2 (345455 downstream)																							GCACTGTGTGTTTTCATTTTA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60153386	60153386	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60153386delG								None (None upstream) : BCL11A (524917 downstream)																							AGAAGTGGGAGGTGAGGTCTG	0.398													4	2	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61583634	61583635	+	Intron	DEL	AT	-	-	rs70963416	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61583634_61583635delAT	uc002sbe.2	-							NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			acacacacacatacacacacac	0.010													5	3	---	---	---	---	
ACTR2	10097	broad.mit.edu	37	2	65454317	65454318	+	5'Flank	INS	-	GAA	GAA	rs143156954	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65454317_65454318insGAA	uc002sdq.2	+						ACTR2_uc010yqf.1_5'Flank|ACTR2_uc002sdp.2_5'Flank|ACTR2_uc010yqg.1_5'Flank	NM_005722	NP_005713	P61160	ARP2_HUMAN	actin-related protein 2 isoform b						cellular component movement	Arp2/3 protein complex|cell projection|cytoplasm	actin binding|ATP binding				0						TGGGACTACTGGAAGGAGGCGG	0.411													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	69195175	69195182	+	IGR	DEL	AGGAAGGA	-	-	rs71397315		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69195175_69195182delAGGAAGGA								GKN2 (15073 upstream) : GKN1 (6523 downstream)																							AGAGAGAAAGaggaaggaaggaaggaag	0.120													5	3	---	---	---	---	
ANTXR1	84168	broad.mit.edu	37	2	69428976	69428976	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69428976delG	uc002sfg.2	+							NM_032208	NP_115584	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1 isoform 1 precursor						actin cytoskeleton reorganization|substrate adhesion-dependent cell spreading	filopodium membrane|integral to membrane|lamellipodium membrane	actin filament binding|collagen binding|metal ion binding|protein binding|transmembrane receptor activity			ovary(2)|skin(2)	4						cagtgcctgtgggacatccaa	0.040									Familial_Infantile_Hemangioma				4	2	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71845519	71845520	+	Intron	DEL	GT	-	-	rs138739904	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71845519_71845520delGT	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						ggtagaggtggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
EXOC6B	23233	broad.mit.edu	37	2	72761330	72761330	+	Intron	DEL	A	-	-	rs78415868		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72761330delA	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						GGGTCAAACCAAAAAAAAAAT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	81825079	81825079	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81825079delT								CTNNA2 (949175 upstream) : None (None downstream)																							GGGAACATGGTTTTGGATGAC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82147290	82147290	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82147290delT								None (None upstream) : None (None downstream)																							gttcaattccttgttaacttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82211229	82211230	+	IGR	INS	-	GT	GT	rs150552142	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82211229_82211230insGT								None (None upstream) : None (None downstream)																							TAGATATTCTAgtgtgtgtgtg	0.153													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82648020	82648021	+	IGR	DEL	AC	-	-	rs112152645		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82648020_82648021delAC								None (None upstream) : None (None downstream)																							acacacagaaacacacacacac	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85667623	85667624	+	IGR	INS	-	TT	TT	rs149457005	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85667623_85667624insTT								SH2D6 (3473 upstream) : MAT2A (98664 downstream)																							taatttttgtattttttttagt	0.000													4	3	---	---	---	---	
VPS24	51652	broad.mit.edu	37	2	86858475	86858476	+	Intron	DEL	AA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86858475_86858476delAA	uc010ytl.1	-							NM_001005753	NP_001005753	Q9Y3E7	CHMP3_HUMAN	vacuolar protein sorting 24 isoform 2						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1						tctcaaaaagaaaaaaaaaaaG	0.139													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87586723	87586724	+	Intron	INS	-	ATG	ATG	rs150079111	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87586723_87586724insATG	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						ggagagtggaaatgagatgaaa	0.015													5	4	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87587193	87587194	+	Intron	INS	-	GATTG	GATTG			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87587193_87587194insGATTG	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						tgagatgatgagatgagatgaa	0.000													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87629598	87629598	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87629598delA	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						tccatctcagaaaaaaaaaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89860599	89860603	+	IGR	DEL	ATTCC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89860599_89860603delATTCC								FLJ40330 (754474 upstream) : None (None downstream)																							attgcattctattccattccattcc	0.000													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90451097	90451097	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90451097delT	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		cttggaaatatttttttcata	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90485492	90485496	+	IGR	DEL	CTGAC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90485492_90485496delCTGAC								None (None upstream) : None (None downstream)																							gctggcttggctgactggcttggct	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91798819	91798820	+	IGR	INS	-	AA	AA	rs71204456		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91798819_91798820insAA								None (None upstream) : LOC654342 (6372 downstream)																							aaaaacaaaCCCCCCCCCCATA	0.114													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91944753	91944754	+	IGR	DEL	GT	-	-	rs62142720	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91944753_91944754delGT								LOC654342 (96778 upstream) : GGT8P (18614 downstream)																							gtgtgtttgcgtgtgtgtgtgt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92044379	92044380	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92044379_92044380insA								GGT8P (74226 upstream) : FKSG73 (84779 downstream)																							gaccaagaaagaaaagaaatca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92053988	92053988	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92053988delA								GGT8P (83835 upstream) : FKSG73 (75171 downstream)																							caaaaaaaccaaaactataga	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92095670	92095670	+	IGR	DEL	G	-	-	rs112963197		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92095670delG								GGT8P (125517 upstream) : FKSG73 (33489 downstream)																							Aagaacaatagggaatcctcc	0.100													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92188404	92188405	+	IGR	INS	-	G	G	rs150975516		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92188404_92188405insG								FKSG73 (57910 upstream) : None (None downstream)																							AAAGTCtttatttttttttttt	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106105724	106105724	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106105724delA								FHL2 (50494 upstream) : NCK2 (255630 downstream)																							ggaaggaaggaaaggaaggaa	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106126541	106126542	+	IGR	INS	-	CGTAGTTCTCT	CGTAGTTCTCT			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106126541_106126542insCGTAGTTCTCT								FHL2 (71311 upstream) : NCK2 (234812 downstream)																							TATGTCTTTCACCTAGTTCTCT	0.262													4	2	---	---	---	---	
UXS1	80146	broad.mit.edu	37	2	106782272	106782273	+	Intron	INS	-	G	G	rs142942979	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106782272_106782273insG	uc002tdm.2	-						UXS1_uc002tdn.2_Intron|UXS1_uc002tdo.2_Intron|UXS1_uc010ywh.1_Intron	NM_025076	NP_079352	Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1						cellular metabolic process	Golgi cisterna membrane|integral to membrane	coenzyme binding|UDP-glucuronate decarboxylase activity			ovary(2)	2						CAAGGAGGGAAGCGGGGGTGGC	0.441													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	111926790	111926791	+	IGR	DEL	GT	-	-	rs72091170		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111926790_111926791delGT								BCL2L11 (768 upstream) : LOC541471 (38568 downstream)																							TTAATCTGCAgtgtgtgtgtgt	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113449450	113449450	+	IGR	DEL	T	-	-	rs111373542		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113449450delT								SLC20A1 (28052 upstream) : CKAP2L (45994 downstream)																							TGATTtcttcttttttttttt	0.184													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119505887	119505887	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119505887delG								INSIG2 (638291 upstream) : EN1 (93861 downstream)																							GGGTGAAGGAGGGGACaatat	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122591278	122591279	+	IGR	INS	-	T	T	rs113949175		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122591278_122591279insT								TSN (65852 upstream) : None (None downstream)																							TCAAATGCATGttttttttttt	0.248													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122981767	122981768	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122981767_122981768insT								TSN (456341 upstream) : None (None downstream)																							gtttttgataattttttttgaa	0.030													4	2	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	125427793	125427800	+	Intron	DEL	TCTTTCTT	-	-	rs78152095		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125427793_125427800delTCTTTCTT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		cttctttccctctttctttctttctttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126131730	126131731	+	IGR	INS	-	A	A	rs78799773		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126131730_126131731insA								CNTNAP5 (458869 upstream) : None (None downstream)																							gactccgtctcaaaaaaaaaaa	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129535593	129535593	+	IGR	DEL	C	-	-	rs5834228		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129535593delC								HS6ST1 (459422 upstream) : None (None downstream)																							ATAAATACCTCTGGGGGGACA	0.527													4	2	---	---	---	---	
TUBA3D	113457	broad.mit.edu	37	2	132238484	132238484	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132238484delT	uc002tsu.3	+							NM_080386	NP_525125	Q13748	TBA3C_HUMAN	tubulin, alpha 3d						'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(221;0.13)		CAGTGAtttcttttttttttt	0.219													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132779425	132779425	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132779425delT								C2orf27B (220191 upstream) : NCRNA00164 (125739 downstream)																							AACAAGTATCTTTTAAAAACA	0.418													8	5	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	132980959	132980960	+	Intron	DEL	TT	-	-	rs112386828		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132980959_132980960delTT	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						tgaaacactctttttgtagaat	0.000													5	3	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	133008670	133008670	+	Intron	DEL	T	-	-	rs111946818		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133008670delT	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						TAATCTTCAGTTTTTTTCCTC	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133021900	133021900	+	IGR	DEL	C	-	-	rs75477623	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133021900delC								NCRNA00164 (6358 upstream) : GPR39 (152247 downstream)																							ATAGTGCTAGCTTCTGCTGAC	0.318													13	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133062601	133062604	+	Intron	DEL	CTCA	-	-	rs4063334	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133062601_133062604delCTCA	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		AGCGCTTGGGCTCAGTTTGGGGAG	0.583													6	5	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	134016321	134016322	+	Intron	INS	-	A	A	rs77114113		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134016321_134016322insA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002ttt.1_Intron|NCKAP5_uc002tts.1_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						ctgtctcaattaaaaaaaaaaa	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134583143	134583143	+	IGR	DEL	G	-	-	rs146663827		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134583143delG								NCKAP5 (257112 upstream) : MGAT5 (428687 downstream)																							ACATCATGCAGGAAAAAAAGG	0.433													4	2	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	138346051	138346052	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138346051_138346052insT	uc002tva.1	+						THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		ATTTTTCAGTGTTTTTTTTTTT	0.198													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	139987796	139987796	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139987796delG								NXPH2 (449985 upstream) : None (None downstream)																							TTCTGCCTCTGGACACCCTAG	0.269													4	2	---	---	---	---	
KYNU	8942	broad.mit.edu	37	2	143700506	143700506	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143700506delC	uc002tvl.2	+						KYNU_uc002tvk.2_Intron|KYNU_uc010fnm.2_Intron	NM_003937	NP_003928	Q16719	KYNU_HUMAN	kynureninase (L-kynurenine hydrolase) isoform a						anthranilate metabolic process|NAD biosynthetic process|quinolinate biosynthetic process|response to interferon-gamma|response to vitamin B6	cytosol|mitochondrion|soluble fraction	kynureninase activity|protein homodimerization activity			skin(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.072)	L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)	aggcattcttcccttaccagc	0.000													4	2	---	---	---	---	
FMNL2	114793	broad.mit.edu	37	2	153394405	153394406	+	Intron	INS	-	AC	AC	rs151210210	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153394405_153394406insAC	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						ACCTTacacatacacacacaca	0.158													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	154149516	154149516	+	IGR	DEL	T	-	-	rs10177602	byFrequency	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154149516delT								ARL6IP6 (531749 upstream) : RPRM (184336 downstream)																							TTTGTTAAGGTTTTTTTCCCT	0.343													4	2	---	---	---	---	
GPD2	2820	broad.mit.edu	37	2	157390763	157390764	+	Intron	INS	-	CTT	CTT	rs74905756		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157390763_157390764insCTT	uc002tzf.3	+						GPD2_uc010zch.1_Intron|GPD2_uc002tzd.3_Intron|GPD2_uc002tze.1_Intron	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,						cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1						tctcttctctcctctgctgtgc	0.000													1	5	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	160060227	160060228	+	Intron	INS	-	C	C	rs150932397	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160060227_160060228insC	uc002uag.2	+						TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron|TANC1_uc010fon.2_Intron	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						acaggcatgagccaccacacct	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	160769824	160769824	+	IGR	DEL	T	-	-	rs5835775		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160769824delT								LY75 (8562 upstream) : PLA2R1 (28188 downstream)																							agccaatcTCTTAAGTGGCTT	0.234													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	161606723	161606726	+	IGR	DEL	CTGT	-	-	rs113182188		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161606723_161606726delCTGT								RBMS1 (256405 upstream) : TANK (386740 downstream)																							ATGGGAATAActgtctgtctgtct	0.250													4	2	---	---	---	---	
FIGN	55137	broad.mit.edu	37	2	164514010	164514011	+	Intron	INS	-	TGTG	TGTG	rs139473125	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164514010_164514011insTGTG	uc002uck.1	-							NM_018086	NP_060556	Q5HY92	FIGN_HUMAN	fidgetin							nuclear matrix	ATP binding|nucleoside-triphosphatase activity			large_intestine(2)|ovary(1)|skin(1)	4						CAGAGGGAGTCtgtgtgtgtgt	0.356													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	166580960	166580960	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166580960delT								CSRNP3 (43757 upstream) : GALNT3 (23353 downstream)																							AAAAATACAATTTTTTTTTTC	0.348													3	3	---	---	---	---	
ABCB11	8647	broad.mit.edu	37	2	169804452	169804452	+	Intron	DEL	T	-	-	rs4148800		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169804452delT	uc002ueo.1	-						ABCB11_uc010zda.1_Intron|ABCB11_uc010zdb.1_Intron	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),						bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)	GTTGAATCTCTTTTTTTTTTT	0.229													4	2	---	---	---	---	
SP3	6670	broad.mit.edu	37	2	174828742	174828744	+	Intron	DEL	CTC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174828742_174828744delCTC	uc002uig.2	-						SP3_uc002uie.2_5'UTR|SP3_uc002uif.2_Intron|SP3_uc010zel.1_Intron	NM_003111	NP_003102	Q02447	SP3_HUMAN	Sp3 transcription factor isoform 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	protein binding|zinc ion binding		EWSR1/SP3(3)	soft_tissue(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.185)			AGCCCGCGCTctcctcctcctcc	0.532													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	176099231	176099231	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176099231delC								ATP5G3 (52741 upstream) : KIAA1715 (691179 downstream)																							AACAAGGAGGCCATGAGAAAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	186133641	186133652	+	IGR	DEL	CTTCCTTCCTTG	-	-	rs4667022		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186133641_186133652delCTTCCTTCCTTG								ZNF804A (329429 upstream) : None (None downstream)																							ttcttccttccttccttccttgcttccttcct	0.028													4	5	---	---	---	---	
SLC40A1	30061	broad.mit.edu	37	2	190426410	190426410	+	3'UTR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190426410delC	uc002uqp.3	-	8						NM_014585	NP_055400	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated						anatomical structure morphogenesis|cellular iron ion homeostasis	cytoplasm|integral to plasma membrane	iron ion transmembrane transporter activity|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			AATTTTTTTTCCATGCCTCAA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	198247169	198247169	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198247169delA								ANKRD44 (71674 upstream) : SF3B1 (9531 downstream)																							actccgtctcaaaaaaaaaaa	0.194													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	212175585	212175585	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212175585delT								CPS1 (631756 upstream) : ERBB4 (64857 downstream)																							tcccttcacctgtgcttttat	0.000													4	2	---	---	---	---	
ERBB4	2066	broad.mit.edu	37	2	212708140	212708141	+	Intron	INS	-	CA	CA	rs147810608	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212708140_212708141insCA	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		GCGTGCGTGTGcacacacacac	0.386										TSP Lung(8;0.080)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	217914432	217914432	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217914432delG								TNP1 (189650 upstream) : DIRC3 (234316 downstream)																							AAAGGGGGAAGGAGTGGGACA	0.458													3	5	---	---	---	---	
NHEJ1	79840	broad.mit.edu	37	2	220006101	220006102	+	Intron	INS	-	A	A	rs78514937		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220006101_220006102insA	uc002vjp.3	-						NHEJ1_uc002vjq.3_Intron	NM_024782	NP_079058	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1						B cell differentiation|central nervous system development|DNA recombination|double-strand break repair via nonhomologous end joining|positive regulation of ligase activity|response to ionizing radiation|T cell differentiation	nonhomologous end joining complex|nucleus	DNA binding|identical protein binding			lung(1)	1		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		gacttggtctcaaaaaaaaaaa	0.000								Direct_reversal_of_damage|NHEJ					3	3	---	---	---	---	
AP1S3	130340	broad.mit.edu	37	2	224658663	224658663	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224658663delC	uc010fwx.1	-						AP1S3_uc002vnn.2_Intron|AP1S3_uc010fww.2_Intron|AP1S3_uc002vno.2_Intron	NM_001039569	NP_001034658	Q96PC3	AP1S3_HUMAN	adaptor-related protein complex 1, sigma 3						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane coat	protein transporter activity				0		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)		gcccagccTACAATTTTTAAA	0.164													4	2	---	---	---	---	
FBXO36	130888	broad.mit.edu	37	2	230840186	230840186	+	Intron	DEL	T	-	-	rs67276148		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230840186delT	uc002vqa.2	+						FBXO36_uc002vpz.2_Intron|FBXO36_uc002vqb.2_Intron|FBXO36_uc010fxi.1_Intron|FBXO36_uc002vqc.2_Intron	NM_174899	NP_777559	Q8NEA4	FBX36_HUMAN	F-box protein 36											ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		ACCTGATGGAttttttttttt	0.194													5	3	---	---	---	---	
IQCA1	79781	broad.mit.edu	37	2	237245218	237245219	+	Intron	INS	-	T	T	rs140848387	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237245218_237245219insT	uc002vvz.1	-						IQCA1_uc002vwb.2_Intron|IQCA1_uc002vwa.1_Intron|IQCA1_uc010zni.1_Intron	NM_024726	NP_079002	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1								ATP binding			ovary(1)	1						TCCCAACACCCTCCCCAGAGCC	0.520													5	3	---	---	---	---	
RAB17	64284	broad.mit.edu	37	2	238496476	238496476	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238496476delA	uc002vwz.1	-						RAB17_uc002vxa.1_Intron|RAB17_uc002vxb.1_Intron	NM_022449	NP_071894	Q9H0T7	RAB17_HUMAN	RAB17, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|protein binding				0		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)		TGTGTTTCTTaaaaaaaaaaa	0.095													4	2	---	---	---	---	
HDLBP	3069	broad.mit.edu	37	2	242213268	242213268	+	5'Flank	DEL	T	-	-	rs111935616		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242213268delT	uc002waz.2	-						HDLBP_uc002wba.2_Intron|HDLBP_uc002wbb.2_5'Flank|HDLBP_uc010fzn.1_5'Flank	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein						cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		ATCAGACGTGTTTTTTTTTTT	0.383													4	3	---	---	---	---	
CNTN6	27255	broad.mit.edu	37	3	1444398	1444398	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1444398delA	uc003boz.2	+						CNTN6_uc011asj.1_Intron|CNTN6_uc003bpa.2_Intron	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor						axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AGAGAACAGGAAAAAAAATCT	0.274													4	2	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2626583	2626586	+	Intron	DEL	AGGT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2626583_2626586delAGGT	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		cgaagtaggaaggtaggtaggtag	0.172													4	2	---	---	---	---	
SUMF1	285362	broad.mit.edu	37	3	4263099	4263100	+	Intron	DEL	GT	-	-	rs72052515		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4263099_4263100delGT	uc003bps.1	-							NM_182760		Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		GTTTTTTGGGgtgtgtgtgtgt	0.277													3	3	---	---	---	---	
FBLN2	2199	broad.mit.edu	37	3	13581628	13581629	+	Intron	INS	-	G	G	rs140695523	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13581628_13581629insG	uc011auz.1	+							NM_001998	NP_001989	P98095	FBLN2_HUMAN	fibulin 2 isoform b precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			TTGAAGCACCTGGGGGAAAGCG	0.604													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	23081881	23081881	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23081881delA								ZNF385D (667758 upstream) : UBE2E2 (162772 downstream)																							tttctgtctcaaaaaaaaaaa	0.134													4	2	---	---	---	---	
NEK10	152110	broad.mit.edu	37	3	27158433	27158433	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27158433delT	uc010hfk.2	-						NEK10_uc010hfj.2_Intron			Q6ZWH5	NEK10_HUMAN	RecName: Full=Serine/threonine-protein kinase Nek10;          EC=2.7.11.1; AltName: Full=NimA-related protein kinase 10;								ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13						ccagcatgcattagctattta	0.000													4	2	---	---	---	---	
GADL1	339896	broad.mit.edu	37	3	30799908	30799909	+	Intron	INS	-	TTT	TTT	rs140177086	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30799908_30799909insTTT	uc003cep.2	-							NM_207359	NP_997242	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)	TGCCTTTTATCTTTCCCGTCTT	0.441													4	2	---	---	---	---	
GADL1	339896	broad.mit.edu	37	3	30825141	30825143	+	Intron	DEL	AAG	-	-	rs144129799		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30825141_30825143delAAG	uc003cep.2	-							NM_207359	NP_997242	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)	GTGTAATAAAAAGAAAAGCGGCA	0.335													4	2	---	---	---	---	
ITGA9	3680	broad.mit.edu	37	3	37547130	37547130	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37547130delG	uc003chd.2	+						ITGA9_uc003chc.2_Intron	NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		tctgggtggtggttgcatggc	0.025													4	2	---	---	---	---	
SCN10A	6336	broad.mit.edu	37	3	38758623	38758623	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38758623delG	uc003ciq.2	-							NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha						sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	ATAGATGGAAGGAAGTTTAGA	0.149													4	2	---	---	---	---	
ZNF621	285268	broad.mit.edu	37	3	40564593	40564593	+	5'Flank	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40564593delT	uc003ckm.2	+						ZNF621_uc003ckn.2_5'Flank|ZNF621_uc003cko.2_5'Flank|ZNF621_uc011aze.1_5'Flank	NM_001098414	NP_001091884	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)		ccacagaaccttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	40759979	40759979	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40759979delT								ZNF621 (178936 upstream) : CTNNB1 (476422 downstream)																							ATAGGCAGACTTTTTTTTTTG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	41059097	41059098	+	IGR	INS	-	ACG	ACG	rs138487348	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41059097_41059098insACG								ZNF621 (478054 upstream) : CTNNB1 (177303 downstream)																							gatgattatactgtgctgtccg	0.000													2	4	---	---	---	---	
ZNF445	353274	broad.mit.edu	37	3	44513352	44513353	+	Intron	INS	-	A	A	rs138407033	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44513352_44513353insA	uc003cnf.2	-						ZNF445_uc011azw.1_Intron	NM_181489	NP_852466	P59923	ZN445_HUMAN	zinc finger protein 445						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		GTATTCAAAGGAAAAAAAAAAG	0.406													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	46140733	46140733	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46140733delC								XCR1 (71754 upstream) : CCR3 (64363 downstream)																							tgcctccacacccagctaact	0.000													4	2	---	---	---	---	
BSN	8927	broad.mit.edu	37	3	49616588	49616588	+	Intron	DEL	T	-	-	rs111577896		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49616588delT	uc003cxe.3	+							NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein						synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		gcctggctaattttttttttt	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	52076402	52076403	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52076402_52076403insA								RPL29 (46444 upstream) : DUSP7 (6536 downstream)																							aggaaggaaggaaggaaggaag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	55110616	55110616	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55110616delG								CACNA2D3 (2034 upstream) : WNT5A (389128 downstream)																							GTCCACAGcaggggttctctg	0.129													4	2	---	---	---	---	
ARF4	378	broad.mit.edu	37	3	57586077	57586080	+	5'Flank	DEL	TTTC	-	-	rs112082137		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57586077_57586080delTTTC	uc003dix.3	-						ARF4_uc003diy.3_5'Flank|ARF4_uc010hnd.2_5'Flank|ARF4_uc003diz.3_5'Flank	NM_001660	NP_001651	P18085	ARF4_HUMAN	ADP-ribosylation factor 4						protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	Golgi apparatus	GTP binding|GTPase activity			upper_aerodigestive_tract(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0449)|Kidney(284;0.0561)		ctcttttctttttctttctttcct	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	63256743	63256744	+	IGR	INS	-	T	T	rs148523759	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63256743_63256744insT								LOC285401 (146008 upstream) : SYNPR (7170 downstream)																							TACCTTCTCTCTTTTAAGTGTT	0.188													3	4	---	---	---	---	
FOXP1	27086	broad.mit.edu	37	3	71006305	71006306	+	3'UTR	INS	-	T	T	rs71869606		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71006305_71006306insT	uc003dol.2	-	17					FOXP1_uc003dom.2_3'UTR|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_3'UTR|FOXP1_uc003dop.2_3'UTR|FOXP1_uc003doi.2_3'UTR|FOXP1_uc003doj.2_3'UTR|FOXP1_uc003dok.2_3'UTR	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GCATACATTCATTTTTTTTTTG	0.347			T	PAX5	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	87936166	87936166	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87936166delA								POU1F1 (610429 upstream) : HTR1F (95560 downstream)																							ccacattgccaagacaaccct	0.000													0	6	---	---	---	---	
ABI3BP	25890	broad.mit.edu	37	3	100562387	100562388	+	Intron	DEL	GA	-	-	rs57891258		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100562387_100562388delGA	uc003dun.2	-						ABI3BP_uc003duo.2_Intron|ABI3BP_uc011bhd.1_Intron|ABI3BP_uc003dum.2_Intron	NM_015429	NP_056244	Q7Z7G0	TARSH_HUMAN	ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4						gtgtgtgtgtgagagagagaga	0.149													3	3	---	---	---	---	
BOC	91653	broad.mit.edu	37	3	112979753	112979753	+	Intron	DEL	C	-	-	rs71319363		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112979753delC	uc003dzx.2	+						BOC_uc010hqi.2_Intron|BOC_uc003dzy.2_Intron|BOC_uc003dzz.2_Intron	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor						cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)			ccaaaaccatcccccccagtc	0.030													4	2	---	---	---	---	
ZBTB20	26137	broad.mit.edu	37	3	114229345	114229345	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114229345delT	uc003ebj.2	-						ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		CACACTGAGCTTTTTTTTTTT	0.453													4	2	---	---	---	---	
ZBTB20	26137	broad.mit.edu	37	3	114369308	114369308	+	Intron	DEL	A	-	-	rs63738460		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114369308delA	uc003ebk.2	-						ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		ATCTATTTACAAAAAAATATT	0.318													2	4	---	---	---	---	
LSAMP	4045	broad.mit.edu	37	3	115596101	115596102	+	Intron	INS	-	T	T	rs138898769	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115596101_115596102insT	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		AAAGCTCCCTGTTTTTTTTTTC	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116412839	116412840	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116412839_116412840insA								LSAMP (888821 upstream) : LOC285194 (15795 downstream)																							ATGGCCTGCTGAAAAAAAAAGA	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117087005	117087008	+	IGR	DEL	CACA	-	-	rs57266851		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117087005_117087008delCACA								LOC285194 (651120 upstream) : None (None downstream)																							cacacacgtgcacacacacacaca	0.142													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117111298	117111299	+	IGR	DEL	CT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117111298_117111299delCT								LOC285194 (675413 upstream) : None (None downstream)																							ctctctgttgctctctctctct	0.248													3	3	---	---	---	---	
LRRC58	116064	broad.mit.edu	37	3	120058124	120058124	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120058124delC	uc003edr.2	-							NM_001099678	NP_001093148	Q96CX6	LRC58_HUMAN	leucine rich repeat containing 58												0				GBM - Glioblastoma multiforme(114;0.147)		CAAACACATACCCATGCTCTC	0.363													4	2	---	---	---	---	
FSTL1	11167	broad.mit.edu	37	3	120142236	120142237	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120142236_120142237insA	uc003eds.2	-						FSTL1_uc011bjh.1_Intron|FSTL1_uc010hrb.2_Intron	NM_007085	NP_009016	Q12841	FSTL1_HUMAN	follistatin-like 1 precursor						BMP signaling pathway	extracellular space	calcium ion binding|heparin binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.189)		CTGTGTTCTGCAATGGTCTTGT	0.431													4	2	---	---	---	---	
POLQ	10721	broad.mit.edu	37	3	121171341	121171341	+	Intron	DEL	T	-	-	rs113058029		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121171341delT	uc003eee.3	-						POLQ_uc003eed.2_Intron	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta						DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		gttactcctgttttttttttt	0.249								DNA_polymerases_(catalytic_subunits)					3	4	---	---	---	---	
ILDR1	286676	broad.mit.edu	37	3	121717830	121717831	+	Intron	INS	-	C	C	rs139872172	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121717830_121717831insC	uc003ees.2	-						ILDR1_uc003eeq.2_Intron|ILDR1_uc003eer.2_Intron|ILDR1_uc010hrg.2_Intron	NM_175924	NP_787120	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor							cytosol|integral to membrane|plasma membrane	receptor activity			skin(1)	1				GBM - Glioblastoma multiforme(114;0.156)		catcttttaaaagagatgactt	0.000													4	2	---	---	---	---	
SEC22A	26984	broad.mit.edu	37	3	122924523	122924527	+	Intron	DEL	CAAAA	-	-	rs66811125		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122924523_122924527delCAAAA	uc003ege.2	+						SEC22A_uc003egf.2_5'Flank	NM_012430	NP_036562	Q96IW7	SC22A_HUMAN	SEC22 vesicle trafficking protein homolog A						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane	transporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0548)		gaccctgtttcaaaacaaaacaaaa	0.122													3	5	---	---	---	---	
ITGB5	3693	broad.mit.edu	37	3	124606767	124606768	+	5'Flank	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124606767_124606768insT	uc003eho.2	-							NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(2)	2				GBM - Glioblastoma multiforme(114;0.163)		tttttcttttcttttttttttt	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127037739	127037742	+	IGR	DEL	TCAT	-	-	rs6781039		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127037739_127037742delTCAT								PLXNA1 (281511 upstream) : TPRA1 (254166 downstream)																							CTAAGAAGCCtcattcattcattc	0.338													4	2	---	---	---	---	
KIAA1257	57501	broad.mit.edu	37	3	128655342	128655343	+	Intron	DEL	AG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128655342_128655343delAG	uc003elh.1	-						KIAA1257_uc003elg.1_Intron			Q9ULG3	K1257_HUMAN	RecName: Full=Uncharacterized protein FLJ43738;												0						caactaaaacagagtcgacagg	0.000													0	6	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131495642	131495642	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131495642delT	uc003eok.2	-						CPNE4_uc011blq.1_Intron|CPNE4_uc003eol.2_Intron|CPNE4_uc003eom.2_Intron	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						TGATAGTTGATTAAGGACCTC	0.423													4	2	---	---	---	---	
RAB6B	51560	broad.mit.edu	37	3	133556564	133556564	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133556564delC	uc003epy.2	-						RAB6B_uc011blu.1_Intron	NM_016577	NP_057661	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family						protein transport|retrograde vesicle-mediated transport, Golgi to ER|small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle|Golgi membrane	GTP binding|GTPase activity|protein binding			pancreas(1)	1						TAGGCTCTTTCCCCCAGGCCT	0.532													4	3	---	---	---	---	
STAG1	10274	broad.mit.edu	37	3	136140495	136140495	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136140495delG	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						GAGAGGGAAAGAGGAAGAAGT	0.363													4	2	---	---	---	---	
ESYT3	83850	broad.mit.edu	37	3	138153197	138153197	+	5'Flank	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138153197delT	uc003esk.2	+						ESYT3_uc010hug.2_5'Flank	NM_031913	NP_114119	A0FGR9	ESYT3_HUMAN	family with sequence similarity 62 (C2 domain							integral to membrane|plasma membrane					0						TTAGGTGATGTTTATCCATGA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	141380746	141380747	+	IGR	INS	-	T	T	rs139979459	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141380746_141380747insT								RASA2 (49549 upstream) : RNF7 (76304 downstream)																							AGCATTCAACATCCtggattag	0.356													5	5	---	---	---	---	
SLC9A9	285195	broad.mit.edu	37	3	143157265	143157266	+	Intron	INS	-	GT	GT	rs145312416	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143157265_143157266insGT	uc003evn.2	-							NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						ATCTCCCTGGCgtgtgtgtgtg	0.431													2	6	---	---	---	---	
SLC9A9	285195	broad.mit.edu	37	3	143374524	143374525	+	Intron	DEL	AC	-	-	rs35702068		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143374524_143374525delAC	uc003evn.2	-						SLC9A9_uc011bnk.1_Intron	NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						atgcacatgtacacacacacac	0.267													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144687132	144687132	+	IGR	DEL	T	-	-	rs66593030		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144687132delT								C3orf58 (975923 upstream) : None (None downstream)																							GGTATTAGTGTTTTTAAAAAA	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	146274118	146274118	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146274118delT								PLSCR1 (11490 upstream) : PLSCR5 (20225 downstream)																							aacccagtcctttttttggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	156504800	156504801	+	Intron	DEL	TG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156504800_156504801delTG	uc003fax.1	-											Homo sapiens cDNA FLJ31839 fis, clone NT2RP7000086.																		TGAGTTTTATTGTGTGGGGTTT	0.282													6	4	---	---	---	---	
