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
CCNL2	81669	broad.mit.edu	37	1	1325625	1325625	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1325625G>C	uc001afi.2	-	8	1023	c.991C>G	c.(991-993)CCT>GCT	p.P331A	CCNL2_uc010nym.1_RNA|CCNL2_uc001aff.1_Missense_Mutation_p.P109A|CCNL2_uc001afg.1_Missense_Mutation_p.P109A|CCNL2_uc001afh.2_3'UTR|CCNL2_uc001afj.2_3'UTR|CCNL2_uc001afk.2_3'UTR	NM_030937	NP_112199	Q96S94	CCNL2_HUMAN	cyclin L2 isoform A	331					regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nuclear speck	protein kinase binding			ovary(2)|central_nervous_system(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		TTGGGGGCAGGAGAGAACCCC	0.587													6	70	---	---	---	---	PASS
CCNL2	81669	broad.mit.edu	37	1	1325636	1325636	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1325636G>A	uc001afi.2	-	8	1012	c.980C>T	c.(979-981)TCG>TTG	p.S327L	CCNL2_uc010nym.1_RNA|CCNL2_uc001aff.1_Missense_Mutation_p.S105L|CCNL2_uc001afg.1_Missense_Mutation_p.S105L|CCNL2_uc001afh.2_3'UTR|CCNL2_uc001afj.2_3'UTR|CCNL2_uc001afk.2_3'UTR	NM_030937	NP_112199	Q96S94	CCNL2_HUMAN	cyclin L2 isoform A	327					regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nuclear speck	protein kinase binding			ovary(2)|central_nervous_system(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		AGAGAACCCCGAGGTACCATC	0.592													8	72	---	---	---	---	PASS
CDK11A	728642	broad.mit.edu	37	1	1636454	1636454	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1636454C>A	uc009vks.2	-	13	1455	c.1347G>T	c.(1345-1347)GTG>GTT	p.V449V	CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agv.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc001ahj.3_5'UTR|CDK11A_uc009vkp.2_Silent_p.V66V|CDK11A_uc009vkq.2_RNA|CDK11A_uc009vkr.2_Silent_p.V439V|CDK11A_uc010nys.1_Silent_p.V439V|CDK11A_uc010nyt.1_Silent_p.V449V	NM_024011	NP_076916	Q9UQ88	CD11A_HUMAN	cell division cycle 2-like 2 isoform 1	452	Protein kinase.				apoptosis|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			stomach(1)	1						GCTTTAGAGCCACAATTTCAT	0.532													6	129	---	---	---	---	PASS
CHD5	26038	broad.mit.edu	37	1	6206373	6206373	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6206373C>A	uc001amb.1	-	11	1801	c.1701G>T	c.(1699-1701)AAG>AAT	p.K567N	CHD5_uc001ama.1_5'Flank|CHD5_uc001amc.1_RNA	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	567					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TGTTCTTCCTCTTCTCGCTCT	0.527													5	52	---	---	---	---	PASS
PLEKHG5	57449	broad.mit.edu	37	1	6556583	6556583	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6556583G>T	uc001ano.1	-	2	152	c.51C>A	c.(49-51)CCC>CCA	p.P17P	PLEKHG5_uc001ann.1_5'UTR|PLEKHG5_uc001anq.1_Silent_p.P38P|PLEKHG5_uc001anp.1_Silent_p.P38P	NM_001042663	NP_001036128	O94827	PKHG5_HUMAN	pleckstrin homology domain containing family G	17					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		CCATGCAGGCGGGGTTCTGAC	0.682													4	19	---	---	---	---	PASS
TNFRSF9	3604	broad.mit.edu	37	1	7995201	7995201	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7995201C>A	uc001aot.2	-	6	544	c.416G>T	c.(415-417)TGT>TTT	p.C139F		NM_001561	NP_001552	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily,	139	Extracellular (Potential).|TNFR-Cys 4.				induction of apoptosis|negative regulation of cell proliferation	integral to plasma membrane	binding|receptor activity			large_intestine(1)|lung(1)|ovary(1)|skin(1)	4	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|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;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		ATCCAAAGAACAGCTTAGACA	0.433													5	32	---	---	---	---	PASS
PTCHD2	57540	broad.mit.edu	37	1	11589653	11589653	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11589653G>C	uc001ash.3	+	14	2977	c.2839G>C	c.(2839-2841)GGG>CGG	p.G947R		NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	947	Extracellular (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CCCCTTCCACGGGCGCGTATG	0.627													8	41	---	---	---	---	PASS
MUL1	79594	broad.mit.edu	37	1	20827489	20827489	+	Silent	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20827489T>A	uc001bdi.3	-	4	910	c.753A>T	c.(751-753)ACA>ACT	p.T251T		NM_024544	NP_078820	Q969V5	MUL1_HUMAN	mitochondrial ubiquitin ligase activator of NFKB	251	Helical; (Potential).				activation of caspase activity|activation of JUN kinase activity|induction of apoptosis|mitochondrial fission|mitochondrion localization|negative regulation of cell growth|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to mitochondrial outer membrane|nucleus|peroxisome	identical protein binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding				0		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00748)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000137)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		GGGTGGCACATGTGGCAAAGC	0.592													11	62	---	---	---	---	PASS
EPHB2	2048	broad.mit.edu	37	1	23236992	23236992	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23236992G>A	uc009vqj.1	+	14	2765	c.2620G>A	c.(2620-2622)GGC>AGC	p.G874S	EPHB2_uc001bge.2_Missense_Mutation_p.G875S|EPHB2_uc001bgf.2_Missense_Mutation_p.G874S|EPHB2_uc010odu.1_Missense_Mutation_p.G816S	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	874	Cytoplasmic (Potential).|Protein kinase.				axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		GCCCAAGTTCGGCCAAATTGT	0.627									Hereditary_Prostate_Cancer				8	21	---	---	---	---	PASS
ASAP3	55616	broad.mit.edu	37	1	23763444	23763444	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23763444T>A	uc001bha.2	-	15	1560	c.1436A>T	c.(1435-1437)CAG>CTG	p.Q479L	ASAP3_uc001bgy.1_5'Flank|ASAP3_uc001bgz.1_RNA|ASAP3_uc010odz.1_Missense_Mutation_p.Q348L|ASAP3_uc010oea.1_Missense_Mutation_p.Q470L|ASAP3_uc001bhb.2_Missense_Mutation_p.Q2L	NM_017707	NP_060177	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH	479	Arf-GAP.				regulation of ARF GTPase activity	cytoplasm	ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3						GGTGAGTGACTGCATGCGCGA	0.657													3	6	---	---	---	---	PASS
HMGCL	3155	broad.mit.edu	37	1	24143192	24143192	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24143192G>T	uc001bib.2	-	4	365	c.321C>A	c.(319-321)ACC>ACA	p.T107T	HMGCL_uc010oec.1_Silent_p.T107T|HMGCL_uc009vqr.2_Intron|HMGCL_uc001bic.2_Silent_p.T82T|HMGCL_uc009vqs.1_Silent_p.T107T|HMGCL_uc001bid.1_Silent_p.T107T	NM_000191	NP_000182	P35914	HMGCL_HUMAN	3-hydroxy-3-methylglutaryl CoA lyase isoform 1	107					acetoacetic acid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA lyase activity|metal ion binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)		TCAAATTTGGGGTCAGGACTG	0.517													7	145	---	---	---	---	PASS
MYOM3	127294	broad.mit.edu	37	1	24418729	24418729	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24418729G>T	uc001bin.3	-	11	1330	c.1167C>A	c.(1165-1167)CTC>CTA	p.L389L	MYOM3_uc001bim.3_Silent_p.L46L|MYOM3_uc001bio.2_Silent_p.L389L|MYOM3_uc001bip.1_Silent_p.L46L	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3	389	Fibronectin type-III 1.									skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		AAGTCAGGATGAGGCAGTCTC	0.657													4	15	---	---	---	---	PASS
COL16A1	1307	broad.mit.edu	37	1	32138087	32138087	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32138087C>A	uc001btk.1	-	47	3400	c.3035G>T	c.(3034-3036)GGA>GTA	p.G1012V	COL16A1_uc001bti.1_5'Flank|COL16A1_uc001btj.1_Missense_Mutation_p.G825V	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	1012	Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		GCCAGGATCTCCCTCACTGTT	0.597													22	19	---	---	---	---	PASS
C1orf94	84970	broad.mit.edu	37	1	34667845	34667845	+	Silent	SNP	C	A	A	rs114850350	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34667845C>A	uc001bxs.3	+	4	1260	c.861C>A	c.(859-861)ACC>ACA	p.T287T	C1orf94_uc001bxt.2_Silent_p.T477T	NM_032884	NP_116273	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform b	287							protein binding				0		Myeloproliferative disorder(586;0.0393)				ATCACTCTACCTTCTTGCAGT	0.552													5	63	---	---	---	---	PASS
MAP7D1	55700	broad.mit.edu	37	1	36636743	36636743	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36636743G>T	uc001bzz.2	+	2	434	c.218G>T	c.(217-219)GGG>GTG	p.G73V	MAP7D1_uc001caa.2_Missense_Mutation_p.G73V|MAP7D1_uc001cab.2_Missense_Mutation_p.G73V|MAP7D1_uc001cac.2_5'Flank	NM_018067	NP_060537	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	73	Pro-rich.					cytoplasm|spindle				ovary(3)|breast(2)	5		Myeloproliferative disorder(586;0.0393)				AGCCCCTCAGGGCAGGTCGGG	0.657													6	33	---	---	---	---	PASS
MTF1	4520	broad.mit.edu	37	1	38323190	38323190	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38323190G>T	uc001cce.1	-	2	282	c.141C>A	c.(139-141)ACC>ACA	p.T47T	MTF1_uc009vvj.1_5'UTR	NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	47						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TAAGAACAGTGGTCCTATCAT	0.498													5	49	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39844973	39844973	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39844973C>A	uc010oiu.1	+	18	8826	c.8695C>A	c.(8695-8697)CTC>ATC	p.L2899I	MACF1_uc010ois.1_Missense_Mutation_p.L2397I|MACF1_uc001cda.1_Missense_Mutation_p.L2284I|MACF1_uc001cdc.1_Missense_Mutation_p.L1463I	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	4464					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TCAGGCTATCCTCAACAGAAT	0.478													9	248	---	---	---	---	PASS
PRDX1	5052	broad.mit.edu	37	1	45980172	45980172	+	Intron	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45980172G>T	uc001cnz.2	-						PRDX1_uc001coa.2_Intron|PRDX1_uc001cob.2_Intron|PRDX1_uc001coc.2_Intron	NM_181697	NP_859048	Q06830	PRDX1_HUMAN	peroxiredoxin 1						cell proliferation|cell redox homeostasis|hydrogen peroxide catabolic process|skeletal system development	melanosome|mitochondrion|nucleus	protein binding|thioredoxin peroxidase activity				0	Acute lymphoblastic leukemia(166;0.155)					TCAGACAGATGGCTTACCTTC	0.328													7	191	---	---	---	---	PASS
AKR1A1	10327	broad.mit.edu	37	1	46034829	46034829	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46034829C>A	uc001cod.2	+	9	1304	c.840C>A	c.(838-840)ACC>ACA	p.T280T	AKR1A1_uc001coe.2_Silent_p.T280T|AKR1A1_uc001cof.2_Silent_p.T86T|AKR1A1_uc001cog.2_RNA	NM_006066	NP_006057	P14550	AK1A1_HUMAN	aldo-keto reductase family 1, member A1	280					glucose metabolic process		alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)					TTGACTTCACCTTTAGCCCAG	0.473													7	72	---	---	---	---	PASS
FAF1	11124	broad.mit.edu	37	1	50957443	50957443	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50957443T>C	uc009vyx.1	-	17	1588	c.1525A>G	c.(1525-1527)AGA>GGA	p.R509G	FAF1_uc009vyw.1_RNA|FAF1_uc001cse.1_Missense_Mutation_p.R509G|FAF1_uc010onc.1_Missense_Mutation_p.R267G	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1	509					apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		TCTTGCTCTCTCTTCACATTT	0.338													15	68	---	---	---	---	PASS
CC2D1B	200014	broad.mit.edu	37	1	52821867	52821867	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52821867T>G	uc001ctq.1	-	18	2201	c.2063A>C	c.(2062-2064)CAG>CCG	p.Q688P	CC2D1B_uc001ctr.2_Missense_Mutation_p.Q228P|CC2D1B_uc001cts.2_Missense_Mutation_p.Q373P	NM_032449	NP_115825	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	688	C2.									ovary(2)	2						CCTCACAGTCTGGAATGTCTT	0.612													16	23	---	---	---	---	PASS
C8A	731	broad.mit.edu	37	1	57333307	57333307	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57333307G>A	uc001cyo.2	+	2	235	c.103G>A	c.(103-105)GCA>ACA	p.A35T		NM_000562	NP_000553	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	35					complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular space|membrane attack complex				ovary(1)|central_nervous_system(1)|skin(1)	3						AGCTACACCCGCAGCAGTTAC	0.448													6	28	---	---	---	---	PASS
C8A	731	broad.mit.edu	37	1	57378134	57378134	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57378134G>T	uc001cyo.2	+	10	1571	c.1439G>T	c.(1438-1440)CGC>CTC	p.R480L		NM_000562	NP_000553	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	480	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular space|membrane attack complex				ovary(1)|central_nervous_system(1)|skin(1)	3						GAGGCCAAGCGCCAGAACCTG	0.622													15	25	---	---	---	---	PASS
HOOK1	51361	broad.mit.edu	37	1	60325921	60325921	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60325921G>T	uc009wad.2	+	16	1555	c.1453G>T	c.(1453-1455)GAG>TAG	p.E485*	HOOK1_uc001czo.2_Nonsense_Mutation_p.E485*|HOOK1_uc001czp.2_RNA|HOOK1_uc010oor.1_Nonsense_Mutation_p.E443*	NM_015888	NP_056972	Q9UJC3	HOOK1_HUMAN	hook homolog 1	485	Sufficient for interaction with microtubules.|Potential.				early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|multicellular organismal development|protein transport	FHF complex|microtubule	identical protein binding			ovary(1)|breast(1)	2	all_cancers(7;0.000129)					AGAAGGCTCTGAGAATGAACG	0.373													6	159	---	---	---	---	PASS
NFIA	4774	broad.mit.edu	37	1	61554058	61554058	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61554058G>T	uc001czw.2	+	2	749	c.265G>T	c.(265-267)GAG>TAG	p.E89*	NFIA_uc001czy.2_Nonsense_Mutation_p.E81*|NFIA_uc010oos.1_Nonsense_Mutation_p.E134*|NFIA_uc001czv.2_Nonsense_Mutation_p.E89*	NM_001134673	NP_001128145	Q12857	NFIA_HUMAN	nuclear factor I/A isoform 1	89	CTF/NF-I.				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						CGAATATCGAGAGGATTTTGT	0.463													7	124	---	---	---	---	PASS
L1TD1	54596	broad.mit.edu	37	1	62675520	62675520	+	Silent	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62675520A>T	uc001dae.3	+	4	1376	c.1074A>T	c.(1072-1074)CTA>CTT	p.L358L		NM_019079	NP_061952	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	358										ovary(1)|skin(1)	2						TGAGCTTCCTATTTCTTAAAG	0.383													24	116	---	---	---	---	PASS
PDE4B	5142	broad.mit.edu	37	1	66379032	66379032	+	Missense_Mutation	SNP	C	G	G	rs12038033		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66379032C>G	uc001dcn.2	+	2	226	c.35C>G	c.(34-36)GCT>GGT	p.A12G	PDE4B_uc009war.2_5'UTR|PDE4B_uc001dco.2_Missense_Mutation_p.A12G	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1	12					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)	ACGGTGATGGCTGATGATGTA	0.398													16	33	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75037158	75037158	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75037158C>T	uc001dgg.2	-	14	4455	c.4236G>A	c.(4234-4236)GGG>GGA	p.G1412G		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	1412	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						GCACTTCCTCCCCACTCCGTG	0.557													17	55	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75065401	75065401	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75065401A>C	uc001dgg.2	-	11	1923	c.1704T>G	c.(1702-1704)AGT>AGG	p.S568R	uc001dgh.2_Intron|C1orf173_uc001dgi.3_Missense_Mutation_p.S362R	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	568	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						CTTCCAGTTCACTCTCAGAGC	0.388													26	36	---	---	---	---	PASS
C1orf173	127254	broad.mit.edu	37	1	75107029	75107029	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75107029T>A	uc001dgg.2	-	5	649	c.430A>T	c.(430-432)AGT>TGT	p.S144C		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	144										ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						GCTAACGGACTGGAATGTCCT	0.428													6	36	---	---	---	---	PASS
ZZZ3	26009	broad.mit.edu	37	1	78097971	78097971	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78097971C>A	uc001dhq.2	-	5	1545	c.1069G>T	c.(1069-1071)GTT>TTT	p.V357F	ZZZ3_uc001dhr.2_Intron|ZZZ3_uc009wbz.1_Missense_Mutation_p.V357F|ZZZ3_uc001dhp.2_Missense_Mutation_p.V357F	NM_015534	NP_056349	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	357					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5						CAGTCTAGAACAGGAGATGGT	0.468													17	51	---	---	---	---	PASS
WDR63	126820	broad.mit.edu	37	1	85559204	85559204	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85559204C>A	uc001dkt.2	+	9	1112	c.921C>A	c.(919-921)CTC>CTA	p.L307L	WDR63_uc009wcl.2_Silent_p.L268L	NM_145172	NP_660155	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	307										upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		GGAAATACCTCGCAGAAGAAG	0.388													7	158	---	---	---	---	PASS
CCBL2	56267	broad.mit.edu	37	1	89414865	89414865	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89414865T>A	uc001dmp.2	-	11	1427	c.1050A>T	c.(1048-1050)AGA>AGT	p.R350S	CCBL2_uc001dmq.2_Missense_Mutation_p.R316S|CCBL2_uc001dmr.2_Missense_Mutation_p.R186S	NM_001008661	NP_001008661	Q6YP21	KAT3_HUMAN	kynurenine aminotransferase III isoform 1	350					biosynthetic process|kynurenine metabolic process|tryptophan catabolic process		cysteine-S-conjugate beta-lyase activity|kynurenine-glyoxylate transaminase activity|kynurenine-oxoglutarate transaminase activity|pyridoxal phosphate binding			ovary(1)	1		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	CCATCCGATCTCTTTTTACTT	0.408													13	24	---	---	---	---	PASS
GBP1	2633	broad.mit.edu	37	1	89523674	89523674	+	Splice_Site	SNP	C	T	T	rs139189718	byFrequency	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89523674C>T	uc001dmx.2	-	6	1094	c.874_splice	c.e6+1	p.R292_splice		NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,						interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		AGGGGACTTACGAGGCCCGTT	0.423													35	39	---	---	---	---	PASS
EVI5	7813	broad.mit.edu	37	1	93070917	93070917	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93070917T>C	uc001dox.2	-	16	1979	c.1969A>G	c.(1969-1971)AGC>GGC	p.S657G	EVI5_uc010otf.1_Missense_Mutation_p.S668G|EVI5_uc001doy.1_RNA	NM_005665	NP_005656	O60447	EVI5_HUMAN	ecotropic viral integration site 5	657	Targeting to the centrosomes.|Potential.|Dimerization.|Interaction with AURKB and INCENP.				cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		GCAGCTATGCTATCTGCTTCC	0.333													27	55	---	---	---	---	PASS
MTF2	22823	broad.mit.edu	37	1	93602335	93602335	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93602335G>T	uc009wdj.2	+	15	1825	c.1533G>T	c.(1531-1533)CAG>CAT	p.Q511H	MTF2_uc010oth.1_Missense_Mutation_p.Q409H|MTF2_uc009wdk.2_Missense_Mutation_p.Q454H|MTF2_uc001dpi.3_Missense_Mutation_p.Q238H|MTF2_uc010oti.1_Missense_Mutation_p.Q409H|MTF2_uc001dpj.3_Missense_Mutation_p.Q409H|MTF2_uc001dpl.3_Missense_Mutation_p.Q409H|MTF2_uc001dpm.3_Missense_Mutation_p.Q180H	NM_007358	NP_031384	Q9Y483	MTF2_HUMAN	metal response element binding transcription	511						nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)		TCCAGACTCAGAACTCAGAAA	0.418													16	72	---	---	---	---	PASS
DPH5	51611	broad.mit.edu	37	1	101460686	101460686	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101460686C>A	uc001dts.2	-	6	657	c.510G>T	c.(508-510)CAG>CAT	p.Q170H	DPH5_uc001dtr.2_Missense_Mutation_p.Q170H|DPH5_uc001dtq.2_RNA|DPH5_uc001dtt.2_Missense_Mutation_p.Q170H|DPH5_uc001dtu.2_RNA|DPH5_uc001dtv.2_RNA|DPH5_uc001dtw.2_RNA|DPH5_uc001dtx.2_Missense_Mutation_p.Q170H|DPH5_uc001dty.2_Missense_Mutation_p.Q49H|DPH5_uc001dtz.2_RNA	NM_015958	NP_057042	Q9H2P9	DPH5_HUMAN	diphthine synthase isoform a	170					peptidyl-diphthamide biosynthetic process from peptidyl-histidine		diphthine synthase activity				0		all_epithelial(167;3.1e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0385)|all cancers(265;0.043)|COAD - Colon adenocarcinoma(174;0.151)|Colorectal(144;0.173)|Lung(183;0.198)		TTTCCAAAGACTGCTCCTTTA	0.294													7	16	---	---	---	---	PASS
PRMT6	55170	broad.mit.edu	37	1	107600083	107600083	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107600083G>A	uc010ous.1	+	1	817	c.746G>A	c.(745-747)CGG>CAG	p.R249Q		NM_018137	NP_060607	Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	249					base-excision repair|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone binding|histone methyltransferase activity (H2A-R3 specific)|histone methyltransferase activity (H3-R2 specific)|histone methyltransferase activity (H4-R3 specific)|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity				0		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		GTGCTGGCCCGGCCGCAGCGC	0.687													6	13	---	---	---	---	PASS