RSRC1	51319	broad.mit.edu	37	3	158013054	158013055	+	Intron	INS	-	A	A	rs138038048	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158013054_158013055insA	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			attttaggtaggggTGAAAGTG	0.193													6	4	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	158832102	158832103	+	Intron	INS	-	TTT	TTT	rs5853852		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158832102_158832103insTTT	uc003fcq.1	+						IQCJ_uc003fco.2_Intron|IQCJ_uc010hvy.1_Intron|IQCJ_uc003fcp.1_Intron	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			GTTTCTAAATGttttttttttt	0.153													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161792702	161792705	+	IGR	DEL	TCTC	-	-	rs7624912		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161792702_161792705delTCTC								OTOL1 (570974 upstream) : None (None downstream)																							tttctttctttctctctctctctc	0.172													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162313951	162313952	+	IGR	DEL	GT	-	-	rs71649722		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162313951_162313952delGT								None (None upstream) : None (None downstream)																							gtgtgcacacgtgtgtgtgtgt	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163582825	163582826	+	IGR	DEL	TT	-	-	rs35207734		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163582825_163582826delTT								None (None upstream) : MIR1263 (306433 downstream)																							ATTTACTCTCTTGTGTCATGGT	0.272													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165663574	165663574	+	IGR	DEL	A	-	-	rs144993512		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165663574delA								BCHE (108321 upstream) : None (None downstream)																							TACTAGATTGAAAAAAAAAAC	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166110793	166110793	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166110793delT								BCHE (555540 upstream) : ZBBX (847288 downstream)																							agtagccatctttttttttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	168132868	168132868	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168132868delT								GOLIM4 (319451 upstream) : MIR551B (136774 downstream)																							TTAAATTGCCTTTTTTTTTTT	0.249													3	4	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170360569	170360572	+	Intron	DEL	ACAC	-	-	rs111378123		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170360569_170360572delACAC	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)			TTATAAGCAAacacacacacacac	0.196													4	3	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173187429	173187430	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173187429_173187430insA	uc003fio.1	+							NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TTTTAAAAACTAAAAAAAAAAA	0.203													4	2	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173345192	173345193	+	Intron	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173345192_173345193delAC	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			tttttccattacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176983189	176983189	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176983189delT								TBL1XR1 (68141 upstream) : None (None downstream)																							ggccagaaaatttttttttta	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	178042179	178042179	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178042179delC								None (None upstream) : KCNMB2 (212045 downstream)																							AAGAAGACTACCAGTGTATAG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180475628	180475629	+	Intron	INS	-	AGGA	AGGA			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180475628_180475629insAGGA	uc003fko.2	-											Homo sapiens mRNA; cDNA DKFZp434A128 (from clone DKFZp434A128).																		aagaaagaaagaggaaggaagg	0.000													9	10	---	---	---	---	
KLHL24	54800	broad.mit.edu	37	3	183377548	183377549	+	Intron	INS	-	A	A	rs77124026		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183377548_183377549insA	uc003flv.2	+						KLHL24_uc003flw.2_Intron|KLHL24_uc003flx.2_Intron	NM_017644	NP_060114	Q6TFL4	KLH24_HUMAN	DRE1 protein							axon|cytoplasm|perikaryon				ovary(1)	1	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			GTTGACATATTACAAGTTCAGT	0.322													4	3	---	---	---	---	
PARL	55486	broad.mit.edu	37	3	183582692	183582692	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183582692delT	uc003fmd.2	-						PARL_uc003fme.2_Intron	NM_018622	NP_061092	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like isoform 1						proteolysis	integral to membrane|mitochondrial inner membrane|nucleus	serine-type endopeptidase activity				0	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TCCATATTTCTTTTTTTTTTT	0.318													3	3	---	---	---	---	
PARL	55486	broad.mit.edu	37	3	183598910	183598912	+	Intron	DEL	TTT	-	-	rs111529578		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183598910_183598912delTTT	uc003fmd.2	-						PARL_uc003fme.2_Intron	NM_018622	NP_061092	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like isoform 1						proteolysis	integral to membrane|mitochondrial inner membrane|nucleus	serine-type endopeptidase activity				0	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			CCTTTGTGCAttttttttttttt	0.030													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184173950	184173951	+	IGR	INS	-	T	T	rs78737623		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184173950_184173951insT								CHRD (66331 upstream) : EPHB3 (105636 downstream)																							GTCACAATCTGGTTTTTTTTTT	0.441													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	185691994	185691995	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185691994_185691995insA	uc010hyn.1	+						uc010hyo.1_Intron					Homo sapiens cDNA, FLJ99355.																		gactccatctgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
DGKG	1608	broad.mit.edu	37	3	185865776	185865776	+	3'UTR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185865776delT	uc003fqa.2	-	25					DGKG_uc003fqb.2_3'UTR|DGKG_uc003fqc.2_3'UTR|DGKG_uc011brx.1_3'UTR	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	ATCTTGCTCCTAGGTGGTCCT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187201991	187201994	+	IGR	DEL	AAAC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187201991_187201994delAAAC								RTP4 (112624 upstream) : SST (184702 downstream)																							ctcagtctcgaaacaaacaaacaa	0.191													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187821336	187821339	+	IGR	DEL	TGTT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187821336_187821339delTGTT								BCL6 (357861 upstream) : LPP (50380 downstream)																							tgataatatgtgtttgtttgtttg	0.000													6	4	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188559182	188559182	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188559182delT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TCTGAAtttgttttttttttt	0.209			T	HMGA2|MLL|C12orf9	lipoma|leukemia								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190717524	190717525	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190717524_190717525insA								SNAR-I (121685 upstream) : OSTN (212797 downstream)																							aggaaggaaggaaggaaggaag	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193775979	193775986	+	Intron	DEL	ACCCAGGG	-	-	rs66526632		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193775979_193775986delACCCAGGG	uc003ftp.3	-											Homo sapiens cDNA clone IMAGE:4828668.																		TGAAGGACCCACCCAGGGAGGAGGCTGA	0.438													4	2	---	---	---	---	
LRRC15	131578	broad.mit.edu	37	3	194092595	194092596	+	5'Flank	DEL	AT	-	-	rs112884343	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194092595_194092596delAT	uc003ftu.2	-						LRRC15_uc003ftt.2_5'Flank	NM_130830	NP_570843	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15 isoform b							integral to membrane				ovary(3)	3	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		acacaaacacatacacacacac	0.020													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194267706	194267706	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194267706delC								ATP13A3 (78738 upstream) : TMEM44 (40697 downstream)																							gagcgaaactccatctcaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194445983	194445983	+	IGR	DEL	G	-	-	rs35955114		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194445983delG								FAM43A (36219 upstream) : C3orf21 (343032 downstream)																							ctgaaaatcagggggggtgta	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195353385	195353386	+	IGR	DEL	CG	-	-	rs111429267		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195353385_195353386delCG								APOD (42309 upstream) : SDHAP2 (31524 downstream)																							catgcacacacgcgcacacaca	0.030													6	3	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195481652	195481653	+	Intron	DEL	TG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195481652_195481653delTG	uc011bto.1	-						MUC4_uc010hzq.2_5'Flank|MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						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)		catgtatgtatgtgtgtatcca	0.045													4	2	---	---	---	---	
OSTalpha	200931	broad.mit.edu	37	3	195956560	195956561	+	Intron	INS	-	AA	AA	rs150331848		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195956560_195956561insAA	uc003fwd.2	+						OSTalpha_uc010iac.1_Intron|OSTalpha_uc003fwe.2_Intron	NM_152672	NP_689885	Q86UW1	OSTA_HUMAN	organic solute transporter alpha							integral to membrane|plasma membrane	transporter activity			ovary(1)	1	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;8.83e-25)|all cancers(36;8.38e-23)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;7.51e-07)|Lung(62;1.06e-06)	GBM - Glioblastoma multiforme(46;0.00202)		tctctattattaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	196167323	196167324	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196167323_196167324insA								UBXN7 (7978 upstream) : RNF168 (31305 downstream)																							gagactgtctcaaaaaaaaatt	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	196560144	196560145	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196560144_196560145insA								PAK2 (628 upstream) : SENP5 (34582 downstream)																							tactaaaatacaaaaaaaaatc	0.000													4	2	---	---	---	---	
KIAA0226	9711	broad.mit.edu	37	3	197431787	197431787	+	Intron	DEL	T	-	-	rs80272519		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197431787delT	uc003fyc.2	-						KIAA0226_uc003fyd.3_Intron|KIAA0226_uc003fyf.2_Intron|KIAA0226_uc003fyg.2_Intron	NM_014687	NP_055502	Q92622	RUBIC_HUMAN	hypothetical protein LOC9711 isoform 2.						autophagy|endocytosis|negative regulation of autophagy|negative regulation of endocytosis	early endosome|late endosome|lysosome	protein binding				0	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		GGTTTGCATGTTTTTTTTTTT	0.423													4	2	---	---	---	---	
LRCH3	84859	broad.mit.edu	37	3	197550367	197550367	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197550367delT	uc011bul.1	+						LRCH3_uc003fyj.1_Intron|LRCH3_uc011bum.1_Intron|LRCH3_uc011bun.1_Intron	NM_032773	NP_116162	Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH)							extracellular region				ovary(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		CCTTTGACTCttttttttttt	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	1184045	1184045	+	IGR	DEL	A	-	-	rs78089906		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1184045delA								SPON2 (17065 upstream) : LOC100130872 (5527 downstream)																							gaatagacctaacacaaatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3610868	3610868	+	IGR	DEL	A	-	-	rs11321586		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3610868delA								LRPAP1 (76644 upstream) : ADRA2C (157207 downstream)																							gggctctcccaagccccgatg	0.149													6	4	---	---	---	---	
EVC2	132884	broad.mit.edu	37	4	5657458	5657458	+	Intron	DEL	A	-	-	rs67146324		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5657458delA	uc003gij.2	-						EVC2_uc011bwb.1_Intron|EVC2_uc003gik.2_Intron	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin							integral to membrane				large_intestine(3)|ovary(2)	5						ATCCACATGTAAAAAAAAAAA	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18991408	18991408	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18991408delA								LCORL (968023 upstream) : None (None downstream)																							AGATCAAAGGAAAAAAAATAG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	38734537	38734537	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38734537delA								KLF3 (31409 upstream) : TLR10 (39726 downstream)																							agactctgtcaaaaaaaaaaa	0.189													4	2	---	---	---	---	
ATP8A1	10396	broad.mit.edu	37	4	42435160	42435160	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42435160delC	uc003gwr.2	-						ATP8A1_uc003gwq.2_Intron|ATP8A1_uc003gws.2_Intron	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	TCATTTTCTGCCTTGGTAACA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49142865	49142869	+	IGR	DEL	CACTG	-	-	rs150026397		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49142865_49142869delCACTG								CWH43 (78772 upstream) : None (None downstream)																							cattgcattccactggggttgattc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58819861	58819862	+	IGR	INS	-	GAGG	GAGG	rs149047630	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58819861_58819862insGAGG								IGFBP7 (843322 upstream) : None (None downstream)																							aaagaaagaaagagggagggag	0.025													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	61045184	61045186	+	IGR	DEL	TGT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61045184_61045186delTGT								None (None upstream) : None (None downstream)																							TATTTCATACTGTTGTTGTTGTT	0.394													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69232225	69232226	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69232225_69232226insT								YTHDC1 (16401 upstream) : UGT2B15 (280090 downstream)																							tcagttaaaccttttttttaaa	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	71366925	71366925	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71366925delA								MUC7 (18212 upstream) : AMTN (17373 downstream)																							caatcaagttaacactcaata	0.000													4	2	---	---	---	---	
ADAMTS3	9508	broad.mit.edu	37	4	73203047	73203047	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73203047delA	uc003hgk.1	-							NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTAAAACATAAAATGCATCA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	80811647	80811647	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80811647delG								GDEP (27248 upstream) : ANTXR2 (11126 downstream)																							aaattaccttgggcagtatgg	0.000													4	2	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81821278	81821281	+	Intron	DEL	GTGT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81821278_81821281delGTGT	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						GTGGAAGAAAgtgtgtgtgtgtgt	0.172													3	3	---	---	---	---	
HPSE	10855	broad.mit.edu	37	4	84228561	84228562	+	Intron	INS	-	GCA	GCA	rs139326664	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84228561_84228562insGCA	uc003hoj.3	-						HPSE_uc010ika.2_Intron|HPSE_uc011ccq.1_Intron|HPSE_uc011ccr.1_Intron|HPSE_uc011ccs.1_Intron|HPSE_uc011cct.1_Intron|HPSE_uc003hok.3_Intron	NM_001098540	NP_001092010	Q9Y251	HPSE_HUMAN	heparanase precursor						carbohydrate metabolic process|cell adhesion|proteoglycan metabolic process	extracellular region|lysosomal membrane|nucleus	beta-glucuronidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Heparin(DB01109)	GGCAACTGCATgcagcagcagc	0.307													3	3	---	---	---	---	
AFF1	4299	broad.mit.edu	37	4	88020145	88020145	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88020145delA	uc003hqj.3	+						AFF1_uc011ccy.1_Intron|AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926	P51825	AFF1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TGTTTATTGTAATATAAAATT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	90591407	90591408	+	IGR	DEL	TC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90591407_90591408delTC								GPRIN3 (362246 upstream) : SNCA (53843 downstream)																							tctccctccttctctctctctc	0.030													4	2	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91048720	91048721	+	5'UTR	DEL	CT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91048720_91048721delCT	uc003hsv.3	+	1					FAM190A_uc003hsu.3_5'UTR|FAM190A_uc010ikv.2_RNA	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						TCCGCCTCTCCTCTCTCTCTCT	0.594													3	3	---	---	---	---	
GRID2	2895	broad.mit.edu	37	4	93852775	93852776	+	Intron	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93852775_93852776delAC	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron|GRID2_uc011cdv.1_Intron	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	GATAGAAGATacacacacacac	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	95313890	95313891	+	IGR	INS	-	AAA	AAA	rs146390824	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95313890_95313891insAAA								HPGDS (49863 upstream) : PDLIM5 (59147 downstream)																							gtcaaaatggcaccccatctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	107809008	107809009	+	IGR	DEL	CA	-	-	rs35056289		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107809008_107809009delCA								AIMP1 (538629 upstream) : DKK2 (33951 downstream)																							cacacacatgcacacacacaca	0.158													4	2	---	---	---	---	
LOC285419	285419	broad.mit.edu	37	4	124786491	124786491	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124786491delG	uc011cgn.1	+						LOC285419_uc003ifd.2_RNA	NR_027105				Homo sapiens mRNA; cDNA DKFZp686P12109 (from clone DKFZp686P12109).												0						GTCTAAGGATGGCACAATGGC	0.358													4	2	---	---	---	---	
FAT4	79633	broad.mit.edu	37	4	126285877	126285877	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126285877delC	uc003ifj.3	+							NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						gttttttcagctggtgcatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	134201515	134201516	+	IGR	DEL	GT	-	-	rs143252293		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134201515_134201516delGT								PCDH10 (88784 upstream) : PABPC4L (915975 downstream)																							ttttctattcgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	140184468	140184468	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140184468delT								ELF2 (86096 upstream) : C4orf49 (2849 downstream)																							atttgtggacttttttttttt	0.000													4	2	---	---	---	---	
GAB1	2549	broad.mit.edu	37	4	144381841	144381841	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144381841delA	uc003ije.2	+						GAB1_uc003ijd.2_Intron|GAB1_uc011chq.1_Intron	NM_002039	NP_002030	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1 isoform b						cell proliferation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	cytosol	SH3/SH2 adaptor activity			breast(2)|lung(1)|skin(1)	4	all_hematologic(180;0.158)					TAAATGAGTTAAAAAAAAAAA	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	149611454	149611454	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149611454delA								NR3C2 (247811 upstream) : None (None downstream)																							GCGACCTTGGAACCTGACTTT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153959586	153959586	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153959586delA								FHDC1 (58738 upstream) : TRIM2 (114684 downstream)																							CTCAGTTACCAAAAAATGATC	0.234													4	2	---	---	---	---	
KIAA0922	23240	broad.mit.edu	37	4	154390467	154390468	+	Intron	DEL	AC	-	-	rs34231481		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154390467_154390468delAC	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				GGTAAGGGAGacacacacacac	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	158577367	158577367	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158577367delT								LOC340017 (80072 upstream) : FAM198B (468366 downstream)																							TAAAGTCCACTACAATTGCCT	0.348													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164537871	164537872	+	Intron	DEL	AC	-	-	rs112359062		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164537871_164537872delAC	uc003iqs.1	-							NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				gtctctgaaaacacacacacac	0.000													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164590754	164590754	+	Intron	DEL	T	-	-	rs71600626		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164590754delT	uc003iqs.1	-							NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				gatgtttatcttttttttttt	0.000													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164672979	164672980	+	Intron	INS	-	GTGTGA	GTGTGA	rs139079372	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164672979_164672980insGTGTGA	uc003iqs.1	-							NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				tgtgtgtgtgtgatgaggaaat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	165628858	165628859	+	IGR	INS	-	A	A	rs138546703	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165628858_165628859insA								MARCH1 (323656 upstream) : TRIM61 (246741 downstream)																							CAAACACCCCCACCCCACCCCA	0.302													3	5	---	---	---	---	
TLL1	7092	broad.mit.edu	37	4	167023998	167023998	+	3'UTR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167023998delT	uc003irh.1	+	21					TLL1_uc011cjn.1_3'UTR|TLL1_uc011cjo.1_3'UTR	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		TAGATGAGCCTTTTAGTAGAG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	168842610	168842610	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168842610delG								SPOCK3 (686869 upstream) : ANXA10 (171097 downstream)																							aacacacactggggcctgttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	175922845	175922846	+	IGR	DEL	GT	-	-	rs112532837		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175922845_175922846delGT								ADAM29 (23515 upstream) : GPM6A (631243 downstream)																							attacagCACgtgtgtgtgtgt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	178370845	178370846	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178370845_178370846insT	uc003iux.1	+											Homo sapiens cDNA FLJ37626 fis, clone BRCOC2014748.																		catagttcatattttttttttt	0.000													2	5	---	---	---	---	
CCDC111	201973	broad.mit.edu	37	4	185578560	185578560	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185578560delA	uc003iwk.2	+						CCDC111_uc010isd.1_Intron|CCDC111_uc003iwj.2_Intron|CCDC111_uc003iwl.2_Intron|CCDC111_uc003iwm.2_Intron|CCDC111_uc003iwn.2_Intron	NM_152683	NP_689896	Q96LW4	CC111_HUMAN	coiled-coil domain containing 111						DNA replication, synthesis of RNA primer		DNA primase activity			central_nervous_system(1)	1		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.00531)|Hepatocellular(41;0.00932)|Renal(120;0.0246)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|all_neural(102;0.131)		all cancers(43;5.84e-27)|Epithelial(43;2.2e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.28e-11)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.03e-05)|Colorectal(24;7.57e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000249)|COAD - Colon adenocarcinoma(29;0.000502)|LUSC - Lung squamous cell carcinoma(40;0.00995)|READ - Rectum adenocarcinoma(43;0.173)		TCAGTTCTTTAAAAAAAAAAG	0.179													4	2	---	---	---	---	
SORBS2	8470	broad.mit.edu	37	4	186651075	186651075	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186651075delA	uc003iyl.2	-						SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Intron|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cky.1_Intron|SORBS2_uc003iyp.2_Intron	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TTTACTGTCTAATTCCTTCTG	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190551719	190551720	+	IGR	INS	-	CTCCCA	CTCCCA	rs150684825		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190551719_190551720insCTCCCA								None (None upstream) : FRG1 (310254 downstream)																							AGCCATTTCTCCCCCCGCCAAA	0.450													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190617583	190617584	+	IGR	INS	-	AAGTAT	AAGTAT	rs138661908		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190617583_190617584insAAGTAT								None (None upstream) : FRG1 (244390 downstream)																							TACTGTATCTCAAGTATAAGTT	0.361													7	6	---	---	---	---	
NKD2	85409	broad.mit.edu	37	5	1022533	1022534	+	Intron	INS	-	A	A	rs33911086		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1022533_1022534insA	uc003jbt.1	+						NKD2_uc010itf.1_Intron	NM_033120	NP_149111	Q969F2	NKD2_HUMAN	naked cuticle homolog 2						exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding				0	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			TCCCACCCGCTGTGGGCGTCTC	0.658													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1043778	1043779	+	IGR	INS	-	ATGG	ATGG	rs112604190		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1043778_1043779insATGG								NKD2 (4853 upstream) : SLC12A7 (6712 downstream)																							tgtgtgaatgagtgggttagtg	0.099													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1938165	1938165	+	IGR	DEL	C	-	-	rs5865399		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1938165delC								IRX4 (55285 upstream) : IRX2 (808116 downstream)																							GTCTAGGACTCTACCTGTTAA	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3127238	3127239	+	IGR	DEL	TT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3127238_3127239delTT								C5orf38 (371726 upstream) : IRX1 (468929 downstream)																							TCTCCGGGGGTTTCTCAGCCAG	0.619													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3382294	3382294	+	IGR	DEL	A	-	-	rs68053951		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3382294delA								C5orf38 (626782 upstream) : IRX1 (213874 downstream)																							GTAGGTTTGTAAAAGGAAGGG	0.453													6	3	---	---	---	---	
ADCY2	108	broad.mit.edu	37	5	7787796	7787799	+	Intron	DEL	TAGA	-	-	rs67569911		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7787796_7787799delTAGA	uc003jdz.1	+						ADCY2_uc011cmo.1_Intron|ADCY2_uc010itm.1_Intron	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						ggtaggtaggtagatagataggta	0.225													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10157191	10157192	+	IGR	INS	-	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10157191_10157192insG								LOC285692 (253255 upstream) : FAM173B (69246 downstream)																							ttgccctagtaggggctgtctg	0.000													4	2	---	---	---	---	
FAM173B	134145	broad.mit.edu	37	5	10248340	10248344	+	Intron	DEL	CTAGT	-	-	rs144678576		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10248340_10248344delCTAGT	uc003jeo.2	-						FAM173B_uc003jep.2_Intron|FAM173B_uc010itr.2_Intron|CCT5_uc011cmq.1_5'Flank|CCT5_uc003jeq.2_5'Flank|CCT5_uc003jer.2_5'Flank|CCT5_uc010its.2_5'Flank|CCT5_uc011cmr.1_5'Flank|CCT5_uc011cms.1_5'Flank|CCT5_uc011cmt.1_5'Flank	NM_199133	NP_954584	Q6P4H8	F173B_HUMAN	hypothetical protein LOC134145							integral to membrane				kidney(1)|central_nervous_system(1)	2						CTTTCTTATACTAGTCTAATGTCAT	0.361													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10777990	10777991	+	IGR	DEL	AT	-	-	rs35631063		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10777990_10777991delAT								DAP (16603 upstream) : CTNND2 (193961 downstream)																							AATTGATAACATGTGCTCCAGT	0.337													6	3	---	---	---	---	
CDH18	1016	broad.mit.edu	37	5	19840396	19840397	+	Intron	DEL	AG	-	-	rs10941513		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19840396_19840397delAG	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					aaaaaaaaaaagaaaaaaaaaa	0.149													3	3	---	---	---	---	
CDH18	1016	broad.mit.edu	37	5	19935929	19935930	+	Intron	INS	-	TA	TA	rs72403163		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19935929_19935930insTA	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					ctctctctctctctctctcact	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20938835	20938848	+	IGR	DEL	AATGTTCTATAATA	-	-	rs148017022		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20938835_20938848delAATGTTCTATAATA								CDH18 (950528 upstream) : GUSBP1 (403094 downstream)																							TACACTTTCTAATGTTCTATAATAAATTCTAAAG	0.271													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28112232	28112232	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28112232delT								None (None upstream) : None (None downstream)																							TCCATTTTACTTTTAAGAGAG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28591548	28591549	+	IGR	INS	-	A	A	rs117293687	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28591548_28591549insA								None (None upstream) : None (None downstream)																							gatggtgtctcaaaaaaaaaaa	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30054409	30054409	+	IGR	DEL	A	-	-	rs139930695		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30054409delA								None (None upstream) : None (None downstream)																							tcggtttcagaaaaaaaaaat	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30337510	30337511	+	IGR	DEL	CA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30337510_30337511delCA								None (None upstream) : CDH6 (856285 downstream)																							cacactacagcacacacacaca	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	32580944	32580944	+	IGR	DEL	T	-	-	rs76681075		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32580944delT								ZFR (136100 upstream) : SUB1 (4661 downstream)																							ctacacactgttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	34518641	34518641	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34518641delT								C1QTNF3 (475324 upstream) : RAI14 (137792 downstream)																							actggggacattgtaaaatgg	0.000													4	2	---	---	---	---	
IL7R	3575	broad.mit.edu	37	5	35861814	35861815	+	Intron	INS	-	T	T	rs144722239	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35861814_35861815insT	uc003jjs.2	+						IL7R_uc011coo.1_Intron|IL7R_uc011cop.1_Intron	NM_002185	NP_002176	P16871	IL7RA_HUMAN	interleukin 7 receptor precursor						immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)|skin(1)	5	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			GGAAAAGAGTCTGGTTTGAAAG	0.376													1	7	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38255753	38255753	+	5'Flank	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38255753delT	uc003jlc.1	+						EGFLAM_uc003jlb.1_5'Flank	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					TTTGAACAGATTTTTTTTTTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	75228282	75228283	+	IGR	INS	-	A	A	rs141539631	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75228282_75228283insA								POC5 (214969 upstream) : SV2C (151022 downstream)																							aaagtgggatcgggggctaaca	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	78628774	78628774	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78628774delA								JMY (5738 upstream) : HOMER1 (41013 downstream)																							ctgtaaattgaaggcagtaat	0.000													4	2	---	---	---	---	
SERINC5	256987	broad.mit.edu	37	5	79505169	79505170	+	Intron	INS	-	AC	AC	rs143586858	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79505169_79505170insAC	uc003kgj.2	-						SERINC5_uc003kgk.2_Intron|SERINC5_uc003kgl.2_Intron|SERINC5_uc003kgm.2_Intron|SERINC5_uc011ctj.1_Intron	NM_178276	NP_840060	Q86VE9	SERC5_HUMAN	developmentally regulated protein TPO1						phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(167;0.00328)|all_lung(232;0.00356)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.93e-46)|Epithelial(54;5.59e-40)|all cancers(79;1.89e-34)		agaagaggaggacacacacaca	0.000													4	3	---	---	---	---	
MSH3	4437	broad.mit.edu	37	5	80074816	80074817	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80074816_80074817insT	uc003kgz.2	+							NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		tttttttttacttttttttttt	0.134								MMR					3	3	---	---	---	---	
KCNN2	3781	broad.mit.edu	37	5	113721217	113721218	+	Intron	DEL	CA	-	-	rs146876609		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113721217_113721218delCA	uc003kqo.2	+							NM_021614	NP_067627	Q9H2S1	KCNN2_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding|small conductance calcium-activated potassium channel activity			ovary(2)	2		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)		cacatgcgcgcacacacacaca	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	114889126	114889126	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114889126delT								FEM1C (8535 upstream) : TMED7-TICAM2 (25214 downstream)																							taggtaggtgttttcgcaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	117664155	117664155	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117664155delT								None (None upstream) : DTWD2 (508416 downstream)																							CTCAGCCAGCTTACACTCATA	0.423													4	2	---	---	---	---	
SNX24	28966	broad.mit.edu	37	5	122343757	122343758	+	3'UTR	DEL	CT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122343757_122343758delCT	uc011cwo.1	+	7					SNX24_uc010jcy.2_3'UTR	NM_014035	NP_054754	Q9Y343	SNX24_HUMAN	SBBI31 protein						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)		AACAAAGCCACTCTCTGCTTCA	0.431													0	6	---	---	---	---	
CHSY3	337876	broad.mit.edu	37	5	129326070	129326071	+	Intron	INS	-	GT	GT	rs142840698	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129326070_129326071insGT	uc003kvd.2	+							NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3							Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		tgagtgagtgagtgtgtgtgtg	0.332													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129951290	129951291	+	IGR	DEL	CA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129951290_129951291delCA								CHSY3 (428964 upstream) : HINT1 (543584 downstream)																							acacaacacccacacacacaca	0.337													4	2	---	---	---	---	
STK32A	202374	broad.mit.edu	37	5	146761616	146761616	+	Intron	DEL	G	-	-	rs79595434		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146761616delG	uc010jgn.1	+						STK32A_uc011dbw.1_Intron	NM_001112724	NP_001106195	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A isoform 1								ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			gccatcctgaggcacatgtgg	0.000													1	5	---	---	---	---	
GRIA1	2890	broad.mit.edu	37	5	152885877	152885884	+	Intron	DEL	GTGTGTGT	-	-	rs71896761		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152885877_152885884delGTGTGTGT	uc003lva.3	+						GRIA1_uc003luy.3_Intron|GRIA1_uc003luz.3_Intron|GRIA1_uc011dcv.1_Intron|GRIA1_uc011dcw.1_Intron|GRIA1_uc011dcx.1_Intron|GRIA1_uc011dcy.1_Intron|GRIA1_uc011dcz.1_Intron|GRIA1_uc010jia.1_Intron	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GGCAAGAAGGgtgtgtgtgtgtgtgtgt	0.231													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	158043671	158043672	+	IGR	INS	-	A	A	rs147196479	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158043671_158043672insA								CLINT1 (757503 upstream) : EBF1 (79252 downstream)																							aaatttacaagaaaaaaaaaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162985268	162985269	+	IGR	INS	-	GT	GT	rs143714105	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162985268_162985269insGT								MAT2B (38935 upstream) : None (None downstream)																							TGTGTGAGGGAgtgtgtgtgtg	0.149													5	3	---	---	---	---	
DOCK2	1794	broad.mit.edu	37	5	169225328	169225330	+	Intron	DEL	ACA	-	-	rs138493543		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169225328_169225330delACA	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTATCTATAGACAGCAACCTACT	0.365													2	4	---	---	---	---	
C5orf47	133491	broad.mit.edu	37	5	173401208	173401209	+	Intron	INS	-	TGG	TGG	rs72534839		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173401208_173401209insTGG	uc003mcv.2	+									Q569G3	CE047_HUMAN	Homo sapiens chromosome 5 open reading frame 47, mRNA (cDNA clone IMAGE:4823612), partial cds.												0						TCCCAAGAGGCtggtggtggtg	0.455													8	4	---	---	---	---	
CPLX2	10814	broad.mit.edu	37	5	175277976	175277977	+	Intron	INS	-	AA	AA	rs72536776		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175277976_175277977insAA	uc003mde.1	+							NM_006650	NP_006641	Q6PUV4	CPLX2_HUMAN	complexin 2						mast cell degranulation|positive regulation of synaptic plasticity|vesicle docking involved in exocytosis	cytosol				ovary(1)	1	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGCAGAGAGACGAGATCTCAGG	0.579													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	1399677	1399678	+	IGR	DEL	AG	-	-	rs71901740		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1399677_1399678delAG								FOXF2 (3846 upstream) : FOXC1 (211003 downstream)																							ggagagagacagagggagagaa	0.099													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	2557742	2557744	+	IGR	DEL	TCT	-	-	rs113332174		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2557742_2557744delTCT								GMDS (311896 upstream) : C6orf195 (65228 downstream)																							TACATCAGCCTCTTCTTGGGTTT	0.429													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3990690	3990691	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3990690_3990691insT								FAM50B (139140 upstream) : PRPF4B (30878 downstream)																							caagtttctccttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18558175	18558176	+	Intron	DEL	CA	-	-	rs35053329		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18558175_18558176delCA	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																		tcatcatcatcatttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19819393	19819393	+	IGR	DEL	A	-	-	rs113624685		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19819393delA								None (None upstream) : ID4 (18224 downstream)																							ctgaggagttaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	20294798	20294799	+	IGR	INS	-	CTTT	CTTT	rs138877653	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20294798_20294799insCTTT								MBOAT1 (82128 upstream) : E2F3 (107338 downstream)																							TTCTGATTGACCTAAGATTTGC	0.356													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	21584964	21584965	+	IGR	DEL	AT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21584964_21584965delAT								CDKAL1 (352332 upstream) : SOX4 (9007 downstream)																							agttaggtgcatatatatatag	0.000													4	2	---	---	---	---	
FLJ22536	401237	broad.mit.edu	37	6	21726382	21726383	+	Intron	INS	-	CA	CA	rs12183824		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21726382_21726383insCA	uc010jpp.1	+						FLJ22536_uc003ndj.2_Intron|FLJ22536_uc011djk.1_Intron|FLJ22536_uc011djj.1_Intron					Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0						gcgcgcgcgcgcacacacacac	0.168													2	4	---	---	---	---	
ALDH5A1	7915	broad.mit.edu	37	6	24522706	24522707	+	Intron	INS	-	GT	GT	rs72282015		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24522706_24522707insGT	uc003neg.2	+						ALDH5A1_uc003nef.2_Intron	NM_001080	NP_001071	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5A1 isoform 2 precursor						acetate metabolic process|central nervous system development|galactosylceramide metabolic process|gamma-aminobutyric acid catabolic process|glucose metabolic process|glutamate metabolic process|glutamine metabolic process|glutathione metabolic process|glycerophospholipid metabolic process|neurotransmitter catabolic process|neurotransmitter secretion|protein homotetramerization|respiratory electron transport chain|short-chain fatty acid metabolic process|succinate metabolic process	mitochondrial matrix|soluble fraction	succinate-semialdehyde dehydrogenase activity				0					Chlormerodrin(DB00534)|NADH(DB00157)|Succinic acid(DB00139)	TCTTTTCTTTCgtgtgtgtgtg	0.391													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26739800	26739801	+	IGR	INS	-	CAAG	CAAG	rs79214601		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26739800_26739801insCAAG								ZNF322A (79837 upstream) : GUSBL1 (99465 downstream)																							ACATGTGCTCACACGTCtgcat	0.074													3	4	---	---	---	---	
ZNF184	7738	broad.mit.edu	37	6	27422387	27422403	+	Intron	DEL	TGGCAGATCTCCAACCC	-	-	rs141331564		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27422387_27422403delTGGCAGATCTCCAACCC	uc003njj.2	-						ZNF184_uc010jqv.2_Intron|ZNF184_uc003nji.2_Intron	NM_007149	NP_009080	Q99676	ZN184_HUMAN	zinc finger protein 184						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						TGCATGGAAGTGGCAGATCTCCAACCCTGGTTGGAGT	0.419													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28151858	28151859	+	IGR	INS	-	A	A	rs71548306		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28151858_28151859insA								ZNF389 (14483 upstream) : LOC222699 (31257 downstream)																							tgatatgcattaaaaaaaaaaa	0.005													4	3	---	---	---	---	
PSORS1C1	170679	broad.mit.edu	37	6	31092744	31092745	+	Intron	INS	-	A	A	rs139842431		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31092744_31092745insA	uc003nsl.1	+						PSORS1C1_uc010jsj.1_Intron|PSORS1C1_uc003nsn.1_5'Flank	NM_014068	NP_054787	Q9UIG5	PS1C1_HUMAN	SEEK1 protein											ovary(1)	1						gactccgtctcaaaaaaaaaaa	0.233													4	2	---	---	---	---	
BAT1	7919	broad.mit.edu	37	6	31505650	31505651	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31505650_31505651insA	uc003ntt.2	-						BAT1_uc003nts.2_Intron|BAT1_uc011dnn.1_Intron|BAT1_uc003ntu.2_Intron|BAT1_uc003ntv.2_Intron|BAT1_uc003ntw.2_Intron|BAT1_uc003ntx.2_Intron|BAT1_uc011dno.1_Intron|BAT1_uc011dnp.1_Intron|SNORD117_uc003nty.1_5'Flank|BAT1_uc011dnq.1_Intron	NM_004640	NP_004631	Q13838	DX39B_HUMAN	HLA-B associated transcript 1						intronless viral mRNA export from host nucleus|RNA secondary structure unwinding|spliceosome assembly	nuclear speck|spliceosomal complex|transcription export complex	ATP binding|ATP-dependent protein binding|ATP-dependent RNA helicase activity|identical protein binding|U4 snRNA binding|U6 snRNA binding				0						ctgtcactactaaaaaaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	31818965	31818965	+	IGR	DEL	A	-	-	rs71793294		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31818965delA								C6orf48 (11426 upstream) : NEU1 (7865 downstream)																							accctgtctcaaaaaaaaaaa	0.179													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	35169928	35169929	+	IGR	INS	-	C	C	rs149690958	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35169928_35169929insC								TCP11 (60741 upstream) : SCUBE3 (12261 downstream)																							TGCAGAAGCCACCTGCTGTATG	0.525													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	35729336	35729337	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35729336_35729337insA								C6orf81 (12648 upstream) : C6orf126 (15055 downstream)																							tctcaaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
BTBD9	114781	broad.mit.edu	37	6	38567073	38567074	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38567073_38567074insA	uc003ooa.3	-						BTBD9_uc010jwx.2_Intron	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a						cell adhesion						0						TGCAGGTACTTAAAAAAAAAAG	0.158													4	2	---	---	---	---	
UNC5CL	222643	broad.mit.edu	37	6	41012133	41012133	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41012133delG	uc010jxe.1	-							NM_173561	NP_775832	Q8IV45	UN5CL_HUMAN	unc-5 homolog C-like						signal transduction	cytoplasm|integral to membrane				ovary(2)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)					GCGGCAGAGTGGGATAGAAGC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	41280196	41280196	+	IGR	DEL	A	-	-	rs11342970		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41280196delA								TREM1 (25739 upstream) : NCR2 (23332 downstream)																							ACTGCCCTTGAAAAAAAAAAA	0.264													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	42068155	42068155	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42068155delA								TAF8 (12956 upstream) : C6orf132 (1830 downstream)																							aggcagagccaggatgtgggg	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	45523947	45523948	+	IGR	INS	-	A	A	rs148031592	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45523947_45523948insA								RUNX2 (5129 upstream) : CLIC5 (342242 downstream)																							GCCTGTTTCAGAAAAAAAGTTG	0.460													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50592243	50592243	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50592243delC								DEFB112 (575879 upstream) : TFAP2D (89014 downstream)																							gcccacatcaccaagtcaatc	0.000													4	2	---	---	---	---	
GCLC	2729	broad.mit.edu	37	6	53405465	53405466	+	Intron	INS	-	CA	CA	rs143043423	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53405465_53405466insCA	uc003pbw.1	-						GCLC_uc003pbx.2_Intron	NM_001498	NP_001489	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit						anti-apoptosis|cell redox homeostasis|cysteine metabolic process|glutamate metabolic process|glutathione biosynthetic process|negative regulation of transcription, DNA-dependent|regulation of blood vessel size|response to heat|response to hormone stimulus|response to oxidative stress|xenobiotic metabolic process	cytosol	ADP binding|ATP binding|coenzyme binding|glutamate binding|glutamate-cysteine ligase activity|magnesium ion binding			ovary(1)|central_nervous_system(1)	2	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)	aagtgtCTTGCcacacacacac	0.015													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57208555	57208555	+	Intron	DEL	A	-	-	rs11324461		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57208555delA	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	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)		AGtgttaaagaaaaaaaatta	0.174													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57232208	57232213	+	Intron	DEL	TAAAAC	-	-	rs66996024		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57232208_57232213delTAAAAC	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	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)		AAAAAATGTTTAAAACTAACTTATTT	0.252													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57238019	57238020	+	Intron	INS	-	AGT	AGT	rs149497221		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57238019_57238020insAGT	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	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)		cactgacattgttttttttttc	0.000													6	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57301956	57301963	+	Intron	DEL	ACACTTAA	-	-	rs146504937		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57301956_57301963delACACTTAA	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)		caggcactggacacttaaacaactagat	0.000													5	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57416838	57416839	+	Intron	INS	-	A	A	rs138010997		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57416838_57416839insA	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)		aagcaatggggaaaggactgcc	0.000													4	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57438418	57438418	+	Intron	DEL	T	-	-	rs66509138		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57438418delT	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)		AAATCCTAGATTTTTTTCTAA	0.303													4	6	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57438823	57438823	+	Intron	DEL	G	-	-	rs145954948		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57438823delG	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)		GCAGGTTTGTGGGATATGATG	0.348													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57461972	57461973	+	Intron	INS	-	T	T	rs138866737		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57461972_57461973insT	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)		attataaaggatgttttaaggg	0.000													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57474770	57474774	+	Intron	DEL	ATAGG	-	-	rs139550998	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57474770_57474774delATAGG	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)		CTTAAGCATCATAGGATTGTTCATT	0.302													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57499442	57499442	+	Intron	DEL	A	-	-	rs11360933		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57499442delA	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)		tatgcaaatgaacaggtatga	0.020													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57517011	57517012	+	IGR	INS	-	TTAA	TTAA	rs138904532		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57517011_57517012insTTAA								PRIM2 (3636 upstream) : GUSBL2 (729147 downstream)																							AAATACTGCATTTAAGACTGAC	0.356													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57537973	57537975	+	IGR	DEL	ATA	-	-	rs67691807		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57537973_57537975delATA								PRIM2 (24598 upstream) : GUSBL2 (708184 downstream)																							ACACATACACATATACAGACACG	0.305													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57577557	57577558	+	IGR	INS	-	A	A	rs150323846	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57577557_57577558insA								PRIM2 (64182 upstream) : GUSBL2 (668601 downstream)																							cttagcagtttaaagtccttgt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57591255	57591256	+	IGR	INS	-	A	A	rs34026510		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57591255_57591256insA								PRIM2 (77880 upstream) : GUSBL2 (654903 downstream)																							caagactctccaaaaaaaaaaa	0.025													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57603993	57603995	+	IGR	DEL	TGC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57603993_57603995delTGC								PRIM2 (90618 upstream) : GUSBL2 (642164 downstream)																							ttatgaataatgctgcagtaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	62187865	62187865	+	IGR	DEL	G	-	-	rs36027385		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62187865delG								None (None upstream) : KHDRBS2 (202000 downstream)																							aaggtatagtgggagtgcatt	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	62202932	62202933	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62202932_62202933insA								None (None upstream) : KHDRBS2 (186932 downstream)																							cacagattcttaaaaaaaatgt	0.000													4	4	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65500964	65500964	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65500964delA	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						ATAAAAGCCTAAAGTGGGTTT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	66781227	66781228	+	IGR	DEL	TG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66781227_66781228delTG								MCART3P (281852 upstream) : None (None downstream)																							AGGAGTTGACtgtgtgtgtgtg	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	71966198	71966198	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71966198delT								B3GAT2 (299410 upstream) : OGFRL1 (32279 downstream)																							AGTGACTCCATTTTGGACATT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82362570	82362570	+	IGR	DEL	A	-	-	rs72429669		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82362570delA								None (None upstream) : FAM46A (92878 downstream)																							AAAGCTGCAGAAAAAAAAAAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	83433198	83433198	+	IGR	DEL	C	-	-	rs140756337	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83433198delC								TPBG (356584 upstream) : UBE2CBP (168988 downstream)																							acaacaacaacaaAAAAAAAc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	84558947	84558948	+	IGR	INS	-	TT	TT	rs71549568		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84558947_84558948insTT								SNAP91 (139820 upstream) : RIPPLY2 (4037 downstream)																							TACTGAAACACTCtctttctct	0.233													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	87262925	87262926	+	IGR	INS	-	T	T	rs148604296	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87262925_87262926insT								SNHG5 (874474 upstream) : HTR1E (384098 downstream)																							ATCTTTAAGTGCTCAGATATTT	0.337													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	91147439	91147440	+	IGR	INS	-	T	T	rs150050166	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91147439_91147440insT								BACH2 (140877 upstream) : MAP3K7 (77913 downstream)																							actgtttgtccttttttttgtc	0.000													4	3	---	---	---	---	
LACE1	246269	broad.mit.edu	37	6	108664561	108664562	+	Intron	INS	-	T	T	rs151221050	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108664561_108664562insT	uc003psj.2	+							NM_145315	NP_660358	Q8WV93	LACE1_HUMAN	lactation elevated 1								ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)		cAACCTTTTTGTTTTTTTTTAG	0.203													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112277775	112277776	+	IGR	INS	-	GT	GT	rs144749595	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112277775_112277776insGT								FYN (83148 upstream) : WISP3 (97502 downstream)																							gtcaccaaagagtgtgtgtgtg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	136071121	136071122	+	IGR	DEL	TT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136071121_136071122delTT								C6orf217 (33929 upstream) : PDE7B (101712 downstream)																							tctctctctctttctgtgtgtg	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138937668	138937669	+	IGR	DEL	AG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138937668_138937669delAG								NHSL1 (44000 upstream) : CCDC28A (156988 downstream)																							aggcagagacagagagagagag	0.248													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	142360424	142360425	+	IGR	INS	-	CA	CA	rs9321854		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142360424_142360425insCA								None (None upstream) : NMBR (36321 downstream)																							CCACTTATacgcacacacacac	0.342													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	147477962	147477962	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147477962delC	uc003qlt.1	-						uc003qlu.1_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																		TTTTCTCCATCCATCCACGTT	0.473													4	2	---	---	---	---	
PLEKHG1	57480	broad.mit.edu	37	6	151132771	151132772	+	Intron	INS	-	A	A	rs113949195		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151132771_151132772insA	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron|PLEKHG1_uc011eem.1_Intron|PLEKHG1_uc003qnz.2_Intron	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		AGACCTGCATTAAAAAAAAAAA	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	167846747	167846749	+	IGR	DEL	GGT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167846747_167846749delGGT								TCP10 (48749 upstream) : C6orf123 (338472 downstream)																							tgtggatggaggtggtggtggca	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168556750	168556751	+	IGR	INS	-	T	T	rs145368471	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168556750_168556751insT								FRMD1 (76911 upstream) : DACT2 (150835 downstream)																							TGCATCTCCCATCCCCCCGGTG	0.604													4	4	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	2199699	2199700	+	Intron	INS	-	A	A	rs141314037	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2199699_2199700insA	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		cccgtctctgcaaaaaaaatac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	3251845	3251846	+	IGR	INS	-	GCGC	GCGC			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3251845_3251846insGCGC								CARD11 (168266 upstream) : SDK1 (89234 downstream)																							caccccagggtgcgcacacaca	0.035													3	3	---	---	---	---	
DFNA5	1687	broad.mit.edu	37	7	24747303	24747304	+	Intron	DEL	AC	-	-	rs66969664		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24747303_24747304delAC	uc010kus.1	-						DFNA5_uc003swz.2_Intron|DFNA5_uc003sxa.1_Intron|DFNA5_uc010kut.1_Intron	NM_001127453	NP_001120925	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5 protein isoform						sensory perception of sound					ovary(1)	1						aaaggagaagacacacacacac	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	26621617	26621617	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26621617delG								KIAA0087 (43173 upstream) : C7orf71 (55873 downstream)																							GCTGTGGCAAGGGGACACTTC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	28287410	28287410	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28287410delA								JAZF1 (66973 upstream) : LOC402644 (31432 downstream)																							TAAAGGAAATAAAAAAAAAAA	0.119													4	3	---	---	---	---	
CHN2	1124	broad.mit.edu	37	7	29469206	29469207	+	Intron	INS	-	AG	AG	rs28624792		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29469206_29469207insAG	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058	P52757	CHIO_HUMAN	beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2						cagacacacacacacacCCATA	0.332													1	7	---	---	---	---	
FAM188B	84182	broad.mit.edu	37	7	30794253	30794256	+	Intron	DEL	ATCC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30794253_30794256delATCC	uc010kwe.2	+						INMT_uc010kwc.1_Intron|INMT_uc010kwd.1_Intron|INMT_uc003tbs.1_Intron	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182												0						atatccatctatccatccatccat	0.039													4	2	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33471701	33471702	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33471701_33471702insT	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc003tdr.1_Intron|BBS9_uc003tds.1_Intron|BBS9_uc003tdt.2_Intron	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			ttctttctttcttttttttttt	0.114									Bardet-Biedl_syndrome				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35089252	35089253	+	IGR	INS	-	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35089252_35089253insC								DPY19L1 (11599 upstream) : DPY19L2P1 (30348 downstream)																							CTTCTCTGGAGCCCCAGAACAG	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	37714981	37714981	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37714981delT								ELMO1 (226451 upstream) : GPR141 (65015 downstream)																							TTTAGCATTGTTCCCAGGAAA	0.343													4	2	---	---	---	---	
OGDH	4967	broad.mit.edu	37	7	44644510	44644510	+	5'Flank	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44644510delA	uc003tln.2	+						OGDH_uc003tlm.2_5'Flank|OGDH_uc011kbx.1_5'Flank|OGDH_uc011kby.1_5'Flank	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor						glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)	atcctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
CCM2	83605	broad.mit.edu	37	7	45036446	45036447	+	5'Flank	INS	-	GT	GT			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45036446_45036447insGT	uc003tmn.2	+									Q9BSQ5	CCM2_HUMAN	Homo sapiens PP10187 mRNA, complete cds.						endothelial tube morphogenesis|integrin-mediated signaling pathway|stress-activated MAPK cascade|vasculogenesis	cytoplasm	protein binding				0						atttctcatgggtgtgtgtgtg	0.000									Familial_Cerebral_Cavernous_Angioma				4	2	---	---	---	---	
SUN3	256979	broad.mit.edu	37	7	48028695	48028696	+	Intron	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48028695_48028696delAC	uc003tof.2	-						SUN3_uc010kyq.2_Intron|SUN3_uc003tog.2_Intron|SUN3_uc011kcf.1_Intron	NM_152782	NP_689995	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 1							integral to membrane				central_nervous_system(1)	1						agatggatggacacacagacag	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54584927	54584928	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54584927_54584928insT								HPVC1 (314813 upstream) : VSTM2A (25091 downstream)																							atctagcaggatttttttggca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56439441	56439442	+	IGR	INS	-	G	G	rs140774664		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56439441_56439442insG								PSPH (255351 upstream) : DKFZp434L192 (124474 downstream)																							GTGTGAGGCAAGGGGCTCACGC	0.708													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57274577	57274577	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57274577delT								ZNF479 (67006 upstream) : ZNF716 (235306 downstream)																							CACCtctttctttttttttct	0.065													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57625746	57625747	+	IGR	INS	-	A	A	rs142046463		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57625746_57625747insA								ZNF716 (92481 upstream) : None (None downstream)																							GAGATTGCTCCACAATCCATTT	0.287													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57748875	57748875	+	IGR	DEL	A	-	-	rs112740084		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57748875delA								ZNF716 (215610 upstream) : None (None downstream)																							cagtgtctttaatccttgtta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57774292	57774292	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57774292delA								ZNF716 (241027 upstream) : None (None downstream)																							cactatacccagctatttttt	0.000													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61794323	61794324	+	IGR	INS	-	AAC	AAC			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61794323_61794324insAAC								None (None upstream) : LOC643955 (957348 downstream)																							aaacgaatggaatcatcgaatg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61816353	61816353	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61816353delG								None (None upstream) : LOC643955 (935319 downstream)																							ATGACTGAATGAATGCGGTTC	0.473													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61866347	61866347	+	IGR	DEL	T	-	-	rs111371066		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61866347delT								None (None upstream) : LOC643955 (885325 downstream)																							agcttcattctttttttttat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62474185	62474186	+	IGR	INS	-	G	G	rs140692461		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62474185_62474186insG								None (None upstream) : LOC643955 (277486 downstream)																							GGGAAGGGGATGAAGGAAGGGC	0.460													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67218066	67218069	+	IGR	DEL	AGAG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67218066_67218069delAGAG								STAG3L4 (431554 upstream) : None (None downstream)																							aagaagaaatagagagagaaagag	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67967965	67967966	+	IGR	INS	-	T	T	rs145533217	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67967965_67967966insT								None (None upstream) : None (None downstream)																							aattttttatattttggtagag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68052213	68052214	+	IGR	INS	-	T	T	rs150190706		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68052213_68052214insT								None (None upstream) : None (None downstream)																							ACTCAAAtttcttttttttttt	0.203													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68268329	68268329	+	IGR	DEL	G	-	-	rs71910280		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68268329delG								None (None upstream) : AUTS2 (795576 downstream)																							TAAATGTGATGGGGGGGTGGT	0.388													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	72010141	72010144	+	IGR	DEL	AAGA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72010141_72010144delAAGA								CALN1 (98005 upstream) : TYW1B (13585 downstream)																							ggaaggaaggaagaaagaaagaaa	0.064													7	5	---	---	---	---	
SPDYE8P	389517	broad.mit.edu	37	7	74970249	74970249	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74970249delA	uc010lcv.2	+						PMS2L2_uc011kfp.1_Intron|PMS2L2_uc011kfq.1_Intron|PMS2L2_uc003uch.1_Intron|SPDYE8P_uc011kfs.1_Intron|PMS2L2_uc003uco.1_Intron|PMS2L2_uc003ucq.2_Intron					RecName: Full=Putative WBSCR19-like protein 4;												0						TTATAGTCTCaaaaaaaaaaa	0.418													12	7	---	---	---	---	
PHTF2	57157	broad.mit.edu	37	7	77447484	77447484	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77447484delT	uc003ugq.3	+						PHTF2_uc003ugo.3_Intron|PHTF2_uc003ugp.2_Intron|PHTF2_uc010ldv.2_Intron	NM_001127358	NP_001120830	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1						attaattccctgtcccatgaa	0.000													4	2	---	---	---	---	
PHTF2	57157	broad.mit.edu	37	7	77453577	77453577	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77453577delT	uc003ugq.3	+						PHTF2_uc003ugo.3_Intron|PHTF2_uc003ugp.2_Intron|PHTF2_uc010ldv.2_Intron	NM_001127358	NP_001120830	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1						TCCTGGTTTGTTTTTTTTTTT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	81092166	81092167	+	IGR	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81092166_81092167delAC								SEMA3C (540491 upstream) : HGF (239278 downstream)																							acacacacatacacacacacac	0.272													4	2	---	---	---	---	
GRM3	2913	broad.mit.edu	37	7	86311812	86311812	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86311812delT	uc003uid.2	+						GRM3_uc010lef.2_Intron|GRM3_uc010leg.2_Intron|GRM3_uc010leh.2_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor						synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	TGCTTATTTATTATCATTGGT	0.284													4	2	---	---	---	---	
DYNC1I1	1780	broad.mit.edu	37	7	95479411	95479411	+	Intron	DEL	T	-	-	rs148725818		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95479411delT	uc003uoc.3	+						DYNC1I1_uc003uod.3_Intron|DYNC1I1_uc003uob.2_Intron|DYNC1I1_uc003uoe.3_Intron|DYNC1I1_uc010lfl.2_Intron	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1						vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole|vesicle	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			tttctgaaggttttttagtga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	96975128	96975130	+	IGR	DEL	AAA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96975128_96975130delAAA								ACN9 (164055 upstream) : TAC1 (386141 downstream)																							cgtctcaaggaaaaaaaaaaaGC	0.217													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98202861	98202861	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98202861delA								BAIAP2L1 (172434 upstream) : NPTX2 (43736 downstream)																							attccatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ZNF789	285989	broad.mit.edu	37	7	99072217	99072217	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99072217delA	uc003uqq.1	+						ZNF789_uc003uqp.2_Intron|ZNF789_uc010lfw.1_Intron	NM_213603	NP_998768	Q5FWF6	ZN789_HUMAN	zinc finger protein 789 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|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)					actccacctcaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100615378	100615378	+	IGR	DEL	C	-	-	rs33957279		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100615378delC								ACHE (120839 upstream) : MUC12 (32697 downstream)																							GATCCAGAGACCCCCTGCCCT	0.328													7	5	---	---	---	---	
C7orf52	375607	broad.mit.edu	37	7	100822650	100822651	+	Intron	INS	-	A	A	rs5886168		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100822650_100822651insA	uc003uxy.1	-						C7orf52_uc003uxz.1_Intron|C7orf52_uc003uya.1_5'Flank|C7orf52_uc003uyb.1_Intron	NM_198571	NP_940973	Q8N8M0	CG052_HUMAN	hypothetical protein LOC375607								N-acetyltransferase activity			ovary(1)	1	Lung NSC(181;0.168)|all_lung(186;0.215)					CCCAGCAGATGAAAAAAAAAAA	0.609													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101967482	101967482	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101967482delA								SH2B2 (5305 upstream) : SPDYE6 (18711 downstream)																							ACTCTGTCTCAAAAAAAAAAA	0.189													6	3	---	---	---	---	
COG5	10466	broad.mit.edu	37	7	107145328	107145329	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107145328_107145329insT	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4						tttgaatcttcttttttttctt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	113720144	113720145	+	IGR	INS	-	AGAA	AGAA	rs145948358	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113720144_113720145insAGAA								PPP1R3A (161062 upstream) : FOXP2 (6237 downstream)																							aggaggaaaatagagggaaata	0.223													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114449116	114449116	+	IGR	DEL	A	-	-	rs35598602		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114449116delA								FOXP2 (118024 upstream) : MDFIC (113093 downstream)																							CAGACTGGTTAAAAAAAAAAA	0.343													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114972547	114972550	+	IGR	DEL	GTGC	-	-	rs61421473		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114972547_114972550delGTGC								MDFIC (313284 upstream) : TFEC (602652 downstream)																							gtgtgtgtgtgtgcgcgcgcgtgt	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	118114344	118114344	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118114344delA								ANKRD7 (231562 upstream) : None (None downstream)																							agggttttctaaaggtgcaga	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	120559267	120559268	+	IGR	DEL	GT	-	-	rs10557184		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120559267_120559268delGT								TSPAN12 (61090 upstream) : ING3 (31549 downstream)																							AAgtgtgtgagtgtgtgtgtgt	0.342													3	4	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122281917	122281917	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122281917delA	uc010lkp.2	-						CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						ATGTTACGTTAAAAAAAAAAA	0.323													4	2	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122452078	122452078	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122452078delT	uc010lkp.2	-						CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						AATTCACCTATTTTTTTTTTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	122684192	122684193	+	IGR	INS	-	T	T	rs138633699	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122684192_122684193insT								TAS2R16 (48438 upstream) : SLC13A1 (69396 downstream)																							tccttccttcctccttccttcc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	123745264	123745264	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123745264delA	uc011koc.1	+											Homo sapiens disrupted in Rett 1 mRNA sequence.																		gaaatttaataaaagtgacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124947018	124947025	+	IGR	DEL	ACTCACTC	-	-	rs141552763		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124947018_124947025delACTCACTC								POT1 (376981 upstream) : None (None downstream)																							ttcacttactactcactcactcactcac	0.058													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128569765	128569765	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128569765delT								KCP (18992 upstream) : IRF5 (8004 downstream)																							ATTTCTTCCCTCTGCCTGCAA	0.458													4	2	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	131922088	131922088	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131922088delG	uc003vra.3	-							NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						ACTCAGAGATGGGGAGGGTGC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	132891548	132891548	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132891548delG								CHCHD3 (124720 upstream) : EXOC4 (46275 downstream)																							TGAATTGGCTGGGTGGCAAGT	0.537													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133023991	133023992	+	Intron	DEL	TG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133023991_133023992delTG	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vri.2_Intron|EXOC4_uc003vrj.2_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				tccatggtTTTGTGTGTGTGTG	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	134659239	134659240	+	IGR	INS	-	C	C	rs146757175		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134659239_134659240insC								CALD1 (3769 upstream) : AGBL3 (12019 downstream)																							ctactgtattgtcccccttgac	0.089													2	5	---	---	---	---	
DGKI	9162	broad.mit.edu	37	7	137507878	137507878	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137507878delA	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3						aaaaggtcccaaaacccatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	140215504	140215504	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140215504delT								MKRN1 (36135 upstream) : DENND2A (2723 downstream)																							gcccACCTTCTTTTTTTTTCc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142109561	142109562	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142109561_142109562insA	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		CCATGCACAGGCTGCTCAGAAA	0.535													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151900273	151900273	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151900273delA	uc003wla.2	-						MLL3_uc003wkz.2_Intron	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)		CTTTTTGAACAAAAAAATCTC	0.259			N		medulloblastoma								4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151971449	151971450	+	Intron	INS	-	C	C	rs79820593		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151971449_151971450insC	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)		AGACTCACAGAAAAAAACACAA	0.287			N		medulloblastoma								3	5	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152112561	152112562	+	Intron	INS	-	TGTCTTAAAG	TGTCTTAAAG	rs149892943		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152112561_152112562insTGTCTTAAAG	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)		CTTAGAGCAAATATGTCATACA	0.213			N		medulloblastoma								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	5662747	5662747	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5662747delA								CSMD1 (810419 upstream) : MCPH1 (601374 downstream)																							ttcatgatataaaacccatta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	8052963	8052964	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8052963_8052964insA								MIR548I3 (106352 upstream) : FLJ10661 (33128 downstream)																							aataagtaaacaaaaaaaaagc	0.000													4	2	---	---	---	---	
MFHAS1	9258	broad.mit.edu	37	8	8703388	8703388	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8703388delA	uc003wsj.1	-							NM_004225	NP_004216	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified												0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		ttgtcaggccaaaaacctttg	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	9815758	9815759	+	IGR	INS	-	TCCTGT	TCCTGT	rs145278049	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9815758_9815759insTCCTGT								MIR124-1 (54776 upstream) : MSRA (96071 downstream)																							gcacgcacacctcctgttacgt	0.000													6	4	---	---	---	---	
XKR6	286046	broad.mit.edu	37	8	10921027	10921028	+	Intron	DEL	AA	-	-	rs35995429		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10921027_10921028delAA	uc003wtk.1	-							NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		gccctgtctcaaaaaaaaaaaa	0.163													4	2	---	---	---	---	
C8orf79	57604	broad.mit.edu	37	8	12831171	12831171	+	Intron	DEL	A	-	-	rs34721055		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12831171delA	uc010lsq.2	+						C8orf79_uc011kxw.1_Intron	NM_020844	NP_065895	Q9P272	K1456_HUMAN	hypothetical protein LOC57604 isoform 1								methyltransferase activity				0						ggggtggatgacatggaactg	0.000													5	4	---	---	---	---	
SGCZ	137868	broad.mit.edu	37	8	15015829	15015829	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15015829delT	uc003wwq.2	-							NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		AAATTTTTCCTTTTTTGCTAG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	16314245	16314246	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16314245_16314246insA								MSR1 (263945 upstream) : FGF20 (536088 downstream)																							aggaagggaggaagggagggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	18346325	18346325	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18346325delA								NAT2 (87602 upstream) : PSD3 (38489 downstream)																							caggcaagggaaaaaaaataa	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20747007	20747007	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20747007delT								LZTS1 (634204 upstream) : GFRA2 (802523 downstream)																							CCTGCTTGTGTTTTTTTTTTC	0.498													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23362659	23362659	+	IGR	DEL	A	-	-	rs111727100		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23362659delA								ENTPD4 (47415 upstream) : SLC25A37 (23704 downstream)																							actccgtctcaaaaaaaaaaa	0.020													4	2	---	---	---	---	
GTF2E2	2961	broad.mit.edu	37	8	30453684	30453684	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30453684delC	uc003xig.2	-							NM_002095	NP_002086	P29084	T2EB_HUMAN	general transcription factor IIE, polypeptide 2,						regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIE complex	DNA binding|protein binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.113)|Kidney(114;0.135)		ctctgagcttcacagatcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	31177253	31177253	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31177253delT								WRN (145977 upstream) : NRG1 (320015 downstream)																							AGTATCCAGCTTCCAAGTTTT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	33064121	33064121	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33064121delG								NRG1 (441563 upstream) : FUT10 (164225 downstream)																							tggagtcattggtgacattta	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37399573	37399574	+	IGR	INS	-	TGTG	TGTG	rs150837338	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37399573_37399574insTGTG								KCNU1 (605932 upstream) : ZNF703 (153727 downstream)																							TCAGAAGGAGAtgtgtgtgtgt	0.223													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	38464046	38464047	+	IGR	INS	-	GGCATGTG	GGCATGTG	rs150922347	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38464046_38464047insGGCATGTG								RNF5P1 (5271 upstream) : TACC1 (121657 downstream)																							ATGAAAGTGCCGGCATGTGTCT	0.455													5	3	---	---	---	---	
TACC1	6867	broad.mit.edu	37	8	38600811	38600814	+	Intron	DEL	TGAA	-	-	rs71862752		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38600811_38600814delTGAA	uc011lbz.1	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc003xmb.3_Intron	NM_006283	NP_006274	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			ATATATTTGTtgaatgaatgaatg	0.328													3	3	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40501309	40501309	+	Intron	DEL	A	-	-	rs145640905		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40501309delA	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			gtgtgtgtgcaaaaaaaaaaa	0.000													5	4	---	---	---	---	
MYST3	7994	broad.mit.edu	37	8	41829415	41829416	+	Intron	INS	-	A	A	rs140089536	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41829415_41829416insA	uc010lxb.2	-						MYST3_uc010lxc.2_Intron|MYST3_uc003xon.3_Intron|MYST3_uc010lxd.2_Intron	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic						histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)			gtatgacagagaaaaaaaaaat	0.074													5	3	---	---	---	---	
MYST3	7994	broad.mit.edu	37	8	41856980	41856981	+	Intron	DEL	CC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41856980_41856981delCC	uc010lxb.2	-						MYST3_uc010lxc.2_Intron|MYST3_uc003xon.3_Intron|MYST3_uc010lxd.2_Intron	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic						histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)			TATGCAATCTCCTCCATAGACT	0.386													4	2	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48325686	48325686	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48325686delG	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|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	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				TGTGGTGGATGGTGAACTATC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55263426	55263426	+	IGR	DEL	T	-	-	rs113896196		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55263426delT								MRPL15 (202352 upstream) : SOX17 (107069 downstream)																							TAAAAAGAAAttttttttttt	0.134													4	2	---	---	---	---	
CA8	767	broad.mit.edu	37	8	61105497	61105498	+	Intron	DEL	CA	-	-	rs34956420	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61105497_61105498delCA	uc003xtz.1	-							NM_004056	NP_004047	P35219	CAH8_HUMAN	carbonic anhydrase VIII						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)				caacatcatgcacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61310875	61310876	+	IGR	INS	-	T	T	rs71557785		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61310875_61310876insT								CA8 (116921 upstream) : RAB2A (118683 downstream)																							atgcctggctattttttttttt	0.000													4	2	---	---	---	---	