SLC25A24	29957	broad.mit.edu	37	1	108700228	108700228	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108700228C>A	uc001dvn.3	-	5	739	c.525G>T	c.(523-525)GGG>GGT	p.G175G	SLC25A24_uc001dvm.2_Silent_p.G156G	NM_013386	NP_037518	Q6NUK1	SCMC1_HUMAN	solute carrier family 25 member 24 isoform 1	175	Mitochondrial intermembrane (Potential).				transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding			ovary(1)	1		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)		TTAAGCTATCCCCTATGTCAA	0.403													7	109	---	---	---	---	PASS
CTTNBP2NL	55917	broad.mit.edu	37	1	112999276	112999276	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112999276G>A	uc001ebx.2	+	6	1390	c.1162G>A	c.(1162-1164)GAG>AAG	p.E388K	CTTNBP2NL_uc001ebz.2_5'Flank	NM_018704	NP_061174	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	388						actin cytoskeleton	protein binding			central_nervous_system(2)|ovary(1)	3		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAAACCAGTGGAGAATGGTGG	0.552													22	72	---	---	---	---	PASS
PTPN22	26191	broad.mit.edu	37	1	114381218	114381218	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114381218C>A	uc001eds.2	-	12	1070	c.940G>T	c.(940-942)GAG>TAG	p.E314*	PTPN22_uc009wgq.2_Nonsense_Mutation_p.E259*|PTPN22_uc010owo.1_Nonsense_Mutation_p.E70*|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Nonsense_Mutation_p.E314*|PTPN22_uc009wgs.2_Nonsense_Mutation_p.E187*|PTPN22_uc001edu.2_Nonsense_Mutation_p.E314*	NM_015967	NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type	314					negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGATTTTTCTCAGGAATACAA	0.328													5	52	---	---	---	---	PASS
TRIM33	51592	broad.mit.edu	37	1	114949569	114949569	+	Silent	SNP	A	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114949569A>C	uc001eew.2	-	14	2496	c.2412T>G	c.(2410-2412)GCT>GCG	p.A804A	TRIM33_uc010owr.1_Silent_p.A418A|TRIM33_uc010ows.1_Silent_p.A436A|TRIM33_uc001eex.2_Silent_p.A804A|TRIM33_uc001eey.1_5'UTR	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform	804					negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTACCATGCAAGCACTCCTCC	0.433			T	RET	papillary thyroid								17	63	---	---	---	---	PASS
NBPF7	343505	broad.mit.edu	37	1	120386969	120386969	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120386969C>T	uc010oxk.1	-	1	811	c.190G>A	c.(190-192)GTA>ATA	p.V64I		NM_001047980	NP_001041445	P0C2Y1	NBPF7_HUMAN	hypothetical protein LOC343505	64						cytoplasm				ovary(1)|skin(1)	2	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;3.66e-05)|Lung NSC(69;0.000192)|all_epithelial(167;0.0347)		Lung(183;0.0103)|LUSC - Lung squamous cell carcinoma(189;0.0544)		ATTTGAGTTACAAGAAATTTC	0.423											OREG0013730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	22	86	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144886153	144886153	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144886153C>T	uc001elw.3	-	23	3372	c.3081G>A	c.(3079-3081)CTG>CTA	p.L1027L	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Silent_p.L1093L|PDE4DIP_uc001elv.3_Silent_p.L34L	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1027	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTAGCTCCTTCAGTTCCTCCT	0.522			T	PDGFRB	MPD								21	117	---	---	---	---	PASS
ACP6	51205	broad.mit.edu	37	1	147120111	147120111	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147120111G>T	uc001epr.2	-	9	1544	c.1080C>A	c.(1078-1080)ACC>ACA	p.T360T		NM_016361	NP_057445	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic precursor	360					lipid metabolic process	extracellular region|mitochondrion	acid phosphatase activity|protein binding			ovary(4)	4	all_hematologic(923;0.0276)					AAAGTTCCATGGTCAGGTCAA	0.512													5	54	---	---	---	---	PASS
SV2A	9900	broad.mit.edu	37	1	149879602	149879602	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149879602G>T	uc001etg.2	-	9	2027	c.1536C>A	c.(1534-1536)TTC>TTA	p.F512L	SV2A_uc009wlk.2_5'Flank|SV2A_uc001eth.2_Missense_Mutation_p.F512L	NM_014849	NP_055664	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2	512	Extracellular (Potential).				neurotransmitter transport	cell junction|endoplasmic reticulum|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(6)|pancreas(1)	7	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	ACTTGTCATTGAAGTACTGCC	0.488													26	59	---	---	---	---	PASS
TCHHL1	126637	broad.mit.edu	37	1	152057617	152057617	+	Silent	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152057617A>T	uc001ezo.1	-	3	2606	c.2541T>A	c.(2539-2541)TCT>TCA	p.S847S		NM_001008536	NP_001008536	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	847							calcium ion binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			TGAAAAAGACAGAACAATCTG	0.502													30	51	---	---	---	---	PASS
LCE2D	353141	broad.mit.edu	37	1	152636867	152636867	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152636867C>T	uc001fag.2	+	2	341	c.286C>T	c.(286-288)CCT>TCT	p.P96S		NM_178430	NP_848517	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	96	Cys-rich.				keratinization						0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGAGAGTGAACCTTCTGGGGC	0.642													13	35	---	---	---	---	PASS
NUP210L	91181	broad.mit.edu	37	1	153984787	153984787	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153984787G>T	uc001fdw.2	-	34	4785	c.4713C>A	c.(4711-4713)ACC>ACA	p.T1571T	NUP210L_uc009woq.2_Silent_p.T480T|NUP210L_uc010peh.1_Silent_p.T1571T	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	1571						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)			TGAGGGTATTGGTGAGATAAG	0.403													6	104	---	---	---	---	PASS
TDRD10	126668	broad.mit.edu	37	1	154514508	154514508	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154514508G>T	uc009wow.2	+	7	1216	c.378G>T	c.(376-378)GAG>GAT	p.E126D	TDRD10_uc001ffd.2_Missense_Mutation_p.E126D|TDRD10_uc001ffe.2_Missense_Mutation_p.E47D	NM_001098475	NP_001091945	Q5VZ19	TDR10_HUMAN	tudor domain containing 10 isoform a	126							nucleotide binding|RNA binding			ovary(1)	1	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			AGGTGTTGGAGAAGGCTTCTG	0.488													6	23	---	---	---	---	PASS
TRIM46	80128	broad.mit.edu	37	1	155148375	155148375	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155148375T>C	uc001fhs.1	+	3	420	c.337T>C	c.(337-339)TAC>CAC	p.Y113H	RAG1AP1_uc010pey.1_Intron|KRTCAP2_uc001fho.2_5'Flank|KRTCAP2_uc001fhp.1_5'Flank|TRIM46_uc009wpe.1_RNA|TRIM46_uc010pez.1_Missense_Mutation_p.Y100H|TRIM46_uc001fhq.2_RNA|TRIM46_uc001fhr.2_Missense_Mutation_p.Y113H|TRIM46_uc001fht.1_RNA|TRIM46_uc010pfa.1_5'UTR|TRIM46_uc001fhu.1_Missense_Mutation_p.Y90H|TRIM46_uc009wpg.1_Missense_Mutation_p.Y100H|TRIM46_uc009wpf.2_3'UTR|TRIM46_uc001fhv.3_Missense_Mutation_p.Y100H|TRIM46_uc001fhw.1_RNA	NM_025058	NP_079334	Q7Z4K8	TRI46_HUMAN	tripartite motif-containing 46	113						intracellular	zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CTTTGGGACATACCCTGGGAG	0.552													40	94	---	---	---	---	PASS
FCER1A	2205	broad.mit.edu	37	1	159275910	159275910	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159275910G>T	uc001ftq.2	+	5	563	c.464G>T	c.(463-465)TGG>TTG	p.W155L		NM_002001	NP_001992	P12319	FCERA_HUMAN	Fc fragment of IgE, high affinity I, receptor	155	Ig-like 2.|Extracellular (Potential).					integral to plasma membrane				lung(2)|skin(2)|prostate(1)	5	all_hematologic(112;0.0429)				Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043)	CTCAAGTACTGGTATGAGAAC	0.493													5	83	---	---	---	---	PASS
VSIG8	391123	broad.mit.edu	37	1	159827692	159827692	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159827692C>T	uc001fuh.2	-	4	631	c.495G>A	c.(493-495)CTG>CTA	p.L165L	C1orf204_uc001fuf.1_5'Flank|C1orf204_uc001fug.1_5'Flank	NM_001013661	NP_001013683	Q5VU13	VSIG8_HUMAN	V-set and immunoglobulin domain containing 8	165	Extracellular (Potential).|Ig-like V-type 2.					integral to membrane				central_nervous_system(1)	1	all_hematologic(112;0.0597)					CATAGCACTTCAGCACCACAT	0.592													4	16	---	---	---	---	PASS
ATP1A2	477	broad.mit.edu	37	1	160109474	160109474	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160109474C>A	uc001fvc.2	+	21	3017	c.2885C>A	c.(2884-2886)GCT>GAT	p.A962D	ATP1A2_uc001fvd.2_Missense_Mutation_p.A681D	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein	962	Helical; (Potential).				ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			ACGGCGTTGGCTGCCTTTCTC	0.577													11	28	---	---	---	---	PASS
PVRL4	81607	broad.mit.edu	37	1	161042499	161042499	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161042499C>A	uc001fxo.2	-	9	1784	c.1485G>T	c.(1483-1485)AAG>AAT	p.K495N	ARHGAP30_uc001fxk.2_5'Flank|ARHGAP30_uc001fxl.2_5'Flank|ARHGAP30_uc001fxm.2_5'Flank|ARHGAP30_uc009wtx.2_5'Flank|ARHGAP30_uc001fxn.1_5'Flank|PVRL4_uc010pjy.1_Missense_Mutation_p.K149N|PVRL4_uc010pjz.1_Missense_Mutation_p.K204N	NM_030916	NP_112178	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4 precursor	495	Cytoplasmic (Potential).				adherens junction organization|cell adhesion|cell junction assembly	adherens junction|extracellular region|integral to membrane				ovary(2)	2	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			TGCCCGTGGGCTTGGCCCGTA	0.597													24	36	---	---	---	---	PASS
C1orf111	284680	broad.mit.edu	37	1	162344105	162344105	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162344105G>T	uc001gbx.2	-	3	583	c.519C>A	c.(517-519)TCC>TCA	p.S173S		NM_182581	NP_872387	Q5T0L3	CA111_HUMAN	hypothetical protein LOC284680	173										ovary(1)	1	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			GGTGCCACCTGGAAGCCATTA	0.582													7	185	---	---	---	---	PASS
UAP1	6675	broad.mit.edu	37	1	162551080	162551080	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162551080G>T	uc001gce.3	+	5	994	c.665G>T	c.(664-666)GGG>GTG	p.G222V		NM_003115	NP_003106	Q16222	UAP1_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1	222					dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol|nucleus|plasma membrane	UDP-N-acetylglucosamine diphosphorylase activity			ovary(2)|skin(2)|kidney(1)	5	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			TTTCCAGATGGGAATGGTGGT	0.388													7	142	---	---	---	---	PASS
DDR2	4921	broad.mit.edu	37	1	162729778	162729778	+	Intron	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162729778G>A	uc001gcf.2	+						DDR2_uc001gcg.2_Intron	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2						cell adhesion	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			AGGTCAGTGGGGTCGGGTGTG	0.308													24	25	---	---	---	---	PASS
ILDR2	387597	broad.mit.edu	37	1	166905975	166905975	+	Splice_Site	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166905975C>A	uc001gdx.1	-	5	613	c.557_splice	c.e5-1	p.E186_splice		NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor							integral to membrane				ovary(1)	1						AACACCCACTCTGGAAGGATG	0.602													5	24	---	---	---	---	PASS
MAEL	84944	broad.mit.edu	37	1	166963298	166963298	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166963298A>T	uc001gdy.1	+	5	586	c.515A>T	c.(514-516)CAG>CTG	p.Q172L	MAEL_uc001gdz.1_Missense_Mutation_p.Q141L|MAEL_uc009wvf.1_RNA	NM_032858	NP_116247	Q96JY0	MAEL_HUMAN	maelstrom homolog	172					cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|multicellular organismal development|piRNA metabolic process|spermatogenesis	piP-body	DNA binding			skin(1)	1						TTTCATTGTCAGGCTGCAAGT	0.323													5	11	---	---	---	---	PASS
DNM3	26052	broad.mit.edu	37	1	172050971	172050971	+	Splice_Site	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172050971G>T	uc001gie.2	+	12	1599	c.1423_splice	c.e12-1	p.V475_splice	DNM3_uc001gid.3_Splice_Site_p.V475_splice|DNM3_uc009wwb.2_Splice_Site_p.V475_splice|DNM3_uc001gif.2_Splice_Site_p.V475_splice	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						TTGACTTATAGGTATTGCTAT	0.338													6	72	---	---	---	---	PASS
GAS5	60674	broad.mit.edu	37	1	173835447	173835447	+	Intron	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173835447C>T	uc001gji.2	-						GAS5_uc001gjj.2_Intron|GAS5_uc001gjk.2_Intron|SNORD81_uc009wwi.1_5'Flank|SNORD47_uc001gjl.2_5'Flank|SNORD80_uc009wwj.1_5'Flank|SNORD79_uc009wwk.1_5'Flank|SNORD78_uc009wwl.2_5'Flank|SNORD44_uc001gjn.1_5'Flank|ZBTB37_uc001gjp.1_5'Flank|ZBTB37_uc001gjq.3_5'Flank|ZBTB37_uc009wwp.1_5'Flank|ZBTB37_uc001gjr.2_5'Flank					Homo sapiens mRNA; cDNA DKFZp564D0164 (from clone DKFZp564D0164).												0						CCAGATACATCAGACAGATAG	0.313													17	41	---	---	---	---	PASS
TNN	63923	broad.mit.edu	37	1	175092614	175092614	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175092614C>A	uc001gkl.1	+	12	2842	c.2729C>A	c.(2728-2730)GCC>GAC	p.A910D		NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N precursor	910	Fibronectin type-III 8.				cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		CCGGTTCAGGCCACCATTGAC	0.537													19	40	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175334299	175334299	+	Missense_Mutation	SNP	C	G	G	rs139055042		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175334299C>G	uc001gkp.1	-	10	2515	c.2434G>C	c.(2434-2436)GAT>CAT	p.D812H	TNR_uc009wwu.1_Missense_Mutation_p.D812H	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	812	Fibronectin type-III 6.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					TCCTCCTCATCCCTGGGGCTG	0.517													19	34	---	---	---	---	PASS
CACNA1E	777	broad.mit.edu	37	1	181767670	181767670	+	Silent	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181767670G>C	uc001gow.2	+	47	6678	c.6513G>C	c.(6511-6513)CCG>CCC	p.P2171P	CACNA1E_uc009wxs.2_Silent_p.P2059P|CACNA1E_uc009wxt.2_Silent_p.P1440P	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	2214	Cytoplasmic (Potential).				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						CCAACTCTCCGCACCCCCAGC	0.622													3	24	---	---	---	---	PASS
CFHR5	81494	broad.mit.edu	37	1	196967353	196967353	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196967353C>A	uc001gts.3	+	7	1194	c.1066C>A	c.(1066-1068)CGT>AGT	p.R356S		NM_030787	NP_110414	Q9BXR6	FHR5_HUMAN	complement factor H-related 5 precursor	356	Sushi 6.				complement activation, alternative pathway	extracellular region				breast(1)|skin(1)	2						TTCTAGAATACGTTACAGATG	0.348													11	19	---	---	---	---	PASS
KDM5B	10765	broad.mit.edu	37	1	202700083	202700083	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202700083G>T	uc001gyf.2	-	25	4246	c.4130C>A	c.(4129-4131)GCT>GAT	p.A1377D	KDM5B_uc009xag.2_Missense_Mutation_p.A1413D|KDM5B_uc001gyg.1_Missense_Mutation_p.A1219D	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B	1377					negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5						AGTCTGCTGAGCAGGGCTTGG	0.532													14	22	---	---	---	---	PASS
ATP2B4	493	broad.mit.edu	37	1	203652420	203652420	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203652420G>T	uc001gzw.2	+	2	971	c.87G>T	c.(85-87)CTG>CTT	p.L29L	ATP2B4_uc001gzv.2_Silent_p.L29L|ATP2B4_uc009xaq.2_Silent_p.L29L	NM_001684	NP_001675	P23634	AT2B4_HUMAN	plasma membrane calcium ATPase 4 isoform 4b	29	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|skin(1)	3	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TAATGGAACTGAGGAAGCTCA	0.522													6	152	---	---	---	---	PASS
SYT14	255928	broad.mit.edu	37	1	210334198	210334198	+	Silent	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210334198A>G	uc009xcv.2	+	8	1551	c.1479A>G	c.(1477-1479)CTA>CTG	p.L493L	SYT14_uc001hhs.3_Silent_p.L557L|SYT14_uc001hht.3_Silent_p.L512L|SYT14_uc001hhu.3_RNA|SYT14_uc010psn.1_Silent_p.L538L|SYT14_uc010pso.1_Silent_p.L455L|SYT14_uc010psp.1_Silent_p.L31L	NM_153262	NP_694994	Q8NB59	SYT14_HUMAN	synaptotagmin XIV isoform 4	493	Cytoplasmic (Potential).|C2 2.					integral to membrane				ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.085)		AAGTGGCCCTATTTCAGCTTT	0.418													23	71	---	---	---	---	PASS
GPATCH2	55105	broad.mit.edu	37	1	217793409	217793409	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217793409C>A	uc001hlf.1	-	2	585	c.489G>T	c.(487-489)AAG>AAT	p.K163N	GPATCH2_uc001hlg.3_Missense_Mutation_p.K163N	NM_018040	NP_060510	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	163						intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		TGCGTTTTACCTTTCTCCTCC	0.453													7	101	---	---	---	---	PASS
IARS2	55699	broad.mit.edu	37	1	220276788	220276788	+	Splice_Site	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220276788G>T	uc001hmc.2	+	8	1055	c.951_splice	c.e8-1	p.K317_splice		NM_018060	NP_060530	Q9NSE4	SYIM_HUMAN	mitochondrial isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	TTTTATGTTAGGTATGCTGTT	0.313													5	60	---	---	---	---	PASS
C1orf65	164127	broad.mit.edu	37	1	223568305	223568305	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223568305G>T	uc001hoa.2	+	1	1591	c.1488G>T	c.(1486-1488)GAG>GAT	p.E496D		NM_152610	NP_689823	Q8N715	CA065_HUMAN	hypothetical protein LOC164127	496	Potential.									central_nervous_system(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0704)		GGGAGTCAGAGGAACAGAGGA	0.607													18	28	---	---	---	---	PASS
PARP1	142	broad.mit.edu	37	1	226556023	226556023	+	Splice_Site	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226556023C>A	uc001hqd.3	-	16	2326	c.2155_splice	c.e16-1	p.A719_splice		NM_001618	NP_001609	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase family, member 1						cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nuclear envelope|nucleolus|transcription factor complex	DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding			lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1)	10	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		GAGACACCGCCTGGAGAGGAG	0.587								Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					21	30	---	---	---	---	PASS
PSEN2	5664	broad.mit.edu	37	1	227079536	227079536	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227079536G>A	uc009xeo.1	+	11	1490	c.1063G>A	c.(1063-1065)GAG>AAG	p.E355K	PSEN2_uc009xep.1_Missense_Mutation_p.E354K|PSEN2_uc001hqk.2_RNA	NM_000447	NP_000438	P49810	PSN2_HUMAN	presenilin 2 isoform 1	355	Cytoplasmic (Potential).				amyloid precursor protein catabolic process|anti-apoptosis|apoptosis|beta-amyloid metabolic process|calcium ion transport|induction of apoptosis by extracellular signals|intracellular signal transduction|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity	apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear inner membrane|perinuclear region of cytoplasm|Z disc	aspartic-type endopeptidase activity|protein binding			lung(2)	2		Prostate(94;0.0771)				GCTGGAGGAAGAGGAGGAAAG	0.602													9	19	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228473926	228473926	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228473926A>G	uc009xez.1	+	34	9196	c.9152A>G	c.(9151-9153)AAT>AGT	p.N3051S	OBSCN_uc001hsn.2_Missense_Mutation_p.N3051S|OBSCN_uc001hsq.1_Missense_Mutation_p.N307S	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	3051	Ig-like 30.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				AACGAGCTCAATGAGATCGAT	0.652													5	7	---	---	---	---	PASS
SIPA1L2	57568	broad.mit.edu	37	1	232581528	232581528	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232581528A>G	uc001hvg.2	-	9	3258	c.3100T>C	c.(3100-3102)TGT>CGT	p.C1034R	SIPA1L2_uc001hvf.2_Missense_Mutation_p.C108R	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	1034					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				AGCTCTGAACACCCTCTGTTG	0.552													36	66	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240497432	240497432	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240497432C>A	uc010pyd.1	+	13	4893	c.4668C>A	c.(4666-4668)CTC>CTA	p.L1556L	FMN2_uc010pye.1_Silent_p.L1560L|FMN2_uc010pyf.1_Silent_p.L202L|FMN2_uc010pyg.1_Silent_p.L152L	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1556	FH2.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AACAGTGCCTCTTTCCACTGC	0.358													75	73	---	---	---	---	PASS
ZNF496	84838	broad.mit.edu	37	1	247492858	247492858	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247492858C>A	uc001ico.2	-	3	488	c.23G>T	c.(22-24)CGA>CTA	p.R8L	ZNF496_uc009xgv.2_Missense_Mutation_p.R8L|ZNF496_uc001icp.2_Missense_Mutation_p.R8L|ZNF496_uc010pyv.1_Missense_Mutation_p.R8L	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	zinc finger protein 496	8					positive regulation of transcription, DNA-dependent|viral reproduction		DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			AGCCAAGACTCGGGGGCACAG	0.582													16	60	---	---	---	---	PASS
NLRP3	114548	broad.mit.edu	37	1	247588563	247588563	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247588563G>A	uc001icr.2	+	5	1956	c.1818G>A	c.(1816-1818)CTG>CTA	p.L606L	NLRP3_uc001ics.2_Silent_p.L606L|NLRP3_uc001icu.2_Silent_p.L606L|NLRP3_uc001icw.2_Silent_p.L606L|NLRP3_uc001icv.2_Silent_p.L606L|NLRP3_uc010pyw.1_Silent_p.L604L|NLRP3_uc001ict.1_Silent_p.L604L	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	606					detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding			lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1)	26	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			AAATCAGGCTGGAGCTGCTGA	0.458													17	54	---	---	---	---	PASS
OR2B11	127623	broad.mit.edu	37	1	247614643	247614643	+	Silent	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247614643G>C	uc010pyx.1	-	1	642	c.642C>G	c.(640-642)CCC>CCG	p.P214P		NM_001004492	NP_001004492	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B,	214	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			upper_aerodigestive_tract(1)	1	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			TGAGAGCCAGGGGCACCAACA	0.577													13	25	---	---	---	---	PASS
OR2W3	343171	broad.mit.edu	37	1	248059311	248059311	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248059311C>A	uc001idp.1	+	3	692	c.423C>A	c.(421-423)TGC>TGA	p.C141*	OR2W3_uc010pzb.1_Nonsense_Mutation_p.C141*	NM_001001957	NP_001001957	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W,	141	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|pancreas(1)	3	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			CCAGGCTCTGCCGGGGCTTGG	0.627													17	19	---	---	---	---	PASS
ASAP2	8853	broad.mit.edu	37	2	9475236	9475236	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9475236G>T	uc002qzh.2	+	9	1117	c.777G>T	c.(775-777)CAG>CAT	p.Q259H	ASAP2_uc002qzi.2_Missense_Mutation_p.Q259H	NM_003887	NP_003878	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH	259	Potential.				regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0						AACAGGCCCAGGATGAAGAAA	0.413													6	61	---	---	---	---	PASS
DDX1	1653	broad.mit.edu	37	2	15770898	15770898	+	Splice_Site	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15770898A>T	uc002rce.2	+	26	2381	c.2093_splice	c.e26-2	p.G698_splice		NM_004939	NP_004930	Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1						DNA duplex unwinding|double-strand break repair|multicellular organismal development|regulation of transcription, DNA-dependent|regulation of translational initiation|spliceosome assembly|transcription, DNA-dependent	cleavage body|stress granule|tRNA-splicing ligase complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|DNA/RNA helicase activity|exonuclease activity|poly(A) RNA binding|protein binding|RNA helicase activity|transcription cofactor activity			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		TGTGTGATGCAGGTGGAAGCT	0.408													84	88	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21232877	21232877	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21232877T>A	uc002red.2	-	26	6991	c.6863A>T	c.(6862-6864)CAC>CTC	p.H2288L		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	2288					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	AGCCTCAATGTGTTGTTTTAA	0.348													24	126	---	---	---	---	PASS
NCOA1	8648	broad.mit.edu	37	2	24930637	24930637	+	Silent	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24930637G>C	uc002rfk.2	+	11	2556	c.2298G>C	c.(2296-2298)CTG>CTC	p.L766L	NCOA1_uc010eye.2_Silent_p.L766L|NCOA1_uc002rfi.2_Silent_p.L615L|NCOA1_uc002rfj.2_Silent_p.L766L|NCOA1_uc002rfl.2_Silent_p.L766L	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1	766									PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCCAAACCTGAGCCTGGATG	0.383			T	PAX3	alveolar rhadomyosarcoma								20	32	---	---	---	---	PASS
DNAJC27	51277	broad.mit.edu	37	2	25186269	25186269	+	Intron	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25186269C>T	uc002rft.1	-						DNAJC27_uc010ykn.1_Intron|DNAJC27_uc002rfu.1_Intron|DNAJC27_uc010eyg.1_Intron	NM_016544	NP_057628	Q9NZQ0	DJC27_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 27						protein folding|small GTPase mediated signal transduction		GTP binding|heat shock protein binding|unfolded protein binding			skin(1)	1						AAAAGGCTTTCTTACCTCATA	0.363													10	22	---	---	---	---	PASS
DNMT3A	1788	broad.mit.edu	37	2	25468908	25468908	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25468908C>G	uc002rgc.2	-	12	1712	c.1455G>C	c.(1453-1455)CAG>CAC	p.Q485H	DNMT3A_uc002rgd.2_Missense_Mutation_p.Q485H|DNMT3A_uc010eyi.2_RNA|DNMT3A_uc002rgb.2_Missense_Mutation_p.Q296H	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	485	ADD.				regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3)	140	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCGGCACTTCTGCCGCACCT	0.612			Mis|F|N|S		AML								9	43	---	---	---	---	PASS
GALNT14	79623	broad.mit.edu	37	2	31168726	31168726	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31168726C>A	uc002rnr.2	-	7	1284	c.665G>T	c.(664-666)CGG>CTG	p.R222L	GALNT14_uc002rnq.2_Missense_Mutation_p.R202L|GALNT14_uc002rns.2_Missense_Mutation_p.R227L|GALNT14_uc010ymr.1_Missense_Mutation_p.R187L|GALNT14_uc010ezo.1_Missense_Mutation_p.R189L|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	222	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					GCACACCACCCGCGTGTAGTC	0.388													4	19	---	---	---	---	PASS
MEMO1	51072	broad.mit.edu	37	2	32145975	32145975	+	Nonsense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32145975T>A	uc002rnx.2	-	4	599	c.217A>T	c.(217-219)AGA>TGA	p.R73*	MEMO1_uc010ymu.1_Nonsense_Mutation_p.R50*|MEMO1_uc010ezq.2_Nonsense_Mutation_p.R73*|MEMO1_uc002rny.2_RNA|MEMO1_uc002rnz.2_RNA|MEMO1_uc010ymv.1_RNA	NM_015955	NP_057039	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1 isoform 1	73					regulation of microtubule-based process	cytosol|nucleus				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)					ATGAAAATTCTCCGGCTAGGA	0.378													22	35	---	---	---	---	PASS
MAP4K3	8491	broad.mit.edu	37	2	39509664	39509664	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39509664G>T	uc002rro.2	-	22	1710	c.1619C>A	c.(1618-1620)CCT>CAT	p.P540H	MAP4K3_uc002rrp.2_Missense_Mutation_p.P519H|MAP4K3_uc010yns.1_Missense_Mutation_p.P93H	NM_003618	NP_003609	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase	540					JNK cascade		ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(3)|lung(3)|stomach(1)|pancreas(1)	8		all_hematologic(82;0.211)				ATGCACTTTAGGTGTTGGAGG	0.323													5	43	---	---	---	---	PASS
MSH6	2956	broad.mit.edu	37	2	48027425	48027425	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48027425C>A	uc002rwd.3	+	4	2455	c.2303C>A	c.(2302-2304)CCT>CAT	p.P768H	MSH6_uc002rwc.2_Missense_Mutation_p.P768H|MSH6_uc010fbj.2_Missense_Mutation_p.P466H|MSH6_uc010yoi.1_Missense_Mutation_p.P638H|MSH6_uc010yoj.1_Missense_Mutation_p.P466H	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	768					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGCCATACTCCTTTTGGTAAG	0.423			Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				10	248	---	---	---	---	PASS
FBXO11	80204	broad.mit.edu	37	2	48040932	48040932	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48040932G>A	uc010fbl.2	-	17	1943	c.1829C>T	c.(1828-1830)TCT>TTT	p.S610F	FBXO11_uc002rwe.2_Missense_Mutation_p.S610F|FBXO11_uc002rwf.2_Missense_Mutation_p.S610F|FBXO11_uc010fbk.2_Missense_Mutation_p.S118F	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1	694	PbH1 14.				ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AAACATACCAGAATTATAAAC	0.274													18	33	---	---	---	---	PASS
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48869555	48869555	+	Intron	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48869555C>A	uc010yol.1	+						STON1-GTF2A1L_uc002rwp.1_Missense_Mutation_p.P792T|GTF2A1L_uc002rws.1_Missense_Mutation_p.P88T|GTF2A1L_uc010yom.1_Missense_Mutation_p.P54T|GTF2A1L_uc002rwt.2_Missense_Mutation_p.P88T	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ATTAGTTATTCCTGCTGGTAG	0.294													7	15	---	---	---	---	PASS
FSHR	2492	broad.mit.edu	37	2	49191003	49191003	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49191003C>T	uc002rww.2	-	10	1031	c.957G>A	c.(955-957)GAG>GAA	p.E319E	FSHR_uc002rwx.2_Silent_p.E257E|FSHR_uc010fbn.2_Silent_p.E293E	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	319	Extracellular (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)	TGTAGCTGGACTCATTGTCTT	0.443									Gonadal_Dysgenesis_46_XX				113	117	---	---	---	---	PASS
CHAC2	494143	broad.mit.edu	37	2	54001477	54001477	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54001477C>A	uc002rxk.1	+	3	465	c.370C>A	c.(370-372)CTG>ATG	p.L124M	ASB3_uc002rxg.1_Intron|ASB3_uc002rxh.1_Intron|ASB3_uc002rxi.3_Intron|ASB3_uc010yoo.1_Intron	NM_001008708	NP_001008708	Q8WUX2	CHAC2_HUMAN	ChaC, cation transport regulator-like 2	124											0			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			TCCTGCACCTCTGGAAGACAT	0.358													6	110	---	---	---	---	PASS
C2orf63	130162	broad.mit.edu	37	2	55449476	55449476	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55449476C>A	uc002ryi.2	-	3	418	c.72G>T	c.(70-72)TTG>TTT	p.L24F	C2orf63_uc002ryh.2_5'UTR|C2orf63_uc002ryj.2_Intron	NM_152385	NP_689598	Q8NHS4	CB063_HUMAN	hypothetical protein LOC130162 isoform 1	24							binding			ovary(2)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(58;0.179)|Lung(47;0.189)			GCACACTTTCCAAAAATTCCT	0.363													6	99	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61475683	61475683	+	Silent	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61475683T>A	uc002sbe.2	-	49	6379	c.6357A>T	c.(6355-6357)ACA>ACT	p.T2119T	USP34_uc002sbf.2_Silent_p.T269T	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	2119					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)			GAAAATCTTCTGTATAGGGCG	0.358													19	33	---	---	---	---	PASS
PPP3R1	5534	broad.mit.edu	37	2	68415796	68415796	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68415796C>A	uc002sei.1	-	3	462	c.70G>T	c.(70-72)GGA>TGA	p.G24*		NM_000945	NP_000936	P63098	CANB1_HUMAN	protein phosphatase 3, regulatory subunit B,	24	EF-hand 1.				activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	calcineurin complex|cytosol	calcium ion binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding				0					Pimecrolimus(DB00337)	AATCTCTTTCCTAGCCTTTTA	0.368													5	53	---	---	---	---	PASS
GKN2	200504	broad.mit.edu	37	2	69173541	69173541	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69173541G>T	uc002sfa.2	-	5	476	c.367C>A	c.(367-369)CTG>ATG	p.L123M	GKN2_uc002sfb.3_Missense_Mutation_p.L123M	NM_182536	NP_872342	Q86XP6	GKN2_HUMAN	trefoil factor interactions(z) 1 precursor	123	BRICHOS.					extracellular region					0						AGAGACTCCAGAGGGTTGTAC	0.413													7	179	---	---	---	---	PASS
DYSF	8291	broad.mit.edu	37	2	71709007	71709007	+	Splice_Site	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71709007A>T	uc002sie.2	+	3	521	c.145_splice	c.e3-2	p.G49_splice	DYSF_uc010feg.2_Splice_Site_p.G49_splice|DYSF_uc010feh.2_Splice_Site_p.G49_splice|DYSF_uc002sig.3_Splice_Site_p.G49_splice|DYSF_uc010yqx.1_Splice_Site|DYSF_uc010fee.2_Splice_Site_p.G49_splice|DYSF_uc010fef.2_Splice_Site_p.G49_splice|DYSF_uc010fei.2_Splice_Site_p.G49_splice|DYSF_uc010fek.2_Splice_Site_p.G50_splice|DYSF_uc010fej.2_Splice_Site_p.G50_splice|DYSF_uc010fel.2_Splice_Site_p.G50_splice|DYSF_uc010feo.2_Splice_Site_p.G50_splice|DYSF_uc010fem.2_Splice_Site_p.G50_splice|DYSF_uc010fen.2_Splice_Site_p.G50_splice|DYSF_uc002sif.2_Splice_Site_p.G50_splice	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						TTTTTCTTCCAGGGATTTGAA	0.323													7	18	---	---	---	---	PASS
TET3	200424	broad.mit.edu	37	2	74275351	74275351	+	Silent	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74275351A>T	uc002skb.3	+	1	1902	c.1902A>T	c.(1900-1902)TCA>TCT	p.S634S	TET3_uc010fez.1_Silent_p.S634S	NM_144993	NP_659430	O43151	TET3_HUMAN	tet oncogene family member 3	634							metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						CTGTGCTCTCAACCACCTGCT	0.577													4	22	---	---	---	---	PASS
REG3G	130120	broad.mit.edu	37	2	79255403	79255403	+	3'UTR	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79255403G>T	uc002snw.2	+	6					REG3G_uc002snx.2_3'UTR|REG3G_uc010ffu.2_3'UTR	NM_198448	NP_940850	Q6UW15	REG3G_HUMAN	regenerating islet-derived 3 gamma precursor						acute-phase response	extracellular region	sugar binding				0						CAAGGACTAGGGCAGGTGGGA	0.478													22	39	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90249397	90249397	+	Splice_Site	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90249397C>G	uc010fhm.2	+	28		c.3939_splice	c.e28+1							Parts of antibodies, mostly variable regions.																		AGTACCCCTCCCACAGTGTTA	0.517													34	106	---	---	---	---	PASS
TEKT4	150483	broad.mit.edu	37	2	95542369	95542369	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95542369A>G	uc002stw.1	+	6	1256	c.1163A>G	c.(1162-1164)CAG>CGG	p.Q388R	uc002stv.1_Intron|TEKT4_uc010fhr.1_RNA	NM_144705	NP_653306	Q8WW24	TEKT4_HUMAN	tektin 4	388	Potential.				cell projection organization|microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(1)|breast(1)|skin(1)	3						GAAGCGGAGCAGTCCCTGCGC	0.597													9	16	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109365585	109365585	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109365585G>T	uc002tem.3	+	9	1399	c.1273G>T	c.(1273-1275)GGT>TGT	p.G425C		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	425					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						ATACGATGTTGGTAAGTTATA	0.269													7	166	---	---	---	---	PASS
CKAP2L	150468	broad.mit.edu	37	2	113514469	113514469	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113514469C>A	uc002tie.2	-	4	558	c.479G>T	c.(478-480)GGT>GTT	p.G160V	CKAP2L_uc002tif.2_Splice_Site_p.M1_splice|CKAP2L_uc010yxp.1_5'UTR|CKAP2L_uc010yxq.1_5'UTR	NM_152515	NP_689728	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	160						centrosome					0						TATACATTTACCATTTCCTTG	0.343													10	40	---	---	---	---	PASS
DDX18	8886	broad.mit.edu	37	2	118579815	118579815	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118579815G>C	uc002tlh.1	+	7	1143	c.1044G>C	c.(1042-1044)AAG>AAC	p.K348N		NM_006773	NP_006764	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	348	Helicase ATP-binding.						ATP binding|ATP-dependent RNA helicase activity|RNA binding			breast(2)|ovary(1)|lung(1)	4						AGGAATTAAAGCAAATTATTA	0.358													10	37	---	---	---	---	PASS
ZRANB3	84083	broad.mit.edu	37	2	135965099	135965099	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135965099C>A	uc002tum.2	-	19	3031	c.2914G>T	c.(2914-2916)GCA>TCA	p.A972S	ZRANB3_uc002tuk.2_Missense_Mutation_p.A515S|ZRANB3_uc002tul.2_Missense_Mutation_p.A970S	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	972						intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)		AGTTCTTGTGCGTTCACATTA	0.413													5	138	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141359117	141359117	+	Silent	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141359117A>T	uc002tvj.1	-	42	7863	c.6891T>A	c.(6889-6891)ACT>ACA	p.T2297T		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2297	Extracellular (Potential).|LDL-receptor class B 24.				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)		TCTGGTCCACAGTGTGTCTGG	0.512										TSP Lung(27;0.18)			6	17	---	---	---	---	PASS
KYNU	8942	broad.mit.edu	37	2	143798134	143798134	+	Silent	SNP	G	T	T	rs145299669		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143798134G>T	uc002tvl.2	+	13	1309	c.1179G>T	c.(1177-1179)CCG>CCT	p.P393P	KYNU_uc010fnm.2_Silent_p.P393P	NM_003937	NP_003928	Q16719	KYNU_HUMAN	kynureninase (L-kynurenine hydrolase) isoform a	393					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)	TAATTACTCCGTCTCATGTAG	0.393													9	27	---	---	---	---	PASS
ARHGAP15	55843	broad.mit.edu	37	2	144244987	144244987	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144244987G>T	uc002tvm.3	+	9	900	c.749G>T	c.(748-750)CGA>CTA	p.R250L	ARHGAP15_uc002tvn.2_Missense_Mutation_p.R16L	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15	250					regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)		GACAAAAATCGAGTTAAAAGC	0.338													4	63	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152512796	152512796	+	Silent	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152512796G>C	uc010fnx.2	-	49	6557	c.6366C>G	c.(6364-6366)GTC>GTG	p.V2122V		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	2122	Nebulin 56.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		TTGCAGCCGTGACACTGAGCA	0.473													41	86	---	---	---	---	PASS
PSMD14	10213	broad.mit.edu	37	2	162242088	162242088	+	Intron	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162242088G>A	uc002ubu.2	+							NM_005805	NP_005796	O00487	PSDE_HUMAN	proteasome 26S subunit, non-ATPase 14						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K63-linked deubiquitination|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	endopeptidase activator activity|metal ion binding|metallopeptidase activity|proteasome binding|ubiquitin thiolesterase activity			breast(1)	1						TCCAGGTATTGCCTATATTTG	0.318													6	18	---	---	---	---	PASS
TTC21B	79809	broad.mit.edu	37	2	166802149	166802149	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166802149C>A	uc002udk.2	-	4	447	c.314G>T	c.(313-315)GGA>GTA	p.G105V	TTC21B_uc002udl.2_Missense_Mutation_p.G105V|uc002udm.1_Intron	NM_024753	NP_079029	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	105						cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5						CTCTCCAGCTCCTTTACGTTG	0.368													13	26	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170127413	170127413	+	Splice_Site	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170127413C>A	uc002ues.2	-	16	2533	c.2320_splice	c.e16+1	p.G774_splice	LRP2_uc010zdf.1_Intron	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	ACCTTTCTCACCTGTGCCATC	0.279													4	24	---	---	---	---	PASS