MTFR1	9650	broad.mit.edu	37	8	66571662	66571662	+	Intron	DEL	T	-	-	rs35841835		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66571662delT	uc003xvm.2	+						MTFR1_uc011lep.1_Intron	NM_014637	NP_055452	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1 isoform 1							mitochondrion|plasma membrane				pancreas(1)	1			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			aaaggagaggttttttttttt	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	66846399	66846399	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66846399delT								PDE7A (92644 upstream) : DNAJC5B (87392 downstream)																							ccatgacatattcttagcttc	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	67189627	67189627	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67189627delA								CRH (98929 upstream) : RRS1 (151636 downstream)																							GTGAATGTATATTAATAGTCA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	69926312	69926312	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69926312delA	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																		ttttcttcttaaaaaaaaatc	0.189													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70269648	70269648	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70269648delC								C8orf34 (538392 upstream) : SULF1 (109211 downstream)																							tgttcctattcggccatcttg	0.129													4	2	---	---	---	---	
SLCO5A1	81796	broad.mit.edu	37	8	70623248	70623248	+	Intron	DEL	T	-	-	rs10715743		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70623248delT	uc003xyl.2	-						SLCO5A1_uc010lzb.2_Intron|SLCO5A1_uc011lfa.1_Intron|SLCO5A1_uc003xyk.2_Intron|SLCO5A1_uc010lzc.2_Intron	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,							integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			CTTCATACTGTCCCCCCCACT	0.567													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	71017690	71017691	+	IGR	INS	-	A	A	rs144729155	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71017690_71017691insA								PRDM14 (34128 upstream) : NCOA2 (6576 downstream)																							tggatgtagtggctatggttat	0.015													2	4	---	---	---	---	
TRPA1	8989	broad.mit.edu	37	8	72973182	72973183	+	Intron	DEL	TG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72973182_72973183delTG	uc003xza.2	-							NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1							integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	tgtgtgtgcttgtgtgtgtgtg	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	84606776	84606776	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84606776delA								None (None upstream) : RALYL (488677 downstream)																							gtagatgtctaaaagtgaaac	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	85080811	85080814	+	IGR	DEL	TGTG	-	-	rs71896863		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85080811_85080814delTGTG								None (None upstream) : RALYL (14639 downstream)																							TCACCCtgtttgtgtgtgtgtgtg	0.260													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	85891683	85891684	+	IGR	DEL	TT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85891683_85891684delTT								RALYL (57612 upstream) : LRRCC1 (127693 downstream)																							tatttttgtatttttagtagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	87859835	87859836	+	IGR	INS	-	AGGA	AGGA			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87859835_87859836insAGGA								CNGB3 (103934 upstream) : CNBD1 (18840 downstream)																							gggagggagggaggaaggaagg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	89883046	89883047	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89883046_89883047insT								MMP16 (543329 upstream) : RIPK2 (886928 downstream)																							tgtcttcttgattttttttcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	90829200	90829200	+	IGR	DEL	A	-	-	rs67731695		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90829200delA								RIPK2 (25909 upstream) : OSGIN2 (84896 downstream)																							CTGGAGCTGTAAAAAAATACA	0.463													4	2	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100819943	100819943	+	Intron	DEL	G	-	-	rs34184716		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100819943delG	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ACGCACACGTGTGTTTTCTTA	0.224													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101337994	101337995	+	IGR	INS	-	AC	AC	rs143644146	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101337994_101337995insAC								RNF19A (15667 upstream) : ANKRD46 (183992 downstream)																							GAGTATGTATTACACACACACA	0.317													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101439017	101439018	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101439017_101439018insT								RNF19A (116690 upstream) : ANKRD46 (82969 downstream)																							accaccaccacctcactaccac	0.000													4	2	---	---	---	---	
PABPC1	26986	broad.mit.edu	37	8	101726153	101726154	+	Intron	INS	-	A	A	rs142785641	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101726153_101726154insA	uc003yjs.1	-						PABPC1_uc011lhc.1_Intron|PABPC1_uc011lhd.1_Intron|PABPC1_uc003yjt.1_Intron|PABPC1_uc003yju.2_Intron	NM_002568	NP_002559	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1						mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation	catalytic step 2 spliceosome|cytosol	nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity				0	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			GAAAGACAGGGAAAAAAAATTC	0.391													4	2	---	---	---	---	
DCAF13	25879	broad.mit.edu	37	8	104454009	104454010	+	Intron	INS	-	T	T	rs71575961		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104454009_104454010insT	uc003yln.2	+						DCAF13_uc003ylo.2_Intron	NM_015420	NP_056235	Q9NV06	DCA13_HUMAN	WD repeats and SOF1 domain containing						rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1						tttcttttttcttttttttttt	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	109298703	109298704	+	IGR	DEL	AG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109298703_109298704delAG								EIF3E (37744 upstream) : TTC35 (157149 downstream)																							tctcaaaaaaaGAGAGAGAGAG	0.238													4	2	---	---	---	---	
SAMD12	401474	broad.mit.edu	37	8	119360616	119360617	+	Intron	INS	-	T	T	rs113186433		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119360616_119360617insT	uc010mda.1	-						SAMD12_uc010mdb.1_Intron	NM_001101676	NP_001095146	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			ccACTTATTACttttttttttt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	123377349	123377349	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123377349delT								HAS2AS (720416 upstream) : ZHX2 (416552 downstream)																							ctgggcagggtttttagtatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	123716334	123716334	+	IGR	DEL	A	-	-	rs74542816		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123716334delA								None (None upstream) : ZHX2 (77567 downstream)																							CACTCTATTTAAAAAAAAAAA	0.239													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124682455	124682456	+	IGR	DEL	CT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124682455_124682456delCT								KLHL38 (17265 upstream) : ANXA13 (10579 downstream)																							tcctccccaccttcctcctcct	0.144													6	3	---	---	---	---	
NSMCE2	286053	broad.mit.edu	37	8	126325345	126325345	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126325345delA	uc003yrw.2	+							NM_173685	NP_775956	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			cttaaagtggaaaaaaaaaaa	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128624982	128624982	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128624982delT								LOC727677 (130598 upstream) : MYC (122783 downstream)																							ataaaaggaatttttcctccc	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129689359	129689359	+	IGR	DEL	A	-	-	rs35214084		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129689359delA								MIR1208 (526925 upstream) : None (None downstream)																							tggaactgccaaaattatata	0.209													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130108928	130108929	+	IGR	DEL	TC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130108928_130108929delTC								MIR1208 (946494 upstream) : GSDMC (651514 downstream)																							tttttttctttctctctctctc	0.074													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130416758	130416758	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130416758delA								None (None upstream) : GSDMC (343685 downstream)																							AAAGAAAAATAATAAACTCTT	0.159													4	2	---	---	---	---	
GSDMC	56169	broad.mit.edu	37	8	130791096	130791096	+	Intron	DEL	A	-	-	rs61071273	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130791096delA	uc003ysr.2	-							NM_031415	NP_113603	Q9BYG8	GSDMC_HUMAN	melanoma-derived leucine zipper, extra-nuclear							mitochondrion				ovary(2)|skin(1)	3						acaatcgtataaaaaaaaaag	0.000													4	2	---	---	---	---	
ADCY8	114	broad.mit.edu	37	8	131916612	131916612	+	Intron	DEL	T	-	-	rs35578806		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131916612delT	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)			AAAACAGTGATTTTTTTTTTC	0.383										HNSCC(32;0.087)			2	4	---	---	---	---	
LRRC6	23639	broad.mit.edu	37	8	133640658	133640658	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133640658delA	uc003ytk.2	-						LRRC6_uc003ytl.2_Intron	NM_012472	NP_036604	Q86X45	LRRC6_HUMAN	leucine rich repeat containing 6							cytoplasm				ovary(1)|kidney(1)	2	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			actccatctcaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	135739375	135739376	+	IGR	INS	-	A	A	rs13272908		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135739375_135739376insA								ZFAT (14094 upstream) : MIR30B (73387 downstream)																							ACACGAAGtggagaaaaaaaaa	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136783851	136783852	+	IGR	DEL	GC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136783851_136783852delGC								KHDRBS3 (124005 upstream) : None (None downstream)																							gttgaagcttgcccatagtgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139063514	139063518	+	IGR	DEL	AGTTT	-	-	rs139255629		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139063514_139063518delAGTTT								None (None upstream) : FAM135B (78750 downstream)																							aagagaagaaagtttagaagagaag	0.132													4	3	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141246179	141246180	+	Intron	DEL	TT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141246179_141246180delTT	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						ctgtatttcctttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142315233	142315233	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142315233delA								SLC45A4 (51008 upstream) : LOC731779 (35415 downstream)																							TACTCGGGGGAAAAGGCCACT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142946521	142946522	+	IGR	INS	-	AGAC	AGAC	rs148565558	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142946521_142946522insAGAC								MIR1302-7 (78847 upstream) : NCRNA00051 (333195 downstream)																							aaaaacagaatagacagacaga	0.198													3	3	---	---	---	---	
TSNARE1	203062	broad.mit.edu	37	8	143337296	143337296	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143337296delC	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_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)					atcaccatcaccatcaccacc	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143757708	143757708	+	IGR	DEL	T	-	-	rs2978980	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143757708delT								JRK (6307 upstream) : PSCA (4167 downstream)																							ATTCTGTGGGTCAGGAATTTG	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144493006	144493008	+	IGR	DEL	TGG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144493006_144493008delTGG								RHPN1 (26617 upstream) : MAFA (18507 downstream)																							gtgatggtgatggtggtggtggt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144743624	144743625	+	IGR	INS	-	CTT	CTT	rs34691044		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144743624_144743625insCTT								ZNF623 (7724 upstream) : ZNF707 (22997 downstream)																							CCTTCCTGCTCCTTCACTCGCC	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	19383920	19383921	+	IGR	DEL	TG	-	-	rs111414173		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19383920_19383921delTG								RPS6 (3685 upstream) : ACER2 (13886 downstream)																							AAAAAAGATTtgtgtgtgtgtg	0.228													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	23518500	23518500	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23518500delT	uc003zpr.2	-											Homo sapiens mRNA; cDNA DKFZp781D1719 (from clone DKFZp781D1719).																		acaagctctctttttgcctgc	0.000													4	2	---	---	---	---	
C9orf11	54586	broad.mit.edu	37	9	27291192	27291193	+	Intron	INS	-	T	T	rs138227130	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27291192_27291193insT	uc003zql.2	-						C9orf11_uc011lnq.1_Intron	NM_020641	NP_065692	Q9NQ60	AFAF_HUMAN	Acr formation associated factor isoform 1							acrosomal membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(39;7.39e-08)|Lung(218;1.26e-05)|LUSC - Lung squamous cell carcinoma(38;0.000106)		tgtgtcagacctgtggttggca	0.054													5	4	---	---	---	---	
LINGO2	158038	broad.mit.edu	37	9	28002264	28002264	+	Intron	DEL	T	-	-	rs71931826		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28002264delT	uc003zqu.1	-						LINGO2_uc010mjf.1_Intron|LINGO2_uc003zqv.1_Intron	NM_152570	NP_689783	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		CTTCCCTCCATTTTTTTTTTG	0.358													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	29410519	29410519	+	IGR	DEL	T	-	-	rs11292769		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29410519delT								MIR873 (521566 upstream) : None (None downstream)																							TGTTTGCTTGTTTTTTTTTTT	0.328													2	4	---	---	---	---	
MELK	9833	broad.mit.edu	37	9	36627051	36627052	+	Intron	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36627051_36627052delAC	uc003zzn.2	+						MELK_uc011lpm.1_Intron|MELK_uc011lpn.1_Intron|MELK_uc011lpo.1_Intron|MELK_uc010mll.2_Intron|MELK_uc011lpp.1_Intron|MELK_uc010mlm.2_Intron|MELK_uc011lpq.1_Intron|MELK_uc011lpr.1_Intron|MELK_uc011lps.1_Intron	NM_014791	NP_055606	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase							cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			ACAAGCGCAAacacacacacac	0.228													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	43397585	43397585	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43397585delA								LOC642929 (252101 upstream) : FAM75A6 (226919 downstream)																							gaggaactagaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	46208066	46208066	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:46208066delA								FAM27A (479784 upstream) : KGFLP1 (479500 downstream)																							tttggaggccaaggcatgtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66463598	66463600	+	Intron	DEL	TGT	-	-	rs149401867	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66463598_66463600delTGT	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		CCTTTGTAAGTGTTGCTGCAGCT	0.345													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66464673	66464674	+	Intron	DEL	TG	-	-	rs113415960		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66464673_66464674delTG	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		GTCAAAACACTGTACTGATTCC	0.356													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66486940	66486940	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66486940delA								FAM74A4 (992554 upstream) : LOC442421 (9530 downstream)																							CCCGCCCCCCAATACCTGCCC	0.731													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66510122	66510122	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66510122delT								LOC442421 (7095 upstream) : AQP7P1 (744145 downstream)																							aatttcctgattttggcaaca	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66799030	66799031	+	IGR	INS	-	TCTT	TCTT	rs112529174		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66799030_66799031insTCTT								LOC442421 (296003 upstream) : AQP7P1 (455236 downstream)																							ttttgaaacactttgtgaatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67340073	67340073	+	IGR	DEL	G	-	-	rs79998190		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67340073delG								AQP7P1 (50581 upstream) : FAM27B (452857 downstream)																							GGGGAGTGGAGCCTGGGCctg	0.373													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68356752	68356752	+	IGR	DEL	C	-	-	rs75577840		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68356752delC								FAM27B (562563 upstream) : MIR1299 (645487 downstream)																							GAAGTCTCATCCCCATATTTT	0.368													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68390793	68390794	+	IGR	DEL	CT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68390793_68390794delCT								FAM27B (596604 upstream) : MIR1299 (611445 downstream)																							tgctgtcttcctttttgtctaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68424724	68424724	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68424724delA								FAM27B (630535 upstream) : MIR1299 (577515 downstream)																							CATGTTACAGAGGAAGCACTG	0.473													21	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69828717	69828717	+	IGR	DEL	C	-	-	rs59138657		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69828717delC								LOC100133920 (163768 upstream) : FOXD4L5 (346992 downstream)																							TTCATCTTGGCTTCTTCTCTG	0.244													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69833589	69833590	+	IGR	DEL	AT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69833589_69833590delAT								LOC100133920 (168640 upstream) : FOXD4L5 (342119 downstream)																							ttctttcacaatatatgtttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	70837214	70837214	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70837214delA								CBWD3 (337151 upstream) : FOXD4L3 (80569 downstream)																							tggaattcagaagccatatag	0.000													4	3	---	---	---	---	
FAM189A2	9413	broad.mit.edu	37	9	71957261	71957261	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71957261delA	uc010mon.1	+						FAM189A2_uc004ahg.2_Intron	NM_001127608	NP_001121080	Q15884	F1892_HUMAN	chromosome 9 open reading frame 61 precursor							integral to membrane					0						ttgggctcctagttcattgct	0.149													4	2	---	---	---	---	
TMC1	117531	broad.mit.edu	37	9	75218465	75218466	+	Intron	INS	-	TGT	TGT	rs147532102	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75218465_75218466insTGT	uc004aiz.1	+						TMC1_uc010moz.1_Intron	NM_138691	NP_619636	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1						sensory perception of sound	integral to membrane				ovary(1)	1						GTTTAGTTTAGtgttgttgttg	0.193													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85178386	85178387	+	IGR	INS	-	AC	AC	rs138100887	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85178386_85178387insAC								FLJ46321 (568216 upstream) : RASEF (418930 downstream)																							tcccTGAACAGacacacacaca	0.015													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	87120146	87120146	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87120146delT								SLC28A3 (136733 upstream) : NTRK2 (163320 downstream)																							gaggatgagatttaggattag	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92178314	92178314	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92178314delC								SEMA4D (65426 upstream) : GADD45G (41613 downstream)																							TCACATCAGTCCACTGCCCAT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	95800468	95800468	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95800468delA								FGD3 (1950 upstream) : SUSD3 (20521 downstream)																							CATGGGTGTCAGGGAGGGACT	0.652													4	2	---	---	---	---	
HSD17B3	3293	broad.mit.edu	37	9	99025097	99025097	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99025097delC	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)	ttttgattttcccagtatatg	0.100													4	2	---	---	---	---	
TRIM14	9830	broad.mit.edu	37	9	100837622	100837623	+	Intron	INS	-	AG	AG	rs146097524	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100837622_100837623insAG	uc004ayd.2	-						NANS_uc004ayb.2_Intron|NANS_uc004ayc.2_Intron|NANS_uc004aye.1_5'Flank	NM_033220	NP_150089	Q14142	TRI14_HUMAN	tripartite motif protein TRIM14 isoform alpha							cytoplasm|intracellular	zinc ion binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.0559)				AAAAATAAAGCAGAGGAAGAGC	0.124													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102230076	102230076	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102230076delA								SEC61B (237176 upstream) : NR4A3 (354061 downstream)																							Caagaagaggaggggaaagaa	0.239													4	2	---	---	---	---	
TMEFF1	8577	broad.mit.edu	37	9	103271154	103271154	+	Intron	DEL	A	-	-	rs72170452		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103271154delA	uc004baz.1	+						TMEFF1_uc004bay.1_Intron	NM_003692	NP_003683	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two						multicellular organismal development	integral to membrane|plasma membrane					0		Acute lymphoblastic leukemia(62;0.0452)				TTTTTAAGCCAAAAAAAAAAA	0.284													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107862452	107862452	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107862452delT								ABCA1 (172016 upstream) : SLC44A1 (144477 downstream)																							ttcattactcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107963794	107963794	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107963794delA								ABCA1 (273358 upstream) : SLC44A1 (43135 downstream)																							tgtctcaaagaaaaaaaaaaa	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	115753027	115753028	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115753027_115753028insT								SLC46A2 (99834 upstream) : ZNF883 (6374 downstream)																							tggtcctgggctttttttttgt	0.000													4	2	---	---	---	---	
TNFSF8	944	broad.mit.edu	37	9	117678053	117678054	+	Intron	INS	-	G	G	rs148692901	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117678053_117678054insG	uc004bji.1	-							NM_001244	NP_001235	P32971	TNFL8_HUMAN	tumor necrosis factor (ligand) superfamily,						cell proliferation|cell-cell signaling|immune response|induction of apoptosis|signal transduction	extracellular space|integral to plasma membrane	cytokine activity|tumor necrosis factor receptor binding			lung(3)|skin(2)|ovary(1)	6						TCACAGTCCCATGGGGATTAtt	0.069													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120269831	120269831	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120269831delC								ASTN2 (92514 upstream) : TLR4 (196629 downstream)																							cttgggggaaccagggacagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122351804	122351804	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122351804delA								DBC1 (220065 upstream) : MIR147 (655453 downstream)																							CTTGTGATTTAAAAAAAAAAT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	123097405	123097405	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123097405delC								MIR147 (90077 upstream) : CDK5RAP2 (53743 downstream)																							tgcccaacgtcccccacctag	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132233878	132233879	+	IGR	INS	-	AAGGGC	AAGGGC	rs140052417	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132233878_132233879insAAGGGC								C9orf106 (148996 upstream) : C9orf50 (140627 downstream)																							CAGACCCCAGAAAGTCTGCTAC	0.500													4	3	---	---	---	---	
FNBP1	23048	broad.mit.edu	37	9	132701669	132701670	+	Intron	INS	-	A	A	rs35702684		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132701669_132701670insA	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848	Q96RU3	FNBP1_HUMAN	formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		cctccgtcccgaaaaataaaaa	0.144			T	MLL	AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	134664476	134664477	+	IGR	INS	-	T	T	rs140538983	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134664476_134664477insT								RAPGEF1 (49259 upstream) : MED27 (71022 downstream)																							ttctttctttcttttctttctt	0.010													3	5	---	---	---	---	
NOTCH1	4851	broad.mit.edu	37	9	139430311	139430311	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139430311delA	uc004chz.2	-							NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein						aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GATCCCTCCCAGGGGCAATGG	0.667			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			3	3	---	---	---	---	
MAN1B1	11253	broad.mit.edu	37	9	139985243	139985243	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139985243delC	uc004cld.2	+						MAN1B1_uc004clc.2_Intron|MAN1B1_uc011meo.1_Intron|MAN1B1_uc011mep.1_Intron|MAN1B1_uc010ncc.2_Intron	NM_016219	NP_057303	Q9UKM7	MA1B1_HUMAN	alpha 1,2-mannosidase						oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|endoplasmic reticulum quality control compartment|integral to membrane	alpha-mannosidase activity|calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(1)|central_nervous_system(1)	2	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		cccacctcagccccccaaagt	0.065													4	2	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1633853	1633854	+	Intron	DEL	CG	-	-	rs56004358		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1633853_1633854delCG	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)		GAGGCGTGcacgcacacacaca	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	5525459	5525459	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5525459delT								NET1 (25035 upstream) : CALML5 (15199 downstream)																							cactccagcatgggcaacaga	0.100													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	6303982	6303983	+	IGR	INS	-	AA	AA	rs111259697		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6303982_6303983insAA								PFKFB3 (26477 upstream) : PRKCQ (165122 downstream)																							aaacaaaaaacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
PRKCQ	5588	broad.mit.edu	37	10	6513200	6513200	+	Intron	DEL	C	-	-	rs146987709		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6513200delC	uc001ijj.1	-						PRKCQ_uc009xim.1_Intron|PRKCQ_uc001iji.1_Intron|PRKCQ_uc009xin.1_Intron|PRKCQ_uc010qax.1_Intron	NM_006257	NP_006248	Q04759	KPCT_HUMAN	protein kinase C, theta						axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6						AAACATGCATCTTGGTATCAA	0.403													2	4	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14502996	14502996	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14502996delC	uc001imv.2	-						FRMD4A_uc001imw.1_Intron			Q9P2Q2	FRM4A_HUMAN	Homo sapiens mRNA for KIAA1294 protein, partial cds.							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						gctactttctcccctagggca	0.000													4	2	---	---	---	---	
ST8SIA6	338596	broad.mit.edu	37	10	17453172	17453173	+	Intron	DEL	TG	-	-	rs72283269		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17453172_17453173delTG	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						TTGAACTCTTtgtgtgtgtgtg	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	19399693	19399693	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19399693delT								ARL5B (432753 upstream) : PLXDC2 (705679 downstream)																							cagcaatgtctttatatatct	0.149													4	2	---	---	---	---	
MLLT10	8028	broad.mit.edu	37	10	21958032	21958033	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21958032_21958033insT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001ira.2_Intron|MLLT10_uc001iqz.2_Intron	NM_004641	NP_004632	P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2						GTAAAATGGGATTTTTTTTTTC	0.307			T	MLL|PICALM|CDK6	AL								4	2	---	---	---	---	
DNAJC1	64215	broad.mit.edu	37	10	22047456	22047456	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22047456delG	uc001irc.2	-						DNAJC1_uc001ird.2_Intron	NM_022365	NP_071760	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1						negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				GCTACCAGCAGGGAGAAAGGC	0.612													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	22739786	22739787	+	IGR	INS	-	A	A	rs144369481	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22739786_22739787insA								SPAG6 (33248 upstream) : PIP4K2A (83980 downstream)																							cccatctctacaaaaaaaaaca	0.000													4	2	---	---	---	---	
KIAA1217	56243	broad.mit.edu	37	10	24419622	24419622	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24419622delT	uc001irs.2	+							NM_001098500	NP_001091970	Q5T5P2	SKT_HUMAN	sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7						CCGATTGGAATTACCTTTTCA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	26945857	26945857	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26945857delC								LOC731789 (3475 upstream) : PDSS1 (40738 downstream)																							atcttcctttcttgtctgctt	0.000													4	2	---	---	---	---	
NCRNA00202	387644	broad.mit.edu	37	10	27225419	27225421	+	Intron	DEL	GAG	-	-	rs147078790		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27225419_27225421delGAG	uc001itf.2	-							NR_026795				Homo sapiens cDNA FLJ40086 fis, clone TESTI2003031.												0						AGGGGAAGAAGAGGAGGAAACAG	0.438													3	3	---	---	---	---	
ARMC4	55130	broad.mit.edu	37	10	28217423	28217423	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28217423delA	uc009xky.2	-						ARMC4_uc010qds.1_Intron|ARMC4_uc010qdt.1_Intron|ARMC4_uc001itz.2_Intron	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4								binding			ovary(4)|skin(2)	6						ACCTCAAAACAAAATCCAAAT	0.403													4	2	---	---	---	---	
SVIL	6840	broad.mit.edu	37	10	29796491	29796492	+	Intron	INS	-	ACAC	ACAC	rs145651487	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29796491_29796492insACAC	uc001iut.1	-						SVIL_uc010qdw.1_Intron|SVIL_uc001iuu.1_Intron	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2						cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)				cactcatagatacacactctca	0.084													3	3	---	---	---	---	
MTPAP	55149	broad.mit.edu	37	10	30638286	30638286	+	5'Flank	DEL	A	-	-	rs10826784		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30638286delA	uc001iva.3	-						MTPAP_uc001ivb.3_Intron|MTPAP_uc001ivc.2_5'Flank	NM_018109	NP_060579	Q9NVV4	PAPD1_HUMAN	PAP associated domain containing 1 precursor						cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1						GTCGGGGGGGAGGGGGGGGGC	0.512													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	32076219	32076219	+	IGR	DEL	T	-	-	rs11355159		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32076219delT								ZEB1 (258092 upstream) : ARHGAP12 (19006 downstream)																							ttttcttttcttttttttttt	0.000													3	3	---	---	---	---	
NRP1	8829	broad.mit.edu	37	10	33569458	33569459	+	Intron	INS	-	A	A	rs144550143	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33569458_33569459insA	uc001iwx.3	-						NRP1_uc001iwv.3_Intron|NRP1_uc009xlz.2_Intron|NRP1_uc001iww.3_Intron|NRP1_uc001iwy.3_Intron|NRP1_uc001iwz.2_Intron|NRP1_uc001ixa.2_Intron|NRP1_uc001ixb.1_Intron|NRP1_uc001ixc.1_Intron	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a						axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)	GTTCTTCAGGGAAAAAAAAATA	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	33713814	33713814	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33713814delT								NRP1 (89808 upstream) : PARD3 (686284 downstream)																							TCTTTGTTCATTTTTTTTTTC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38590039	38590040	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38590039_38590040insA								LOC100129055 (86767 upstream) : HSD17B7P2 (55268 downstream)																							gaccctgccttaaaaaaaaaaa	0.079													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38795783	38795797	+	IGR	DEL	GAATGGAATGGAATG	-	-	rs140352723		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38795783_38795797delGAATGGAATGGAATG								LOC399744 (54703 upstream) : None (None downstream)																							gagtggactcgaatggaatggaatggaatggaatg	0.047													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	39081263	39081263	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39081263delT								LOC399744 (340183 upstream) : None (None downstream)																							ctccattccatttttttccaa	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	39146085	39146089	+	IGR	DEL	GAATC	-	-	rs61713023		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39146085_39146089delGAATC								LOC399744 (405005 upstream) : None (None downstream)																							gaatggaatggaatcgaatggaatg	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42368677	42368681	+	IGR	DEL	ATACA	-	-	rs112096796	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42368677_42368681delATACA								None (None upstream) : LOC441666 (458634 downstream)																							attccattccatacaattccattcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42642538	42642538	+	IGR	DEL	A	-	-	rs74632924	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42642538delA								None (None upstream) : LOC441666 (184777 downstream)																							GTTGCTTTTTATTTCCTTACT	0.443													4	2	---	---	---	---	
BMS1	9790	broad.mit.edu	37	10	43310526	43310527	+	Intron	INS	-	A	A	rs146360022		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43310526_43310527insA	uc001jaj.2	+							NM_014753	NP_055568	Q14692	BMS1_HUMAN	BMS1-like, ribosome assembly protein						ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3						ctattatttcTTAGGAGGGTAT	0.193													1	5	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47018728	47018728	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47018728delA	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						aaaacaaaacaaaaaaacaac	0.000													6	4	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47051071	47051071	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47051071delA	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						CTAGCATCAGAAAGATTTTAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	49203360	49203361	+	IGR	DEL	AT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49203360_49203361delAT								FRMPD2L1 (339728 upstream) : FRMPD2 (161247 downstream)																							CAATGTACACATGTCATGGCTT	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	50645548	50645548	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50645548delT								DRGX (45641 upstream) : ERCC6 (18944 downstream)																							gagaatagtgtttactagctg	0.000													4	2	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53113207	53113207	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53113207delA	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		aaacaactctacaggaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	55309154	55309154	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55309154delT								MBL2 (777694 upstream) : PCDH15 (253381 downstream)																							ctatttttgcttttttttttg	0.000													4	2	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	56336852	56336852	+	Intron	DEL	T	-	-	rs11318408		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56336852delT	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				TTTTAAtttcttttttttttt	0.179										HNSCC(58;0.16)			0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	59317825	59317826	+	IGR	INS	-	G	G	rs35257384		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59317825_59317826insG								None (None upstream) : IPMK (637792 downstream)																							gagagagagaaaagaagaggaa	0.079													6	4	---	---	---	---	
BICC1	80114	broad.mit.edu	37	10	60273190	60273193	+	Intron	DEL	CGGC	-	-	rs10571555		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60273190_60273193delCGGC	uc001jki.1	+							NM_001080512	NP_001073981	Q9H694	BICC1_HUMAN	bicaudal C homolog 1						multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4						CTCCAGCCTACGGCCGGCCGGTTT	0.667													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	63388908	63388909	+	IGR	DEL	TG	-	-	rs72135721		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63388908_63388909delTG								TMEM26 (175700 upstream) : C10orf107 (33810 downstream)																							gtgtgggctctgtgtgtgtgtg	0.257													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65596399	65596400	+	IGR	DEL	CA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65596399_65596400delCA								REEP3 (214428 upstream) : ANXA2P3 (988885 downstream)																							catgtgcatgcacacacacaca	0.282													3	5	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	68372427	68372427	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68372427delC	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						AATAATTGTTCCACCCAAAAT	0.333													4	2	---	---	---	---	
SLC25A16	8034	broad.mit.edu	37	10	70251571	70251572	+	Intron	INS	-	TTGA	TTGA	rs12773696	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70251571_70251572insTTGA	uc001joi.2	-						SLC25A16_uc010qix.1_Intron|SLC25A16_uc010qiy.1_Intron|SLC25A16_uc001joj.2_Intron	NM_152707	NP_689920	P16260	GDC_HUMAN	solute carrier family 25, member 16						coenzyme biosynthetic process|pantothenate metabolic process	integral to membrane|mitochondrial inner membrane	binding|solute:solute antiporter activity				0						tgcttgcttgcttgattgattg	0.000													3	3	---	---	---	---	
ZMIZ1	57178	broad.mit.edu	37	10	81052825	81052825	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81052825delT	uc001kaf.2	+						ZMIZ1_uc001kag.2_Intron|ZMIZ1_uc001kah.1_Intron	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17						transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CCCTGCACACTTTCCTGGTTT	0.537											OREG0020307	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SH2D4B	387694	broad.mit.edu	37	10	82297088	82297088	+	5'Flank	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82297088delT	uc001kck.1	+							NM_207372	NP_997255	Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B isoform 1												0			Colorectal(32;0.229)			TCCAGTGTGCTTCTGATCAGG	0.488													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	84145356	84145357	+	Intron	INS	-	CT	CT			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84145356_84145357insCT	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		AAATGGAGAGACTCTATACAAG	0.351													4	2	---	---	---	---	
GRID1	2894	broad.mit.edu	37	10	87950657	87950658	+	Intron	INS	-	CATG	CATG	rs142684911	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87950657_87950658insCATG	uc001kdl.1	-						GRID1_uc009xsu.1_Intron	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	atgagtgtgtacgtgcatgcat	0.327										Multiple Myeloma(13;0.14)			4	3	---	---	---	---	
TM9SF3	56889	broad.mit.edu	37	10	98312907	98312908	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98312907_98312908insA	uc001kmm.3	-						TM9SF3_uc010qot.1_Intron|TM9SF3_uc001kmn.1_5'Flank	NM_020123	NP_064508	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3 precursor							integral to membrane	binding				0		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		TTAATGCAAAGAAAAAAAAAAG	0.322													6	3	---	---	---	---	
CNNM2	54805	broad.mit.edu	37	10	104754958	104754958	+	Intron	DEL	T	-	-	rs112724495		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104754958delT	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron	NM_017649	NP_060119	Q9H8M5	CNNM2_HUMAN	cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		ctcttcctcctccttcctctt	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	111313359	111313360	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111313359_111313360insT								None (None upstream) : XPNPEP1 (311164 downstream)																							tatataccacatttttcctatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113687634	113687635	+	IGR	INS	-	T	T	rs145419779	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113687634_113687635insT								ADRA2A (846974 upstream) : GPAM (221987 downstream)																							tcagtggttccttttttTTCCC	0.168													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	115065950	115065951	+	IGR	INS	-	C	C	rs77172264	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115065950_115065951insC								TCF7L2 (138516 upstream) : HABP2 (246827 downstream)																							gtgatgttggactctagaccct	0.015													1	5	---	---	---	---	
PPAPDC1A	196051	broad.mit.edu	37	10	122235423	122235423	+	Intron	DEL	C	-	-	rs71958067		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122235423delC	uc001lev.1	+						PPAPDC1A_uc010qtd.1_Intron|PPAPDC1A_uc009xzl.1_Intron|PPAPDC1A_uc001lew.1_Intron|PPAPDC1A_uc001lex.1_Intron	NM_001030059	NP_001025230	Q5VZY2	PPC1A_HUMAN	phosphatidic acid phosphatase type 2 domain						phospholipid dephosphorylation	integral to membrane	phosphatidate phosphatase activity			breast(1)	1		Lung NSC(174;0.1)|all_lung(145;0.132)		all cancers(201;0.0117)		GCGGGGGGCACCAGTGTCCAC	0.403													3	3	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127582669	127582670	+	Intron	DEL	AT	-	-	rs141033053		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127582669_127582670delAT	uc001ljg.1	-						FANK1_uc010quk.1_5'Flank|FANK1_uc001ljh.3_5'Flank|FANK1_uc009yan.2_5'Flank	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				ACTTAAAAAAATATATATAGAA	0.297													6	3	---	---	---	---	
ADAM12	8038	broad.mit.edu	37	10	127952041	127952042	+	Intron	INS	-	T	T	rs79087114	byFrequency	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127952041_127952042insT	uc001ljk.2	-						ADAM12_uc010qul.1_Intron|ADAM12_uc001ljm.2_Intron|ADAM12_uc001ljn.2_Intron|ADAM12_uc001ljl.3_Intron	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1						cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CCTCTTTGCTGTTTTTTTGTTT	0.198													4	2	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	128782362	128782362	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128782362delC	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)		AGGGTGCTGTCCTAGCCTTCT	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132297517	132297518	+	IGR	DEL	GT	-	-	rs150637124		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132297517_132297518delGT								GLRX3 (314733 upstream) : TCERG1L (593138 downstream)																							AGCAATTGACgtgtgtgtgtgt	0.396													4	3	---	---	---	---	
JAKMIP3	282973	broad.mit.edu	37	10	133968346	133968347	+	Intron	INS	-	AGC	AGC	rs75394942		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133968346_133968347insAGC	uc001lkx.3	+						JAKMIP3_uc009yba.1_Intron	NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		gtgatggtggtggcggtggtgg	0.064													4	3	---	---	---	---	
KNDC1	85442	broad.mit.edu	37	10	134980252	134980253	+	Intron	INS	-	G	G	rs142632830	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134980252_134980253insG	uc001llz.1	+						KNDC1_uc001lma.1_5'Flank	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		tgcatgtgcatggggggggtgt	0.267													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	321076	321077	+	Intron	INS	-	A	A	rs144605457	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:321076_321077insA	uc001loz.2	+						IFITM3_uc001lpa.2_5'Flank					Homo sapiens cDNA clone IMAGE:5200448, partial cds.																		TAGTGGTGTGGGGTCCTGGAGA	0.609													3	5	---	---	---	---	
RNH1	6050	broad.mit.edu	37	11	509370	509370	+	5'Flank	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:509370delG	uc001lpl.1	-						RNH1_uc001lpm.1_5'Flank|RNH1_uc001lpn.1_5'Flank|RNH1_uc001lpo.1_5'Flank|RNH1_uc009ybw.1_5'Flank|RNH1_uc001lpp.1_5'Flank|RNH1_uc001lpt.1_5'Flank|RNH1_uc001lpq.1_5'Flank|RNH1_uc001lpr.1_5'Flank|RNH1_uc001lps.1_5'Flank|RNH1_uc009ybx.1_5'Flank	NM_002939	NP_002930	P13489	RINI_HUMAN	ribonuclease/angiogenin inhibitor						mRNA catabolic process|regulation of angiogenesis	angiogenin-PRI complex|cytoplasm	protein binding|ribonuclease inhibitor activity				0		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		ATTTGTTCGTGGCAATTCTCA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	640743	640743	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:640743delG								DRD4 (40 upstream) : DEAF1 (3482 downstream)																							GATGGGGAGTGGGGAAGAGGG	0.597													2	6	---	---	---	---	
OSBPL5	114879	broad.mit.edu	37	11	3118201	3118202	+	Intron	DEL	AG	-	-	rs75882608		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3118201_3118202delAG	uc001lxk.2	-						OSBPL5_uc010qxq.1_Intron|OSBPL5_uc009ydw.2_Intron|OSBPL5_uc001lxl.2_Intron|OSBPL5_uc009ydx.2_Intron|OSBPL5_uc001lxj.2_5'Flank	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform						cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		agaagaggaaagagggggaagg	0.064													16	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	4749934	4749934	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4749934delT								OR51E2 (30858 upstream) : OR51F1 (40276 downstream)																							AGTCTTCCCCTTTTTTTCTTA	0.139													4	2	---	---	---	---	
OR51S1	119692	broad.mit.edu	37	11	4870804	4870804	+	5'Flank	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4870804delT	uc010qyo.1	-							NM_001004758	NP_001004758	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTTATCCATATTTTTTTCTCT	0.368													4	2	---	---	---	---	
PPFIBP2	8495	broad.mit.edu	37	11	7587271	7587272	+	Intron	DEL	CA	-	-	rs113156891		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7587271_7587272delCA	uc001mfj.3	+							NM_003621	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2						cell communication|DNA integration	intracellular	DNA binding|integrase activity|protein binding			ovary(2)|breast(2)	4				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		TTTAAGATTTCACACACACACA	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	7895845	7895845	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7895845delA	uc001mfs.1	-											Homo sapiens cDNA FLJ34536 fis, clone HLUNG2008384.																		gggactctccaaaatgatgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	12295426	12295426	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12295426delG								MICAL2 (10097 upstream) : MICALCL (13021 downstream)																							ggaggtcactgtggactgtgc	0.229													4	2	---	---	---	---	
PLEKHA7	144100	broad.mit.edu	37	11	17018483	17018483	+	Intron	DEL	A	-	-	rs112441884		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17018483delA	uc001mmo.2	-						PLEKHA7_uc010rcu.1_Intron	NM_175058	NP_778228	Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3						actccgtctcaaaaaaaaaaa	0.244													4	2	---	---	---	---	
SLC6A5	9152	broad.mit.edu	37	11	20644333	20644334	+	Intron	INS	-	CTTC	CTTC	rs145782666	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20644333_20644334insCTTC	uc001mqd.2	+						SLC6A5_uc009yic.2_Intron	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter						synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	CTCCGTCACCTCTTCCATCCTC	0.525													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	22072499	22072500	+	IGR	INS	-	T	T	rs76166830		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22072499_22072500insT								NELL1 (475272 upstream) : ANO5 (142222 downstream)																							tgcccactttgttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	24233912	24233912	+	IGR	DEL	A	-	-	rs111850765		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24233912delA								None (None upstream) : LUZP2 (284644 downstream)																							ccgctccatgaaaaaccacac	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	29230434	29230434	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29230434delG								METT5D1 (875380 upstream) : KCNA4 (801332 downstream)																							TGGATAATATGAAATAAAAGG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	29643310	29643310	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29643310delC								None (None upstream) : KCNA4 (388456 downstream)																							aacatctgctccgtttctggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	32483022	32483023	+	IGR	INS	-	GT	GT	rs137869496	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32483022_32483023insGT								WIT1 (14761 upstream) : EIF3M (122368 downstream)																							tgggactacaggtgcgaaccac	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35021638	35021638	+	IGR	DEL	A	-	-	rs67789628		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35021638delA								PDHX (3964 upstream) : CD44 (138779 downstream)																							CTCTAGGTATAAAAAAAAAAT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35662802	35662802	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35662802delA								FJX1 (20383 upstream) : TRIM44 (21551 downstream)																							AGAATAATAGAAAGGCACACA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39971023	39971023	+	IGR	DEL	A	-	-	rs6485164	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39971023delA								None (None upstream) : LRRC4C (164730 downstream)																							aattatatttaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42233237	42233237	+	IGR	DEL	A	-	-	rs11336355		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42233237delA								LRRC4C (751914 upstream) : None (None downstream)																							atgcatatagaaaaaaaaatg	0.100													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	43003990	43003991	+	IGR	INS	-	ACAC	ACAC	rs139565276	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43003990_43003991insACAC								None (None upstream) : API5 (329514 downstream)																							tcccagaacttaCACACACACA	0.158													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	43004740	43004740	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43004740delA								None (None upstream) : API5 (328765 downstream)																							GATAATTCCCAAAAGGGGGAG	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44978052	44978053	+	IGR	INS	-	T	T	rs150132474	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44978052_44978053insT								TP53I11 (5212 upstream) : LOC221122 (17400 downstream)																							GGACCACCCCCACCCCAGTGAA	0.465													4	4	---	---	---	---	
AGBL2	79841	broad.mit.edu	37	11	47703813	47703814	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47703813_47703814insA	uc001ngg.2	-						AGBL2_uc001ngf.2_Intron|AGBL2_uc010rhq.1_Intron|AGBL2_uc001ngh.1_Intron	NM_024783	NP_079059	Q5U5Z8	CBPC2_HUMAN	carboxypeptidase 2, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2						tattacaggggaaaaaggagtt	0.059													4	2	---	---	---	---	
PTPRJ	5795	broad.mit.edu	37	11	48090655	48090656	+	Intron	INS	-	T	T	rs150807752		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48090655_48090656insT	uc001ngp.3	+						PTPRJ_uc001ngo.3_Intron	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8						TTCAAATGttcttttttttttt	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48888361	48888361	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48888361delT								OR4A47 (377089 upstream) : FOLH1 (279827 downstream)																							tgaaccttccttttgagagag	0.000													3	3	---	---	---	---	
MS4A8B	83661	broad.mit.edu	37	11	60474783	60474784	+	Intron	DEL	GA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60474783_60474784delGA	uc001npv.2	+						MS4A8B_uc009yne.1_Intron	NM_031457	NP_113645	Q9BY19	M4A8B_HUMAN	membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity				0						TATGgagagcgagagagagaga	0.470													6	3	---	---	---	---	
C11orf66	220004	broad.mit.edu	37	11	61255461	61255461	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61255461delT	uc001nru.1	+						C11orf66_uc009ynq.1_Intron	NM_145017	NP_659454	Q7Z5V6	CK066_HUMAN	IIIG9 protein											ovary(1)	1						cttcttcttcttttttttttt	0.249													4	2	---	---	---	---	
SF3B2	10992	broad.mit.edu	37	11	65835244	65835245	+	Intron	INS	-	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65835244_65835245insC	uc001ogy.1	+						PACS1_uc001ogz.1_5'Flank|PACS1_uc001oha.1_5'Flank	NM_006842	NP_006833	Q13435	SF3B2_HUMAN	splicing factor 3B subunit 2						interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3						GCACTGTGCCACCCCCCCGCCC	0.579											OREG0021094	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	4	---	---	---	---	
PACS1	55690	broad.mit.edu	37	11	65903733	65903734	+	Intron	INS	-	AC	AC	rs143893859	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65903733_65903734insAC	uc001oha.1	+						PACS1_uc001ogz.1_Intron	NM_018026	NP_060496	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1						interspecies interaction between organisms|regulation of defense response to virus by virus|viral reproduction	cytosol	protein binding			ovary(6)	6						CAATCCCGCTAacacacacaca	0.356													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	67311269	67311269	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67311269delC								CABP2 (20370 upstream) : GSTP1 (39797 downstream)																							aagtggtcagccctctctggg	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	68797547	68797548	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68797547_68797548insT								MRGPRF (16697 upstream) : TPCN2 (18802 downstream)																							tttctctagacttttttttttt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69865669	69865670	+	IGR	INS	-	TGTG	TGTG	rs145164577	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69865669_69865670insTGTG								FGF3 (231477 upstream) : ANO1 (58738 downstream)																							cccgagccaattgtatcttccc	0.010													4	2	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70862836	70862837	+	Intron	INS	-	G	G	rs147640187	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70862836_70862837insG	uc001oqc.2	-							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)			CAAGAGCAGGCAGAGACCGTCC	0.649													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	70991771	70991771	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70991771delA								SHANK2 (55963 upstream) : DHCR7 (153688 downstream)																							ccagatatataaaagcctaga	0.000													4	2	---	---	---	---	
POLD3	10714	broad.mit.edu	37	11	74350463	74350463	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74350463delA	uc001ovf.1	+						POLD3_uc009yua.1_Intron	NM_006591	NP_006582	Q15054	DPOD3_HUMAN	DNA-directed DNA polymerase delta 3						base-excision repair|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|mismatch repair|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	delta DNA polymerase complex|nucleoplasm	DNA-directed DNA polymerase activity|protein binding			kidney(2)|ovary(1)	3	Breast(11;3.21e-06)					TCTTTAATGGAAAAAAAAACC	0.239													4	2	---	---	---	---	
UVRAG	7405	broad.mit.edu	37	11	75738016	75738016	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75738016delA	uc001oxc.2	+						UVRAG_uc010rrw.1_Intron|UVRAG_uc001oxd.2_Intron|UVRAG_uc010rrx.1_Intron	NM_003369	NP_003360	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated						DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6						AATCAAGGTGAAAAAAAAAAA	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79949011	79949022	+	IGR	DEL	TGTGTGTGTGTG	-	-	rs12287446		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79949011_79949022delTGTGTGTGTGTG								ODZ4 (797316 upstream) : None (None downstream)																							TCGCTCTCTCtgtgtgtgtgtgtgtgtgtgtg	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	87758726	87758726	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87758726delA								TMEM135 (724158 upstream) : RAB38 (87705 downstream)																							ttgactttttaataatagcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91479581	91479582	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91479581_91479582insT								MIR1261 (877211 upstream) : FAT3 (605680 downstream)																							tattgaggtggttttttttgtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93007799	93007802	+	IGR	DEL	AGAA	-	-	rs138473041		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93007799_93007802delAGAA								SLC36A4 (76704 upstream) : CCDC67 (55354 downstream)																							AGAGACAAAGAGAAAGAAGCAACC	0.147													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	94808517	94808517	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94808517delT								SFRS2B (4130 upstream) : ENDOD1 (14500 downstream)																							GCGTGATGTGTTTAGTAAAGC	0.294													4	2	---	---	---	---	
GRIA4	2893	broad.mit.edu	37	11	105668828	105668829	+	Intron	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105668828_105668829delAC	uc001pix.2	+						GRIA4_uc001piu.1_Intron|GRIA4_uc001piw.2_Intron|GRIA4_uc001piv.2_Intron|GRIA4_uc009yxk.1_Intron	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	acacacacatacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109007884	109007884	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109007884delT								DDX10 (196238 upstream) : C11orf87 (284991 downstream)																							catttgtccatttttactttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114189676	114189676	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114189676delA								NNMT (6438 upstream) : C11orf71 (72494 downstream)																							tctcaaaaggaaaaaaaaaaa	0.169													4	2	---	---	---	---	
SIK3	23387	broad.mit.edu	37	11	116767743	116767744	+	Intron	DEL	AA	-	-	rs34854326		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116767743_116767744delAA	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						actctgtttcaaaaaaaaaaaa	0.178													4	4	---	---	---	---	
DSCAML1	57453	broad.mit.edu	37	11	117319827	117319827	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117319827delG	uc001prh.1	-							NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		aaaagaagctggacaaatggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	118750506	118750506	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118750506delT								DDX6 (88534 upstream) : CXCR5 (4035 downstream)																							AAGGTAAttcttttttttttt	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119951730	119951731	+	IGR	INS	-	C	C	rs142820249	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119951730_119951731insC								PVRL1 (352295 upstream) : TRIM29 (30264 downstream)																							TGCTGGCTCAGCCCTGGCTCTA	0.569													4	2	---	---	---	---	
UBASH3B	84959	broad.mit.edu	37	11	122559160	122559160	+	Intron	DEL	G	-	-	rs112598984		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122559160delG	uc001pyi.3	+							NM_032873	NP_116262	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing,							cytoplasm|nucleus	protein tyrosine phosphatase activity			central_nervous_system(1)	1		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		TGGtttgtttgtttttttttt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	123192763	123192768	+	IGR	DEL	TTTGTT	-	-	rs111443689		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123192763_123192768delTTTGTT								ASAM (126756 upstream) : GRAMD1B (203760 downstream)																							TCCTCTGCTAtttgtttttgtttttg	0.214													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	126978533	126978534	+	IGR	INS	-	GAG	GAG	rs146571596	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126978533_126978534insGAG								KIRREL3 (105178 upstream) : None (None downstream)																							TGCAGGCTGTTGACCTGAGGCC	0.564													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128125980	128125980	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128125980delA								None (None upstream) : ETS1 (202676 downstream)																							tgtaatttatagggcattagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128745423	128745423	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128745423delA								KCNJ1 (8155 upstream) : KCNJ5 (15890 downstream)																							tagaaagattaaaattacagc	0.070													4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131434763	131434764	+	Intron	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131434763_131434764delAC	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						acacacacatacacacacacac	0.351													4	2	---	---	---	---	
B4GALNT3	283358	broad.mit.edu	37	12	658074	658078	+	Intron	DEL	CAAAA	-	-	rs67058437		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:658074_658078delCAAAA	uc001qii.1	+						B4GALNT3_uc001qij.1_Intron	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			gcctcaaaagcaaaacaaaacaaca	0.127													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	1767934	1767934	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1767934delG								WNT5B (11557 upstream) : ADIPOR2 (32313 downstream)																							CAGAGGACCTGGCTTCCCAAC	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	2829228	2829229	+	IGR	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2829228_2829229delAC								CACNA1C (22113 upstream) : FKBP4 (74879 downstream)																							acacacacagacacacacacac	0.000													4	2	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	5737834	5737835	+	Intron	DEL	GT	-	-	rs72150450		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5737834_5737835delGT	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						taagcAGAGAGTgtgtgtgtgt	0.054													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8729390	8729390	+	IGR	DEL	A	-	-	rs66610266		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8729390delA								CLEC4E (35832 upstream) : AICDA (25372 downstream)																							CATTATTCTTAAAACTCCTTG	0.189													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8826197	8826197	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8826197delT								MFAP5 (10764 upstream) : RIMKLB (8019 downstream)																							ctcgagcttcttttttttttt	0.000													4	2	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11330845	11330845	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11330845delA	uc001qzf.1	-							NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						gtgagccaagattgcgccatt	0.005										HNSCC(22;0.051)			3	3	---	---	---	---	
DUSP16	80824	broad.mit.edu	37	12	12643024	12643025	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12643024_12643025insT	uc001rao.1	-						DUSP16_uc001ran.1_Intron	NM_030640	NP_085143	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16						inactivation of MAPK activity|MAPK export from nucleus|MAPK phosphatase export from nucleus, leptomycin B sensitive	cytoplasmic membrane-bounded vesicle|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		atttttaaacattttttttgta	0.000													4	2	---	---	---	---	
AEBP2	121536	broad.mit.edu	37	12	19634410	19634411	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19634410_19634411insT	uc001ref.2	+						AEBP2_uc001ree.2_Intron|AEBP2_uc001reg.1_Intron	NM_001114176	NP_001107648	Q6ZN18	AEBP2_HUMAN	AE binding protein 2 isoform b						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)|Esophageal squamous(101;0.143)					cttttcttttctttttttttTT	0.005													3	3	---	---	---	---	
SLCO1B3	28234	broad.mit.edu	37	12	21068872	21068873	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21068872_21068873insA	uc001rek.2	+						SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					ATACTGGGGAGAAAAAAATGTA	0.272													9	6	---	---	---	---	
SLCO1A2	6579	broad.mit.edu	37	12	21509477	21509479	+	Intron	DEL	ATA	-	-	rs140977876		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21509477_21509479delATA	uc001res.2	-						SLCO1A2_uc010siq.1_Intron	NM_134431	NP_602307	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A						bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						agtcatgatcataatatttgaaa	0.099													4	5	---	---	---	---	
TM7SF3	51768	broad.mit.edu	37	12	27133722	27133722	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27133722delA	uc010sjl.1	-							NM_016551	NP_057635	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3 precursor							integral to membrane|plasma membrane				upper_aerodigestive_tract(2)	2	Colorectal(261;0.0847)					CATTCAGAAGAAAAAAAAAAT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	27304823	27304826	+	IGR	DEL	GGAG	-	-	rs147156884		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27304823_27304826delGGAG								C12orf71 (69368 upstream) : STK38L (92252 downstream)																							atgtcagccaggaggaagaggcat	0.088													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	27968736	27968737	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27968736_27968737insA								KLHDC5 (12764 upstream) : PTHLH (142281 downstream)																							acgtaatttataaaaaaaagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30209809	30209812	+	IGR	DEL	TTAT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30209809_30209812delTTAT								TMTC1 (272117 upstream) : IPO8 (572111 downstream)																							gcctgcctgattatttacccacgt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31405736	31405737	+	IGR	INS	-	AA	AA	rs140519491	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31405736_31405737insAA								DDX11 (148011 upstream) : FAM60A (27790 downstream)																							TTTTGACATCCAAAAAAAAAAG	0.267													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	39934080	39934080	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39934080delT								KIF21A (97162 upstream) : ABCD2 (10942 downstream)																							ctgatttttcttatcttgccc	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	43415534	43415535	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43415534_43415535insT								PRICKLE1 (431962 upstream) : ADAMTS20 (332478 downstream)																							ttcctgtcaaattttttgctgt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	43715930	43715931	+	IGR	INS	-	CTCA	CTCA	rs143937475	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43715930_43715931insCTCA								PRICKLE1 (732358 upstream) : ADAMTS20 (32082 downstream)																							tctctctctctcacacacacac	0.267													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48646657	48646657	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48646657delC								OR10AD1 (49582 upstream) : H1FNT (76106 downstream)																							cattcttatgcctttgcatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48840999	48841000	+	IGR	INS	-	TGTA	TGTA	rs150944515		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48840999_48841000insTGTA								ZNF641 (95978 upstream) : ANP32D (25448 downstream)																							cttactctgtgtgtgtgtgtgt	0.020													6	3	---	---	---	---	
FAIM2	23017	broad.mit.edu	37	12	50274662	50274663	+	Intron	INS	-	GA	GA			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50274662_50274663insGA	uc001rvj.1	-						FAIM2_uc001rvi.1_Intron|FAIM2_uc001rvk.1_Intron	NM_012306	NP_036438	Q9BWQ8	FAIM2_HUMAN	Fas apoptotic inhibitory molecule 2						anti-apoptosis|apoptosis	cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|ovary(1)|skin(1)	3						tgcgtgaatgtgagtgtgtgtg	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	51952545	51952546	+	IGR	DEL	TT	-	-	rs76816770		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51952545_51952546delTT								SLC4A8 (42998 upstream) : SCN8A (32474 downstream)																							aaaatttcactttgttatgaga	0.104													2	7	---	---	---	---	
ZNF385A	25946	broad.mit.edu	37	12	54782611	54782611	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54782611delT	uc001sfy.3	-						ZNF385A_uc001sfz.3_Intron	NM_001130967	NP_001124439	Q96PM9	Z385A_HUMAN	zinc finger protein 385A isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|zinc ion binding			ovary(1)	1						CCCCTGGGTCTTTTTTACCAA	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55070545	55070546	+	IGR	INS	-	AA	AA	rs139553988	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55070545_55070546insAA								DCD (28396 upstream) : MUCL1 (177753 downstream)																							AAAGGTCCACCaaaaaaaaaca	0.104													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55325216	55325216	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55325216delA								MUCL1 (73044 upstream) : KIAA0748 (18649 downstream)																							agcagtgagtaaatcaaggcc	0.000													3	3	---	---	---	---	
RAP1B	5908	broad.mit.edu	37	12	69021111	69021112	+	Intron	INS	-	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69021111_69021112insC	uc001sub.2	+						RAP1B_uc010ste.1_Intron|RAP1B_uc001suc.2_Intron|RAP1B_uc010stf.1_Intron|RAP1B_uc010stg.1_Intron|RAP1B_uc010sth.1_Intron|RAP1B_uc010sti.1_Intron	NM_001089704	NP_001083173	P61224	RAP1B_HUMAN	SubName: Full=Ras-related protein Rap-1A; SubName: Full=cDNA FLJ75985, highly similar to Homo sapiens RAP1A, member of RAS oncogene family (RAP1A), transcript variant 2, mRNA; SubName: Full=RAP1A, member of RAS oncogene family;						blood coagulation|energy reserve metabolic process|regulation of establishment of cell polarity|regulation of insulin secretion	cell-cell junction|cytosol	GDP binding|GTP binding|GTPase activity|protein binding				0	Breast(13;1.24e-05)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)	GBM - Glioblastoma multiforme(7;0.000306)		TGCACACTGGGCCCCCCCATGA	0.470													9	9	---	---	---	---	
SLC35E3	55508	broad.mit.edu	37	12	69143782	69143782	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69143782delA	uc001suh.2	+							NM_018656	NP_061126	Q7Z769	S35E3_HUMAN	solute carrier family 35, member E2							integral to membrane					0	Breast(13;2.31e-06)|Renal(347;0.0684)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00372)			AAGGAAGGGTAAAAGGCAGAG	0.522													4	2	---	---	---	---	
CPSF6	11052	broad.mit.edu	37	12	69654100	69654100	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69654100delT	uc001sut.3	+						CPSF6_uc001suu.3_Intron|CPSF6_uc010stk.1_Intron	NM_007007	NP_008938	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6,						mRNA polyadenylation|protein tetramerization	mRNA cleavage factor complex|paraspeckles|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			gctggagtggttttttttttt	0.114													4	2	---	---	---	---	
YEATS4	8089	broad.mit.edu	37	12	69771232	69771233	+	Intron	INS	-	A	A	rs146041012	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69771232_69771233insA	uc001sux.2	+							NM_006530	NP_006521	O95619	YETS4_HUMAN	glioma-amplified sequence-41						histone H2A acetylation|histone H4 acetylation|mitosis|positive regulation of transcription, DNA-dependent|regulation of growth	NuA4 histone acetyltransferase complex|nuclear matrix	DNA binding|protein C-terminus binding|sequence-specific DNA binding transcription factor activity|structural constituent of cytoskeleton				0	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)			tggagctggggatctcgctgtg	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	73113875	73113875	+	IGR	DEL	T	-	-	rs11300674		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73113875delT								TRHDE (54454 upstream) : None (None downstream)																							tgtgtacatattttgttgtgt	0.040													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	73601855	73601855	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73601855delA								TRHDE (542434 upstream) : None (None downstream)																							ttgaatctataaattaccttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	91809248	91809249	+	IGR	DEL	TG	-	-	rs72063010		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91809248_91809249delTG								DCN (232442 upstream) : BTG1 (569617 downstream)																							tgtgtgtttatgtgtgtgtgtg	0.292													4	2	---	---	---	---	
CRADD	8738	broad.mit.edu	37	12	94176370	94176371	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94176370_94176371insA	uc001tda.2	+						CRADD_uc010sur.1_Intron|CRADD_uc010sus.1_Intron	NM_003805	NP_003796	P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1						tccgtctcaggaaaaaaaaaaa	0.030													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	98401877	98401879	+	IGR	DEL	GAA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98401877_98401879delGAA								RMST (443084 upstream) : LOC100128191 (504874 downstream)																							agaggaagaggaagaagaagaag	0.000													3	4	---	---	---	---	
PAH	5053	broad.mit.edu	37	12	103250051	103250051	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103250051delA	uc001tjq.1	-						PAH_uc010swc.1_Intron	NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase						catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	ggattctagtaagctccccag	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108865755	108865756	+	IGR	DEL	CT	-	-	rs71854494		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108865755_108865756delCT								CMKLR1 (132661 upstream) : FICD (43295 downstream)																							AGCAGGTACCCTGAGTGTCCTC	0.574													5	4	---	---	---	---	
IQCD	115811	broad.mit.edu	37	12	113636482	113636482	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113636482delT	uc001tuu.2	-							NM_138451	NP_612460	Q96DY2	IQCD_HUMAN	IQ motif containing D											ovary(1)	1						tattttgaggtgataatgttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114117547	114117548	+	IGR	INS	-	AA	AA	rs10637671		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114117547_114117548insAA								LHX5 (207670 upstream) : RBM19 (136995 downstream)																							accttgtttctaaaaaaaaaaa	0.168													2	4	---	---	---	---	
TBX5	6910	broad.mit.edu	37	12	114821242	114821242	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114821242delG	uc001tvo.2	-						TBX5_uc001tvp.2_Intron|TBX5_uc001tvq.2_Intron|TBX5_uc010syv.1_Intron	NM_181486	NP_852259	Q99593	TBX5_HUMAN	T-box 5 isoform 1						cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(6)|pancreas(1)|skin(1)	8	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		gacaaacctaggggggtggcc	0.199													4	2	---	---	---	---	
RNFT2	84900	broad.mit.edu	37	12	117289549	117289549	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117289549delA	uc009zwn.2	+						RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron|RNFT2_uc001twc.3_Intron|RNFT2_uc001twd.2_RNA	NM_001109903	NP_001103373	Q96EX2	RNFT2_HUMAN	transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		gactctgtctaaaaaaaaaaa	0.109													4	2	---	---	---	---	
SPPL3	121665	broad.mit.edu	37	12	121327604	121327604	+	Intron	DEL	G	-	-	rs34133865		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121327604delG	uc001tzd.2	-						SPPL3_uc009zwz.2_Intron	NM_139015	NP_620584	Q8TCT6	PSL4_HUMAN	signal peptide peptidase 3							integral to membrane	aspartic-type endopeptidase activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGATTGTTATGAAGGTAGGTC	0.294													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126407383	126407384	+	IGR	DEL	GA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126407383_126407384delGA								TMEM132B (263794 upstream) : LOC100128554 (519643 downstream)																							gagggcaggggagagagagaga	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130505517	130505517	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130505517delA								TMEM132D (117305 upstream) : LOC100190940 (12482 downstream)																							cctgtctcttaaaaaaaaaaa	0.149													4	2	---	---	---	---	
GOLGA3	2802	broad.mit.edu	37	12	133403691	133403691	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133403691delC	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CTTTCTGCTTCCCCCACACCT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19089447	19089447	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19089447delG								None (None upstream) : LOC284232 (319096 downstream)																							aaggtaagtagcaccaaagtt	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	20690042	20690043	+	IGR	DEL	AT	-	-	rs75472712		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20690042_20690043delAT								ZMYM2 (29104 upstream) : GJA3 (22352 downstream)																							cctgggcaacatagcgagatcc	0.025													3	4	---	---	---	---	
SGCG	6445	broad.mit.edu	37	13	23838478	23838478	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23838478delA	uc001uom.2	+						SGCG_uc009zzv.2_Intron|SGCG_uc009zzw.2_Intron	NM_000231	NP_000222	Q13326	SGCG_HUMAN	gamma sarcoglycan						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		caatggttacaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	28523032	28523032	+	IGR	DEL	T	-	-	rs35109122		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28523032delT								ATP5EP2 (3323 upstream) : CDX2 (13247 downstream)																							ctccatatccttttttttttt	0.000													2	4	---	---	---	---	
STARD13	90627	broad.mit.edu	37	13	33751960	33751962	+	Intron	DEL	AGG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33751960_33751962delAGG	uc001uuw.2	-						STARD13_uc001uuu.2_Intron|STARD13_uc001uuv.2_Intron|STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron|STARD13_uc010abh.1_Intron	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		gaaggaaggaaggaaggaaggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	41258978	41258979	+	IGR	INS	-	GCTT	GCTT	rs113918840		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41258978_41258979insGCTT								FOXO1 (18244 upstream) : MIR320D-1 (42985 downstream)																							GGCTGGTTGAAgcttgcttgct	0.119													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	42576146	42576146	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42576146delG								KIAA0564 (40925 upstream) : DGKH (38026 downstream)																							CTATGGCTCTGATGATGGTCC	0.254													4	2	---	---	---	---	
DGKH	160851	broad.mit.edu	37	13	42748078	42748079	+	Intron	DEL	TG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42748078_42748079delTG	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_Intron|DGKH_uc010tfi.1_Intron|DGKH_uc010tfj.1_Intron|DGKH_uc001uyn.1_Intron|DGKH_uc001uyo.1_Intron|DGKH_uc001uyp.2_Intron	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		AGTTCATGAAtgtgtgtgtgtg	0.193													6	3	---	---	---	---	
TNFSF11	8600	broad.mit.edu	37	13	43136256	43136257	+	5'Flank	DEL	AA	-	-	rs10538049		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43136256_43136257delAA	uc001uyt.2	+							NM_033012	NP_143026	O14788	TNF11_HUMAN	tumor necrosis factor ligand superfamily, member						immune response|monocyte chemotaxis|osteoclast differentiation|positive regulation of bone resorption|positive regulation of corticotropin-releasing hormone secretion|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling|positive regulation of fever generation by positive regulation of prostaglandin secretion|positive regulation of homotypic cell-cell adhesion|positive regulation of NF-kappaB transcription factor activity|positive regulation of osteoclast differentiation|positive regulation of T cell activation	cytoplasm|extracellular space|integral to plasma membrane	cytokine activity|receptor activity|tumor necrosis factor receptor binding				0		Lung NSC(96;1.11e-05)|Breast(139;0.00868)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000249)|GBM - Glioblastoma multiforme(144;0.00119)|BRCA - Breast invasive adenocarcinoma(63;0.073)		ttttgctgagaaaaaaactttc	0.000													2	5	---	---	---	---	
TSC22D1	8848	broad.mit.edu	37	13	45023028	45023029	+	Intron	INS	-	GT	GT	rs150896509		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45023028_45023029insGT	uc001uzn.3	-						TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358	Q15714	T22D1_HUMAN	TSC22 domain family, member 1 isoform 1						transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		ATTCTAGATCCgtgtgtgtgtg	0.347													4	5	---	---	---	---	
ITM2B	9445	broad.mit.edu	37	13	48816631	48816631	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48816631delA	uc001vbz.3	+							NM_021999	NP_068839	Q9Y287	ITM2B_HUMAN	integral membrane protein 2B						nervous system development	Golgi membrane|integral to membrane|nucleus|plasma membrane	beta-amyloid binding				0		all_cancers(8;2.2e-31)|all_epithelial(8;6.77e-15)|all_lung(13;9.67e-07)|all_hematologic(8;9.72e-06)|Lung NSC(96;8.3e-05)|Breast(56;0.000141)|Acute lymphoblastic leukemia(8;0.00045)|Prostate(109;0.000669)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;1.97e-06)		TGAGAGTCATAATCATCTTGG	0.269													4	2	---	---	---	---	