RBM45	129831	broad.mit.edu	37	2	178988945	178988945	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178988945C>A	uc002ulv.2	+	8	1252	c.1160C>A	c.(1159-1161)CCT>CAT	p.P387H		NM_152945	NP_694453	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	389					cell differentiation|nervous system development	cytoplasm|nucleus	nucleotide binding|RNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			GCTGAAACTCCTGTGAAAGAA	0.343													6	161	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179399281	179399281	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179399281G>T	uc010zfg.1	-	307	94581	c.94357C>A	c.(94357-94359)CAA>AAA	p.Q31453K	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.Q25148K|TTN_uc010zfi.1_Missense_Mutation_p.Q25081K|TTN_uc010zfj.1_Missense_Mutation_p.Q24956K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	32380							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)			ATGATCTGTTGGTTAGTTTCA	0.418													7	172	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179468828	179468828	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179468828A>G	uc010zfg.1	-	231	47106	c.46882T>C	c.(46882-46884)TCT>CCT	p.S15628P	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.S9323P|TTN_uc010zfi.1_Missense_Mutation_p.S9256P|TTN_uc010zfj.1_Missense_Mutation_p.S9131P	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16555							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)			GTAATTGGAGAGCCACCATTG	0.493													15	180	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179469536	179469536	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179469536C>A	uc010zfg.1	-	230	46800	c.46576G>T	c.(46576-46578)GGC>TGC	p.G15526C	uc002umo.2_RNA|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.G9221C|TTN_uc010zfi.1_Missense_Mutation_p.G9154C|TTN_uc010zfj.1_Missense_Mutation_p.G9029C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16453							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)			ATTTCACTGCCACCATTATCA	0.443													7	147	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179471753	179471753	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179471753G>T	uc010zfg.1	-	227	46096	c.45872C>A	c.(45871-45873)CCA>CAA	p.P15291Q	uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.P8986Q|TTN_uc010zfi.1_Missense_Mutation_p.P8919Q|TTN_uc010zfj.1_Missense_Mutation_p.P8794Q	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16218							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)			TTTACCTAGTGGATCAACTGC	0.393													7	179	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179472360	179472360	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179472360C>A	uc010zfg.1	-	226	45575	c.45351G>T	c.(45349-45351)ATG>ATT	p.M15117I	uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.M8812I|TTN_uc010zfi.1_Missense_Mutation_p.M8745I|TTN_uc010zfj.1_Missense_Mutation_p.M8620I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16044							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)			TCTTCCCAGCCATTATTTGTA	0.448													6	142	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179577134	179577134	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179577134G>T	uc010zfg.1	-	92	24007	c.23783C>A	c.(23782-23784)CCA>CAA	p.P7928Q	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.P4589Q	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	8855							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)			TGTGCTACTTGGAATTTCCAG	0.403													9	244	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179617883	179617883	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179617883C>T	uc010zfg.1	-	45	10552	c.10328G>A	c.(10327-10329)AGG>AAG	p.R3443K	TTN_uc010zfh.1_Missense_Mutation_p.R3589K|TTN_uc010zfi.1_Missense_Mutation_p.R3522K|TTN_uc010zfj.1_Missense_Mutation_p.R3397K|TTN_uc002umz.1_Missense_Mutation_p.R104K|TTN_uc002unb.2_Missense_Mutation_p.R3443K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							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)			TTGTTCAATCCTCTCATGCAA	0.299													8	66	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179654793	179654793	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179654793G>A	uc010zfg.1	-	12	2074	c.1850C>T	c.(1849-1851)ACA>ATA	p.T617I	TTN_uc010zfh.1_Missense_Mutation_p.T571I|TTN_uc010zfi.1_Missense_Mutation_p.T571I|TTN_uc010zfj.1_Missense_Mutation_p.T571I|TTN_uc002unb.2_Missense_Mutation_p.T617I|TTN_uc010frg.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	617							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)			GACTTTGGGTGTGGCAACTAT	0.333													68	29	---	---	---	---	PASS
CCDC141	285025	broad.mit.edu	37	2	179742795	179742795	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179742795C>T	uc002unf.1	-	2	127	c.70G>A	c.(70-72)GCC>ACC	p.A24T	CCDC141_uc002ung.2_Missense_Mutation_p.A599T	NM_173648	NP_775919	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	24							protein binding			ovary(7)|pancreas(2)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			CAATGCTTGGCTTTAGCATCA	0.363													53	41	---	---	---	---	PASS
C2orf66	401027	broad.mit.edu	37	2	197672176	197672176	+	Silent	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197672176G>C	uc002utv.2	-	2	1234	c.345C>G	c.(343-345)CTC>CTG	p.L115L		NM_213608	NP_998773	Q6UXQ4	CB066_HUMAN	hypothetical protein LOC401027 precursor	115						extracellular region					0						TTCAGCCTTTGAGATAATTGT	0.388													16	84	---	---	---	---	PASS
SGOL2	151246	broad.mit.edu	37	2	201436176	201436176	+	Silent	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201436176T>C	uc002uvw.2	+	7	1220	c.1107T>C	c.(1105-1107)GCT>GCC	p.A369A	SGOL2_uc010zhd.1_Silent_p.A369A|SGOL2_uc010zhe.1_Silent_p.A369A	NM_152524	NP_689737	Q562F6	SGOL2_HUMAN	shugoshin-like 2 isoform 1	369					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding			ovary(2)|skin(2)	4						ATTTAACTGCTAGTGAAGTCA	0.343													10	34	---	---	---	---	PASS
FAM126B	285172	broad.mit.edu	37	2	201857011	201857011	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201857011G>T	uc002uws.3	-	10	1012	c.824C>A	c.(823-825)CCA>CAA	p.P275Q	FAM126B_uc002uwu.2_Missense_Mutation_p.P193Q|FAM126B_uc002uwv.2_Missense_Mutation_p.P275Q	NM_173822	NP_776183	Q8IXS8	F126B_HUMAN	hypothetical protein LOC285172	275						intracellular				ovary(1)	1						TACCAATAGTGGTTGAGAAAA	0.338													5	76	---	---	---	---	PASS
ALS2CR4	65062	broad.mit.edu	37	2	202494079	202494079	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202494079T>C	uc002uyh.1	-	10	844	c.743A>G	c.(742-744)TAT>TGT	p.Y248C	ALS2CR4_uc002uyg.1_Missense_Mutation_p.Y240C|ALS2CR4_uc010zho.1_Missense_Mutation_p.Y43C|ALS2CR4_uc010zhp.1_RNA	NM_001044385	NP_001037850	Q96Q45	TM237_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	272						integral to membrane	protein binding				0						TGCTAGAACATATATCACAAC	0.408													24	21	---	---	---	---	PASS
C2orf80	389073	broad.mit.edu	37	2	209046009	209046009	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209046009C>A	uc002vcr.2	-	5	399	c.227G>T	c.(226-228)AGA>ATA	p.R76I		NM_001099334	NP_001092804	Q0P641	CB080_HUMAN	hypothetical protein LOC389073	76										skin(1)	1						ATATATGGGTCTGCCATGGAG	0.353													18	29	---	---	---	---	PASS
PTH2R	5746	broad.mit.edu	37	2	209358352	209358352	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209358352G>T	uc002vdb.2	+	13	1834	c.1621G>T	c.(1621-1623)GGA>TGA	p.G541*	PTH2R_uc010zjb.1_Nonsense_Mutation_p.G552*|PTH2R_uc010fuo.1_Intron	NM_005048	NP_005039	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor precursor	541	Cytoplasmic (Potential).					integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)		AGACACTGAAGGATGCCAAGG	0.498													17	70	---	---	---	---	PASS
C2orf67	151050	broad.mit.edu	37	2	211019273	211019273	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211019273C>A	uc002vds.2	-	2	242	c.34G>T	c.(34-36)GGT>TGT	p.G12C	C2orf67_uc002vdt.2_Missense_Mutation_p.G12C|C2orf67_uc002vdw.2_Missense_Mutation_p.G12C|C2orf67_uc002vdy.1_Missense_Mutation_p.G12C|C2orf67_uc002vdv.2_Missense_Mutation_p.G12C|C2orf67_uc002vdx.1_Missense_Mutation_p.G12C	NM_152519	NP_689732	A0AUZ9	CB067_HUMAN	hypothetical protein LOC151050	12										ovary(3)	3		Renal(323;0.202)		Epithelial(149;0.00435)|Lung(261;0.0529)|LUSC - Lung squamous cell carcinoma(261;0.0551)|all cancers(144;0.0696)		AAGCTGATACCCTTTGCTGTT	0.413													8	176	---	---	---	---	PASS
ACADL	33	broad.mit.edu	37	2	211081131	211081131	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211081131G>T	uc002vdz.3	-	4	704	c.476C>A	c.(475-477)CCC>CAC	p.P159H		NM_001608	NP_001599	P28330	ACADL_HUMAN	long-chain acyl-CoA dehydrogenase precursor	159					carnitine catabolic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|negative regulation of fatty acid biosynthetic process|negative regulation of fatty acid oxidation|regulation of cholesterol metabolic process|temperature homeostasis	mitochondrial matrix	long-chain-acyl-CoA dehydrogenase activity|palmitoyl-CoA oxidase activity				0		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		AGTCATCTGGGGAATAAAGTG	0.398													7	117	---	---	---	---	PASS
CPS1	1373	broad.mit.edu	37	2	211456551	211456551	+	Intron	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211456551C>G	uc002vee.3	+						CPS1_uc010fur.2_Intron|CPS1_uc010fus.2_5'Flank	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b						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)		CCTTTTCTCTCCAGAGGGCAG	0.378													4	87	---	---	---	---	PASS
WDR69	164781	broad.mit.edu	37	2	228770955	228770955	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228770955G>T	uc002vpn.1	+	9	838	c.759G>T	c.(757-759)AAG>AAT	p.K253N	WDR69_uc010zlw.1_Missense_Mutation_p.K238N|WDR69_uc002vpo.1_RNA	NM_178821	NP_849143	Q8N136	WDR69_HUMAN	WD repeat domain 69	253	WD 4.									breast(1)	1		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;1.22e-10)|all cancers(144;8.11e-08)|Lung(261;0.011)|LUSC - Lung squamous cell carcinoma(224;0.0148)		GTTGTAGGAAGGTAAATATCT	0.358													5	63	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228883619	228883619	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228883619C>A	uc002vpq.2	-	7	1998	c.1951G>T	c.(1951-1953)GCT>TCT	p.A651S	SPHKAP_uc002vpp.2_Missense_Mutation_p.A651S|SPHKAP_uc010zlx.1_Missense_Mutation_p.A651S	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	651						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GACTTTGAAGCAGTTTCCATG	0.463													18	58	---	---	---	---	PASS
INPP5D	3635	broad.mit.edu	37	2	234094557	234094557	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234094557G>A	uc010zmo.1	+	20	2497	c.2344G>A	c.(2344-2346)GAG>AAG	p.E782K	INPP5D_uc010zmp.1_Missense_Mutation_p.E781K	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a	782					apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		GAAGTTTGGTGAGACTCTTCC	0.488													12	12	---	---	---	---	PASS
SPP2	6694	broad.mit.edu	37	2	234969103	234969103	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234969103G>T	uc002vvk.1	+	4	509	c.424G>T	c.(424-426)GAG>TAG	p.E142*	SPP2_uc010fyl.1_Nonsense_Mutation_p.E62*	NM_006944	NP_008875	Q13103	SPP24_HUMAN	secreted phosphoprotein 2, 24kDa precursor	142					bone remodeling|skeletal system development	extracellular region	endopeptidase inhibitor activity				0		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)		CTCCACGTCTGAGTCTTACAG	0.562													13	20	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238285988	238285988	+	Splice_Site	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238285988C>T	uc002vwl.2	-	7	2783	c.2498_splice	c.e7-1	p.E833_splice	COL6A3_uc002vwo.2_Splice_Site_p.E627_splice|COL6A3_uc010znj.1_Splice_Site_p.E226_splice|COL6A3_uc002vwq.2_Splice_Site_p.E627_splice|COL6A3_uc002vwr.2_Splice_Site_p.E426_splice|COL6A3_uc010znk.1_Intron	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CGCTTGCTCTCTGCAATGAAG	0.478													30	25	---	---	---	---	PASS
PRR21	643905	broad.mit.edu	37	2	240982214	240982214	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240982214C>T	uc010zod.1	-	1	186	c.186G>A	c.(184-186)ACG>ACA	p.T62T		NM_001080835	NP_001074304	Q8WXC7	PRR21_HUMAN	proline rich 21	62	Pro-rich.									ovary(1)|skin(1)	2						GGTGAAGAGCCGTGGATGAAG	0.612													10	13	---	---	---	---	PASS
MYEOV2	150678	broad.mit.edu	37	2	241066130	241066130	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241066130G>T	uc002vyu.1	-	5	609	c.609C>A	c.(607-609)ACC>ACA	p.T203T		NM_138336	NP_612209	Q8WXC6	MYOV2_HUMAN	hypothetical protein LOC150678 isoform 1	Error:Variant_position_missing_in_Q8WXC6_after_alignment											0		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)		TGCTTCTTGTGGTTCTGAGCA	0.468													5	62	---	---	---	---	PASS
IL17RE	132014	broad.mit.edu	37	3	9956415	9956415	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9956415C>A	uc003btu.2	+	16	1518	c.1401C>A	c.(1399-1401)ACC>ACA	p.T467T	CIDEC_uc003bto.2_Intron|IL17RC_uc010hcr.2_5'Flank|IL17RC_uc011ato.1_5'Flank|IL17RC_uc010hcs.2_5'Flank|IL17RC_uc003btz.2_5'Flank|IL17RC_uc011atp.1_5'Flank|IL17RC_uc003bud.2_5'Flank|IL17RC_uc003bua.2_5'Flank|IL17RC_uc003bub.2_5'Flank|IL17RC_uc010hct.2_5'Flank|IL17RC_uc010hcu.2_5'Flank|IL17RC_uc010hcv.2_5'Flank|IL17RC_uc011atq.1_5'Flank|IL17RC_uc003buc.2_5'Flank|IL17RE_uc003btw.2_Silent_p.T467T|IL17RE_uc003btx.2_Silent_p.T351T|IL17RE_uc010hcq.2_Missense_Mutation_p.P492T|IL17RE_uc003bty.2_RNA	NM_153483	NP_705616	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E isoform 1	467	Helical; (Potential).					cytoplasm|extracellular region|integral to membrane	receptor activity			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		CCCTCCTCACCCTACTGGGTG	0.612													5	40	---	---	---	---	PASS
RAF1	5894	broad.mit.edu	37	3	12633208	12633208	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12633208G>T	uc003bxf.3	-	11	1607	c.1192C>A	c.(1192-1194)CGC>AGC	p.R398S	RAF1_uc011aut.1_Missense_Mutation_p.R183S|RAF1_uc011auu.1_Missense_Mutation_p.R316S	NM_002880	NP_002871	P04049	RAF1_HUMAN	v-raf-1 murine leukemia viral oncogene homolog	398	Protein kinase.				activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|SRGAP3/RAF1(4)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14					Sorafenib(DB00398)	TCTACTCACCGCAGAACAGCC	0.547			T	SRGAP3	pilocytic astrocytoma				Noonan_syndrome				18	13	---	---	---	---	PASS
SLC4A7	9497	broad.mit.edu	37	3	27439274	27439274	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27439274G>T	uc003cdv.2	-	18	2648	c.2577C>A	c.(2575-2577)ATC>ATA	p.I859I	SLC4A7_uc011awu.1_RNA|SLC4A7_uc011awv.1_RNA|SLC4A7_uc003cdu.3_Silent_p.I740I|SLC4A7_uc011aww.1_Silent_p.I868I|SLC4A7_uc011awx.1_Silent_p.I855I|SLC4A7_uc011awy.1_Silent_p.I851I|SLC4A7_uc011awz.1_RNA|SLC4A7_uc011axa.1_Silent_p.I740I|SLC4A7_uc011axb.1_Silent_p.I855I|SLC4A7_uc010hfl.2_Silent_p.I409I|SLC4A7_uc003cdw.2_Silent_p.I735I	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate	859	Cytoplasmic (Potential).					apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5						CAAAATCACTGATTGTCGATC	0.303													4	20	---	---	---	---	PASS
SCN5A	6331	broad.mit.edu	37	3	38655263	38655263	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38655263C>T	uc003cio.2	-	6	868	c.674G>A	c.(673-675)CGG>CAG	p.R225Q	SCN5A_uc003cin.2_Missense_Mutation_p.R225Q|SCN5A_uc003cil.3_Intron|SCN5A_uc010hhi.2_Intron|SCN5A_uc010hhk.2_Intron|SCN5A_uc011ayr.1_Intron|SCN5A_uc010hhl.1_Intron	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha	225	Helical; Voltage-sensor; Name=S4 of repeat I; (Potential).		R -> W (in PFHB1A).|R -> Q (in LQT3).		blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)	TTTCAGGGCCCGGAGGACTCG	0.498													6	3	---	---	---	---	PASS
WDR48	57599	broad.mit.edu	37	3	39136189	39136189	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39136189G>C	uc003cit.2	+	19	1999	c.1989G>C	c.(1987-1989)AAG>AAC	p.K663N	WDR48_uc011ayt.1_Missense_Mutation_p.K654N|WDR48_uc011ayu.1_Missense_Mutation_p.K581N|WDR48_uc011ayv.1_Missense_Mutation_p.K388N|WDR48_uc003ciu.2_RNA	NM_020839	NP_065890	Q8TAF3	WDR48_HUMAN	WD repeat domain 48	663					interspecies interaction between organisms|protein deubiquitination	lysosome|nucleus	protein binding			ovary(1)|breast(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TCATATGGAAGAGCGGTGGAG	0.418													18	33	---	---	---	---	PASS
NKTR	4820	broad.mit.edu	37	3	42681131	42681131	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42681131G>T	uc003clo.2	+	13	4082	c.3935G>T	c.(3934-3936)AGG>ATG	p.R1312M	NKTR_uc003clm.1_Missense_Mutation_p.R1059M|NKTR_uc003clp.2_Missense_Mutation_p.R1059M|NKTR_uc011azp.1_Intron|NKTR_uc003clq.1_Missense_Mutation_p.R1202M|NKTR_uc003clr.1_Missense_Mutation_p.R1059M|NKTR_uc003cls.2_Missense_Mutation_p.R1012M	NM_005385	NP_005376	P30414	NKTR_HUMAN	natural killer-tumor recognition sequence	1312	Arg/Ser tandem repeat-rich.				protein folding	membrane	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.24)		AGCCAGTCCAGGAGTCCAAGT	0.448													5	53	---	---	---	---	PASS
KIF15	56992	broad.mit.edu	37	3	44893441	44893441	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44893441C>A	uc003cnx.3	+	33	4118	c.3969C>A	c.(3967-3969)TCC>TCA	p.S1323S	KIF15_uc010hiq.2_Silent_p.S1226S|KIF15_uc010hir.2_Silent_p.S371S	NM_020242	NP_064627	Q9NS87	KIF15_HUMAN	kinesin family member 15	1323	Potential.				blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		AGAGAACATCCCAGGTGTGCT	0.383													6	70	---	---	---	---	PASS
SCAP	22937	broad.mit.edu	37	3	47465535	47465535	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47465535G>T	uc003crh.1	-	9	1293	c.1038C>A	c.(1036-1038)GGC>GGA	p.G346G	SCAP_uc011baz.1_Silent_p.G91G|SCAP_uc003crg.2_5'UTR	NM_012235	NP_036367	Q12770	SCAP_HUMAN	SREBF chaperone protein	346	SSD.|Helical; Name=4; (Potential).				cholesterol metabolic process|negative regulation of cholesterol biosynthetic process|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane	unfolded protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		GGAAAATCTCGCTGGGGACAG	0.567													6	7	---	---	---	---	PASS
NCKIPSD	51517	broad.mit.edu	37	3	48717141	48717141	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48717141G>T	uc003cun.2	-	8	1450	c.1356C>A	c.(1354-1356)CAC>CAA	p.H452Q	NCKIPSD_uc003cum.2_Missense_Mutation_p.H445Q	NM_016453	NP_057537	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain isoform	452	Leu-rich.				cytoskeleton organization|NLS-bearing substrate import into nucleus|signal transduction	intermediate filament|nucleus	cytoskeletal protein binding|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GTGATGCTCGGTGTTCCTGGC	0.587													20	14	---	---	---	---	PASS
SEMA3F	6405	broad.mit.edu	37	3	50220346	50220346	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50220346G>T	uc003cyj.2	+	10	1111	c.913G>T	c.(913-915)GGT>TGT	p.G305C	SEMA3F_uc003cyk.2_Missense_Mutation_p.G274C	NM_004186	NP_004177	Q13275	SEM3F_HUMAN	semaphorin 3F precursor	305	Sema.				axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		GAACGATGACGGTGGTCACTG	0.602													3	12	---	---	---	---	PASS
NISCH	11188	broad.mit.edu	37	3	52525432	52525432	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52525432C>A	uc011beg.1	+	21	3879	c.3807C>A	c.(3805-3807)CTC>CTA	p.L1269L	NISCH_uc003ded.3_Silent_p.L1269L|NISCH_uc003dee.3_Silent_p.L758L|NISCH_uc003deg.1_RNA|NISCH_uc003deh.3_Silent_p.L18L	NM_007184	NP_009115	Q9Y2I1	NISCH_HUMAN	nischarin	1269					apoptosis|cell communication	cytosol|early endosome|plasma membrane|recycling endosome	phosphatidylinositol binding|receptor activity			ovary(3)|central_nervous_system(1)	4				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)		ACTGCTTCCTCCAGCACCTCA	0.622													10	10	---	---	---	---	PASS
ATXN7	6314	broad.mit.edu	37	3	63973883	63973883	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63973883A>T	uc003dlw.3	+	9	1797	c.1244A>T	c.(1243-1245)CAT>CTT	p.H415L	ATXN7_uc003dlv.2_Missense_Mutation_p.H415L|ATXN7_uc010hnv.2_Missense_Mutation_p.H415L|ATXN7_uc011bfn.1_Missense_Mutation_p.H270L	NM_000333	NP_000324	O15265	ATX7_HUMAN	ataxin 7 isoform a	415	Pro-rich.				cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		AGGGACCCGCATCCCGCCCCT	0.512													23	37	---	---	---	---	PASS
ABI3BP	25890	broad.mit.edu	37	3	100567705	100567705	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100567705T>A	uc003dun.2	-	16	1475	c.1390A>T	c.(1390-1392)ACA>TCA	p.T464S	ABI3BP_uc003duo.2_Missense_Mutation_p.T506S|ABI3BP_uc011bhd.1_5'Flank|ABI3BP_uc003dum.2_5'Flank	NM_015429	NP_056244	Q7Z7G0	TARSH_HUMAN	ABI gene family, member 3 (NESH) binding protein	464	Pro-rich.					extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4						GGGATAGATGTAGTTTGCTGG	0.368													11	55	---	---	---	---	PASS
DPPA2	151871	broad.mit.edu	37	3	109033356	109033356	+	Splice_Site	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109033356C>A	uc003dxo.2	-	2	280	c.33_splice	c.e2+1	p.K11_splice		NM_138815	NP_620170	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2							nucleus	nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)	3						ATGAAACTTACCTTCTTGCTG	0.388													8	22	---	---	---	---	PASS
GPR156	165829	broad.mit.edu	37	3	119886143	119886143	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119886143C>A	uc011bjf.1	-	9	2181	c.2181G>T	c.(2179-2181)TGG>TGT	p.W727C	GPR156_uc011bjg.1_Missense_Mutation_p.W723C	NM_153002	NP_694547	Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	727	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.19)		GCACTGGGGGCCACAGCTGCC	0.602													4	15	---	---	---	---	PASS
ZXDC	79364	broad.mit.edu	37	3	126185161	126185161	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126185161G>A	uc003eiv.2	-	5	1332	c.1278C>T	c.(1276-1278)TGC>TGT	p.C426C	ZXDC_uc010hsh.2_RNA|ZXDC_uc003eix.2_Silent_p.C426C	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1	426	C2H2-type 9.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)		AGAACCTCGCGCAACATCCTG	0.502													13	13	---	---	---	---	PASS
ACAD9	28976	broad.mit.edu	37	3	128627878	128627878	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128627878C>A	uc003ela.3	+	14	1623	c.1421C>A	c.(1420-1422)TCC>TAC	p.S474Y	ACAD9_uc010hsw.1_3'UTR|ACAD9_uc011bks.1_Missense_Mutation_p.S351Y|ACAD9_uc003elb.2_Missense_Mutation_p.S351Y|ACAD9_uc003eld.1_RNA|ACAD9_uc003ele.2_Missense_Mutation_p.S126Y	NM_014049	NP_054768	Q9H845	ACAD9_HUMAN	acyl-Coenzyme A dehydrogenase family, member 9	474						mitochondrion	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding			ovary(2)|central_nervous_system(1)	3						CTTCGGGACTCCCTGGGCCGA	0.582													6	22	---	---	---	---	PASS
COL6A6	131873	broad.mit.edu	37	3	130353474	130353474	+	Intron	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130353474C>A	uc010htl.2	+						COL6A6_uc003eni.3_Intron	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor						axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						CCTAAGGTACCGTGTGCTTCC	0.418													3	16	---	---	---	---	PASS
EPHB1	2047	broad.mit.edu	37	3	134873037	134873037	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134873037G>T	uc003eqt.2	+	6	1561	c.1341G>T	c.(1339-1341)ATG>ATT	p.M447I	EPHB1_uc003equ.2_Missense_Mutation_p.M8I	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	447	Fibronectin type-III 2.|Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						GTGCCACTATGAGGAGCATCA	0.542													6	114	---	---	---	---	PASS
PAQR9	344838	broad.mit.edu	37	3	142681040	142681040	+	3'UTR	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142681040G>T	uc003evg.2	-	1					PAQR9_uc003evf.1_Intron	NM_198504	NP_940906	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX							integral to membrane	receptor activity				0						CTCCAAGGCGGAGGCTCACTT	0.473													9	359	---	---	---	---	PASS
GPR87	53836	broad.mit.edu	37	3	151012966	151012966	+	Nonsense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151012966G>C	uc003eyt.2	-	3	429	c.68C>G	c.(67-69)TCA>TGA	p.S23*	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_023915	NP_076404	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	23	Extracellular (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)			CCTGTTGCCTGAATTGTGACT	0.502													10	101	---	---	---	---	PASS
DHX36	170506	broad.mit.edu	37	3	154041955	154041955	+	Intron	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154041955G>T	uc003ezy.3	-						DHX36_uc010hvq.2_Intron|DHX36_uc003ezz.3_Intron	NM_020865	NP_065916	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36							cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TACTGAATCCGAGATTACCTC	0.527													8	245	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164906744	164906744	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164906744G>T	uc003fej.3	-	2	2319	c.1875C>A	c.(1873-1875)GCC>GCA	p.A625A	SLITRK3_uc003fek.2_Silent_p.A625A	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	625	Extracellular (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						CTCCAGGCTGGGCTGGGGATT	0.547										HNSCC(40;0.11)			37	19	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164906901	164906901	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164906901A>T	uc003fej.3	-	2	2162	c.1718T>A	c.(1717-1719)TTT>TAT	p.F573Y	SLITRK3_uc003fek.2_Missense_Mutation_p.F573Y	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	573	LRRCT 2.|Extracellular (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						CCACTGTTTAAAGGGGACCAG	0.522										HNSCC(40;0.11)			91	28	---	---	---	---	PASS
SERPINI2	5276	broad.mit.edu	37	3	167189509	167189509	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167189509G>T	uc003fer.1	-	1	172	c.114C>A	c.(112-114)TCC>TCA	p.S38S	SERPINI2_uc003fes.1_Silent_p.S48S|SERPINI2_uc003fet.1_Silent_p.S38S	NM_006217	NP_006208	O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin),	38					cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3						TATGAGATAAGGAAACCTCTT	0.393													8	201	---	---	---	---	PASS
SERPINI1	5274	broad.mit.edu	37	3	167543034	167543034	+	Splice_Site	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167543034G>T	uc003ffa.3	+	9	1355	c.1157_splice	c.e9-1	p.G386_splice	SERPINI1_uc003ffb.3_Splice_Site_p.G386_splice	NM_001122752	NP_001116224	Q99574	NEUS_HUMAN	neuroserpin precursor						central nervous system development|peripheral nervous system development|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(1)	1						AACCAATACAGGTACAATTCT	0.303													8	171	---	---	---	---	PASS
MECOM	2122	broad.mit.edu	37	3	168810787	168810787	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168810787G>C	uc003ffi.3	-	13	2828	c.2559C>G	c.(2557-2559)AAC>AAG	p.N853K	MECOM_uc010hwk.1_Missense_Mutation_p.N867K|MECOM_uc003ffj.3_Missense_Mutation_p.N918K|MECOM_uc011bpi.1_Missense_Mutation_p.N845K|MECOM_uc003ffn.3_Missense_Mutation_p.N853K|MECOM_uc003ffk.2_Missense_Mutation_p.N844K|MECOM_uc003ffl.2_Missense_Mutation_p.N1004K|MECOM_uc011bpj.1_Missense_Mutation_p.N1041K|MECOM_uc011bpk.1_Missense_Mutation_p.N843K	NM_005241	NP_005232	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform b	853					apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						CATGGTTGCTGTTCCCAATGA	0.413													7	98	---	---	---	---	PASS
LRRC34	151827	broad.mit.edu	37	3	169525366	169525366	+	Intron	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169525366G>T	uc003ffx.2	-						LRRC34_uc003ffy.2_Intron|LRRC34_uc011bpn.1_Intron|LRRC34_uc003ffz.2_Intron|LRRC34_uc003fga.3_Intron	NM_153353	NP_699184	Q8IZ02	LRC34_HUMAN	leucine rich repeat containing 34												0	all_cancers(22;4.12e-22)|all_epithelial(15;7.54e-27)|all_lung(20;1.63e-16)|Lung NSC(18;6.92e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			TGATTCTTATGGAAACATACC	0.323													6	119	---	---	---	---	PASS
ECT2	1894	broad.mit.edu	37	3	172520750	172520750	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172520750C>A	uc003fii.2	+	19	2131	c.1993C>A	c.(1993-1995)CTC>ATC	p.L665I	ECT2_uc010hwv.1_Missense_Mutation_p.L696I|ECT2_uc003fih.2_Missense_Mutation_p.L664I|ECT2_uc003fij.1_Missense_Mutation_p.L665I|ECT2_uc003fik.1_Missense_Mutation_p.L665I|ECT2_uc003fil.1_Missense_Mutation_p.L696I|ECT2_uc003fim.1_5'UTR	NM_018098	NP_060568	Q9H8V3	ECT2_HUMAN	epithelial cell transforming sequence 2 oncogene	665	PH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|ovary(1)|skin(1)	4	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			AACTCTCTTCCTCTTCAATGA	0.378													7	150	---	---	---	---	PASS
TBL1XR1	79718	broad.mit.edu	37	3	176743300	176743300	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176743300C>G	uc003fiw.3	-	16	1791	c.1531G>C	c.(1531-1533)GAC>CAC	p.D511H	TBL1XR1_uc003fix.3_Missense_Mutation_p.D511H|TBL1XR1_uc011bpz.1_Missense_Mutation_p.D183H	NM_024665	NP_078941	Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	511	WD 8.				canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TTCCGAAGGTCTAATACACAA	0.348													19	64	---	---	---	---	PASS
TTC14	151613	broad.mit.edu	37	3	180320739	180320739	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180320739G>T	uc003fkk.2	+	2	354	c.222G>T	c.(220-222)CTG>CTT	p.L74L	TTC14_uc003fkl.2_Silent_p.L74L|TTC14_uc003fkm.2_Silent_p.L74L	NM_133462	NP_597719	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14 isoform a	74							RNA binding			ovary(1)	1	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			AAGCGGATCTGCTTTTTGCAC	0.343													91	19	---	---	---	---	PASS
CCDC39	339829	broad.mit.edu	37	3	180372659	180372659	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180372659C>T	uc010hxe.2	-	7	936	c.821G>A	c.(820-822)GGG>GAG	p.G274E	CCDC39_uc003fkn.2_RNA	NM_181426	NP_852091	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	274					axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TGTGTTATTCCCAATCTCACT	0.333													5	63	---	---	---	---	PASS
MAGEF1	64110	broad.mit.edu	37	3	184428680	184428680	+	3'UTR	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184428680C>A	uc003fpa.2	-	1						NM_022149	NP_071432	Q9HAY2	MAGF1_HUMAN	melanoma antigen family F, 1											ovary(1)	1	all_cancers(143;4.61e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;5.64e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.56e-22)			AACTTTTCACCAACCCTCACC	0.383													5	64	---	---	---	---	PASS
CRYGS	1427	broad.mit.edu	37	3	186256664	186256664	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186256664C>A	uc003fqe.2	-	3	410	c.358G>T	c.(358-360)GAG>TAG	p.E120*	CRYGS_uc003fqf.2_Nonsense_Mutation_p.E120*	NM_017541	NP_060011	P22914	CRBS_HUMAN	crystallin, gamma S	120	Beta/gamma crystallin 'Greek key' 3.						structural constituent of eye lens				0	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.5e-22)	GBM - Glioblastoma multiforme(93;0.0906)		TGAAATTGCTCCATGATGGAA	0.478													8	64	---	---	---	---	PASS
AHSG	197	broad.mit.edu	37	3	186338633	186338633	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186338633C>A	uc003fqk.3	+	7	1099	c.1018C>A	c.(1018-1020)CGC>AGC	p.R340S	AHSG_uc003fql.3_Missense_Mutation_p.R341S|AHSG_uc003fqm.3_Missense_Mutation_p.R339S|AHSG_uc010hyp.2_Missense_Mutation_p.R303S	NM_001622	NP_001613	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	340					acute-phase response|negative regulation of bone mineralization|negative regulation of insulin receptor signaling pathway|pinocytosis|positive regulation of phagocytosis|regulation of inflammatory response|skeletal system development	extracellular space	cysteine-type endopeptidase inhibitor activity|protein binding				0	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		CCGGAAAACACGCACAGTGGT	0.602													9	57	---	---	---	---	PASS
ATP13A4	84239	broad.mit.edu	37	3	193183867	193183867	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193183867C>A	uc003ftd.2	-	11	1327	c.1219G>T	c.(1219-1221)GGA>TGA	p.G407*	ATP13A4_uc003fte.1_Nonsense_Mutation_p.G407*|ATP13A4_uc011bsr.1_Intron|ATP13A4_uc010hzi.2_RNA|ATP13A4_uc003ftf.3_Nonsense_Mutation_p.G113*	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	407	Helical; (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		GTGGCTGTTCCTACAAGGCAC	0.458													9	246	---	---	---	---	PASS
OPA1	4976	broad.mit.edu	37	3	193349400	193349400	+	Splice_Site	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193349400G>T	uc003ftm.2	+	6	859	c.625_splice	c.e6-1	p.V209_splice	OPA1_uc003ftg.2_Splice_Site_p.V264_splice|OPA1_uc003fth.2_Splice_Site_p.V228_splice|OPA1_uc003fti.2_Splice_Site_p.V246_splice|OPA1_uc003ftj.2_Splice_Site_p.V227_splice|OPA1_uc003ftk.2_Splice_Site_p.V210_splice|OPA1_uc003ftl.2_Splice_Site_p.V191_splice|OPA1_uc003ftn.2_Splice_Site_p.V173_splice	NM_015560	NP_056375	O60313	OPA1_HUMAN	optic atrophy 1 isoform 1						apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		TAAACATTTAGGTGTCAGACA	0.279													6	113	---	---	---	---	PASS
PIGG	54872	broad.mit.edu	37	4	502758	502758	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:502758C>T	uc003gak.3	+	5	1036	c.900C>T	c.(898-900)CCC>CCT	p.P300P	PIGG_uc003gaj.3_Silent_p.P300P|PIGG_uc011bux.1_RNA|PIGG_uc010ibf.2_Silent_p.P167P|PIGG_uc003gal.3_Silent_p.P211P|PIGG_uc003gai.2_RNA|PIGG_uc011buw.1_Silent_p.P178P|PIGG_uc003gam.2_Silent_p.P211P|PIGG_uc003gan.2_Silent_p.P211P	NM_001127178	NP_001120650	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	300	Lumenal (Potential).				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	CP2 mannose-ethanolamine phosphotransferase activity			central_nervous_system(2)|ovary(1)|skin(1)	4						AAAGGAAACCCGGTGAGAATT	0.393													28	11	---	---	---	---	PASS
TNIP2	79155	broad.mit.edu	37	4	2746619	2746619	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2746619G>A	uc003gfg.2	-	4	798	c.711C>T	c.(709-711)TAC>TAT	p.Y237Y	TNIP2_uc003gff.2_Silent_p.Y130Y|TNIP2_uc003gfh.2_Intron	NM_024309	NP_077285	Q8NFZ5	TNIP2_HUMAN	A20-binding inhibitor of NF-kappaB activation 2	237						cytosol	protein binding			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GCCCCCTCACGTATTCGTCCC	0.597													7	21	---	---	---	---	PASS
CPZ	8532	broad.mit.edu	37	4	8609097	8609097	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8609097A>T	uc003glm.2	+	7	1298	c.1172A>T	c.(1171-1173)GAC>GTC	p.D391V	CPZ_uc003gll.2_RNA|CPZ_uc003gln.2_Missense_Mutation_p.D254V|CPZ_uc003glo.2_Missense_Mutation_p.D380V|CPZ_uc003glp.2_RNA	NM_001014447	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1	391					proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3						TACCCCTTCGACTTCTCCAAG	0.602											OREG0016100	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	18	9	---	---	---	---	PASS
C1QTNF7	114905	broad.mit.edu	37	4	15437385	15437385	+	Silent	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15437385T>C	uc011bxb.1	+	2	245	c.18T>C	c.(16-18)TAT>TAC	p.Y6Y	C1QTNF7_uc003gno.2_Silent_p.Y13Y|C1QTNF7_uc003gnp.2_Silent_p.Y6Y	NM_001135171	NP_001128643	Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7	6						collagen					0						TCTTGCTCTATGTTACAAGTT	0.463													25	24	---	---	---	---	PASS
GBA3	57733	broad.mit.edu	37	4	22750521	22750521	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22750521C>G	uc003gqp.3	+	4	1236	c.1145C>G	c.(1144-1146)GCG>GGG	p.A382G	GBA3_uc010iep.2_Intron|GBA3_uc011bxo.1_Missense_Mutation_p.A383G	NM_020973	NP_066024	Q9H227	GBA3_HUMAN	cytosolic beta-glucosidase isoform a	382					glycoside catabolic process|glycosylceramide catabolic process	cytosol	beta-galactosidase activity|beta-glucosidase activity|cation binding|glycosylceramidase activity				0						AGTGACCCAGCGCCTCTTGAT	0.373													8	6	---	---	---	---	PASS
PPARGC1A	10891	broad.mit.edu	37	4	23886493	23886493	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23886493G>C	uc003gqs.2	-	2	236	c.116C>G	c.(115-117)TCT>TGT	p.S39C	PPARGC1A_uc003gqt.2_RNA|PPARGC1A_uc011bxp.1_5'Flank|PPARGC1A_uc010ier.1_RNA|PPARGC1A_uc003gqu.3_Missense_Mutation_p.S39C	NM_013261	NP_037393	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor	39					androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding			ovary(2)|lung(2)|kidney(2)|skin(2)	8		Breast(46;0.0503)				ATCTAGTTCAGAAAGATCAAG	0.428													15	11	---	---	---	---	PASS
DHX15	1665	broad.mit.edu	37	4	24541881	24541881	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24541881G>T	uc003gqx.2	-	10	1804	c.1636C>A	c.(1636-1638)CTG>ATG	p.L546M	DHX15_uc003gqw.2_5'Flank	NM_001358	NP_001349	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 15	546					mRNA processing	U12-type spliceosomal complex	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(1)	1		Breast(46;0.0503)				AAAGCAGCCAGGTAATTCAAA	0.418													6	58	---	---	---	---	PASS
CWH43	80157	broad.mit.edu	37	4	49034612	49034612	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49034612T>A	uc003gyv.2	+	12	1720	c.1538T>A	c.(1537-1539)GTG>GAG	p.V513E	CWH43_uc011bzl.1_Missense_Mutation_p.V486E	NM_025087	NP_079363	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog	513					GPI anchor biosynthetic process	integral to membrane				skin(2)|ovary(1)	3						TACCCAATTGTGAAATCTGAG	0.468													96	82	---	---	---	---	PASS
EPHA5	2044	broad.mit.edu	37	4	66197847	66197847	+	Splice_Site	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66197847C>T	uc003hcy.2	-	17	3046	c.2853_splice	c.e17-1	p.R951_splice	EPHA5_uc003hcx.2_Splice_Site_p.R883_splice|EPHA5_uc003hcz.2_Splice_Site_p.R929_splice|EPHA5_uc011cah.1_Splice_Site_p.R952_splice|EPHA5_uc011cai.1_Splice_Site_p.R930_splice|EPHA5_uc003hda.2_Intron	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor						cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						ATTAGATACTCTAAAACACAT	0.338										TSP Lung(17;0.13)			8	18	---	---	---	---	PASS
ANKRD17	26057	broad.mit.edu	37	4	73963958	73963958	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73963958C>G	uc003hgp.2	-	26	4970	c.4853G>C	c.(4852-4854)AGG>ACG	p.R1618T	ANKRD17_uc003hgo.2_Missense_Mutation_p.R1505T|ANKRD17_uc003hgq.2_Missense_Mutation_p.R1367T|ANKRD17_uc003hgr.2_Missense_Mutation_p.R1617T	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	1618	Ser-rich.				interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GCTGGAAATCCTCATGTTATC	0.473													54	113	---	---	---	---	PASS
FAM175A	84142	broad.mit.edu	37	4	84403359	84403359	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84403359C>G	uc003hou.2	-	2	191	c.126G>C	c.(124-126)AAG>AAC	p.K42N	FAM175A_uc003hov.2_5'UTR	NM_139076	NP_620775	Q6UWZ7	F175A_HUMAN	coiled-coil domain containing 98	42	MPN-like.				chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of DNA repair|response to ionizing radiation	BRCA1-A complex	polyubiquitin binding			kidney(1)	1						TAATGCTGTTCTTGGCTTCAC	0.328													7	58	---	---	---	---	PASS
CDS1	1040	broad.mit.edu	37	4	85553014	85553014	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85553014G>T	uc011ccv.1	+	6	1121	c.623G>T	c.(622-624)CGT>CTT	p.R208L	CDS1_uc010ike.1_Missense_Mutation_p.R12L	NM_001263	NP_001254	Q92903	CDS1_HUMAN	CDP-diacylglycerol synthase 1	208					signal transduction|visual perception	endoplasmic reticulum membrane|integral to membrane	diacylglycerol cholinephosphotransferase activity|phosphatidate cytidylyltransferase activity			large_intestine(2)|ovary(1)|breast(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		AAACATTATCGTCTGCAGTTT	0.328													30	87	---	---	---	---	PASS
NUDT9	53343	broad.mit.edu	37	4	88356326	88356326	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88356326G>A	uc003hqq.2	+	2	624	c.301G>A	c.(301-303)GCA>ACA	p.A101T	NUDT9_uc003hqr.2_Missense_Mutation_p.A51T|NUDT9_uc010ikl.2_Missense_Mutation_p.A101T	NM_024047	NP_076952	Q9BW91	NUDT9_HUMAN	nudix-type motif 9 isoform a	101						mitochondrion	ADP-ribose diphosphatase activity				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000937)		GGAATACACTGCAGTCTCTGT	0.483													16	54	---	---	---	---	PASS
MMRN1	22915	broad.mit.edu	37	4	90857906	90857906	+	Silent	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90857906G>C	uc003hst.2	+	6	3146	c.3075G>C	c.(3073-3075)CTG>CTC	p.L1025L	MMRN1_uc010iku.2_Intron|MMRN1_uc011cds.1_Silent_p.L767L	NM_007351	NP_031377	Q13201	MMRN1_HUMAN	multimerin 1	1025					cell adhesion|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen				ovary(4)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		CCACAGTCCTGATAGGCCGGA	0.348													23	51	---	---	---	---	PASS
ENPEP	2028	broad.mit.edu	37	4	111470983	111470983	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111470983A>T	uc003iab.3	+	17	2784	c.2442A>T	c.(2440-2442)CAA>CAT	p.Q814H		NM_001977	NP_001968	Q07075	AMPE_HUMAN	glutamyl aminopeptidase	814	Extracellular (Potential).				cell migration|cell proliferation|cell-cell signaling|proteolysis	integral to plasma membrane	aminopeptidase activity|metalloexopeptidase activity|zinc ion binding			skin(3)|ovary(1)|breast(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)	L-Glutamic Acid(DB00142)	CATTAGCTCAAGAAAAAGAAA	0.363													20	39	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123122179	123122179	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123122179A>T	uc003ieh.2	+	13	1441	c.1396A>T	c.(1396-1398)AGC>TGC	p.S466C	KIAA1109_uc003iei.1_Missense_Mutation_p.S220C|KIAA1109_uc010ins.1_5'UTR	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	466					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						CATCAATGCCAGCTACCCCCG	0.393													13	29	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126402738	126402738	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126402738C>T	uc003ifj.3	+	15	12661	c.12661C>T	c.(12661-12663)CAG>TAG	p.Q4221*	FAT4_uc011cgp.1_Nonsense_Mutation_p.Q2462*|FAT4_uc003ifi.1_Nonsense_Mutation_p.Q1699*	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4221	Laminin G-like 2.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						CCACATGAGTCAGAATGAGAA	0.438													18	62	---	---	---	---	PASS