FNDC3A	22862	broad.mit.edu	37	13	49741126	49741127	+	Intron	INS	-	A	A	rs138791522	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49741126_49741127insA	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		AACTCCACTCCAAAAAAAAGag	0.139													3	3	---	---	---	---	
TPTE2P3	220115	broad.mit.edu	37	13	53151111	53151113	+	Intron	DEL	AAA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53151111_53151113delAAA	uc001vgw.2	+							NR_002793				Homo sapiens TPTE and PTEN homologous inositol lipid phosphatase pseudogene, mRNA (cDNA clone IMAGE:5298506), with apparent retained intron.												0						ACCTTTATGCaaaaaaaaaaaaa	0.330													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	53330553	53330553	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53330553delC								LECT1 (16606 upstream) : MIR759 (53632 downstream)																							aaacattgttctaacaggact	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	53506822	53506822	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53506822delG								PCDH8 (84048 upstream) : OLFM4 (96150 downstream)																							TGGAGATGTCGAGTGTTTTTC	0.448													1	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	58420512	58420513	+	IGR	DEL	CT	-	-	rs146658158		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58420512_58420513delCT								PCDH17 (117447 upstream) : None (None downstream)																							aacttttatgctctgttttcct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	58548779	58548780	+	IGR	INS	-	ACAC	ACAC	rs141761680	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58548779_58548780insACAC								PCDH17 (245714 upstream) : None (None downstream)																							ACAGACACAGAacacacacaca	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59840257	59840257	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59840257delA								None (None upstream) : DIAPH3 (399468 downstream)																							TGATTTAGGGAAAAAAACCTG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	60871606	60871608	+	IGR	DEL	TTG	-	-	rs34862453		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60871606_60871608delTTG								DIAPH3 (133487 upstream) : TDRD3 (98983 downstream)																							ttctgtcaccttgttgtttttgc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	62594854	62594854	+	IGR	DEL	A	-	-	rs73499049	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62594854delA								PCDH20 (592775 upstream) : None (None downstream)																							ccttaaagttaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63591391	63591391	+	IGR	DEL	A	-	-	rs78958510		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63591391delA								None (None upstream) : OR7E156P (720177 downstream)																							gtcctgaaagaaaaaaaaaaa	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63637291	63637291	+	IGR	DEL	T	-	-	rs75453829		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63637291delT								None (None upstream) : OR7E156P (674277 downstream)																							AGGACTCTCCTTAACAATGAG	0.358													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	68969866	68969866	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68969866delC								None (None upstream) : None (None downstream)																							ATTTTGACTTCTTTTTTTTTG	0.269													4	2	---	---	---	---	
KLHL1	57626	broad.mit.edu	37	13	70451169	70451169	+	Intron	DEL	A	-	-	rs80198594		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70451169delA	uc001vip.2	-						KLHL1_uc010thm.1_Intron	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		aactctgtccaaaaaaaaaaa	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	70740749	70740750	+	IGR	INS	-	G	G	rs146714617		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70740749_70740750insG								ATXN8OS (26864 upstream) : None (None downstream)																							aaggacttcattcatgtctaaa	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	82265214	82265214	+	IGR	DEL	A	-	-	rs34280872		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82265214delA								None (None upstream) : None (None downstream)																							GAGTTGTTCTAAAAAAAAAAA	0.174													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	83670347	83670347	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83670347delA								None (None upstream) : SLITRK1 (780997 downstream)																							gcaacagagcaagatagaaag	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	87971831	87971832	+	IGR	DEL	AC	-	-	rs35599892		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87971831_87971832delAC								None (None upstream) : SLITRK5 (353038 downstream)																							acacacaccaacacacacacac	0.228													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	95005516	95005516	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95005516delA	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)				ACCGACAAGCAAAAATGAGTG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	96026657	96026657	+	IGR	DEL	T	-	-	rs34543727		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96026657delT								ABCC4 (72970 upstream) : CLDN10 (59196 downstream)																							gctaattgagttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111447057	111447057	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111447057delC								ING1 (73637 upstream) : C13orf29 (69277 downstream)																							atgcctgctacctcgtgaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19024831	19024832	+	IGR	INS	-	G	G	rs149077501	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19024831_19024832insG								None (None upstream) : OR11H12 (352762 downstream)																							cagtttcttcaaaagagagatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19111820	19111820	+	IGR	DEL	A	-	-	rs112121452		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19111820delA								None (None upstream) : OR11H12 (265774 downstream)																							AAATGAATACAACAGAATAGA	0.219													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19611232	19611233	+	Intron	DEL	TT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19611232_19611233delTT	uc001vvi.2	+											Homo sapiens prostate-specific P775P mRNA sequence.																		gcctggctaatttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20370274	20370274	+	IGR	DEL	C	-	-	rs71431995		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20370274delC								OR4K2 (24903 upstream) : OR4K5 (18492 downstream)																							acatatttttcccccccagat	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	21439973	21439973	+	IGR	DEL	T	-	-	rs67874262		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21439973delT								RNASE2 (15379 upstream) : METT11D1 (17992 downstream)																							GGAGTGGGGGTTTTCTGCATA	0.542											OREG0022560	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22184815	22184815	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22184815delT								OR4E2 (50579 upstream) : DAD1 (848992 downstream)																							TTTTCTTTTCTTTTTTTTTTT	0.443													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	23143167	23143168	+	IGR	INS	-	CC	CC			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23143167_23143168insCC								ABHD4 (61910 upstream) : OXA1L (92563 downstream)																							tgagacaatggttttttctaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	27240751	27240752	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27240751_27240752insT								NOVA1 (173791 upstream) : None (None downstream)																							TCAtttttttcttttttttttt	0.129													4	2	---	---	---	---	
G2E3	55632	broad.mit.edu	37	14	31042616	31042619	+	Intron	DEL	TGTG	-	-	rs10552989		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31042616_31042619delTGTG	uc001wqk.2	+						G2E3_uc010tpe.1_Intron|G2E3_uc010tpf.1_Intron	NM_017769	NP_060239	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin ligase						apoptosis|multicellular organismal development|protein modification process	Golgi apparatus|nucleolus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						caacaggatatgtgtgtgtgtgtg	0.108													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	32644019	32644019	+	IGR	DEL	A	-	-	rs33945955		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32644019delA								ARHGAP5 (15087 upstream) : AKAP6 (154460 downstream)																							gttgatggacaacgtaggttg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	38354509	38354509	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38354509delT	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																		tttgaaagagTTTTTTTTTCT	0.164													4	2	---	---	---	---	
LRFN5	145581	broad.mit.edu	37	14	42277638	42277639	+	Intron	INS	-	GAGG	GAGG	rs142271830	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42277638_42277639insGAGG	uc001wvm.2	+						LRFN5_uc010ana.2_Intron	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III							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)		aaggaagaatcgagggagggag	0.099										HNSCC(30;0.082)			7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	42774743	42774751	+	IGR	DEL	TTGTTGTTG	-	-	rs74046831		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42774743_42774751delTTGTTGTTG								LRFN5 (400993 upstream) : None (None downstream)																							catgttatttttgttgttgttgttgttgt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	45961116	45961116	+	IGR	DEL	T	-	-	rs80178873		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45961116delT								C14orf106 (238511 upstream) : None (None downstream)																							tacctgaagctgggggtgtag	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	45974624	45974627	+	IGR	DEL	AAAG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45974624_45974627delAAAG								C14orf106 (252019 upstream) : None (None downstream)																							gaaaaaatataaagaaagggaaaa	0.000													1	5	---	---	---	---	
MDGA2	161357	broad.mit.edu	37	14	47545764	47545767	+	Intron	DEL	TGTG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47545764_47545767delTGTG	uc001wwj.3	-						MDGA2_uc001wwi.3_Intron|MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						gtgtgtgttatgtgtgtgtgtgtg	0.211													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49513969	49513969	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49513969delC								None (None upstream) : SDCCAG1 (519058 downstream)																							cactcgggcaccctggaagaa	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	54361827	54361828	+	IGR	INS	-	T	T	rs10579622		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54361827_54361828insT								DDHD1 (741781 upstream) : BMP4 (54629 downstream)																							tccttccttccttccttccttc	0.000													4	2	---	---	---	---	
SAMD4A	23034	broad.mit.edu	37	14	55224141	55224142	+	Intron	INS	-	T	T	rs112987358		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55224141_55224142insT	uc001xbb.2	+						SAMD4A_uc001xbc.2_Intron|SAMD4A_uc001xbg.2_Intron	NM_015589	NP_056404	Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0						gtgtgtgtgtgtgtgtTTTGTT	0.257													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	55724522	55724522	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55724522delT								DLGAP5 (66126 upstream) : FBXO34 (13499 downstream)																							CCTTTCTCTATTTTTTTCCCT	0.164													4	2	---	---	---	---	
PELI2	57161	broad.mit.edu	37	14	56628016	56628017	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56628016_56628017insT	uc001xch.2	+							NM_021255	NP_067078	Q9HAT8	PELI2_HUMAN	pellino 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	protein binding			ovary(1)	1						CTGTTCATCTGttttttttttt	0.168													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57552841	57552843	+	IGR	DEL	GAA	-	-	rs137933825		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57552841_57552843delGAA								OTX2 (275657 upstream) : EXOC5 (116353 downstream)																							GGGAGAAAGTGAAGAAGAATAGG	0.488													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	62408409	62408409	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62408409delC								SNAPC1 (145264 upstream) : SYT16 (45394 downstream)																							CTCTGCAGCTCCCTTTAGTAC	0.488													4	2	---	---	---	---	
SYT16	83851	broad.mit.edu	37	14	62566590	62566605	+	Intron	DEL	TGTGTGTCTGTCTGTC	-	-	rs112392786		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62566590_62566605delTGTGTGTCTGTCTGTC	uc001xfu.1	+						SYT16_uc010tse.1_Intron	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like											central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		agcaagaccTtgtgtgtctgtctgtctgtctgtctg	0.074													1	5	---	---	---	---	
PPP2R5E	5529	broad.mit.edu	37	14	63845750	63845750	+	Intron	DEL	T	-	-	rs111381608		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63845750delT	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron	NM_006246	NP_006237	Q16537	2A5E_HUMAN	epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		ACCCAttttcttttttttttt	0.169													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	65152153	65152154	+	IGR	DEL	AC	-	-	rs112556249		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65152153_65152154delAC								C14orf50 (96057 upstream) : PLEKHG3 (19039 downstream)																							CACACAGTATacacacacacac	0.332													4	3	---	---	---	---	
ARG2	384	broad.mit.edu	37	14	68105087	68105087	+	Intron	DEL	A	-	-	rs34647933		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68105087delA	uc001xjs.2	+							NM_001172	NP_001163	P78540	ARGI2_HUMAN	arginase 2 precursor						arginine metabolic process|nitric oxide biosynthetic process|urea cycle	mitochondrial matrix	arginase activity|metal ion binding				0				all cancers(60;0.000582)|OV - Ovarian serous cystadenocarcinoma(108;0.00392)|BRCA - Breast invasive adenocarcinoma(234;0.00928)	L-Arginine(DB00125)|L-Ornithine(DB00129)	caaataatccaaaaaaaaaag	0.159													3	3	---	---	---	---	
RAD51L1	5890	broad.mit.edu	37	14	68562013	68562014	+	Intron	INS	-	A	A	rs35832065		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68562013_68562014insA	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193	O15315	RA51B_HUMAN	RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)		GAAAGAGGGTTAAAAAAAAAAA	0.332			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					4	2	---	---	---	---	
KIAA0247	9766	broad.mit.edu	37	14	70136425	70136425	+	Intron	DEL	T	-	-	rs71754236		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70136425delT	uc001xlk.2	+						KIAA0247_uc010aqz.2_Intron	NM_014734	NP_055549	Q92537	K0247_HUMAN	hypothetical protein LOC9766 precursor							integral to membrane				ovary(3)	3				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)		CATACTTCTCTTTATCCTTCA	0.448													1	5	---	---	---	---	
SFRS5	6430	broad.mit.edu	37	14	70192461	70192462	+	5'Flank	INS	-	CCAG	CCAG	rs147047507	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70192461_70192462insCCAG	uc001xll.2	+							NM_006925	NP_008856	Q13243	SRSF5_HUMAN	splicing factor, arginine/serine-rich 5						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|protein binding|RNA binding				0				all cancers(60;0.00144)|BRCA - Breast invasive adenocarcinoma(234;0.0132)|OV - Ovarian serous cystadenocarcinoma(108;0.0154)		GAAGAAAACACCCAGTGGGGCA	0.450													2	5	---	---	---	---	
TTLL5	23093	broad.mit.edu	37	14	76339993	76340006	+	Intron	DEL	TTTTTTTAGTTTTT	-	-	rs68179861		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76339993_76340006delTTTTTTTAGTTTTT	uc001xrx.2	+						TTLL5_uc010ask.1_Intron|TTLL5_uc001xrz.2_Intron|TTLL5_uc001xsa.2_Intron	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)		atgttttctctttttttagttttttttttttagt	0.000													2	4	---	---	---	---	
C14orf166B	145497	broad.mit.edu	37	14	77309002	77309003	+	Intron	INS	-	CATT	CATT	rs140915508	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77309002_77309003insCATT	uc001xsx.2	+						C14orf166B_uc010asn.1_Intron|C14orf166B_uc001xsw.2_Intron|C14orf166B_uc010aso.1_Intron|C14orf166B_uc010tvg.1_Intron|C14orf166B_uc010tvh.1_Intron	NM_194287	NP_919263	Q0VAA2	CN16B_HUMAN	hypothetical protein LOC145497												0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		TCCAGTGAATGcattcattcat	0.213													6	3	---	---	---	---	
ADCK1	57143	broad.mit.edu	37	14	78378789	78378790	+	Intron	INS	-	TC	TC			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78378789_78378790insTC	uc001xui.2	+						ADCK1_uc010tvo.1_Intron|ADCK1_uc001xuj.2_Intron|ADCK1_uc001xuk.1_Intron	NM_020421	NP_065154	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1 isoform a							extracellular region	ATP binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		gtgtgtgtgtgtgtgtgtgtgt	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	80418922	80418923	+	IGR	INS	-	AC	AC	rs139087133	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80418922_80418923insAC								NRXN3 (88164 upstream) : DIO2 (244947 downstream)																							acacaatacagacacacacaca	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	80786367	80786367	+	Intron	DEL	A	-	-	rs74832626		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80786367delA	uc001xuw.1	+											Homo sapiens, clone IMAGE:5167652, mRNA.																		agactgaaggaaaagaatggc	0.000													1	11	---	---	---	---	
STON2	85439	broad.mit.edu	37	14	81781190	81781191	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81781190_81781191insT	uc010tvu.1	-						STON2_uc001xvk.1_Intron	NM_033104	NP_149095	Q8WXE9	STON2_HUMAN	stonin 2						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)		ATACCTCTTTGTttttttttgt	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82879756	82879756	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82879756delG								SEL1L (879551 upstream) : None (None downstream)																							TGATTTACTTGGtactatggt	0.080													0	8	---	---	---	---	
EML5	161436	broad.mit.edu	37	14	89193382	89193383	+	Intron	INS	-	TTG	TTG	rs139626436	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89193382_89193383insTTG	uc001xxg.2	-							NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like							cytoplasm|microtubule				ovary(3)	3						ctggctatgttttgttgttgtt	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	91310097	91310097	+	IGR	DEL	T	-	-	rs35290296		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91310097delT								TTC7B (27336 upstream) : RPS6KA5 (27070 downstream)																							ctgaccTTAAttttttttttt	0.000													1	5	---	---	---	---	
CCDC88C	440193	broad.mit.edu	37	14	91844984	91844985	+	Intron	DEL	CT	-	-	rs35752674		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91844984_91844985delCT	uc010aty.2	-						CCDC88C_uc010twk.1_Intron	NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)				cattcccatgctcttttttatg	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	92522854	92522854	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92522854delA								TRIP11 (16037 upstream) : ATXN3 (2043 downstream)																							cactagtcacaaaaaaaccct	0.000													4	2	---	---	---	---	
ITPK1	3705	broad.mit.edu	37	14	93571221	93571221	+	Intron	DEL	C	-	-	rs5810620		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93571221delC	uc001ybg.2	-						ITPK1_uc001ybe.2_Intron|ITPK1_uc001ybf.2_Intron|ITPK1_uc001ybh.2_Intron	NM_014216	NP_055031	Q13572	ITPK1_HUMAN	inositol 1,3,4-triphosphate 5/6 kinase isoform						blood coagulation|inositol trisphosphate metabolic process|signal transduction	cytosol	ATP binding|hydrolase activity|inositol tetrakisphosphate 1-kinase activity|inositol-1,3,4-trisphosphate 5/6-kinase activity|isomerase activity|ligase activity|magnesium ion binding				0		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		CCCAGAGTGACCCCAGGCTAA	0.567													1	6	---	---	---	---	
BEGAIN	57596	broad.mit.edu	37	14	101016996	101016997	+	Intron	INS	-	TTG	TTG	rs145727991	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101016996_101016997insTTG	uc010txa.1	-						BEGAIN_uc001yhq.2_Intron	NM_001159531	NP_001153003	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated							cytoplasm|membrane	protein binding				0		Melanoma(154;0.212)				GCCAGGAAAACTTGTCATCTGC	0.639													4	2	---	---	---	---	
MEG3	55384	broad.mit.edu	37	14	101289865	101289865	+	5'Flank	DEL	T	-	-	rs138440770		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101289865delT	uc001yhy.2	+						MEG3_uc010txb.1_5'Flank|MEG3_uc010txc.1_5'Flank|MEG3_uc001yib.2_5'Flank|MEG3_uc010txd.1_5'Flank|MEG3_uc010txe.1_5'Flank|MEG3_uc001yic.2_5'Flank|MEG3_uc010txf.1_5'Flank|MEG3_uc010avz.1_5'Flank|MEG3_uc001yhw.2_5'Flank|MEG3_uc001yie.2_5'Flank|MEG3_uc001yhx.2_5'Flank|MEG3_uc010txg.1_5'Flank|MEG3_uc001yhz.2_5'Flank|MEG3_uc001yia.2_5'Flank|MEG3_uc010txh.1_5'Flank|MEG3_uc001yhv.2_5'Flank	NR_003530				Homo sapiens MEG3 mRNA, partial sequence, imprinted gene.												0						CTCCCCCCCCTCATCATTTTC	0.378													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	105652529	105652530	+	IGR	INS	-	GTGT	GTGT	rs141337690	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105652529_105652530insGTGT								NUDT14 (4869 upstream) : BRF1 (23093 downstream)																							GGGGCTGGGCCgtgtgtgtgtg	0.361													4	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106115737	106115737	+	Intron	DEL	G	-	-	rs33941735		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106115737delG	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron					Parts of antibodies, mostly variable regions.												0						CCTGGGGCCTGGGGGATGCTG	0.632													6	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106524667	106524667	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106524667delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						ggatgctttgaaaaaaaaaaa	0.045													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20449948	20449948	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20449948delC								None (None upstream) : GOLGA6L6 (287146 downstream)																							cgagatcatgccactgcactc	0.144													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20452335	20452335	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20452335delA								None (None upstream) : GOLGA6L6 (284759 downstream)																							cgtggggtttaagtgagtaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20860452	20860453	+	IGR	INS	-	AAG	AAG	rs142144144		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20860452_20860453insAAG								GOLGA8C (79426 upstream) : BCL8 (9603 downstream)																							CATATGTGTAAAAGGGACAAGG	0.257													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20866888	20866889	+	IGR	INS	-	A	A	rs148671060		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20866888_20866889insA								GOLGA8C (85862 upstream) : BCL8 (3167 downstream)																							ATCACCAACTGAAAAAAAACGA	0.332													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22458653	22458653	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22458653delT								OR4N3P (44268 upstream) : MIR1268 (54576 downstream)																							aaggaaactgttaaaaattgg	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	31190113	31190113	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31190113delG								ARHGAP11B (212304 upstream) : MTMR15 (5942 downstream)																							agagtttccagcaccccacgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37575035	37575036	+	IGR	INS	-	GG	GG	rs149521311	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37575035_37575036insGG								MEIS2 (181535 upstream) : TMCO5A (651791 downstream)																							tgtgctgcactggggggggccc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37783349	37783350	+	IGR	DEL	AA	-	-	rs34783149		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37783349_37783350delAA								MEIS2 (389849 upstream) : TMCO5A (443477 downstream)																							CATCTATCTCaaaaaaaaaaaa	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39156384	39156385	+	IGR	INS	-	GT	GT	rs142905818	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39156384_39156385insGT								C15orf53 (164145 upstream) : C15orf54 (386500 downstream)																							TATAGTGTCTCgtgtgtgtgtg	0.257													4	2	---	---	---	---	
MGA	23269	broad.mit.edu	37	15	41967561	41967561	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41967561delT	uc001zog.1	+						MGA_uc010ucy.1_Intron|MGA_uc010ucz.1_Intron	NM_001080541	NP_001074010	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 2							MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)		CTATTGCTGCttttttttttc	0.055													2	4	---	---	---	---	
CAPN3	825	broad.mit.edu	37	15	42662884	42662884	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42662884delA	uc001zpn.1	+						CAPN3_uc001zpk.1_Intron|CAPN3_uc001zpl.1_Intron|CAPN3_uc010udf.1_Intron|CAPN3_uc010udg.1_Intron|CAPN3_uc001zpo.1_Intron|CAPN3_uc001zpp.1_Intron	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a						muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		tgactcggccactagcaagtc	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	44013813	44013813	+	Intron	DEL	A	-	-	rs111972378		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44013813delA	uc010uec.1	-											Homo sapiens cDNA FLJ16411 fis, clone BRACE2016362.																		actctatctcaaaaaaaaaaa	0.035													4	5	---	---	---	---	
SLC28A2	9153	broad.mit.edu	37	15	45566698	45566701	+	Intron	DEL	CAAA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45566698_45566701delCAAA	uc001zva.2	+							NM_004212	NP_004203	O43868	S28A2_HUMAN	solute carrier family 28 (sodium-coupled						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity			ovary(4)	4		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)		tgacagggtgcaaacaaacaaaca	0.162													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46005382	46005383	+	IGR	DEL	CC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46005382_46005383delCC								SQRDL (21904 upstream) : None (None downstream)																							ttccttccttccttccctcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46535436	46535437	+	IGR	INS	-	TG	TG	rs138422797	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46535436_46535437insTG								SQRDL (551958 upstream) : SEMA6D (940966 downstream)																							GTTTCCTCCCAtgtgtgtgtgt	0.366													3	3	---	---	---	---	
SECISBP2L	9728	broad.mit.edu	37	15	49319807	49319807	+	Intron	DEL	A	-	-	rs7177172	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49319807delA	uc001zxe.1	-						SECISBP2L_uc001zxd.1_Intron|SECISBP2L_uc010bep.1_Intron|SECISBP2L_uc010beq.1_Intron	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like											breast(1)|skin(1)	2						AAACCTTATTAtttttttttt	0.129													4	3	---	---	---	---	
USP8	9101	broad.mit.edu	37	15	50779560	50779561	+	Intron	DEL	AG	-	-	rs112249459		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50779560_50779561delAG	uc001zym.3	+						USP8_uc001zyl.3_Intron|USP8_uc001zyn.3_Intron|USP8_uc010ufh.1_Intron	NM_001128611	NP_001122083	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8						cell cycle|cell proliferation|endosome organization|protein K48-linked deubiquitination|protein K63-linked deubiquitination|ubiquitin-dependent protein catabolic process	cytosol|early endosome|extrinsic to plasma membrane|nucleus	cysteine-type endopeptidase activity|SH3 domain binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)|central_nervous_system(1)	2				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		GAGAAAATGAagagagagagag	0.342													5	3	---	---	---	---	
TMOD2	29767	broad.mit.edu	37	15	52093486	52093487	+	Intron	DEL	TC	-	-	rs72529496		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52093486_52093487delTC	uc002abk.2	+						TMOD2_uc002abl.3_Intron|TMOD2_uc010bfb.2_Intron	NM_014548	NP_055363	Q9NZR1	TMOD2_HUMAN	neuronal tropomodulin isoform a						nervous system development	cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(2)	2				all cancers(107;0.00435)		acacacCCTGtctctctctctc	0.144													4	2	---	---	---	---	
WDR72	256764	broad.mit.edu	37	15	53947904	53947905	+	Intron	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53947904_53947905insT	uc002acj.2	-						WDR72_uc010bfi.1_Intron	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)		CATTTTGTAAGttttttttttt	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	55313745	55313745	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55313745delA								UNC13C (392940 upstream) : RSL24D1 (159776 downstream)																							ATAACAGCTCAAAAAAAAAGG	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	56612687	56612688	+	IGR	DEL	AG	-	-	rs36037947		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56612687_56612688delAG								RFX7 (77204 upstream) : TEX9 (44956 downstream)																							ATagagggaaagagagagatag	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	59704195	59704195	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59704195delA								MYO1E (39124 upstream) : FAM81A (26177 downstream)																							AGAAACAAACAAAAAAAAAAA	0.463													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	61265195	61265196	+	Intron	INS	-	A	A	rs34309313		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61265195_61265196insA	uc002agx.2	-							NM_134261	NP_599023	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						GCATTTGGGAGAAAAAAAAAAA	0.411													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62118106	62118107	+	IGR	INS	-	T	T	rs147553899	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62118106_62118107insT								RORA (596604 upstream) : VPS13C (26485 downstream)																							AAAATGATACCGTCTTGTGATG	0.317													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63193188	63193189	+	IGR	INS	-	CA	CA	rs139896802	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63193188_63193189insCA								TLN2 (56361 upstream) : TPM1 (141649 downstream)																							GAAGGCAGAAGCATGGCACCAA	0.564													3	4	---	---	---	---	
DAPK2	23604	broad.mit.edu	37	15	64307142	64307143	+	Intron	DEL	AC	-	-	rs71955602		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64307142_64307143delAC	uc002amr.2	-						DAPK2_uc010uim.1_Intron|DAPK2_uc010bgu.1_Intron	NM_014326	NP_055141	Q9UIK4	DAPK2_HUMAN	death-associated kinase 2						apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)		aaaaaaaaaaaCATTCTGACAT	0.243													4	2	---	---	---	---	
ANKDD1A	348094	broad.mit.edu	37	15	65201132	65201132	+	5'Flank	DEL	T	-	-	rs11299776		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65201132delT	uc002aoa.2	+						ANKDD1A_uc002anx.1_5'Flank|ANKDD1A_uc002any.2_5'Flank|ANKDD1A_uc002anz.2_5'Flank	NM_182703	NP_874362	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A						signal transduction					ovary(1)	1						aggttatgggtttagggtact	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	71064159	71064160	+	IGR	INS	-	A	A	rs142152511	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71064159_71064160insA								UACA (8309 upstream) : LARP6 (59731 downstream)																							aagaaaacagcaatgcaacggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	71105518	71105519	+	IGR	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71105518_71105519delAC								UACA (49668 upstream) : LARP6 (18372 downstream)																							acacacacagacacacacacac	0.342													4	2	---	---	---	---	
PTPN9	5780	broad.mit.edu	37	15	75856936	75856936	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75856936delA	uc002bal.2	-							NM_002833	NP_002824	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2						actacgtctcaaaaaaaaaaa	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	75922962	75922962	+	IGR	DEL	A	-	-	rs74508585		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75922962delA								SNUPN (4243 upstream) : IMP3 (8467 downstream)																							actctgtctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
SGK269	79834	broad.mit.edu	37	15	77568586	77568586	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77568586delA	uc002bcm.2	-							NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member						cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)		gaagacaagtaaaccccaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79399757	79399758	+	IGR	DEL	GT	-	-	rs67542340		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79399757_79399758delGT								RASGRF1 (16542 upstream) : MIR184 (102372 downstream)																							CGAGCTTTTGgtgtgtgtgtgt	0.381													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79952040	79952040	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79952040delG								KIAA1024 (187398 upstream) : MTHFS (185280 downstream)																							CCCTCCCTTTGGCATTATTGA	0.408													4	2	---	---	---	---	
ARNT2	9915	broad.mit.edu	37	15	80698247	80698248	+	Intron	DEL	AG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80698247_80698248delAG	uc002bfr.2	+						ARNT2_uc002bfq.2_Intron	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator						central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)			agagagagacagagagagagag	0.312													4	2	---	---	---	---	
TMC3	342125	broad.mit.edu	37	15	81636087	81636087	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81636087delA	uc002bgo.1	-						TMC3_uc010blr.1_Intron|TMC3_uc002bgp.2_Intron	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3							integral to membrane				ovary(1)|liver(1)	2						AAAAACAGACAAAAAAAAAAA	0.274													4	2	---	---	---	---	
EFTUD1	79631	broad.mit.edu	37	15	82467541	82467541	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82467541delT	uc002bgt.1	-						EFTUD1_uc002bgu.1_Intron	NM_024580	NP_078856	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain						mature ribosome assembly		GTP binding|GTPase activity|ribosome binding|translation elongation factor activity			ovary(1)	1						AAGCTTGGGATTTTTGAGACT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	86341310	86341310	+	IGR	DEL	T	-	-	rs66473925		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86341310delT								KLHL25 (3121 upstream) : AGBL1 (343932 downstream)																							TTCTTGGttcttttttttttt	0.174													4	2	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	86761076	86761076	+	Intron	DEL	T	-	-	rs66607047		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86761076delT	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						cagatttggattttttatcca	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87764129	87764130	+	IGR	INS	-	TGTG	TGTG	rs146149925	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87764129_87764130insTGTG								AGBL1 (191846 upstream) : NCRNA00052 (356030 downstream)																							tcttctatttctgtgtgtgtgt	0.000													4	3	---	---	---	---	
SEMA4B	10509	broad.mit.edu	37	15	90762788	90762788	+	Intron	DEL	G	-	-	rs5814416		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90762788delG	uc002boy.2	+						SEMA4B_uc002boz.2_Intron|SEMA4B_uc010uqd.1_Intron|SEMA4B_uc002bpa.2_5'UTR|SEMA4B_uc010bnv.1_5'Flank	NM_020210	NP_064595			semaphorin 4B precursor											ovary(1)|breast(1)|kidney(1)	3	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			CTAGGCCGAAGGAAAGTTTGC	0.572											OREG0023468	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	91970238	91970239	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91970238_91970239insA								SV2B (131590 upstream) : SLCO3A1 (426699 downstream)																							gtatcagaaagaaaaaaaaaaa	0.183													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93382068	93382068	+	IGR	DEL	T	-	-	rs34974333		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93382068delT								FAM174B (104764 upstream) : CHD2 (47365 downstream)																							aAGCCACCGAttttttttttt	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	97211886	97211887	+	IGR	INS	-	A	A	rs76301544		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97211886_97211887insA								NR2F2 (328396 upstream) : SPATA8 (114792 downstream)																							TTTGTATCTATAAAAAAAAAAG	0.287													4	2	---	---	---	---	
LOC91948	91948	broad.mit.edu	37	15	98400216	98400217	+	Intron	INS	-	GTGT	GTGT	rs72752689	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98400216_98400217insGTGT	uc002buh.1	-						LOC91948_uc002bug.1_Intron	NR_024173				SubName: Full=Putative uncharacterized protein ENSP00000381347;												0						tgagtgagtgagtgtgtgtgtg	0.391													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98955137	98955138	+	IGR	DEL	AG	-	-	rs72017957		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98955137_98955138delAG								ARRDC4 (438070 upstream) : FAM169B (25253 downstream)																							tgagctggaaagagagagagag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98977840	98977841	+	IGR	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98977840_98977841delAC								ARRDC4 (460773 upstream) : FAM169B (2550 downstream)																							acacacacggacacacacacac	0.050													4	2	---	---	---	---	
SYNM	23336	broad.mit.edu	37	15	99654225	99654226	+	Intron	INS	-	GAACT	GAACT	rs141650192	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99654225_99654226insGAACT	uc002bup.2	+						SYNM_uc002buo.2_Intron|SYNM_uc002buq.2_Intron	NM_145728	NP_663780	O15061	SYNEM_HUMAN	desmuslin isoform A						intermediate filament cytoskeleton organization	adherens junction|costamere|intermediate filament|neurofilament cytoskeleton	intermediate filament binding|structural constituent of cytoskeleton|structural constituent of muscle|vinculin binding			ovary(3)|central_nervous_system(1)	4						ttggatcctaggaactggagac	0.109													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	101694342	101694343	+	IGR	DEL	AT	-	-	rs56108350		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101694342_101694343delAT								LRRK1 (84027 upstream) : CHSY1 (21589 downstream)																							gctaccacacatgtgtccatgc	0.000													4	4	---	---	---	---	
MSLN	10232	broad.mit.edu	37	16	810892	810892	+	5'Flank	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:810892delG	uc002cjw.1	+						MSLN_uc002cjt.1_Intron|MSLN_uc002cju.1_Intron|MSLN_uc010brd.1_5'UTR|MSLN_uc002cjv.1_5'Flank|MSLN_uc002cjx.1_5'Flank	NM_013404	NP_037536	Q13421	MSLN_HUMAN	mesothelin isoform 2 preproprotein						cell adhesion	anchored to membrane|extracellular region|Golgi apparatus|plasma membrane				pancreas(1)	1		Hepatocellular(780;0.00335)				GGGGCCACTCGGGACCTGGAG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5406096	5406096	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5406096delA	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																		attctcaagtaaaaataaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8157408	8157409	+	IGR	DEL	GA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8157408_8157409delGA								A2BP1 (394068 upstream) : TMEM114 (462094 downstream)																							ggttgattctgagacactctGA	0.208													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9597983	9597984	+	IGR	INS	-	T	T	rs146541245	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9597983_9597984insT								C16orf72 (384438 upstream) : GRIN2A (249283 downstream)																							aacattttgtgtttttttttta	0.045													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11470366	11470366	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11470366delA								C16orf75 (24749 upstream) : LITAF (171216 downstream)																							ccacatgtgtaagagtttctt	0.000													4	2	---	---	---	---	
NOMO3	408050	broad.mit.edu	37	16	16339110	16339111	+	Intron	INS	-	C	C			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16339110_16339111insC	uc002deq.2	+						NOMO3_uc002dep.2_Intron|NOMO3_uc010bvp.1_Intron	NM_001004067	NP_001004067	P69849	NOMO3_HUMAN	nodal modulator 3 precursor							integral to membrane	carbohydrate binding|carboxypeptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		TGggagtttggattcagggagt	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17762641	17762642	+	IGR	INS	-	GGA	GGA	rs35686708		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17762641_17762642insGGA								XYLT1 (197903 upstream) : NOMO2 (748541 downstream)																							CCAGGCCATGGGGAGGGCAAGG	0.431													3	4	---	---	---	---	