PLK4	10733	broad.mit.edu	37	4	128814582	128814582	+	Intron	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128814582C>A	uc003ifo.2	+						PLK4_uc011cgs.1_Intron|PLK4_uc011cgt.1_Intron	NM_014264	NP_055079	O00444	PLK4_HUMAN	polo-like kinase 4						G2/M transition of mitotic cell cycle|positive regulation of centriole replication|trophoblast giant cell differentiation	centriole|cleavage furrow|cytosol|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0						AGGTACATACCTAATTGTAGG	0.323													6	45	---	---	---	---	PASS
INPP4B	8821	broad.mit.edu	37	4	143003250	143003250	+	Nonsense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143003250G>C	uc003iix.3	-	26	3171	c.2576C>G	c.(2575-2577)TCA>TGA	p.S859*	INPP4B_uc003iiw.3_Nonsense_Mutation_p.S859*|INPP4B_uc011chm.1_RNA|INPP4B_uc011chn.1_Nonsense_Mutation_p.S674*|INPP4B_uc011cho.1_RNA	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,	859					signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					TCTCAAGATTGAGCATTGTTC	0.398													13	53	---	---	---	---	PASS
NR3C2	4306	broad.mit.edu	37	4	149357659	149357659	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149357659G>T	uc003ilj.3	-	2	688	c.354C>A	c.(352-354)TCC>TCA	p.S118S	NR3C2_uc003ilk.3_Silent_p.S118S|NR3C2_uc010iph.2_RNA	NM_000901	NP_000892	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	118	Modulating.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)	GCTGCTCATAGGAATAGTCAG	0.398													6	76	---	---	---	---	PASS
KIAA0922	23240	broad.mit.edu	37	4	154557706	154557706	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154557706C>A	uc003inm.3	+	35	4860	c.4808C>A	c.(4807-4809)TCG>TAG	p.S1603*	KIAA0922_uc010ipp.2_Nonsense_Mutation_p.S1604*|KIAA0922_uc010ipq.2_Nonsense_Mutation_p.S1372*	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2	1603	Cytoplasmic (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				TCTAGAGACTCGAGTTACTGT	0.398													4	69	---	---	---	---	PASS
NPY2R	4887	broad.mit.edu	37	4	156135450	156135450	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156135450C>G	uc003ioq.2	+	2	854	c.359C>G	c.(358-360)CCT>CGT	p.P120R	NPY2R_uc003ior.2_Missense_Mutation_p.P120R	NM_000910	NP_000901	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	120	Extracellular (Potential).				cardiac left ventricle morphogenesis|inhibition of adenylate cyclase activity by G-protein signaling pathway|locomotory behavior|outflow tract morphogenesis	integral to plasma membrane	calcium channel regulator activity			lung(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0854)				AAAATGGGTCCTGTCCTGTGC	0.517													6	23	---	---	---	---	PASS
PDZD2	23037	broad.mit.edu	37	5	32101345	32101345	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32101345G>T	uc003jhl.2	+	24	8741	c.8353G>T	c.(8353-8355)GGT>TGT	p.G2785C	PDZD2_uc003jhm.2_Missense_Mutation_p.G2785C|PDZD2_uc003jhn.2_RNA	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	2785	PDZ 6.				cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						AGTGTACAAAGGTAATGTTCT	0.448													5	29	---	---	---	---	PASS
NUP155	9631	broad.mit.edu	37	5	37293025	37293025	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37293025C>T	uc003jku.1	-	34	4111	c.3993G>A	c.(3991-3993)TTG>TTA	p.L1331L	NUP155_uc003jkt.1_Silent_p.L1272L|NUP155_uc010iuz.1_Silent_p.L1267L	NM_153485	NP_705618	O75694	NU155_HUMAN	nucleoporin 155kDa isoform 1	1331					carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CATATCTTATCAATAATACAT	0.303													13	57	---	---	---	---	PASS
EGFLAM	133584	broad.mit.edu	37	5	38350668	38350668	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38350668G>T	uc003jlc.1	+	4	681	c.357G>T	c.(355-357)CAG>CAT	p.Q119H	EGFLAM_uc003jlb.1_Missense_Mutation_p.Q119H	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G	119	Fibronectin type-III 1.					cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					CTTACAGCCAGGCTGGCAAAG	0.478													10	43	---	---	---	---	PASS
CARD6	84674	broad.mit.edu	37	5	40852638	40852638	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40852638C>A	uc003jmg.2	+	3	1279	c.1204C>A	c.(1204-1206)CAG>AAG	p.Q402K		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	402					apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5						GTATCAGTGCCAGTTTGCTCT	0.453													22	31	---	---	---	---	PASS
C6	729	broad.mit.edu	37	5	41172358	41172358	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41172358G>T	uc003jmk.2	-	9	1470	c.1260C>A	c.(1258-1260)TGC>TGA	p.C420*	C6_uc003jml.1_Nonsense_Mutation_p.C420*	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	420	MACPF.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TGTTGGTGGTGCACCTATGTT	0.428													15	34	---	---	---	---	PASS
PLCXD3	345557	broad.mit.edu	37	5	41382435	41382435	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41382435T>A	uc003jmm.1	-	2	407	c.305A>T	c.(304-306)AAG>ATG	p.K102M		NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X	102	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						GTCTCTGGGCTTGGTGGAAAT	0.448													22	25	---	---	---	---	PASS
PLCXD3	345557	broad.mit.edu	37	5	41382437	41382437	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41382437G>A	uc003jmm.1	-	2	405	c.303C>T	c.(301-303)ACC>ACT	p.T101T		NM_001005473	NP_001005473	Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X	101	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6						CTCTGGGCTTGGTGGAAATTC	0.448													22	26	---	---	---	---	PASS
C5orf34	375444	broad.mit.edu	37	5	43506176	43506176	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43506176G>T	uc003jnz.1	-	5	923	c.606C>A	c.(604-606)ATC>ATA	p.I202I	C5orf34_uc011cpx.1_Silent_p.I88I	NM_198566	NP_940968	Q96MH7	CE034_HUMAN	hypothetical protein LOC375444	202										breast(1)	1	Lung NSC(6;2.07e-05)					TGGATTTCATGATCTGGCAAT	0.373													31	58	---	---	---	---	PASS
NNT	23530	broad.mit.edu	37	5	43645623	43645623	+	Intron	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43645623C>A	uc003joe.2	+						NNT_uc003jof.2_Intron	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase						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)	GTGAGGATACCATTTACCAGG	0.308													5	68	---	---	---	---	PASS
ERBB2IP	55914	broad.mit.edu	37	5	65349881	65349881	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65349881G>T	uc003juk.1	+	21	3043	c.2735G>T	c.(2734-2736)AGG>ATG	p.R912M	ERBB2IP_uc003jui.1_Missense_Mutation_p.R912M|ERBB2IP_uc003juj.1_Missense_Mutation_p.R912M|ERBB2IP_uc011cqx.1_Missense_Mutation_p.R912M|ERBB2IP_uc011cqy.1_Missense_Mutation_p.R912M|ERBB2IP_uc011cqz.1_Intron|ERBB2IP_uc010iwx.1_Missense_Mutation_p.R908M|ERBB2IP_uc003jul.1_Missense_Mutation_p.R908M	NM_018695	NP_061165	Q96RT1	LAP2_HUMAN	ERBB2 interacting protein isoform 2	912					basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)	7		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		AATATAGTCAGGAGCAAGTCT	0.383													11	516	---	---	---	---	PASS
MAP1B	4131	broad.mit.edu	37	5	71495083	71495083	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71495083C>T	uc003kbw.3	+	5	6142	c.5901C>T	c.(5899-5901)CCC>CCT	p.P1967P	MAP1B_uc010iyw.1_Silent_p.P1984P|MAP1B_uc010iyx.1_Silent_p.P1841P|MAP1B_uc010iyy.1_Silent_p.P1841P	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1967	MAP1B 6.					microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CCAGCCCCCCCGAAGTGAGTG	0.478													47	29	---	---	---	---	PASS
CKMT2	1160	broad.mit.edu	37	5	80554960	80554960	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80554960C>T	uc003khc.3	+	9	1143	c.901C>T	c.(901-903)CGA>TGA	p.R301*	RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Nonsense_Mutation_p.R301*|CKMT2_uc003khd.3_Nonsense_Mutation_p.R301*|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816	P17540	KCRS_HUMAN	sarcomeric mitochondrial creatine kinase	301	Phosphagen kinase C-terminal.				creatine metabolic process|muscle contraction	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	AATCCAAGAACGAGGCTGGGA	0.473													39	46	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	89999498	89999498	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89999498C>G	uc003kju.2	+	35	8268	c.8172C>G	c.(8170-8172)TTC>TTG	p.F2724L	GPR98_uc003kjt.2_Missense_Mutation_p.F430L|GPR98_uc003kjv.2_Missense_Mutation_p.F324L	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	2724	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTTTACAATTCCATGTGATAA	0.328													3	4	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140208255	140208255	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140208255G>A	uc003lho.2	+	1	606	c.579G>A	c.(577-579)GGG>GGA	p.G193G	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Silent_p.G193G|PCDHA6_uc011dab.1_Silent_p.G193G	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	193	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACAAATTGGGCTCTTATTAA	0.428													28	31	---	---	---	---	PASS
PCDHB8	56128	broad.mit.edu	37	5	140558864	140558864	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140558864G>T	uc011dai.1	+	1	1435	c.1249G>T	c.(1249-1251)GAG>TAG	p.E417*	PCDHB16_uc003liv.2_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	417	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AAGCAGAGCCGAGTACAACGT	0.507													10	205	---	---	---	---	PASS
PCDHB12	56124	broad.mit.edu	37	5	140590630	140590630	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140590630C>A	uc003liz.2	+	1	2340	c.2151C>A	c.(2149-2151)AGC>AGA	p.S717R	PCDHB12_uc011dak.1_Missense_Mutation_p.S380R|PCDHB13_uc003lja.1_5'Flank	NM_018932	NP_061755	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12 precursor	717	Cytoplasmic (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCAGGAGGAGCAGGGCGGCCC	0.662													27	33	---	---	---	---	PASS
DPYSL3	1809	broad.mit.edu	37	5	146778759	146778759	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146778759G>T	uc003lon.1	-	11	1277	c.1167C>A	c.(1165-1167)GCC>GCA	p.A389A	DPYSL3_uc003loo.2_Silent_p.A503A	NM_001387	NP_001378	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	389					axon guidance|pyrimidine base catabolic process|signal transduction	cytosol|growth cone	dihydropyrimidinase activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAAGATCTTGGCAGCGTTTG	0.448													7	120	---	---	---	---	PASS
CCNG1	900	broad.mit.edu	37	5	162866308	162866308	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162866308C>A	uc003lzb.2	+	3	180	c.46C>A	c.(46-48)CAG>AAG	p.Q16K	CCNG1_uc011dek.1_Intron|CCNG1_uc011del.1_Intron|CCNG1_uc003lzc.2_RNA	NM_199246	NP_954854	P51959	CCNG1_HUMAN	cyclin G1	16					cell division|mitosis|regulation of cyclin-dependent protein kinase activity	nucleus				lung(1)|kidney(1)	2	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)		ACTGCTACACCAGCTGAATGC	0.443													5	75	---	---	---	---	PASS
SLIT3	6586	broad.mit.edu	37	5	168096832	168096832	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168096832T>A	uc003mab.2	-	35	4712	c.4292A>T	c.(4291-4293)TAC>TTC	p.Y1431F	SLIT3_uc010jjg.2_Missense_Mutation_p.Y1438F	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	1431	EGF-like 9.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCACAGGCAGTAGGGCTCCCC	0.552													10	14	---	---	---	---	PASS
CPEB4	80315	broad.mit.edu	37	5	173317590	173317590	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173317590G>T	uc003mcs.3	+	1	2260	c.854G>T	c.(853-855)TGG>TTG	p.W285L	CPEB4_uc010jju.1_Missense_Mutation_p.W285L|CPEB4_uc010jjv.2_Missense_Mutation_p.W285L|CPEB4_uc011dfg.1_Missense_Mutation_p.W285L|CPEB4_uc003mct.3_5'Flank|CPEB4_uc003mcu.3_5'Flank	NM_030627	NP_085130	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding	285							nucleotide binding|RNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CCCTCTCCGTGGAGCAGCTAC	0.582													6	143	---	---	---	---	PASS
GPRIN1	114787	broad.mit.edu	37	5	176026747	176026747	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176026747G>T	uc003meo.1	-	2	264	c.89C>A	c.(88-90)CCA>CAA	p.P30Q		NM_052899	NP_443131	Q7Z2K8	GRIN1_HUMAN	G protein-regulated inducer of neurite outgrowth	30						growth cone|plasma membrane				ovary(2)	2	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCATCCTGTGGGCAGAAGAA	0.637													4	17	---	---	---	---	PASS
HK3	3101	broad.mit.edu	37	5	176317909	176317909	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176317909A>T	uc003mfa.2	-	5	540	c.448T>A	c.(448-450)TTC>ATC	p.F150I	HK3_uc003mez.2_5'Flank	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	150	Regulatory.				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	7	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCATCCAGGAACTCAGACAGG	0.607													15	16	---	---	---	---	PASS
SLC44A4	80736	broad.mit.edu	37	6	31833387	31833387	+	Intron	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31833387G>A	uc010jti.2	-						NEU1_uc003nxq.3_5'Flank|NEU1_uc010jtg.2_5'Flank|NEU1_uc003nxr.3_5'Flank|NEU1_uc010jth.2_5'Flank|NEU1_uc003nxs.3_5'Flank	NM_025257	NP_079533	Q53GD3	CTL4_HUMAN	choline transporter-like protein 4							integral to membrane|plasma membrane	choline transmembrane transporter activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4					Choline(DB00122)	TCCTGGGAGCGAGGAAGGCTC	0.527													31	29	---	---	---	---	PASS
STK38	11329	broad.mit.edu	37	6	36483123	36483123	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36483123C>T	uc003omg.2	-	6	1249	c.661G>A	c.(661-663)GAC>AAC	p.D221N	STK38_uc003omh.2_Missense_Mutation_p.D221N|STK38_uc003omi.2_Missense_Mutation_p.D221N	NM_007271	NP_009202	Q15208	STK38_HUMAN	serine/threonine kinase 38	221	Protein kinase.				intracellular protein kinase cascade|negative regulation of MAP kinase activity	cytoplasm|MLL5-L complex	ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6						ACCTTGCTGTCCAAAAGAAGG	0.468													24	24	---	---	---	---	PASS
DAAM2	23500	broad.mit.edu	37	6	39836641	39836641	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39836641G>T	uc003oow.2	+	7	961	c.805G>T	c.(805-807)GAT>TAT	p.D269Y	DAAM2_uc010jxc.2_Missense_Mutation_p.D269Y|DAAM2_uc003oox.2_Missense_Mutation_p.D269Y	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of	269	GBD/FH3.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					CCGGTACCGGGATGAAGTGAA	0.562													6	11	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51604782	51604782	+	Intron	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51604782A>T	uc003pah.1	-						PKHD1_uc010jzn.1_Intron|PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					GCCTAATTCTACCTGAATGGG	0.403													13	27	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51613076	51613076	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51613076G>T	uc003pah.1	-	58	9614	c.9338C>A	c.(9337-9339)TCT>TAT	p.S3113Y	PKHD1_uc010jzn.1_Missense_Mutation_p.S1096Y|PKHD1_uc003pai.2_Missense_Mutation_p.S3113Y	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3113	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					CAGTTCACAAGAGGAGCACTT	0.483													9	303	---	---	---	---	PASS
BMP5	653	broad.mit.edu	37	6	55684595	55684595	+	Nonsense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55684595G>A	uc003pcq.2	-	2	1253	c.541C>T	c.(541-543)CGA>TGA	p.R181*	BMP5_uc011dxf.1_Nonsense_Mutation_p.R181*	NM_021073	NP_066551	P22003	BMP5_HUMAN	bone morphogenetic protein 5 preproprotein	181					cartilage development|cell differentiation|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(2)	2	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			AGATCAAATCGAAATTCTTTG	0.388													9	9	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56426228	56426228	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56426228G>C	uc003pdf.2	-	51	7859	c.7831C>G	c.(7831-7833)CAG>GAG	p.Q2611E	DST_uc003pcz.3_Missense_Mutation_p.Q2433E|DST_uc011dxj.1_Missense_Mutation_p.Q2462E|DST_uc011dxk.1_Missense_Mutation_p.Q2473E|DST_uc003pcy.3_Missense_Mutation_p.Q2107E	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	4519	Spectrin 4.				cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GATTCTTCCTGAGCCTTTTGC	0.418													28	33	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56462639	56462639	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56462639C>A	uc003pdf.2	-	41	5765	c.5737G>T	c.(5737-5739)GGA>TGA	p.G1913*	DST_uc003pcz.3_Nonsense_Mutation_p.G1735*|DST_uc011dxj.1_Nonsense_Mutation_p.G1764*|DST_uc011dxk.1_Nonsense_Mutation_p.G1775*|DST_uc003pcy.3_Nonsense_Mutation_p.G1409*|DST_uc010kaa.1_RNA	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	3821					cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TCCTCTTCTCCAATTGCTGAC	0.423													35	37	---	---	---	---	PASS
BAI3	577	broad.mit.edu	37	6	69653823	69653823	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69653823G>T	uc003pev.3	+	6	1580	c.1132G>T	c.(1132-1134)GGA>TGA	p.G378*	BAI3_uc010kak.2_Nonsense_Mutation_p.G378*	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	378	Extracellular (Potential).|TSP type-1 2.				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				TCCTCAGTATGGAGGAAGGCC	0.453													5	50	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70900066	70900066	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70900066G>T	uc003pfc.1	+	48	3192	c.3075G>T	c.(3073-3075)GAG>GAT	p.E1025D		NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	1025					cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						TTAATCAAGAGGTCCTAAGGA	0.209													13	21	---	---	---	---	PASS
FILIP1	27145	broad.mit.edu	37	6	76023132	76023132	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76023132G>T	uc003pia.2	-	5	2789	c.2416C>A	c.(2416-2418)CAA>AAA	p.Q806K	FILIP1_uc003phy.1_Missense_Mutation_p.Q806K|FILIP1_uc003phz.2_Missense_Mutation_p.Q707K|FILIP1_uc010kbe.2_Missense_Mutation_p.Q809K|FILIP1_uc003pib.1_Missense_Mutation_p.Q558K	NM_015687	NP_056502	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	806										skin(3)|ovary(1)	4						GCATCAGTTTGGACTCCAGTT	0.473													7	115	---	---	---	---	PASS
GJA10	84694	broad.mit.edu	37	6	90605195	90605195	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90605195C>T	uc011eaa.1	+	1	1008	c.1008C>T	c.(1006-1008)AGC>AGT	p.S336S		NM_032602	NP_115991	Q969M2	CXA10_HUMAN	gap junction protein, alpha 10	336	Cytoplasmic (Potential).				synaptic transmission	connexon complex|integral to membrane	gap junction channel activity				0		all_cancers(76;5.71e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.0915)		ATGTTCACAGCCCGTGTCCCT	0.532											OREG0004442	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=CX62|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	17	23	---	---	---	---	PASS
CCNC	892	broad.mit.edu	37	6	99997415	99997415	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99997415G>A	uc003pqe.2	-	9	854	c.567C>T	c.(565-567)TGC>TGT	p.C189C	uc003pqc.2_Intron|CCNC_uc003pqd.2_Silent_p.C104C|CCNC_uc010kcr.2_RNA|CCNC_uc010kcs.2_Silent_p.C188C|CCNC_uc011eah.1_Silent_p.C104C	NM_005190	NP_005181	P24863	CCNC_HUMAN	cyclin C isoform a	189					regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	DNA-directed RNA polymerase II, holoenzyme	protein kinase binding				0		all_cancers(76;8.46e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.064)		GATACAGTAGGCAAAGATCCG	0.328													4	19	---	---	---	---	PASS
GRIK2	2898	broad.mit.edu	37	6	102511844	102511844	+	Intron	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102511844C>A	uc003pqp.3	+						GRIK2_uc003pqo.3_Missense_Mutation_p.S857Y|GRIK2_uc010kcw.2_Intron	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)	CAGGAATCTTCTATTTGGTTA	0.274													4	6	---	---	---	---	PASS
CLVS2	134829	broad.mit.edu	37	6	123332129	123332129	+	Splice_Site	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123332129G>T	uc003pzi.1	+	3	1259	c.390_splice	c.e3-1	p.R130_splice		NM_001010852	NP_001010852	Q5SYC1	CLVS2_HUMAN	retinaldehyde binding protein 1-like 2						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						GTCGCCGATAGGTACACACTG	0.353													5	74	---	---	---	---	PASS
SASH1	23328	broad.mit.edu	37	6	148711341	148711341	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148711341C>T	uc003qme.1	+	2	703	c.228C>T	c.(226-228)GAC>GAT	p.D76D		NM_015278	NP_056093	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	76							protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GTTTCTCCGACGTGTGCGAGA	0.562													19	52	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152665276	152665276	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152665276G>T	uc010kiw.2	-	74	12767	c.12165C>A	c.(12163-12165)GTC>GTA	p.V4055V	SYNE1_uc003qot.3_Silent_p.V3984V|SYNE1_uc003qou.3_Silent_p.V4055V|SYNE1_uc010kja.1_Silent_p.V760V	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4055	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AATCCGGCTGGACTGCAGAAA	0.478										HNSCC(10;0.0054)			39	18	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152708431	152708431	+	Nonsense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152708431T>A	uc010kiw.2	-	54	8865	c.8263A>T	c.(8263-8265)AAA>TAA	p.K2755*	SYNE1_uc003qot.3_Nonsense_Mutation_p.K2762*|SYNE1_uc003qou.3_Nonsense_Mutation_p.K2755*|SYNE1_uc010kjb.1_Nonsense_Mutation_p.K2738*	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2755	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGTTCTATTTTTTGATCCACT	0.448										HNSCC(10;0.0054)			37	27	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152757184	152757184	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152757184T>G	uc010kiw.2	-	33	4804	c.4202A>C	c.(4201-4203)AAG>ACG	p.K1401T	SYNE1_uc003qot.3_Missense_Mutation_p.K1408T|SYNE1_uc003qou.3_Missense_Mutation_p.K1401T|SYNE1_uc010kjb.1_Missense_Mutation_p.K1384T|SYNE1_uc003qow.2_Missense_Mutation_p.K696T|SYNE1_uc003qox.1_Missense_Mutation_p.K917T	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1401	Potential.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGAAGCTTCCTTTACAAGGTT	0.388										HNSCC(10;0.0054)			9	70	---	---	---	---	PASS
SNX9	51429	broad.mit.edu	37	6	158327175	158327175	+	Silent	SNP	G	A	A	rs138249048		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158327175G>A	uc003qqv.1	+	7	809	c.636G>A	c.(634-636)GCG>GCA	p.A212A		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	212	Critical for tubulation activity.				cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		CTGGATTTGCGAAACCTGGCA	0.333													6	29	---	---	---	---	PASS
UNC93A	54346	broad.mit.edu	37	6	167717471	167717471	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167717471G>T	uc003qvq.2	+	5	865	c.690G>T	c.(688-690)CGG>CGT	p.R230R	UNC93A_uc003qvr.2_Silent_p.R188R	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1	230						integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		ATGTTCAGCGGGAAAGTgaag	0.294													7	81	---	---	---	---	PASS
WIPI2	26100	broad.mit.edu	37	7	5262287	5262287	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5262287C>A	uc003snv.2	+	8	940	c.724C>A	c.(724-726)CGG>AGG	p.R242R	WIPI2_uc003snw.2_Silent_p.R242R|WIPI2_uc003snx.2_Silent_p.R224R|WIPI2_uc003sny.2_Silent_p.R224R|WIPI2_uc010ksv.2_Silent_p.R98R|WIPI2_uc003soa.2_Silent_p.R183R|WIPI2_uc003sob.2_5'UTR	NM_015610	NP_056425	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2	242					autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)		CTTTGAGTTTCGGAGAGGAGT	0.373													5	167	---	---	---	---	PASS
TWISTNB	221830	broad.mit.edu	37	7	19738049	19738049	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19738049G>T	uc003sup.1	-	4	928	c.907C>A	c.(907-909)CAA>AAA	p.Q303K		NM_001002926	NP_001002926	Q3B726	RPA43_HUMAN	TWIST neighbor	303	Lys-rich.					microtubule cytoskeleton|nucleolus	DNA-directed RNA polymerase activity			ovary(1)	1						TGGTCACTTTGGTAACCACTG	0.418													12	722	---	---	---	---	PASS
SP4	6671	broad.mit.edu	37	7	21550868	21550868	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21550868C>A	uc003sva.2	+	6	2517	c.2336C>A	c.(2335-2337)ACC>AAC	p.T779N	SP4_uc003svb.2_Missense_Mutation_p.T466N	NM_003112	NP_003103	Q02446	SP4_HUMAN	Sp4 transcription factor	779					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(3)|skin(2)	5						AATGTTTCAACCAACATGGAA	0.428													51	19	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21757524	21757524	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21757524C>A	uc003svc.2	+	44	7167	c.7136C>A	c.(7135-7137)CCT>CAT	p.P2379H		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2379					microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						ACTTCAATTCCTGAGAGTAGC	0.398									Kartagener_syndrome				11	389	---	---	---	---	PASS
CDCA7L	55536	broad.mit.edu	37	7	21945920	21945920	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21945920C>A	uc010kuk.2	-	6	1028	c.908G>T	c.(907-909)AGG>ATG	p.R303M	CDCA7L_uc003sve.3_Missense_Mutation_p.R269M|CDCA7L_uc010kul.2_Missense_Mutation_p.R257M|CDCA7L_uc003svf.3_Missense_Mutation_p.R302M	NM_018719	NP_061189	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like isoform 1	303					positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0						AATTGTCTTCCTTCTTCGGAA	0.443													9	365	---	---	---	---	PASS
STK31	56164	broad.mit.edu	37	7	23775395	23775395	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23775395C>A	uc003sws.3	+	7	789	c.722C>A	c.(721-723)CCT>CAT	p.P241H	STK31_uc003swt.3_Missense_Mutation_p.P218H|STK31_uc011jze.1_Missense_Mutation_p.P241H|STK31_uc010kuq.2_Missense_Mutation_p.P218H	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a	241							ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						AGCCCCATTCCTTTGTGGGGG	0.453													8	219	---	---	---	---	PASS
TMED4	222068	broad.mit.edu	37	7	44620751	44620751	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44620751G>T	uc003tli.2	-	4	497	c.475C>A	c.(475-477)CGC>AGC	p.R159S	TMED4_uc003tlj.2_Missense_Mutation_p.R100S|TMED4_uc003tlk.2_Missense_Mutation_p.R159S|uc003tll.2_5'Flank	NM_182547	NP_872353	Q7Z7H5	TMED4_HUMAN	transmembrane emp24 protein transport domain	159	Lumenal (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade|transport	endoplasmic reticulum membrane|integral to membrane	signal transducer activity				0						TGGCGGGCGCGGAGCTGTAGC	0.517													4	20	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48266877	48266877	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48266877G>T	uc003toq.2	+	6	512	c.487G>T	c.(487-489)GAG>TAG	p.E163*	ABCA13_uc003top.2_Nonsense_Mutation_p.E163*|ABCA13_uc010kyr.2_5'UTR	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	163					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						CAATAAGACCGAGGAGGTAAT	0.398													5	116	---	---	---	---	PASS
VWC2	375567	broad.mit.edu	37	7	49842319	49842319	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49842319G>T	uc003tot.1	+	3	1265	c.709G>T	c.(709-711)GAG>TAG	p.E237*		NM_198570	NP_940972	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2	237	VWFC 2.				negative regulation of BMP signaling pathway|positive regulation of neuron differentiation	basement membrane|extracellular space					0						GTCTCCATGCGAGAGGTGTCG	0.473													37	42	---	---	---	---	PASS
GNAT3	346562	broad.mit.edu	37	7	80108231	80108231	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80108231C>T	uc011kgu.1	-	4	387	c.387G>A	c.(385-387)CGG>CGA	p.R129R	CD36_uc003uhc.2_Intron	NM_001102386	NP_001095856	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha	129					detection of chemical stimulus involved in sensory perception of bitter taste|G-protein signaling, coupled to cAMP nucleotide second messenger|rhodopsin mediated phototransduction|sensory perception of sweet taste|sensory perception of umami taste	cytoplasm|heterotrimeric G-protein complex|photoreceptor inner segment|photoreceptor outer segment	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1						CTCTCCACAGCCGTTTTATTA	0.443													19	109	---	---	---	---	PASS
SEMA3C	10512	broad.mit.edu	37	7	80418629	80418629	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80418629G>T	uc003uhj.2	-	12	1909	c.1347C>A	c.(1345-1347)CTC>CTA	p.L449L	SEMA3C_uc011kgw.1_Silent_p.L467L	NM_006379	NP_006370	Q99985	SEM3C_HUMAN	semaphorin 3C precursor	449	Sema.				immune response|response to drug	membrane	receptor activity			ovary(1)	1						TACCTGTTCCGAGAAACAGGA	0.393													5	86	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82580167	82580167	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82580167C>A	uc003uhx.2	-	6	10026	c.9737G>T	c.(9736-9738)CGA>CTA	p.R3246L	PCLO_uc003uhv.2_Missense_Mutation_p.R3246L|PCLO_uc010lec.2_Missense_Mutation_p.R211L	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3177	Gln-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						TTCTTGTTCTCGGAACCTTTG	0.473													4	94	---	---	---	---	PASS
CROT	54677	broad.mit.edu	37	7	86983719	86983719	+	Intron	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86983719G>T	uc003uit.2	+						CROT_uc003uis.3_Intron|CROT_uc003uiu.2_Intron	NM_021151	NP_066974	Q9UKG9	OCTC_HUMAN	peroxisomal carnitine O-octanoyltransferase						fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|transport	peroxisomal matrix	carnitine O-octanoyltransferase activity			ovary(2)|lung(1)	3	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	ggatttaactggacctaggaa	0.000													13	664	---	---	---	---	PASS
CDK14	5218	broad.mit.edu	37	7	90585135	90585135	+	Intron	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90585135G>T	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						GACATGTGGTGAGAAATGGAA	0.448													10	59	---	---	---	---	PASS
SAMD9L	219285	broad.mit.edu	37	7	92763543	92763543	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92763543G>A	uc003umh.1	-	5	2958	c.1742C>T	c.(1741-1743)TCT>TTT	p.S581F	SAMD9L_uc003umj.1_Missense_Mutation_p.S581F|SAMD9L_uc003umi.1_Missense_Mutation_p.S581F|SAMD9L_uc010lfb.1_Missense_Mutation_p.S581F|SAMD9L_uc003umk.1_Missense_Mutation_p.S581F|SAMD9L_uc010lfc.1_Missense_Mutation_p.S581F|SAMD9L_uc010lfd.1_Missense_Mutation_p.S581F|SAMD9L_uc011khx.1_Intron	NM_152703	NP_689916	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	581										ovary(4)	4	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TGAGTTTACAGAGATACACAA	0.353													13	66	---	---	---	---	PASS
AGFG2	3268	broad.mit.edu	37	7	100151098	100151098	+	Nonsense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100151098C>G	uc003uvf.2	+	4	696	c.560C>G	c.(559-561)TCA>TGA	p.S187*	AGFG2_uc003uvg.1_Intron|AGFG2_uc010lgy.2_Missense_Mutation_p.Q49E	NM_006076	NP_006067	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	187					regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			central_nervous_system(1)	1						CCGTCTCTCTCAGTTGCTGCC	0.542													11	64	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100677488	100677488	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100677488G>C	uc003uxp.1	+	3	2844	c.2791G>C	c.(2791-2793)GAC>CAC	p.D931H	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	931	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|13.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					AAGTATGCCTGACAGCACCAC	0.507													111	222	---	---	---	---	PASS
LRRC17	10234	broad.mit.edu	37	7	102585004	102585004	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102585004A>G	uc003vau.2	+	4	1665	c.1276A>G	c.(1276-1278)AGA>GGA	p.R426G	FBXL13_uc010liq.1_Intron|FBXL13_uc003vaq.2_Intron|FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Intron|LRRC17_uc003vat.2_3'UTR	NM_001031692	NP_001026862	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17 isoform 1	426					bone marrow development|negative regulation of osteoclast differentiation|ossification	extracellular space				ovary(1)	1						AAAAAAACATAGAGATCACAC	0.338													13	61	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103180820	103180820	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103180820G>C	uc003vca.2	-	44	6914	c.6754C>G	c.(6754-6756)CTC>GTC	p.L2252V	RELN_uc010liz.2_Missense_Mutation_p.L2252V	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2252	BNR 10.				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CCACCGTTGAGAGAATACTGT	0.502													48	69	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103205825	103205825	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103205825G>A	uc003vca.2	-	34	5270	c.5110C>T	c.(5110-5112)CCA>TCA	p.P1704S	RELN_uc010liz.2_Missense_Mutation_p.P1704S	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	1704					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CCAATGGTTGGAGGAACACAC	0.493													10	36	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103230190	103230190	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103230190A>G	uc003vca.2	-	28	4158	c.3998T>C	c.(3997-3999)CTG>CCG	p.L1333P	RELN_uc010liz.2_Missense_Mutation_p.L1333P	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	1333	BNR 5.				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TTCTTTCACCAGAAACCAGGA	0.468													37	79	---	---	---	---	PASS
NRCAM	4897	broad.mit.edu	37	7	107849860	107849860	+	Intron	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107849860T>C	uc003vfb.2	-						NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron	NM_001037132	NP_001032209	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule isoform A						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						TTTTAAACAATATACCTTTAA	0.323													21	42	---	---	---	---	PASS
LRRN3	54674	broad.mit.edu	37	7	110764903	110764903	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110764903C>G	uc003vft.3	+	4	3121	c.2075C>G	c.(2074-2076)ACA>AGA	p.T692R	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.T692R|LRRN3_uc003vfs.3_Missense_Mutation_p.T692R	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	692	Cytoplasmic (Potential).					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		GAAAAAAGTACATCACTGAAA	0.353													9	41	---	---	---	---	PASS
PPP1R3A	5506	broad.mit.edu	37	7	113519652	113519652	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113519652C>G	uc010ljy.1	-	4	1526	c.1495G>C	c.(1495-1497)GAA>CAA	p.E499Q		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	499					glycogen metabolic process	integral to membrane				lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1)	34						TCTGTTGATTCTTTGAGACAT	0.318													16	31	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121668637	121668637	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121668637G>T	uc003vjy.2	+	14	5415	c.5020G>T	c.(5020-5022)GAG>TAG	p.E1674*	PTPRZ1_uc003vjz.2_Nonsense_Mutation_p.E814*|PTPRZ1_uc011knt.1_Nonsense_Mutation_p.E264*	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	1674	Cytoplasmic (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						CTTTTACTTAGAGGACAGTAC	0.388													5	33	---	---	---	---	PASS
FEZF1	389549	broad.mit.edu	37	7	121944015	121944015	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121944015G>T	uc003vkd.2	-	1	551	c.477C>A	c.(475-477)GCC>GCA	p.A159A	FEZF1_uc003vkc.2_Intron|uc010lko.1_RNA|uc003vkf.1_5'Flank	NM_001024613	NP_001019784	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1 isoform 1	159					cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|breast(1)	3						GGTAGCACAAGGCGCCCATGG	0.657													5	3	---	---	---	---	PASS
AKR1B15	441282	broad.mit.edu	37	7	134253033	134253033	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134253033C>A	uc011kpr.1	+	4	573	c.274C>A	c.(274-276)CAA>AAA	p.Q92K	AKR1B15_uc003vrt.2_Missense_Mutation_p.Q64K|AKR1B15_uc011kps.1_Missense_Mutation_p.Q64K	NM_001080538	NP_001074007	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	92							oxidoreductase activity			ovary(1)	1						AGAGAAGATCCAAGAGAAGGC	0.512													8	152	---	---	---	---	PASS
CHRM2	1129	broad.mit.edu	37	7	136699829	136699829	+	Missense_Mutation	SNP	G	T	T	rs11773032		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136699829G>T	uc003vtf.1	+	4	840	c.217G>T	c.(217-219)GGT>TGT	p.G73C	CHRM2_uc003vtg.1_Missense_Mutation_p.G73C|CHRM2_uc003vtj.1_Missense_Mutation_p.G73C|CHRM2_uc003vtk.1_Missense_Mutation_p.G73C|CHRM2_uc003vtl.1_Missense_Mutation_p.G73C|CHRM2_uc003vtm.1_Missense_Mutation_p.G73C|CHRM2_uc003vti.1_Missense_Mutation_p.G73C|CHRM2_uc003vto.1_Missense_Mutation_p.G73C|CHRM2_uc003vtn.1_Missense_Mutation_p.G73C|uc003vtp.1_Intron	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	73	Helical; Name=2; (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)	CCTTATCATAGGTGTTTTCTC	0.478													6	89	---	---	---	---	PASS
DGKI	9162	broad.mit.edu	37	7	137172424	137172424	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137172424C>A	uc003vtt.2	-	23	2315	c.2314G>T	c.(2314-2316)GGT>TGT	p.G772C	DGKI_uc003vtu.2_Missense_Mutation_p.G472C	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	772					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						ACTAGAATACCCAGAGGTATC	0.363													8	161	---	---	---	---	PASS
AKR1D1	6718	broad.mit.edu	37	7	137791988	137791988	+	Intron	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137791988C>G	uc003vtz.2	+						AKR1D1_uc011kqe.1_Intron|AKR1D1_uc011kqf.1_Intron|AKR1D1_uc010lmy.1_RNA	NM_005989	NP_005980	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1						TCCCATACTACGAGTAACTCT	0.463													8	21	---	---	---	---	PASS
ZNF786	136051	broad.mit.edu	37	7	148769495	148769495	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148769495G>T	uc003wfh.2	-	4	506	c.369C>A	c.(367-369)TCC>TCA	p.S123S	ZNF786_uc011kuk.1_Silent_p.S86S|ZNF786_uc003wfi.2_Silent_p.S37S	NM_152411	NP_689624	Q8N393	ZN786_HUMAN	zinc finger protein 786	123					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|skin(1)	4	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			AGGATCCAAAGGAACACTGGC	0.507													4	18	---	---	---	---	PASS
NCAPG2	54892	broad.mit.edu	37	7	158439183	158439183	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158439183C>A	uc003wnv.1	-	25	3293	c.3148G>T	c.(3148-3150)GGA>TGA	p.G1050*	NCAPG2_uc010lqu.1_Nonsense_Mutation_p.G795*|NCAPG2_uc003wnw.1_RNA|NCAPG2_uc003wnx.1_Nonsense_Mutation_p.G1050*|NCAPG2_uc011kwe.1_Nonsense_Mutation_p.G1050*|NCAPG2_uc011kwc.1_Nonsense_Mutation_p.G504*|NCAPG2_uc011kwd.1_Nonsense_Mutation_p.G493*	NM_017760	NP_060230	Q86XI2	CNDG2_HUMAN	leucine zipper protein 5	1050					cell division|chromosome condensation|mitosis	nucleus	methylated histone residue binding			ovary(1)|breast(1)|kidney(1)	3	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		ATTATTATTCCTATTAAACAC	0.398													6	38	---	---	---	---	PASS
MCPH1	79648	broad.mit.edu	37	8	6299593	6299593	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6299593C>A	uc003wqi.2	+	7	654	c.586C>A	c.(586-588)CAA>AAA	p.Q196K	MCPH1_uc003wqh.2_Missense_Mutation_p.Q196K|MCPH1_uc011kwl.1_Missense_Mutation_p.Q148K	NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin	196						microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		TTTAGCTTCCCAAATGATTCA	0.363													5	24	---	---	---	---	PASS
DLC1	10395	broad.mit.edu	37	8	12945993	12945993	+	Intron	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12945993C>T	uc003wwm.2	-						DLC1_uc003wwk.1_Intron|DLC1_uc003wwl.1_Intron|DLC1_uc011kxx.1_Intron	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						GGGAAGCGCTCACCTTAAAAC	0.383													20	23	---	---	---	---	PASS
ASAH1	427	broad.mit.edu	37	8	17942230	17942230	+	5'Flank	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17942230G>T	uc003wyl.2	-						ASAH1_uc010ltb.1_5'Flank|ASAH1_uc003wym.2_5'Flank|ASAH1_uc003wyn.2_Silent_p.T27T|ASAH1_uc003wyo.2_Silent_p.T27T|uc003wyp.1_5'Flank	NM_177924	NP_808592	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase 1 isoform a						ceramide metabolic process	lysosome	ceramidase activity				0				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		TTGAGGCCTCGGTGAAAAGCG	0.572											OREG0018581	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	18	---	---	---	---	PASS
SLC18A1	6570	broad.mit.edu	37	8	20031914	20031914	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20031914G>C	uc011kyq.1	-	6	1060	c.589C>G	c.(589-591)CGA>GGA	p.R197G	SLC18A1_uc003wzl.2_5'Flank|SLC18A1_uc003wzm.2_Missense_Mutation_p.R197G|SLC18A1_uc011kyr.1_Missense_Mutation_p.R197G|SLC18A1_uc003wzn.2_Missense_Mutation_p.R197G|SLC18A1_uc010ltf.2_RNA|SLC18A1_uc003wzo.2_Missense_Mutation_p.R197G	NM_001135691	NP_001129163	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine),	197	Lumenal, vesicle (Potential).				neurotransmitter transport	clathrin sculpted monoamine transport vesicle membrane|integral to membrane|membrane fraction	drug transmembrane transporter activity|monoamine transmembrane transporter activity			ovary(2)	2				Colorectal(74;0.0747)		TGAAGGGTTCGGGCCACAAAG	0.473													16	17	---	---	---	---	PASS