ABCC6P1	653190	broad.mit.edu	37	16	18603566	18603567	+	Intron	INS	-	G	G	rs139400339	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18603566_18603567insG	uc002dfg.2	+						ABCC6P1_uc010vam.1_Intron	NR_003569				SubName: Full=cDNA FLJ51267, highly similar to Multidrug resistance-associated protein 6;												0						tcagaggtactgggggtcgggg	0.000													3	3	---	---	---	---	
EEF2K	29904	broad.mit.edu	37	16	22296556	22296556	+	3'UTR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22296556delT	uc002dki.2	+	18					EEF2K_uc002dkh.2_Intron	NM_013302	NP_037434	O00418	EF2K_HUMAN	elongation factor-2 kinase						insulin receptor signaling pathway|translational elongation	cytosol	ATP binding|calcium ion binding|calmodulin binding|elongation factor-2 kinase activity|translation factor activity, nucleic acid binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(48;0.0223)		TTCCTTGGTGTTTTCTTAGTG	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22704733	22704734	+	IGR	INS	-	T	T	rs5816184		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22704733_22704734insT								LOC653786 (116547 upstream) : HS3ST2 (121126 downstream)																							GATGATGATGAttttttttttt	0.183													5	5	---	---	---	---	
SCNN1B	6338	broad.mit.edu	37	16	23354834	23354835	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23354834_23354835insA	uc002dln.2	+							NM_000336	NP_000327	P51168	SCNNB_HUMAN	sodium channel, nonvoltage-gated 1, beta						excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	gaaggaaaaggaaggaaggaag	0.010													4	2	---	---	---	---	
TNRC6A	27327	broad.mit.edu	37	16	24794848	24794849	+	Intron	INS	-	T	T	rs113077368		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24794848_24794849insT	uc002dmm.2	+						TNRC6A_uc010bxs.2_Intron	NM_014494	NP_055309	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A						negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|micro-ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0394)		ATTATGTACAATTTTTTTTTTT	0.332													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25625095	25625095	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25625095delT								ZKSCAN2 (356240 upstream) : HS3ST4 (78252 downstream)																							AGGGAGTGGCTTTTCAGGATG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26855912	26855912	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26855912delA								HS3ST4 (706904 upstream) : C16orf82 (222307 downstream)																							agactctgtcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27068922	27068925	+	IGR	DEL	TTTG	-	-	rs113114370		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27068922_27068925delTTTG								HS3ST4 (919914 upstream) : C16orf82 (9294 downstream)																							gtgttttatttttgtttgtttgtt	0.108													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27194742	27194742	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27194742delC								C16orf82 (114256 upstream) : JMJD5 (20065 downstream)																							CCAGGTTATACCCTGGATTAG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28229443	28229443	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28229443delA								XPO6 (6253 upstream) : SBK1 (74397 downstream)																							acttcgtctcaaaaaaaaaaa	0.015													4	2	---	---	---	---	
BOLA2	552900	broad.mit.edu	37	16	29770432	29770432	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29770432delA	uc010bzb.1	-						uc002dtf.2_Intron			Q9H3K6	BOLA2_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0						GTGAGAGaggaaggaaggaag	0.050													4	3	---	---	---	---	
SETD1A	9739	broad.mit.edu	37	16	30971062	30971064	+	Intron	DEL	TTC	-	-	rs10540687		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30971062_30971064delTTC	uc002ead.1	+						SETD1A_uc002eae.1_Intron	NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3						ggtcccttcattcttcttcttct	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32546691	32546691	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32546691delG								HERC2P4 (382817 upstream) : TP53TG3B (138150 downstream)																							tctctgagatgaatgcacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32828380	32828381	+	IGR	INS	-	T	T	rs148268914	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32828380_32828381insT								TP53TG3B (139502 upstream) : SLC6A10P (60416 downstream)																							agcatctgtggtttgttaggtc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33361839	33361840	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33361839_33361840insT								SLC6A10P (465376 upstream) : MIR1826 (603668 downstream)																							CTCCCACAAAAttttttttttt	0.257													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33522699	33522699	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33522699delT								SLC6A10P (626236 upstream) : MIR1826 (442809 downstream)																							ATATTTACCCTTACCTACAAG	0.159													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33909505	33909505	+	IGR	DEL	G	-	-	rs138745545	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33909505delG								None (None upstream) : MIR1826 (56003 downstream)																							tgagaaacttgttcgtgatgt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33941513	33941513	+	IGR	DEL	G	-	-	rs140215358		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33941513delG								None (None upstream) : MIR1826 (23995 downstream)																							GGTCTACAAAGCATTTGATTT	0.308													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33951596	33951598	+	IGR	DEL	TTC	-	-	rs148603429		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33951596_33951598delTTC								None (None upstream) : MIR1826 (13910 downstream)																							atttatttttttccccgagacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33987829	33987835	+	IGR	DEL	GATGAAT	-	-	rs113636461		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33987829_33987835delGATGAAT								MIR1826 (22237 upstream) : UBE2MP1 (415967 downstream)																							atctctgtgggatgaatgatgaatgca	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33992552	33992552	+	IGR	DEL	T	-	-	rs113937667		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33992552delT								MIR1826 (26960 upstream) : UBE2MP1 (411250 downstream)																							agcactaaaatatacaattgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46463997	46463998	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46463997_46463998insA								None (None upstream) : ANKRD26P1 (39251 downstream)																							TATATACTTTTAAAAAGCATTG	0.277													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46497282	46497283	+	IGR	INS	-	G	G			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46497282_46497283insG								None (None upstream) : ANKRD26P1 (5966 downstream)																							AGTTTATAACTCACTGTACAAT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	48882426	48882426	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48882426delG								N4BP1 (238306 upstream) : CBLN1 (429785 downstream)																							CTAAGTACCTGGGGCTTGCAG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54970208	54970208	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54970208delA								IRX5 (1815 upstream) : IRX6 (388263 downstream)																							CATTGGCCCTAAACCCTGCCC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	56040307	56040307	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56040307delC								CES7 (80935 upstream) : LOC283856 (86592 downstream)																							AGAGGCAAGACCCCAAAGCTG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64488310	64488311	+	IGR	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64488310_64488311delAC								None (None upstream) : CDH11 (492374 downstream)																							AGACTTGGGGacacacacacac	0.218													4	2	---	---	---	---	
PHLPP2	23035	broad.mit.edu	37	16	71704599	71704600	+	Intron	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71704599_71704600delAC	uc002fax.2	-						PHLPP2_uc002fav.2_Intron|PHLPP2_uc010cgf.2_Intron	NM_015020	NP_055835	Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein							cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)|central_nervous_system(1)	2						GAGGCTGAAAacacacacacac	0.292													6	3	---	---	---	---	
RFWD3	55159	broad.mit.edu	37	16	74682683	74682683	+	Intron	DEL	A	-	-	rs28656043		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74682683delA	uc002fda.2	-						RFWD3_uc010cgq.2_Intron	NM_018124	NP_060594	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3						DNA repair|mitotic cell cycle G1/S transition DNA damage checkpoint|response to ionizing radiation	nucleus	MDM2 binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(1)	3						aaaaaaaaagaaaaaaaaGGG	0.025													4	2	---	---	---	---	
ADAMTS18	170692	broad.mit.edu	37	16	77456437	77456438	+	Intron	INS	-	A	A	rs142217194	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77456437_77456438insA	uc002ffc.3	-						ADAMTS18_uc002ffe.1_Intron|ADAMTS18_uc010vni.1_Intron	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						AGaggagagtgaaaaaaaaaga	0.035													3	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80253041	80253041	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80253041delC								MAF (618419 upstream) : DYNLRB2 (321813 downstream)																							ttggctctgtccccacccaaa	0.164													4	2	---	---	---	---	
CDYL2	124359	broad.mit.edu	37	16	80757021	80757021	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80757021delT	uc002ffs.2	-							NM_152342	NP_689555	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2							nucleus	catalytic activity|protein binding			central_nervous_system(1)	1						GGGCTACCCATTTGCTTCCAA	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86064732	86064733	+	IGR	INS	-	A	A	rs151011405	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86064732_86064733insA								IRF8 (108523 upstream) : LOC732275 (300723 downstream)																							ATTCACATCTGATCTTGCAGTA	0.317													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86160630	86160631	+	IGR	DEL	AA	-	-	rs149247144		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86160630_86160631delAA								IRF8 (204421 upstream) : LOC732275 (204825 downstream)																							TCACATTTACAAAGAGTGTCTT	0.515													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86593299	86593299	+	IGR	DEL	A	-	-	rs76466702		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86593299delA								FLJ30679 (2394 upstream) : FOXC2 (7558 downstream)																							actctgtctcaaaaaaaaaaa	0.259													4	2	---	---	---	---	
FAM38A	9780	broad.mit.edu	37	16	88787608	88787610	+	In_Frame_Del	DEL	CTT	-	-	rs3217718		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88787608_88787610delCTT	uc010vpb.1	-	39	5635_5637	c.5632_5634delAAG	c.(5632-5634)AAGdel	p.K1878del	FAM38A_uc002flp.3_5'Flank|FAM38A_uc002flq.3_5'Flank|FAM38A_uc002flr.3_In_Frame_Del_p.K1446del|FAM38A_uc010cib.2_In_Frame_Del_p.K741del	NM_001142864	NP_001136336	Q92508	PIEZ1_HUMAN	family with sequence similarity 38, member A	1878						endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane|plasma membrane	ion channel activity				0						CTGGGCCCTCCTTCTTCCTTCTT	0.616													2	7	---	---	---	---	
RPH3AL	9501	broad.mit.edu	37	17	203333	203333	+	5'Flank	DEL	A	-	-	rs113666311		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:203333delA	uc002fre.1	-						RPH3AL_uc002frf.1_5'Flank|RPH3AL_uc010cjl.1_5'Flank	NM_006987	NP_008918	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		CCAAGGAGCCAGGGGTGTGGA	0.478													4	3	---	---	---	---	
STX8	9482	broad.mit.edu	37	17	9387702	9387702	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9387702delA	uc002glx.2	-							NM_004853	NP_004844	Q9UNK0	STX8_HUMAN	syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1						ACCTAAGCTCAAAAAAAAAAA	0.294													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	10138889	10138889	+	IGR	DEL	T	-	-	rs72812814	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10138889delT								GAS7 (37021 upstream) : MYH13 (65294 downstream)																							CATCATTAAAttttttttttt	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	11463113	11463113	+	5'Flank	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11463113delG	uc002gnc.1	+											Homo sapiens cDNA FLJ37030 fis, clone BRACE2011183.																		CCTCCAGCCTGGGGGTTGGCA	0.642													4	2	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21211329	21211329	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21211329delG	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		caccacacctggcaaattttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21236300	21236300	+	IGR	DEL	T	-	-	rs66882987		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21236300delT								MAP2K3 (17751 upstream) : KCNJ12 (43399 downstream)																							GCTTCAGGAGTTTTTTAATCC	0.408													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25305912	25305912	+	IGR	DEL	C	-	-	rs144543866	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25305912delC								None (None upstream) : WSB1 (315194 downstream)																							CTACAAGATACTTTAGGCTGC	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25307254	25307254	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25307254delA								None (None upstream) : WSB1 (313852 downstream)																							acttcaatttacaatagcatc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25482529	25482529	+	IGR	DEL	A	-	-	rs77697134		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25482529delA								None (None upstream) : WSB1 (138577 downstream)																							GGGCGACTGGAAAAAAAAAGT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	27691865	27691865	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27691865delC								NUFIP2 (70699 upstream) : TAOK1 (26078 downstream)																							ctcaggtgatccccctacctc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33551050	33551050	+	IGR	DEL	T	-	-	rs146743220		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33551050delT								AMAC1 (29638 upstream) : SLFN5 (19036 downstream)																							aatatttgcattttttttttg	0.040													3	5	---	---	---	---	
HNF1B	6928	broad.mit.edu	37	17	36088302	36088302	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36088302delT	uc002hok.3	-						HNF1B_uc010wdi.1_Intron	NM_000458	NP_000449	P35680	HNF1B_HUMAN	hepatocyte nuclear factor 1-beta isoform 1						endocrine pancreas development|genitalia development|kidney development|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric nephron tubule development|regulation of pronephros size	nucleus	DNA binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			cCACAGAGCGttttttttttt	0.030									Hereditary_Prostate_Cancer				4	2	---	---	---	---	
TBC1D3	729873	broad.mit.edu	37	17	36360943	36360943	+	Intron	DEL	T	-	-	rs112620995		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36360943delT	uc010wdn.1	-						TBC1D3_uc010cvk.2_5'Flank			Q8IZP1	TBC3A_HUMAN	Homo sapiens TBC1D3 mRNA for TBC1 domain family, member 3, complete cds.							intracellular	Rab GTPase activator activity				0	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GACCtttttcttttttttttc	0.040													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39469537	39469537	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39469537delA								KRTAP9-9 (56922 upstream) : KRTAP17-1 (1634 downstream)																							tatgttcaccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39477527	39477527	+	IGR	DEL	A	-	-	rs142778009		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39477527delA								KRTAP17-1 (5580 upstream) : KRT33A (24844 downstream)																							acctggccataaaaaaaaaaa	0.000													3	4	---	---	---	---	
GHDC	84514	broad.mit.edu	37	17	40346196	40346197	+	5'UTR	INS	-	A	A	rs112866882		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40346196_40346197insA	uc002hzd.2	-	1					GHDC_uc002hzg.1_Intron|GHDC_uc010wgg.1_Intron|GHDC_uc002hze.3_Intron|GHDC_uc002hzf.3_Intron|GHDC_uc010cxz.2_Intron	NM_032484	NP_115873	Q8N2G8	GHDC_HUMAN	LGP1 homolog isoform 1							endoplasmic reticulum|nuclear envelope					0		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		gagaccctgtcaaaaaaaaaaa	0.223													6	3	---	---	---	---	
MPP2	4355	broad.mit.edu	37	17	41958264	41958264	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41958264delG	uc010wip.1	-						MPP2_uc002ien.1_Intron|MPP2_uc010wim.1_Intron|MPP2_uc002ieo.1_Intron|MPP2_uc010win.1_Intron|MPP2_uc010wio.1_Intron	NM_005374	NP_005365	Q14168	MPP2_HUMAN	palmitoylated membrane protein 2						signal transduction	cell surface|integral to plasma membrane|membrane fraction	guanylate kinase activity				0		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		TGCACGGTGAGGGAGGGGCGG	0.657											OREG0024443	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	21	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	42449071	42449071	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42449071delT								FAM171A2 (7836 upstream) : ITGA2B (479 downstream)																							CCCTCttttcttttttttttg	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43654859	43654860	+	IGR	INS	-	AA	AA	rs138744706		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43654859_43654860insAA								LRRC37A4 (59343 upstream) : LOC644172 (22631 downstream)																							gactctgtgtcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43776424	43776425	+	Intron	INS	-	TT	TT	rs112972619		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43776424_43776425insTT	uc002ijp.2	+						CRHR1_uc010wjx.1_Intron			P34998	CRFR1_HUMAN	SubName: Full=cDNA FLJ60308, highly similar to Corticotropin-releasing factor receptor 1;						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		cttttcttctcctttttttttt	0.050													5	3	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43803773	43803774	+	Intron	INS	-	G	G	rs147915977	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43803773_43803774insG	uc002ijp.2	+						CRHR1_uc010wjx.1_Intron			P34998	CRFR1_HUMAN	SubName: Full=cDNA FLJ60308, highly similar to Corticotropin-releasing factor receptor 1;						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		GGAAAAGGAAATCAAACATTGG	0.406													2	4	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44274562	44274563	+	Intron	INS	-	A	A	rs150059027	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44274562_44274563insA	uc010dav.2	-							NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				GCTCTGTATCCATCCATCTTTG	0.292													6	3	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44280599	44280599	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44280599delC	uc010dav.2	-							NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				agagcagactccgtctcaaaa	0.164													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46544456	46544457	+	IGR	INS	-	T	T	rs145899852	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46544456_46544457insT								SKAP1 (36862 upstream) : HOXB1 (62350 downstream)																							AGCACTAAGGGTTTTTTTTTTG	0.411													6	3	---	---	---	---	
HLF	3131	broad.mit.edu	37	17	53402152	53402153	+	3'UTR	DEL	GT	-	-	rs72476932		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53402152_53402153delGT	uc002iug.1	+	4					HLF_uc010dce.1_3'UTR|HLF_uc002iuh.2_3'UTR|HLF_uc010wni.1_3'UTR	NM_002126	NP_002117	Q16534	HLF_HUMAN	hepatic leukemia factor						multicellular organismal development|rhythmic process|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						AAGTGTAAGAgtgtgtgtgtgt	0.238			T	TCF3	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53408856	53408857	+	IGR	INS	-	TTC	TTC	rs139085491	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53408856_53408857insTTC								HLF (6430 upstream) : MMD (61118 downstream)																							TATGATCAAAGTTctccaaatg	0.025													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53907051	53907054	+	IGR	DEL	ACAC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53907051_53907054delACAC								PCTP (52304 upstream) : ANKFN1 (323782 downstream)																							aataatttaaacacacacacacac	0.118													4	2	---	---	---	---	
PPM1E	22843	broad.mit.edu	37	17	56833644	56833646	+	In_Frame_Del	DEL	GAG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56833644_56833646delGAG	uc002iwx.2	+	1	413_415	c.286_288delGAG	c.(286-288)GAGdel	p.E100del	PPM1E_uc010ddd.2_5'UTR	NM_014906	NP_055721	Q8WY54	PPM1E_HUMAN	protein phosphatase 1E	100	Glu-rich.|Pro-rich.				protein dephosphorylation	cytoplasm|nucleolus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(3)|lung(1)|skin(1)	5	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			ggttgagggtgaggaggaggagg	0.325													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	60901951	60901952	+	IGR	DEL	TG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60901951_60901952delTG								MARCH10 (16246 upstream) : MIR633 (119624 downstream)																							CACCTCTATAtgtgtgtgtgtg	0.149													4	2	---	---	---	---	
CSH2	1443	broad.mit.edu	37	17	61952775	61952778	+	5'Flank	DEL	TTTC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61952775_61952778delTTTC	uc002jch.2	-						CSH2_uc002jcg.2_5'Flank|CSH2_uc002jci.2_5'Flank|GH2_uc002jcj.2_Intron|CSH2_uc002jck.2_Intron	NM_020991	NP_066271	P01243	CSH_HUMAN	chorionic somatomammotropin hormone 2 isoform 1						female pregnancy|signal transduction	extracellular region	hormone activity|metal ion binding				0						cttctttctttttctttctttctt	0.113													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	63368344	63368344	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63368344delT								RGS9 (144525 upstream) : AXIN2 (156341 downstream)																							TTTATGCTGATTATTGGTTCA	0.363													4	2	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64495266	64495267	+	Intron	INS	-	T	T	rs151141384	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64495266_64495267insT	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)	gattcctatgatttttttttaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	70419432	70419433	+	Intron	INS	-	CA	CA	rs147072575	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70419432_70419433insCA	uc002jix.2	-						uc002jiz.1_Intron|uc002jiy.1_5'Flank					Homo sapiens cDNA FLJ20470 fis, clone KAT06815.																		CCCCTACCCGCcacacacacac	0.480													4	4	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71363645	71363645	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71363645delT	uc010dfm.2	-						SDK2_uc002jjt.3_Intron|SDK2_uc010dfn.2_Intron	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						gcctcttgtcttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75072271	75072272	+	IGR	INS	-	TC	TC	rs143084659	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75072271_75072272insTC								MGAT5B (125801 upstream) : C17orf86 (12453 downstream)																							TCTCCTGTCATTCTCTACCCGC	0.322													4	4	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77328433	77328435	+	Intron	DEL	GGT	-	-	rs10523076		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77328433_77328435delGGT	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			CTGCCAGGGAGGTGGTGTTTTGT	0.537													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	77701765	77701765	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77701765delG								HRNBP3 (223085 upstream) : ENPP7 (3117 downstream)																							CTATGAGATCGCAGAGAAAAT	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	78292119	78292119	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78292119delT	uc002jyf.2	+						uc002jyg.1_Intron	NM_020954	NP_066005			hypothetical protein LOC57714																		ggtttcaggcttttcggctcg	0.040													4	2	---	---	---	---	
AATK	9625	broad.mit.edu	37	17	79115736	79115737	+	Intron	INS	-	T	T	rs139491079	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79115736_79115737insT	uc010dia.2	-							NM_001080395	NP_001073864	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase							integral to membrane|mitochondrion|perinuclear region of cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1)	9	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			tccttccttccttccttccttc	0.109													3	4	---	---	---	---	
FOXK2	3607	broad.mit.edu	37	17	80536059	80536059	+	Intron	DEL	A	-	-	rs3830304		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80536059delA	uc002kfn.2	+						FOXK2_uc002kfm.1_Intron|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			CTTACTGTGCAGAGTGCACAC	0.532													2	4	---	---	---	---	
EMILIN2	84034	broad.mit.edu	37	18	2878495	2878496	+	Intron	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2878495_2878496insA	uc002kln.2	+							NM_032048	NP_114437	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2 precursor						cell adhesion	collagen	extracellular matrix constituent conferring elasticity|protein binding			skin(2)|ovary(1)	3				READ - Rectum adenocarcinoma(2;0.1)		ctcaaggaaggaaaaaaaaaaa	0.089													4	3	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3815489	3815489	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3815489delG	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				TGACTTACCTGGTGTAGCTAC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11498099	11498100	+	IGR	INS	-	C	C	rs35637745	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11498099_11498100insC								FAM38B (796120 upstream) : GNAL (191036 downstream)																							acaacaaaaaaaaGCAGAGTTA	0.203													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	13827974	13827974	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13827974delA								MC5R (1234 upstream) : MC2R (54069 downstream)																							aaaaagaaagaaaaagaaaaa	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15389978	15389978	+	IGR	DEL	A	-	-	rs111591073		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15389978delA								LOC644669 (64060 upstream) : None (None downstream)																							gctttgaaacactttttttgt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15409039	15409039	+	IGR	DEL	A	-	-	rs144372703		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15409039delA								LOC644669 (83121 upstream) : None (None downstream)																							tagacagaacaattctgagaa	0.000													12	6	---	---	---	---	
KCTD1	284252	broad.mit.edu	37	18	24173511	24173512	+	Intron	INS	-	ACA	ACA			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24173511_24173512insACA	uc010xbk.1	-							NM_198991	NP_945342	Q719H9	KCTD1_HUMAN	potassium channel tetramerisation domain						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|voltage-gated potassium channel complex	transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity			ovary(1)	1	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			ggaggaagaagacgaggaggag	0.000													6	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	30095934	30095934	+	IGR	DEL	T	-	-	rs112684458		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30095934delT								WBP11P1 (1338 upstream) : KLHL14 (156700 downstream)																							aattttttaattttttgtaga	0.000													3	3	---	---	---	---	
C18orf34	374864	broad.mit.edu	37	18	30916019	30916019	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30916019delT	uc002kxn.2	-						C18orf34_uc010xbr.1_Intron|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Intron|C18orf34_uc002kxp.2_Intron	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1											ovary(1)	1						cacttaacagtttttaagcac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	32808524	32808524	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32808524delA								MAPRE2 (86147 upstream) : ZNF397 (12474 downstream)																							actccgtctcaaaaaaaaaaa	0.104													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35446056	35446058	+	IGR	DEL	GGA	-	-	rs34243270		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35446056_35446058delGGA								CELF4 (300056 upstream) : None (None downstream)																							aagagaaaagggaggaggaggag	0.300													4	2	---	---	---	---	
SETBP1	26040	broad.mit.edu	37	18	42424312	42424313	+	Intron	INS	-	CG	CG	rs35857171		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42424312_42424313insCG	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)		acgtgcacacacgcgcgcacac	0.401									Schinzel-Giedion_syndrome				5	4	---	---	---	---	
LOXHD1	125336	broad.mit.edu	37	18	44216716	44216716	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44216716delC	uc010xcw.1	-							NM_144612	NP_653213	Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1 isoform 1						sensory perception of sound	stereocilium	protein binding				0						AAATAATAGACCCCATTTTTA	0.254													4	2	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50403738	50403739	+	Intron	DEL	GT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50403738_50403739delGT	uc002lfe.1	+						DCC_uc010xdr.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		AGGGAGGAGGGTGTGTGTGTGT	0.134													4	2	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50769242	50769247	+	Intron	DEL	GTGTGT	-	-	rs144243175		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50769242_50769247delGTGTGT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TGACAAGTAGgtgtgtgtgtgtgtgt	0.350													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	52837287	52837287	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52837287delT								CCDC68 (210548 upstream) : TCF4 (52275 downstream)																							catgattgtgttttgaaatgt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57438567	57438568	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57438567_57438568insA								CCBE1 (73923 upstream) : PMAIP1 (128624 downstream)																							gagactgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57735847	57735856	+	IGR	DEL	GCCTGCCTCA	-	-	rs66723878		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57735847_57735856delGCCTGCCTCA								PMAIP1 (164309 upstream) : MC4R (302708 downstream)																							caggtgatctgcctgcctcagcctcccaaa	0.086													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	61204708	61204708	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61204708delC								SERPINB5 (32391 upstream) : SERPINB12 (18685 downstream)																							TGATGACATACCAGGGGTAAT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62282826	62282826	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62282826delT								C18orf20 (466566 upstream) : None (None downstream)																							AAAGTATTGCTTTAAGATGGG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62452492	62452492	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62452492delA								C18orf20 (636232 upstream) : CDH7 (964996 downstream)																							CATGACTTGGAGTAAAAATGA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62570819	62570820	+	IGR	INS	-	G	G	rs34357100		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62570819_62570820insG								C18orf20 (754559 upstream) : CDH7 (846668 downstream)																							gacttcctccaaaaaaaaaaaa	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68429440	68429441	+	IGR	DEL	CA	-	-	rs34912499		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68429440_68429441delCA								SOCS6 (432006 upstream) : None (None downstream)																							GGGCTGCATGcacacacacaca	0.302													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68534943	68534952	+	IGR	DEL	GTGTGTGTGT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68534943_68534952delGTGTGTGTGT								SOCS6 (537509 upstream) : None (None downstream)																							ttcctaagtagtgtgtgtgtgtgtgtgtgt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71562498	71562499	+	IGR	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71562498_71562499delAC								None (None upstream) : FBXO15 (178089 downstream)																							gctctgcgtgacacacacacac	0.307													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	525152	525153	+	IGR	INS	-	CA	CA	rs72373320		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:525152_525153insCA								C19orf20 (5499 upstream) : CDC34 (6580 downstream)																							CAGCCCTTCACCGCCCCCGGCT	0.688													4	2	---	---	---	---	
ONECUT3	390874	broad.mit.edu	37	19	1768998	1768999	+	Intron	INS	-	GGA	GGA	rs138220122	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1768998_1768999insGGA	uc010xgr.1	+							NM_001080488	NP_001073957	O60422	ONEC3_HUMAN	one cut homeobox 3						endocrine pancreas development		sequence-specific DNA binding				0		Acute lymphoblastic leukemia(61;4.66e-11)|all_hematologic(61;4.59e-07)		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)		gtggaggtgatggtggaggtgg	0.000											OREG0025124	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	4	---	---	---	---	
KLF16	83855	broad.mit.edu	37	19	1860409	1860410	+	Intron	INS	-	CTG	CTG	rs150431611	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1860409_1860410insCTG	uc002luc.2	-						KLF16_uc010xgt.1_Intron	NM_031918	NP_114124	Q9BXK1	KLF16_HUMAN	BTE-binding protein 4							nucleus	DNA binding|zinc ion binding				0		Ovarian(11;1.78e-06)|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)		CCCTGGCCTCCCTGCTCCCAGG	0.629													5	4	---	---	---	---	
THOP1	7064	broad.mit.edu	37	19	2812125	2812125	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2812125delC	uc002lwj.2	+						THOP1_uc010xgz.1_Intron|THOP1_uc002lwk.2_Intron	NM_003249	NP_003240	P52888	THOP1_HUMAN	thimet oligopeptidase 1						proteolysis	cytoplasm	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3				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)		GGCCTCAGAGCCATGGGCTGA	0.592													4	2	---	---	---	---	
TNFAIP8L1	126282	broad.mit.edu	37	19	4645719	4645719	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4645719delA	uc002max.2	+							NM_152362	NP_689575	Q8WVP5	TP8L1_HUMAN	tumor necrosis factor, alpha-induced protein												0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		gatcCGTCTCAAAAAAAAAAA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	6509067	6509068	+	IGR	INS	-	A	A			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6509067_6509068insA								TUBB4 (6737 upstream) : TNFSF9 (21942 downstream)																							TATTTGATCTTAAAAAAAAAAA	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	8256823	8256824	+	IGR	INS	-	GAAGGA	GAAGGA			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8256823_8256824insGAAGGA								FBN3 (44442 upstream) : LASS4 (17393 downstream)																							aagaggaagaggaagaagaaga	0.015													5	4	---	---	---	---	
DNMT1	1786	broad.mit.edu	37	19	10300099	10300099	+	Intron	DEL	T	-	-	rs35245682		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10300099delT	uc002mng.2	-						DNMT1_uc010xlc.1_Intron|DNMT1_uc002mnh.2_Intron|DNMT1_uc010xld.1_Intron	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b						chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)	gcccagcTGAttttttttttt	0.005													2	4	---	---	---	---	
ICAM1	3383	broad.mit.edu	37	19	10397209	10397209	+	3'UTR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10397209delT	uc002mnq.2	+	7					ICAM1_uc010xle.1_3'UTR|ICAM4_uc002mnr.1_5'Flank|ICAM4_uc002mns.1_5'Flank|ICAM4_uc002mnt.1_5'Flank	NM_000201	NP_000192	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1 precursor						adhesion to symbiont|heterophilic cell-cell adhesion|interferon-gamma-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking|positive regulation of cellular extravasation|regulation of immune response|regulation of leukocyte mediated cytotoxicity|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell|virion attachment, binding of host cell surface receptor	extracellular space|integral to plasma membrane	integrin binding|transmembrane receptor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Natalizumab(DB00108)|Simvastatin(DB00641)	gcaaatttgattttttttttt	0.109													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	10705014	10705014	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10705014delC								AP1M2 (7023 upstream) : SLC44A2 (8107 downstream)																							TCCTCTATGGCCCCCCATTGC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13071559	13071560	+	IGR	INS	-	G	G	rs151197677	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13071559_13071560insG								GADD45GIP1 (3509 upstream) : DAND5 (4413 downstream)																							cttgaactcctggctcacctcc	0.000													2	4	---	---	---	---	
CCDC130	81576	broad.mit.edu	37	19	13867955	13867955	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13867955delA	uc002mxb.1	+						CCDC130_uc010xnf.1_Intron|CCDC130_uc002mxc.1_Intron|CCDC130_uc002mxd.1_Intron|CCDC130_uc010dzf.1_Intron	NM_030818	NP_110445	P13994	CC130_HUMAN	coiled-coil domain containing 130						response to virus		protein binding				0			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)			actctgtctcaaaaaaaaaaa	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14473564	14473567	+	IGR	DEL	GGAA	-	-	rs112094421		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14473564_14473567delGGAA								LPHN1 (156567 upstream) : CD97 (18646 downstream)																							agaaagagagggaaggaaggaagg	0.010													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	16418741	16418742	+	IGR	INS	-	G	G	rs143098702	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16418741_16418742insG								AP1M1 (72585 upstream) : KLF2 (16909 downstream)																							gaaggctgacaggtgagtttct	0.149													1	8	---	---	---	---	
CPAMD8	27151	broad.mit.edu	37	19	17030896	17030897	+	Intron	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17030896_17030897delAC	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						TCCTTGTCCTACAGGGTCCCCA	0.317													4	2	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17796908	17796919	+	Intron	DEL	TTCCCCAGCCTT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17796908_17796919delTTCCCCAGCCTT	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						TGTCAACCTCTTCCCCAGCCTTGCCCCTCCCA	0.613													1	7	---	---	---	---	
MAST3	23031	broad.mit.edu	37	19	18256419	18256419	+	Intron	DEL	C	-	-	rs11305984		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18256419delC	uc002nhz.3	+							NM_015016	NP_055831	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase								ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			large_intestine(2)|ovary(2)|stomach(1)	5						agtaggagttcccccaggatc	0.284													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	18930351	18930351	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18930351delT								COMP (28237 upstream) : UPF1 (12393 downstream)																							acaagatgcattttttttttt	0.000													3	3	---	---	---	---	
ZNF682	91120	broad.mit.edu	37	19	20137111	20137112	+	Intron	INS	-	A	A	rs145561353	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20137111_20137112insA	uc002noq.2	-						ZNF682_uc002noo.2_Intron|ZNF682_uc002nop.2_Intron|ZNF682_uc010eck.2_Intron	NM_033196	NP_149973	O95780	ZN682_HUMAN	zinc finger protein 682 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2						ggctccgtctcaaaaaaaaaaC	0.193													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	22492759	22492760	+	IGR	DEL	TT	-	-	rs113892519		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22492759_22492760delTT								ZNF676 (113006 upstream) : ZNF98 (81139 downstream)																							gtttttggggtttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27865258	27865269	+	IGR	DEL	CTTCACATAAAA	-	-	rs147102756	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27865258_27865269delCTTCACATAAAA								None (None upstream) : LOC148189 (416133 downstream)																							aaggaaatatcttcacataaaaactagacaga	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27866551	27866551	+	IGR	DEL	T	-	-	rs111746437		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27866551delT								None (None upstream) : LOC148189 (414851 downstream)																							gtttttggtgttttagagatg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27882741	27882741	+	IGR	DEL	A	-	-	rs113167415		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27882741delA								None (None upstream) : LOC148189 (398661 downstream)																							cctgtggtggaaaaggaaata	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30112063	30112064	+	IGR	INS	-	AG	AG	rs144949120	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30112063_30112064insAG								POP4 (3901 upstream) : PLEKHF1 (44263 downstream)																							aaacatgactcggggtgcctct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30729989	30729989	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30729989delA								C19orf2 (223378 upstream) : ZNF536 (133339 downstream)																							CCCTCACCAGAGGGTATCCCA	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	35704030	35704030	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35704030delC								FXYD5 (43245 upstream) : FAM187B (11674 downstream)																							gactctgtctcaaaaaaaaaa	0.000													4	2	---	---	---	---	
MLL4	9757	broad.mit.edu	37	19	36219343	36219343	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36219343delT	uc010eei.2	+							NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4						chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			gggcaggcactgaagacccag	0.000													4	2	---	---	---	---	
PLD3	23646	broad.mit.edu	37	19	40873275	40873275	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40873275delC	uc002onm.3	+						PLD3_uc002onj.3_Intron|PLD3_uc002onk.3_Intron|PLD3_uc002onl.3_Intron|PLD3_uc002onn.2_Intron|PLD3_uc002ono.2_3'UTR	NM_001031696	NP_001026866	Q8IV08	PLD3_HUMAN	phospholipase D3						lipid catabolic process	endoplasmic reticulum membrane|integral to membrane	NAPE-specific phospholipase D activity|phospholipase D activity|protein binding			skin(2)|ovary(1)	3			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			attgcttgagcccaggagttc	0.030													4	2	---	---	---	---	
ADCK4	79934	broad.mit.edu	37	19	41210879	41210879	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41210879delT	uc002oor.2	-						ADCK4_uc002ooq.1_Intron|ADCK4_uc002oos.2_3'UTR	NM_024876	NP_079152	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4 isoform a							integral to membrane	protein serine/threonine kinase activity				0			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			gtgattcccattttacagatg	0.239													4	2	---	---	---	---	
CYP2S1	29785	broad.mit.edu	37	19	41706982	41706982	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41706982delA	uc002opw.2	+						CYP2F1_uc010xvw.1_Intron|CYP2S1_uc010xvx.1_Intron	NM_030622	NP_085125	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S,						xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity			skin(1)	1						actctgtctcaaaaaaaaaaa	0.204													4	2	---	---	---	---	
KCNN4	3783	broad.mit.edu	37	19	44272893	44272893	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44272893delT	uc002oxl.2	-						KCNN4_uc010eiz.2_Intron	NM_002250	NP_002241	O15554	KCNN4_HUMAN	intermediate conductance calcium-activated						defense response	voltage-gated potassium channel complex	calcium-activated potassium channel activity|calmodulin binding			ovary(2)	2		Prostate(69;0.0352)			Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468)	CTTTGTGCAATTTTTTTTTTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45218125	45218126	+	IGR	INS	-	A	A	rs138139498	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45218125_45218126insA								CEACAM16 (4141 upstream) : BCL3 (33852 downstream)																							ggGAAACAAACAAAAAAAAACT	0.089													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45230319	45230319	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45230319delA								CEACAM16 (16335 upstream) : BCL3 (21659 downstream)																							actctgtctcaaaaaaaaaaa	0.010													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45875405	45875406	+	IGR	INS	-	GCGC	GCGC	rs149564705	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45875405_45875406insGCGC								ERCC2 (1560 upstream) : PPP1R13L (7487 downstream)																							tgtgtgtgtgtgcgcacgtgta	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	46381883	46381884	+	IGR	DEL	TC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46381883_46381884delTC								FOXA3 (4829 upstream) : IRF2BP1 (4982 downstream)																							tctgtctgcttctctctctctc	0.257													4	3	---	---	---	---	
PRKD2	25865	broad.mit.edu	37	19	47212239	47212240	+	Intron	INS	-	G	G	rs11669209		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47212239_47212240insG	uc002pfh.2	-						PRKD2_uc002pfg.2_Intron|PRKD2_uc002pfi.2_Intron|PRKD2_uc002pfj.2_Intron|PRKD2_uc010xye.1_Intron|PRKD2_uc002pfk.2_Intron	NM_001079881	NP_001073350	Q9BZL6	KPCD2_HUMAN	protein kinase D2 isoform A						cell death|intracellular signal transduction|positive regulation of transcription from RNA polymerase II promoter|protein autophosphorylation|T cell receptor signaling pathway	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein kinase C activity			ovary(2)|central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)	7		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		Gttttttttttttttttttttt	0.030													4	2	---	---	---	---	
HSD17B14	51171	broad.mit.edu	37	19	49325587	49325598	+	Intron	DEL	TGGTGATGATGG	-	-	rs142819837		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49325587_49325598delTGGTGATGATGG	uc002pkv.1	-						HSD17B14_uc010emk.1_Intron	NM_016246	NP_057330	Q9BPX1	DHB14_HUMAN	dehydrogenase/reductase (SDR family) member 10						steroid catabolic process	centrosome|cytosol	estradiol 17-beta-dehydrogenase activity|protein binding|testosterone 17-beta-dehydrogenase (NADP+) activity				0		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		atgatggtgatggtgatgatggtggtgatgat	0.000													2	4	---	---	---	---	
HSD17B14	51171	broad.mit.edu	37	19	49327704	49327707	+	Intron	DEL	AGGG	-	-	rs143019364		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49327704_49327707delAGGG	uc002pkv.1	-						HSD17B14_uc010emk.1_Intron	NM_016246	NP_057330	Q9BPX1	DHB14_HUMAN	dehydrogenase/reductase (SDR family) member 10						steroid catabolic process	centrosome|cytosol	estradiol 17-beta-dehydrogenase activity|protein binding|testosterone 17-beta-dehydrogenase (NADP+) activity				0		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		gaaagaaaaaAGGGAGGGAGGGag	0.044													3	4	---	---	---	---	
KCNA7	3743	broad.mit.edu	37	19	49577523	49577524	+	5'Flank	INS	-	T	T	rs111996662		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49577523_49577524insT	uc002pmg.2	-							NM_031886	NP_114092	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related							voltage-gated potassium channel complex	voltage-gated potassium channel activity			central_nervous_system(1)	1		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)		ttctttctttcttttttttttt	0.099													4	2	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50749368	50749369	+	Intron	INS	-	CTTC	CTTC	rs142068028	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50749368_50749369insCTTC	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		tcccttcctttcttccttcctt	0.084													10	5	---	---	---	---	
SIGLECP3	284367	broad.mit.edu	37	19	51674388	51674388	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51674388delT	uc010ycv.1	+						SIGLECP3_uc010ycu.1_Intron|SIGLECP3_uc002pvy.3_Intron|SIGLECP3_uc002pvz.3_Intron					SubName: Full=cDNA FLJ56974, moderately similar to Myeloid cell surface antigen CD33;												0						ttgtgtctgatttttttttca	0.000													4	2	---	---	---	---	
PPP2R1A	5518	broad.mit.edu	37	19	52691813	52691814	+	5'Flank	INS	-	A	A	rs113438272		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52691813_52691814insA	uc002pyp.2	+						PPP2R1A_uc010ydk.1_5'Flank|PPP2R1A_uc010epm.1_5'Flank	NM_014225	NP_055040	P30153	2AAA_HUMAN	alpha isoform of regulatory subunit A, protein						ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity			endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		gactccgtctcaaaaaaaaaaa	0.163			Mis		clear cell ovarian carcinoma								4	4	---	---	---	---	
ZNF415	55786	broad.mit.edu	37	19	53626493	53626493	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53626493delC	uc002qax.2	-						ZNF415_uc002qat.2_Intron|ZNF415_uc002qaw.2_Intron|ZNF415_uc010yds.1_Intron|ZNF415_uc010ydt.1_Intron|ZNF415_uc002qau.2_Intron|ZNF415_uc002qav.2_Intron|ZNF415_uc002qba.2_Intron|ZNF415_uc002qay.2_Intron|ZNF415_uc002qaz.2_Intron	NR_028343		Q09FC8	ZN415_HUMAN	RecName: Full=Zinc finger protein 415;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleolus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.0191)		TCATATGAAGCCAGGGGGTAG	0.537													4	2	---	---	---	---	
CACNG6	59285	broad.mit.edu	37	19	54505344	54505344	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54505344delT	uc002qct.2	+						CACNG6_uc002qcu.2_Intron|CACNG6_uc002qcv.2_Intron	NM_145814	NP_665813	Q9BXT2	CCG6_HUMAN	voltage-dependent calcium channel gamma-6							voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(2)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.168)		tatctctctcttttttttttg	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	55434336	55434337	+	IGR	DEL	AG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55434336_55434337delAG								NCR1 (9897 upstream) : NLRP7 (541 downstream)																							acacagagacagagagagagag	0.238													4	2	---	---	---	---	
NLRP4	147945	broad.mit.edu	37	19	56351711	56351712	+	Intron	DEL	TG	-	-	rs71182920		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56351711_56351712delTG	uc002qmd.3	+							NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4								ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		tgtatgtgtatgtgtgtgtgtg	0.035													5	5	---	---	---	---	
MIMT1	100073347	broad.mit.edu	37	19	57354650	57354651	+	Intron	INS	-	A	A	rs147880916	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57354650_57354651insA	uc010ett.1	+						ZIM2_uc002qnr.2_5'Flank|ZIM2_uc002qnq.2_5'Flank|ZIM2_uc010etp.2_5'Flank|ZIM2_uc010ygs.1_5'Flank|PEG3_uc002qnv.2_5'Flank|PEG3_uc002qnw.2_5'Flank|PEG3_uc002qnx.2_5'Flank|PEG3_uc010etr.2_5'Flank	NR_024059				Homo sapiens MER-repeat containing imprinted transcript 1 mRNA sequence.												0						caaaaaacgacaaaaaaaaccc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57565450	57565450	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57565450delG								MIMT1 (205528 upstream) : USP29 (66059 downstream)																							cactggtttaggcacacttgt	0.000													4	2	---	---	---	---	
RPS5	6193	broad.mit.edu	37	19	58905673	58905674	+	Intron	DEL	TG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58905673_58905674delTG	uc002qsn.2	+						RPS5_uc002qso.2_Intron	NM_001009	NP_001000	P46782	RS5_HUMAN	ribosomal protein S5						endocrine pancreas development|regulation of translational fidelity|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	mRNA binding|structural constituent of ribosome				0		all_cancers(17;1.71e-22)|all_epithelial(17;1.69e-16)|Lung NSC(17;2.25e-06)|all_lung(17;9.97e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Breast(46;0.0194)|Ovarian(87;0.0443)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.171)|GBM - Glioblastoma multiforme(193;0.0323)|Lung(386;0.0543)|LUSC - Lung squamous cell carcinoma(496;0.176)		AACTTCAGCCTGTGTGTGTGTG	0.426													4	2	---	---	---	---	
TMC2	117532	broad.mit.edu	37	20	2590304	2590304	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2590304delA	uc002wgf.1	+						TMC2_uc002wgg.1_Intron|TMC2_uc010zpw.1_Intron|TMC2_uc010zpx.1_Intron	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2							integral to membrane				ovary(3)	3						ACATATAATGAAGGGCAGTGG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	4534906	4534906	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4534906delT								ADRA1D (305247 upstream) : PRNP (131891 downstream)																							GCCCTGGCTCTCCAGCTCTCT	0.473													4	2	---	---	---	---	
C20orf196	149840	broad.mit.edu	37	20	5792186	5792186	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5792186delA	uc002wmf.2	+							NM_152504	NP_689717	Q8IYI0	CT196_HUMAN	hypothetical protein LOC149840												0						AATGGTAGACAAAAAAAAATG	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	11349913	11349914	+	IGR	INS	-	ACAC	ACAC			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11349913_11349914insACAC								JAG1 (695219 upstream) : BTBD3 (521563 downstream)																							cactgtcacatacatacacata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12639571	12639574	+	IGR	DEL	TCTC	-	-	rs11468820		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12639571_12639574delTCTC								BTBD3 (732329 upstream) : SPTLC3 (350053 downstream)																							CAAATATGGTTCTCTCTCTCTGTC	0.392													4	4	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15094410	15094411	+	Intron	DEL	GT	-	-	rs11474632		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15094410_15094411delGT	uc002wou.2	+						MACROD2_uc002wot.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				TAGTCTTGAAgtgtgtgtgtgt	0.297													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16151961	16151964	+	IGR	DEL	GGAA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16151961_16151964delGGAA								MACROD2 (118122 upstream) : KIF16B (100785 downstream)																							agagagggagggaaggaaggaagg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	18002456	18002457	+	IGR	INS	-	GGGAAGG	GGGAAGG	rs141282370	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18002456_18002457insGGGAAGG								C20orf72 (30697 upstream) : OVOL2 (2339 downstream)																							gggaggggaaagaggaagcagg	0.371													0	8	---	---	---	---	
RIN2	54453	broad.mit.edu	37	20	19904979	19904995	+	Intron	DEL	CTCTTCATACCCCACCT	-	-	rs72109502		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19904979_19904995delCTCTTCATACCCCACCT	uc002wro.1	+						RIN2_uc010gcu.1_Intron	NM_018993	NP_061866	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2						endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5						cataccgcacctcttcataccccacctcttcataccc	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	21053762	21053764	+	IGR	DEL	TGT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21053762_21053764delTGT								RALGAPA2 (360496 upstream) : PLK1S1 (52860 downstream)																							ATTACTATTGtgttgttgttgtt	0.167													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23840352	23840353	+	IGR	INS	-	A	A	rs144256985	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23840352_23840353insA								CST2 (33040 upstream) : CST5 (16219 downstream)																							tatgttgctgcaaaaaaaaaac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25742658	25742658	+	IGR	DEL	A	-	-	rs112655215		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25742658delA								ZNF337 (65189 upstream) : FAM182B (1444 downstream)																							aggtggtgatagatactgata	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26113740	26113740	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26113740delT								C20orf191 (19063 upstream) : MIR663 (75082 downstream)																							CCAGAAAAAATATGTGAGAGA	0.328													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26113793	26113794	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26113793_26113794insT								C20orf191 (19116 upstream) : MIR663 (75028 downstream)																							GTGATGCTTCATTTTTTGATTC	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26252429	26252430	+	IGR	DEL	TA	-	-	rs148238331	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26252429_26252430delTA								MIR663 (63515 upstream) : None (None downstream)																							atacatggcttattttttttat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29556637	29556637	+	IGR	DEL	C	-	-	rs73620360		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29556637delC								None (None upstream) : FRG1B (55242 downstream)																							ggaatgagcacaatgggtctg	0.025													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29582544	29582550	+	IGR	DEL	TCTTCCC	-	-	rs111245969		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29582544_29582550delTCTTCCC								None (None upstream) : FRG1B (29329 downstream)																							AGATGCTGTTTCTTCCCTCCTCCCTTG	0.338													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29588351	29588352	+	IGR	DEL	GA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29588351_29588352delGA								None (None upstream) : FRG1B (23527 downstream)																							ttattttgttgagagttttatc	0.000													6	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29648450	29648450	+	Intron	DEL	T	-	-	rs143554592		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29648450delT	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						cagaactccctctcctgtttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	30174548	30174549	+	IGR	INS	-	CA	CA	rs145516816	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30174548_30174549insCA								HM13 (17180 upstream) : ID1 (18543 downstream)																							agatctcggctcactgcaacct	0.000													2	4	---	---	---	---	
ASXL1	171023	broad.mit.edu	37	20	31001331	31001332	+	Intron	INS	-	ATTG	ATTG	rs112981389		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31001331_31001332insATTG	uc002wxs.2	+						ASXL1_uc002wxr.1_Intron|ASXL1_uc010geb.2_Intron	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248						GTGTTCAACGTAtttcattctt	0.059			F|N|Mis		MDS|CMML								0	6	---	---	---	---	
RALY	22913	broad.mit.edu	37	20	32600248	32600249	+	Intron	INS	-	CTCTTCTCTTT	CTCTTCTCTTT	rs138654658	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32600248_32600249insCTCTTCTCTTT	uc002xab.2	+						RALY_uc010zui.1_Intron|RALY_uc002xac.2_Intron|RALY_uc002xad.2_Intron|RALY_uc002xae.1_Intron	NM_016732	NP_057951	Q9UKM9	RALY_HUMAN	RNA binding protein (autoantigenic,							catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(1)	1						GCCTTGCTTGCCTCTTCTCTTT	0.450													3	4	---	---	---	---	
GDF5	8200	broad.mit.edu	37	20	34019157	34019157	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34019157delT	uc010gfc.1	-						uc002xcj.2_5'Flank	NM_000557	NP_000548	P43026	GDF5_HUMAN	growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			gttaaccctcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36038919	36038920	+	IGR	INS	-	T	T	rs74179864		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36038919_36038920insT								SRC (5100 upstream) : BLCAP (106900 downstream)																							tgtttgtttggttttttttttt	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	40502322	40502323	+	IGR	INS	-	AT	AT	rs150531364	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40502322_40502323insAT								CHD6 (255189 upstream) : PTPRT (199070 downstream)																							catgtcaacaaatctgaaggac	0.129													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	40592514	40592514	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40592514delT								CHD6 (345381 upstream) : PTPRT (108879 downstream)																							tgtttgtttgtttattttttg	0.159													4	2	---	---	---	---	
B4GALT5	9334	broad.mit.edu	37	20	48311382	48311383	+	Intron	INS	-	ACAG	ACAG			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48311382_48311383insACAG	uc002xuu.3	-							NM_004776	NP_004767	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	galactosyltransferase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)			cagatacacacacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48998002	48998003	+	IGR	DEL	TG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48998002_48998003delTG								CEBPB (188790 upstream) : PTPN1 (128888 downstream)																							ggtgtgtgtctgtgtgtgtgtg	0.000													8	4	---	---	---	---	
FAM65C	140876	broad.mit.edu	37	20	49211530	49211530	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49211530delC	uc002xvm.2	-						FAM65C_uc010zyt.1_Intron|FAM65C_uc010zyu.1_Intron	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876											ovary(2)	2						GAGGGGAGGTCCCACGGGGCA	0.353													4	2	---	---	---	---	
PFDN4	5203	broad.mit.edu	37	20	52822657	52822657	+	5'Flank	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52822657delC	uc002xwx.2	+							NM_002623	NP_002614	Q9NQP4	PFD4_HUMAN	prefoldin subunit 4						'de novo' posttranslational protein folding	prefoldin complex	chaperone binding|unfolded protein binding				0	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		Colorectal(105;0.124)|STAD - Stomach adenocarcinoma(23;0.206)			CGTCTCCTCTCCCCATGCTGA	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56329968	56329969	+	IGR	INS	-	T	T	rs142525776	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56329968_56329969insT								PMEPA1 (43427 upstream) : C20orf85 (396014 downstream)																							gtccttcctcctttttttttcc	0.010													3	3	---	---	---	---	
LSM14B	149986	broad.mit.edu	37	20	60705077	60705077	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60705077delT	uc010gjy.1	+						LSM14B_uc010gjx.1_Intron|LSM14B_uc002ybv.2_Intron|LSM14B_uc010gjz.1_Intron|LSM14B_uc010zzz.1_Intron	NM_144703	NP_653304	Q9BX40	LS14B_HUMAN	LSM14 homolog B						multicellular organismal development|regulation of translation	ribonucleoprotein complex					0	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)			TCCTGGGCtattttttttttt	0.507													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9672274	9672275	+	IGR	INS	-	T	T			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9672274_9672275insT								None (None upstream) : None (None downstream)																							TTTCTGTTTTGTTTTTTTTTTC	0.317													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9851114	9851115	+	IGR	INS	-	T	T	rs71218859		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9851114_9851115insT								None (None upstream) : None (None downstream)																							tgaaaaattaaaaaaaaaactc	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10463798	10463798	+	Intron	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10463798delG	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		ATTAATTCATGTGAGCTGCCT	0.264													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10807081	10807100	+	IGR	DEL	GGAATGGAGTGGAATGGAGT	-	-	rs75071634		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10807081_10807100delGGAATGGAGTGGAATGGAGT								None (None upstream) : TPTE (99643 downstream)																							ggaatggaacggaatggagtggaatggagtggaatggagt	0.000													10	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14343742	14343743	+	IGR	INS	-	AG	AG			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14343742_14343743insAG								None (None upstream) : C21orf99 (66744 downstream)																							attctccaaaaagtgtttcaaa	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14362029	14362030	+	IGR	INS	-	A	A	rs151036820		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14362029_14362030insA								None (None upstream) : C21orf99 (48457 downstream)																							actggtcaatcaaaagaaaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14363881	14363882	+	IGR	DEL	AG	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14363881_14363882delAG								None (None upstream) : C21orf99 (46605 downstream)																							ttctacaaaaagagagtttcaa	0.000													3	4	---	---	---	---	
C21orf99	149992	broad.mit.edu	37	21	14439999	14439999	+	Intron	DEL	T	-	-	rs142238235		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14439999delT	uc002yja.3	+							NR_026916				Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						ttgcattttcttgatggcttg	0.000													6	3	---	---	---	---	
LIPI	149998	broad.mit.edu	37	21	15518031	15518031	+	Intron	DEL	A	-	-	rs71330038		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15518031delA	uc002yjm.2	-							NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I						lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		AAGTGAAGGGAAAAAAAGTTT	0.224													4	2	---	---	---	---	
LIPI	149998	broad.mit.edu	37	21	15580942	15580947	+	5'Flank	DEL	CGTGCA	-	-	rs68131489		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15580942_15580947delCGTGCA	uc002yjm.2	-							NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I						lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		aagttgtattcgtgcacgtgcacatg	0.000													4	2	---	---	---	---	
NCAM2	4685	broad.mit.edu	37	21	22794405	22794405	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22794405delT	uc002yld.1	+						NCAM2_uc011acb.1_Intron	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor						neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		GGAAGGAGTGTTGCAGGGGTC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	25405478	25405481	+	IGR	DEL	AAAG	-	-	rs67801671		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25405478_25405481delAAAG								None (None upstream) : None (None downstream)																							aaagaaagacaaagaaagaaagaa	0.044													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	35346172	35346172	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35346172delA								ATP5O (58014 upstream) : MRPS6 (99651 downstream)																							CTAGTAACTCAAAAGGGTGGC	0.438													4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37314802	37314803	+	Intron	INS	-	CTTACCT	CTTACCT	rs150332973		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37314802_37314803insCTTACCT	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						atccctacttacctcattacac	0.064			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				3	3	---	---	---	---	
PRDM15	63977	broad.mit.edu	37	21	43226403	43226404	+	Intron	INS	-	CAC	CAC			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43226403_43226404insCAC	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						actaccaccatcaccaccacca	0.000													3	3	---	---	---	---	
COL6A1	1291	broad.mit.edu	37	21	47410424	47410424	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47410424delC	uc002zhu.1	+							NM_001848	NP_001839	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1 precursor						axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			ovary(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)	gtgaaggtgacccggggaggg	0.104													9	4	---	---	---	---	
MICAL3	57553	broad.mit.edu	37	22	18499278	18499279	+	Intron	INS	-	CG	CG	rs149948113	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18499278_18499279insCG	uc002zng.3	-						MICAL3_uc002znh.2_Intron|MICAL3_uc010grf.2_Intron|MICAL3_uc011agm.1_Intron	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		tgtagtcacattctccctccaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	21012123	21012124	+	5'Flank	INS	-	ACG	ACG	rs142838700	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21012123_21012124insACG	uc002zsv.2	-											Homo sapiens, clone IMAGE:5171202, mRNA.																		gggttgggaaaacgacggaaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	23895184	23895185	+	IGR	INS	-	TC	TC	rs138730489	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23895184_23895185insTC								ZDHHC8P1 (150385 upstream) : IGLL1 (20130 downstream)																							TCTCCCTTCAGTCTCCATTCAT	0.262													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	24079059	24079060	+	IGR	INS	-	A	A	rs111420130		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24079059_24079060insA								LOC91316 (19449 upstream) : ZNF70 (1810 downstream)																							aagaaaaaaagaaaaaaaaAAA	0.243													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	24614797	24614797	+	IGR	DEL	A	-	-	rs147772468		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24614797delA								SUSD2 (29723 upstream) : GGT5 (826 downstream)																							tgtttcacagaaaaaaaaaaa	0.010													4	2	---	---	---	---	
LOC644165	644165	broad.mit.edu	37	22	25027248	25027248	+	5'Flank	DEL	A	-	-	rs13055206	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25027248delA	uc011ajv.1	+							NR_024494				Homo sapiens cDNA FLJ57042 complete cds, moderately similar to Breakpoint cluster region protein (EC 2.7.11.1).												0						agggttggggatagggttaca	0.000													4	2	---	---	---	---	
SGSM1	129049	broad.mit.edu	37	22	25228908	25228908	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25228908delT	uc003abg.2	+						SGSM1_uc003abh.2_Intron|SGSM1_uc010guu.1_Intron|SGSM1_uc003abj.2_Intron|SGSM1_uc003abf.2_Intron	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1							Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5						aaatttcctcttttttttttt	0.000													4	2	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26153554	26153554	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26153554delA	uc003abz.1	+							NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						actgcatatcaaaaaaaaaaa	0.214													4	2	---	---	---	---	
ZNRF3	84133	broad.mit.edu	37	22	29310803	29310803	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29310803delA	uc003aeg.2	+							NM_032173	NP_115549	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3							integral to membrane	zinc ion binding			ovary(1)	1						actccgtctcaaaaaaaaaaa	0.194													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	29592435	29592436	+	IGR	DEL	AC	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29592435_29592436delAC								KREMEN1 (28114 upstream) : EMID1 (9517 downstream)																							agatacacagacacacacacac	0.144													4	2	---	---	---	---	
SEC14L2	23541	broad.mit.edu	37	22	30804095	30804095	+	Intron	DEL	A	-	-	rs77169073		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30804095delA	uc003ahr.2	+						SEC14L2_uc003ahq.2_Intron|SEC14L2_uc011akx.1_Intron|SEC14L2_uc003ahs.2_Intron|SEC14L2_uc011aky.1_Intron|SEC14L2_uc003aht.2_5'Flank|SEC14L2_uc003ahu.3_5'Flank|SEC14L2_uc010gvv.2_5'Flank|SEC14L2_uc010gvw.1_5'Flank|MTP18_uc010gvx.1_5'Flank|MTP18_uc003ahv.1_5'Flank|MTP18_uc010gvy.1_5'Flank	NM_012429	NP_036561	O76054	S14L2_HUMAN	SEC14-like 2 isoform 1						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	phospholipid binding|transporter activity|vitamin E binding				0					Vitamin E(DB00163)	actccatctcaaaaaaaaaaa	0.010													3	3	---	---	---	---	
LIMK2	3985	broad.mit.edu	37	22	31642170	31642171	+	Intron	DEL	CA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31642170_31642171delCA	uc003akh.2	+						LIMK2_uc003akg.2_Intron|LIMK2_uc003aki.2_Intron|LIMK2_uc003akj.2_5'Flank|LIMK2_uc003akk.2_5'Flank|LIMK2_uc011aln.1_5'Flank	NM_005569	NP_005560	P53671	LIMK2_HUMAN	LIM domain kinase 2 isoform 2a							mitochondrion|nucleus	ATP binding|protein serine/threonine kinase activity|zinc ion binding			ovary(2)	2						cgcacgcacgcacacacacaca	0.000													4	2	---	---	---	---	
SFI1	9814	broad.mit.edu	37	22	31971049	31971050	+	Intron	DEL	AA	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31971049_31971050delAA	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron|SFI1_uc010gwi.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1						caactcaaagaaaaaaaaaaaa	0.129													4	2	---	---	---	---	
TMPRSS6	164656	broad.mit.edu	37	22	37496454	37496455	+	Intron	INS	-	G	G	rs149146010	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37496454_37496455insG	uc003aqs.1	-						TMPRSS6_uc003aqt.1_Intron|TMPRSS6_uc003aqu.2_Intron	NM_153609	NP_705837	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6						angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|intracellular|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)|skin(1)	6						agagatgtccagggggacagag	0.000													3	4	---	---	---	---	
TRIOBP	11078	broad.mit.edu	37	22	38085880	38085880	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38085880delA	uc003atq.1	+						NOL12_uc011anm.1_Intron|NOL12_uc003ato.1_Intron|NOL12_uc003atp.2_Intron	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6						actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					tattaaaagtaaaaaaattag	0.000													4	2	---	---	---	---	
SCUBE1	80274	broad.mit.edu	37	22	43700594	43700595	+	Intron	DEL	GT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43700594_43700595delGT	uc003bdt.1	-						SCUBE1_uc003bdu.1_Intron	NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1						adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)				GCGGTTGGTCgtgtgtgtgtgt	0.450													5	3	---	---	---	---	
KIAA1644	85352	broad.mit.edu	37	22	44688912	44688913	+	Intron	DEL	GC	-	-	rs71662130		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44688912_44688913delGC	uc003bet.2	-							NM_001099294	NP_001092764	Q3SXP7	K1644_HUMAN	hypothetical protein LOC85352 precursor							integral to membrane				ovary(1)	1		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)				GCTAGACAGGGCCCCGGACCCC	0.584													4	2	---	---	---	---	
FAM118A	55007	broad.mit.edu	37	22	45716319	45716320	+	Intron	DEL	TT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45716319_45716320delTT	uc003bfz.3	+						FAM118A_uc003bga.3_Intron	NM_001104595	NP_001098065	Q9NWS6	F118A_HUMAN	hypothetical protein LOC55007							integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		cttcttcttctttttttttttc	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47010757	47010758	+	IGR	DEL	CA	-	-	rs67259334		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47010757_47010758delCA								CELSR1 (77690 upstream) : GRAMD4 (11900 downstream)																							TTCCCCTGTGCATGTAGGTTCC	0.579													4	3	---	---	---	---	
HDAC10	83933	broad.mit.edu	37	22	50685567	50685567	+	Intron	DEL	T	-	-	rs66462064		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50685567delT	uc003bkg.2	-						TUBGCP6_uc003bkb.1_5'Flank|TUBGCP6_uc010har.1_5'Flank|TUBGCP6_uc010has.1_5'Flank|TUBGCP6_uc010hau.1_5'Flank|HDAC10_uc003bke.2_Intron|HDAC10_uc003bkf.2_Intron|HDAC10_uc010hav.2_Intron|HDAC10_uc003bkh.2_Intron|HDAC10_uc003bki.2_Intron|HDAC10_uc003bkj.2_Intron	NM_032019	NP_114408	Q969S8	HDA10_HUMAN	histone deacetylase 10 isoform 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nucleus	histone deacetylase activity|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		ACGTCTATAAttttttttttt	0.214													4	2	---	---	---	---	
SAPS2	9701	broad.mit.edu	37	22	50857140	50857140	+	Intron	DEL	G	-	-	rs7293044	by1000genomes	TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50857140delG	uc003blb.1	+						SAPS2_uc003bky.1_Intron|SAPS2_uc003bkz.1_Intron|SAPS2_uc003blc.2_Intron|SAPS2_uc003bla.1_Intron	NM_014678	NP_055493	O75170	PP6R2_HUMAN	SAPS domain family, member 2							cytoplasm|intracellular membrane-bounded organelle	protein binding				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.222)		TAAAAAAAAAGAAAAAGTATT	0.274													4	2	---	---	---	---	
ASMTL	8623	broad.mit.edu	37	X	1543890	1543893	+	Intron	DEL	CCAT	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1543890_1543893delCCAT	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				tatccacctaccatccatccatcc	0.010													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	18012377	18012377	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18012377delT								RAI2 (132920 upstream) : BEND2 (168676 downstream)																							TTTCTATCACTTTTGCCTCAT	0.328													4	2	---	---	---	---	
IL1RAPL1	11141	broad.mit.edu	37	X	29019030	29019030	+	Intron	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29019030delT	uc004dby.2	+							NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5						GTTATTGCTCTTTTTTTTTTT	0.338													4	2	---	---	---	---	
HDAC6	10013	broad.mit.edu	37	X	48675659	48675659	+	Intron	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48675659delA	uc011mmi.1	+						HDAC6_uc004dks.1_Intron|HDAC6_uc010nig.1_Intron|HDAC6_uc004dkt.1_Intron|HDAC6_uc011mmk.1_Intron|HDAC6_uc004dkv.1_Intron|HDAC6_uc004dkw.1_Intron|HDAC6_uc004dkx.1_5'Flank	NM_006044	NP_006035	Q9UBN7	HDAC6_HUMAN	histone deacetylase 6						aggresome assembly|cellular response to hydrogen peroxide|Hsp90 deacetylation|lysosome localization|macroautophagy|misfolded or incompletely synthesized protein catabolic process|negative regulation of proteolysis|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|polyubiquitinated misfolded protein transport|positive regulation of apoptosis|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of epithelial cell migration|positive regulation of receptor biosynthetic process|positive regulation of signal transduction|regulation of androgen receptor signaling pathway|regulation of receptor activity|response to growth factor stimulus|response to toxin|transcription, DNA-dependent|tubulin deacetylation	aggresome|caveola|cell leading edge|cytosol|histone deacetylase complex|microtubule associated complex|perinuclear region of cytoplasm	actin binding|alpha-tubulin binding|beta-catenin binding|dynein complex binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|Hsp90 protein binding|microtubule binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|polyubiquitin binding|tau protein binding|tubulin deacetylase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)	4					Vorinostat(DB02546)	actccgtctcaaaaaaaaaaa	0.224													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	58534904	58534904	+	IGR	DEL	T	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:58534904delT								ZXDA (597837 upstream) : None (None downstream)																							gaaaaggaaatatcttcacat	0.000													4	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61891965	61891965	+	IGR	DEL	A	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61891965delA								None (None upstream) : SPIN4 (675143 downstream)																							gtttggaaacagtctttttgc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	103182572	103182572	+	Intron	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103182572delC	uc004eln.1	+						TMSB15B_uc004elo.3_Intron					Homo sapiens cDNA FLJ33654 fis, clone BRAMY2024827.																		GGGTTCATTTCCAATTAAGCA	0.403													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	131037396	131037397	+	IGR	DEL	AC	-	-	rs72188053		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131037396_131037397delAC								LOC286467 (72725 upstream) : MST4 (119848 downstream)																							acacacacatacacacacacac	0.302													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9940581	9940581	+	IGR	DEL	A	-	-	rs112496364		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9940581delA								TTTY22 (289727 upstream) : None (None downstream)																							TTGTTAGtatatttttaaaaa	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9992175	9992175	+	IGR	DEL	C	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9992175delC								TTTY22 (341321 upstream) : None (None downstream)																							ctcctccccaccttcttcagg	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10049888	10049889	+	IGR	INS	-	G	G	rs139978218		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10049888_10049889insG								TTTY22 (399034 upstream) : None (None downstream)																							atcaaaggaaatttcaactgtg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13472716	13472716	+	IGR	DEL	G	-	-			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13472716delG								None (None upstream) : None (None downstream)																							tgtacaaaaagcctggaaatg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13643024	13643025	+	IGR	INS	-	GAT	GAT			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13643024_13643025insGAT								None (None upstream) : None (None downstream)																							cgattccattcgatgattccat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13867074	13867075	+	IGR	INS	-	GACTC	GACTC			TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13867074_13867075insGACTC								None (None upstream) : TTTY15 (907223 downstream)																							ggaatggaattgaatggaatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59013019	59013019	+	IGR	DEL	A	-	-	rs148494923		TCGA-18-3415-01	TCGA-18-3415-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59013019delA								None (None upstream) : None (None downstream)																							gtctcaaaagaaaaaaaaaaT	0.189													7	7	---	---	---	---	