RHOBTB2	23221	broad.mit.edu	37	8	22862901	22862901	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22862901G>T	uc003xcq.2	+	3	746	c.209G>T	c.(208-210)CGA>CTA	p.R70L	RHOBTB2_uc003xcp.2_Missense_Mutation_p.R92L|RHOBTB2_uc011kzp.1_Missense_Mutation_p.R77L	NM_015178	NP_055993	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2 isoform 3	70	Rho-like.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding			ovary(1)|lung(1)	2		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		GAACGCTCCCGAGACGTGGTA	0.607													4	40	---	---	---	---	PASS
NEFM	4741	broad.mit.edu	37	8	24775752	24775752	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24775752C>A	uc003xed.3	+	3	2417	c.2384C>A	c.(2383-2385)TCC>TAC	p.S795Y	NEFM_uc011lac.1_Intron|NEFM_uc010lue.2_Missense_Mutation_p.S419Y	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	795	Tail.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		gccaagggatccaggaaggaa	0.010													3	3	---	---	---	---	PASS
WRN	7486	broad.mit.edu	37	8	31007883	31007883	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31007883G>T	uc003xio.3	+	31	4387	c.3599G>T	c.(3598-3600)AGG>ATG	p.R1200M	WRN_uc010lvk.2_Missense_Mutation_p.R667M	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	1200	HRDC.				base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		AACGTAAAAAGGATTGATGGT	0.353			Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				5	51	---	---	---	---	PASS
ASH2L	9070	broad.mit.edu	37	8	37986347	37986347	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37986347C>A	uc003xkt.3	+	12	1463	c.1405C>A	c.(1405-1407)CAC>AAC	p.H469N	ASH2L_uc011lbk.1_Missense_Mutation_p.H330N|ASH2L_uc003xku.3_Missense_Mutation_p.H375N|ASH2L_uc010lwa.2_Missense_Mutation_p.H375N	NM_004674	NP_004665	Q9UBL3	ASH2L_HUMAN	ash2-like isoform a	469	B30.2/SPRY.				hemopoiesis|histone H3-K4 methylation|positive regulation of cell proliferation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription from RNA polymerase II promoter	Set1C/COMPASS complex	metal ion binding|protein binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)				AACCAAGTTCCACCAGTCCAT	0.423													9	383	---	---	---	---	PASS
FGFR1	2260	broad.mit.edu	37	8	38297823	38297823	+	Intron	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38297823C>A	uc003xlp.2	-						FGFR1_uc011lbo.1_Intron|FGFR1_uc011lbp.1_Intron|FGFR1_uc011lbq.1_Intron|FGFR1_uc010lwk.2_Splice_Site_p.A23_splice|FGFR1_uc011lbs.1_Intron|FGFR1_uc011lbt.1_Intron|FGFR1_uc011lbu.1_Intron|FGFR1_uc011lbv.1_Intron|FGFR1_uc011lbw.1_Intron|FGFR1_uc011lbx.1_Intron|FGFR1_uc003xlv.2_Intron|FGFR1_uc003xlu.2_Intron|FGFR1_uc003xlw.1_Intron	NM_023110	NP_075598	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1 isoform 1						axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)	TGAAAACTTACCTTCGGCTGG	0.532		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						4	7	---	---	---	---	PASS
PXDNL	137902	broad.mit.edu	37	8	52252201	52252201	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52252201T>C	uc003xqu.3	-	21	4230	c.4129A>G	c.(4129-4131)ACA>GCA	p.T1377A	PXDNL_uc003xqt.3_Intron	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	1377					hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CTGAGTGCTGTGATGGTTTCC	0.388													28	59	---	---	---	---	PASS
RRS1	23212	broad.mit.edu	37	8	67342384	67342384	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67342384G>T	uc003xwa.2	+	1	1122	c.1018G>T	c.(1018-1020)GGC>TGC	p.G340C	ADHFE1_uc003xwb.3_5'Flank|ADHFE1_uc003xwd.3_5'Flank|ADHFE1_uc003xwc.3_5'Flank|ADHFE1_uc003xwe.3_5'Flank|ADHFE1_uc003xwf.3_5'Flank|ADHFE1_uc011les.1_5'Flank|ADHFE1_uc011leq.1_5'Flank|ADHFE1_uc011ler.1_5'Flank	NM_015169	NP_055984	Q15050	RRS1_HUMAN	homolog of yeast ribosome biogenesis regulatory	340	Arg/Gly/Lys-rich.				mitotic metaphase plate congression|ribosome biogenesis	condensed nuclear chromosome|nucleolus					0		Lung NSC(129;0.197)	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			GGGCTTGGGAGGCAAGATGAA	0.617													5	61	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77767585	77767585	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77767585A>G	uc003yav.2	+	10	8680	c.8293A>G	c.(8293-8295)ATC>GTC	p.I2765V	ZFHX4_uc003yau.1_Missense_Mutation_p.I2810V|ZFHX4_uc003yaw.1_Missense_Mutation_p.I2765V	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2765						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)			TAATACGGCAATCAGTGACGC	0.468										HNSCC(33;0.089)			17	55	---	---	---	---	PASS
RIPK2	8767	broad.mit.edu	37	8	90782012	90782012	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90782012G>T	uc003yee.2	+	4	810	c.496G>T	c.(496-498)GGT>TGT	p.G166C	RIPK2_uc003yef.2_Missense_Mutation_p.G29C	NM_003821	NP_003812	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	166	Protein kinase.				activation of MAPK activity|anti-apoptosis|apoptosis|inflammatory response|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|CARD domain binding|LIM domain binding|protein homodimerization activity|protein serine/threonine kinase activity|signal transducer activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.0474)			TGCAGATTTTGGTTTATCAAA	0.363													6	127	---	---	---	---	PASS
RUNX1T1	862	broad.mit.edu	37	8	93017415	93017415	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93017415G>T	uc003yfd.2	-	5	753	c.669C>A	c.(667-669)ACC>ACA	p.T223T	RUNX1T1_uc003yfc.1_Silent_p.T196T|RUNX1T1_uc003yfe.1_Silent_p.T186T|RUNX1T1_uc010mao.2_Silent_p.T196T|RUNX1T1_uc011lgi.1_Silent_p.T234T|RUNX1T1_uc003yfb.1_Silent_p.T186T|RUNX1T1_uc003yff.1_Silent_p.T186T	NM_175634	NP_783552	Q06455	MTG8_HUMAN	acute myelogenous leukemia 1 translocation 1	223					generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)			CAGGTGAGGTGGTGCTGGCAT	0.592													31	68	---	---	---	---	PASS
ANKRD46	157567	broad.mit.edu	37	8	101540109	101540109	+	Nonsense_Mutation	SNP	G	T	T	rs140674239		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101540109G>T	uc003yjm.2	-	4	638	c.434C>A	c.(433-435)TCG>TAG	p.S145*	ANKRD46_uc003yjn.1_Nonsense_Mutation_p.S145*|ANKRD46_uc003yjo.1_Nonsense_Mutation_p.S145*|ANKRD46_uc003yjp.1_Nonsense_Mutation_p.S145*	NM_198401	NP_940683	Q86W74	ANR46_HUMAN	ankyrin repeat domain 46	145						integral to membrane					0	all_cancers(14;5.07e-05)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000353)|all_lung(17;0.000998)		Epithelial(11;2.61e-11)|all cancers(13;5.03e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.49e-06)|STAD - Stomach adenocarcinoma(118;0.0957)			CTCCAGTTTCGAGTGGGTTCC	0.368													6	76	---	---	---	---	PASS
RIMS2	9699	broad.mit.edu	37	8	104898026	104898026	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104898026G>T	uc003yls.2	+	2	774	c.533G>T	c.(532-534)CGT>CTT	p.R178L	RIMS2_uc003ylp.2_Missense_Mutation_p.R400L|RIMS2_uc003ylw.2_Missense_Mutation_p.R208L|RIMS2_uc003ylq.2_Missense_Mutation_p.R208L|RIMS2_uc003ylr.2_Missense_Mutation_p.R208L	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	431					intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			ATATCAGAACGTAGAGCTGCC	0.433										HNSCC(12;0.0054)			12	23	---	---	---	---	PASS
TRHR	7201	broad.mit.edu	37	8	110131291	110131291	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110131291G>T	uc003ymz.3	+	2	820	c.804G>T	c.(802-804)CTG>CTT	p.L268L		NM_003301	NP_003292	P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	268	Helical; Name=6; (Potential).					integral to plasma membrane	thyrotropin-releasing hormone receptor activity			skin(2)|lung(1)	3			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			CCAAGATGCTGGCAGTGGTTG	0.403													6	152	---	---	---	---	PASS
SLC30A8	169026	broad.mit.edu	37	8	118184931	118184931	+	3'UTR	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118184931C>G	uc003yoh.2	+	8					SLC30A8_uc010mcz.2_3'UTR|SLC30A8_uc011lia.1_3'UTR|SLC30A8_uc003yog.2_3'UTR	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8						insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			CTCAGTCACACCGTCAGTTTC	0.463													30	79	---	---	---	---	PASS
DEPDC6	64798	broad.mit.edu	37	8	120940802	120940802	+	Silent	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120940802G>C	uc003yow.3	+	2	472	c.285G>C	c.(283-285)CGG>CGC	p.R95R	DEPDC6_uc011lid.1_Intron	NM_022783	NP_073620	Q8TB45	DPTOR_HUMAN	DEP domain containing 6	95	DEP 1.				intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis	intracellular	protein binding				0	Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TAGCAGACCGGGGCATTATTC	0.433													34	65	---	---	---	---	PASS
KCNQ3	3786	broad.mit.edu	37	8	133150161	133150161	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133150161C>G	uc003ytj.2	-	12	1896	c.1671G>C	c.(1669-1671)ATG>ATC	p.M557I	KCNQ3_uc010mdt.2_Missense_Mutation_p.M557I	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein	557					axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			TCCTGGAAAGCATGTCGAGAT	0.458													45	85	---	---	---	---	PASS
FLJ43860	389690	broad.mit.edu	37	8	142477649	142477649	+	Splice_Site	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142477649C>G	uc003ywi.2	-	18	2254	c.2173_splice	c.e18-1	p.D725_splice	FLJ43860_uc011ljs.1_Splice_Site|FLJ43860_uc010meu.1_Splice_Site	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690								binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			GCATGATATCCTGTACAGCGG	0.642													4	35	---	---	---	---	PASS
ZNF696	79943	broad.mit.edu	37	8	144378212	144378212	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144378212C>A	uc003yxy.3	+	3	776	c.367C>A	c.(367-369)CGG>AGG	p.R123R		NM_030895	NP_112157	Q9H7X3	ZN696_HUMAN	zinc finger protein 696	123					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)			CTGGAAGGGGCGGCCTTTCCC	0.677													3	10	---	---	---	---	PASS
TOP1MT	116447	broad.mit.edu	37	8	144406177	144406177	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144406177T>C	uc003yxz.2	-	7	971	c.952A>G	c.(952-954)ATC>GTC	p.I318V	TOP1MT_uc011lkd.1_Missense_Mutation_p.I220V|TOP1MT_uc011lke.1_Missense_Mutation_p.I220V|TOP1MT_uc010mfb.2_Missense_Mutation_p.I220V|TOP1MT_uc011lkf.1_Missense_Mutation_p.I113V|TOP1MT_uc010mfd.1_Missense_Mutation_p.I113V	NM_052963	NP_443195	Q969P6	TOP1M_HUMAN	mitochondrial topoisomerase I precursor	318					DNA topological change	chromosome|mitochondrial nucleoid	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	ACCTTATCGATGAAATACAGG	0.607													12	36	---	---	---	---	PASS
PLEC	5339	broad.mit.edu	37	8	144997715	144997715	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144997715G>A	uc003zaf.1	-	31	6963	c.6793C>T	c.(6793-6795)CGG>TGG	p.R2265W	PLEC_uc003zab.1_Missense_Mutation_p.R2128W|PLEC_uc003zac.1_Missense_Mutation_p.R2132W|PLEC_uc003zad.2_Missense_Mutation_p.R2128W|PLEC_uc003zae.1_Missense_Mutation_p.R2096W|PLEC_uc003zag.1_Missense_Mutation_p.R2106W|PLEC_uc003zah.2_Missense_Mutation_p.R2114W|PLEC_uc003zaj.2_Missense_Mutation_p.R2155W	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	2265	Central fibrous rod domain.|Potential.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9						GCCTGAGCCCGGGCCTGTGCC	0.746													5	4	---	---	---	---	PASS
DOCK8	81704	broad.mit.edu	37	9	312050	312050	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:312050C>T	uc003zgf.2	+	6	737	c.625C>T	c.(625-627)CGG>TGG	p.R209W	DOCK8_uc011lls.1_Missense_Mutation_p.R209W|DOCK8_uc010mgu.2_5'UTR|DOCK8_uc010mgv.2_Missense_Mutation_p.R141W|DOCK8_uc010mgt.2_Missense_Mutation_p.R141W|DOCK8_uc003zgg.2_Missense_Mutation_p.R141W|DOCK8_uc003zgh.2_RNA	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	209					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		GCCTGACAAGCGGCTAGAAAA	0.602													58	28	---	---	---	---	PASS
RFX3	5991	broad.mit.edu	37	9	3270516	3270516	+	Missense_Mutation	SNP	A	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3270516A>C	uc003zhr.2	-	12	1524	c.1212T>G	c.(1210-1212)AGT>AGG	p.S404R	RFX3_uc010mhd.2_Missense_Mutation_p.S404R|RFX3_uc003zhs.1_Missense_Mutation_p.S404R	NM_134428	NP_602304	P48380	RFX3_HUMAN	regulatory factor X3 isoform b	404					cell maturation|ciliary cell motility|cilium assembly|cilium movement involved in determination of left/right asymmetry|endocrine pancreas development|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|regulation of insulin secretion	nuclear chromatin	protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		TTTCTATTTCACTCAGATTGC	0.353													41	15	---	---	---	---	PASS
ERMP1	79956	broad.mit.edu	37	9	5811144	5811144	+	Missense_Mutation	SNP	G	T	T	rs139768756	byFrequency	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5811144G>T	uc003zjm.1	-	7	1348	c.1294C>A	c.(1294-1296)CTG>ATG	p.L432M	ERMP1_uc011lme.1_RNA|ERMP1_uc010mhs.1_Missense_Mutation_p.L46M	NM_024896	NP_079172	Q7Z2K6	ERMP1_HUMAN	aminopeptidase Fxna	432	Cytoplasmic (Potential).				proteolysis	endoplasmic reticulum membrane|integral to membrane	metal ion binding|metallopeptidase activity			ovary(1)	1		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		TTTTTGCCCAGGTACAAAACA	0.403													5	77	---	---	---	---	PASS
RANBP6	26953	broad.mit.edu	37	9	6014019	6014019	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6014019G>A	uc003zjr.2	-	1	1600	c.1589C>T	c.(1588-1590)ACA>ATA	p.T530I	RANBP6_uc011lmf.1_Missense_Mutation_p.T178I|RANBP6_uc003zjs.2_Missense_Mutation_p.T118I	NM_012416	NP_036548	O60518	RNBP6_HUMAN	RAN binding protein 6	530					protein transport	cytoplasm|nucleus	binding			ovary(3)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		TTCTTCTATTGTATCTGCAAC	0.388													51	27	---	---	---	---	PASS
RRAGA	10670	broad.mit.edu	37	9	19049819	19049819	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19049819G>A	uc003znj.2	+	1	448	c.162G>A	c.(160-162)GGG>GGA	p.G54G		NM_006570	NP_006561	Q7L523	RRAGA_HUMAN	Ras-related GTP binding A	54					apoptosis|cellular protein localization|cellular response to amino acid stimulus|positive regulation of cytolysis|positive regulation of TOR signaling cascade|virus-host interaction	Golgi apparatus|lysosome|nucleus	GTP binding|phosphoprotein binding|protein heterodimerization activity|protein homodimerization activity				0						GATTCCTAGGGAACCTGGTGC	0.547													17	10	---	---	---	---	PASS
CDKN2A	1029	broad.mit.edu	37	9	21971003	21971003	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21971003C>A	uc003zpk.2	-	2	567	c.355G>T	c.(355-357)GAG>TAG	p.E119*	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Nonstop_Mutation_p.*174L	NM_000077	NP_000068	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 1	119	ANK 4.		E -> Q (in a biliary tract tumor).		cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(1112)|p.?(13)|p.E119Q(2)|p.E119*(2)|p.A118fs*10(1)|p.A118fs*27(1)		haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3678		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CCCAGCTCCTCAGCCAGGTCC	0.726		17							Uveal_Melanoma_Familial|Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System|Hereditary_Melanoma	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			10	6	---	---	---	---	PASS
TRPM6	140803	broad.mit.edu	37	9	77377029	77377029	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77377029G>T	uc004ajl.1	-	26	4796	c.4558C>A	c.(4558-4560)CAG>AAG	p.Q1520K	TRPM6_uc004ajk.1_Missense_Mutation_p.Q1515K|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajj.1_Missense_Mutation_p.Q476K	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	1520	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						GTGTTTGGCTGAAGCCATGGT	0.488													5	62	---	---	---	---	PASS
TRPM6	140803	broad.mit.edu	37	9	77431640	77431640	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77431640C>G	uc004ajl.1	-	11	1491	c.1253G>C	c.(1252-1254)TGG>TCG	p.W418S	TRPM6_uc004ajk.1_Missense_Mutation_p.W413S|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Missense_Mutation_p.W418S|TRPM6_uc010mpd.1_Missense_Mutation_p.W418S|TRPM6_uc010mpe.1_Intron	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	418	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						CACCCTGTCCCAAGCCATTGC	0.353													21	49	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79259819	79259819	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79259819G>C	uc010mpk.2	-	12	8688	c.8564C>G	c.(8563-8565)ACA>AGA	p.T2855R	PRUNE2_uc011lsk.1_Missense_Mutation_p.T104R|PRUNE2_uc011lsl.1_Missense_Mutation_p.T119R|PRUNE2_uc011lsm.1_Missense_Mutation_p.T120R|PRUNE2_uc004akj.3_Missense_Mutation_p.T309R|PRUNE2_uc010mpl.1_Missense_Mutation_p.T309R	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	2855					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						TTTGTTGGCTGTGGGATCTTC	0.493													15	25	---	---	---	---	PASS
FOXB2	442425	broad.mit.edu	37	9	79635479	79635479	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79635479C>A	uc004ako.1	+	1	909	c.909C>A	c.(907-909)CCC>CCA	p.P303P		NM_001013735	NP_001013757	Q5VYV0	FOXB2_HUMAN	forkhead box B2	303					brain development|embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0						ACCCCGTGCCCGGCCAGCTTG	0.542													3	13	---	---	---	---	PASS
FLJ46321	389763	broad.mit.edu	37	9	84610038	84610038	+	Silent	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84610038T>C	uc004amn.2	+	4	4700	c.4653T>C	c.(4651-4653)TTT>TTC	p.F1551F		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	1551						integral to membrane					0						GCCCTGTGTTTAGTGATGTGC	0.502													5	12	---	---	---	---	PASS
C9orf3	84909	broad.mit.edu	37	9	97844894	97844894	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97844894G>T	uc004ava.2	+	15	2492	c.2357G>T	c.(2356-2358)AGT>ATT	p.S786I	C9orf3_uc004auy.2_Missense_Mutation_p.S687I|C9orf3_uc004avc.2_Intron|C9orf3_uc011luj.1_Missense_Mutation_p.S148I|C9orf3_uc011luk.1_Missense_Mutation_p.S127I|C9orf3_uc004avd.2_Missense_Mutation_p.S148I|MIR23B_hsa-mir-23b|MI0000439_5'Flank|uc004avg.3_5'Flank|MIR27B_hsa-mir-27b|MI0000440_5'Flank	NM_032823	NP_116212	Q8N6M6	AMPO_HUMAN	aminopeptidase O	786					leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		CTGATGGTGAGTGAGGACGCC	0.602													14	19	---	---	---	---	PASS
HEMGN	55363	broad.mit.edu	37	9	100692888	100692888	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100692888T>A	uc004axy.2	-	3	897	c.789A>T	c.(787-789)AAA>AAT	p.K263N	HEMGN_uc004axz.2_Missense_Mutation_p.K263N	NM_197978	NP_932095	Q9BXL5	HEMGN_HUMAN	hemogen	263					cell differentiation|multicellular organismal development					ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)				GCACATCTGGTTTTGGATATG	0.443													53	108	---	---	---	---	PASS
HEMGN	55363	broad.mit.edu	37	9	100693092	100693092	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100693092C>A	uc004axy.2	-	3	693	c.585G>T	c.(583-585)AAG>AAT	p.K195N	HEMGN_uc004axz.2_Missense_Mutation_p.K195N	NM_197978	NP_932095	Q9BXL5	HEMGN_HUMAN	hemogen	195					cell differentiation|multicellular organismal development					ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)				CTTCAGGTTCCTTCATGTCTT	0.388													8	224	---	---	---	---	PASS
ALG2	85365	broad.mit.edu	37	9	101980729	101980729	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101980729G>A	uc004azf.2	-	2	808	c.738C>T	c.(736-738)GCC>GCT	p.A246A	ALG2_uc004azg.2_Silent_p.A153A	NM_033087	NP_149078	Q9H553	ALG2_HUMAN	alpha-1,3-mannosyltransferase ALG2	246					dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in endoplasmic reticulum|protein N-linked glycosylation via asparagine|response to calcium ion	endoplasmic reticulum membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	alpha-1,3-mannosyltransferase activity|calcium-dependent protein binding|glycolipid 3-alpha-mannosyltransferase activity|protein anchor|protein heterodimerization activity|protein N-terminus binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.0559)				GCTGTACTAGGGCTTCCAGTG	0.488													21	114	---	---	---	---	PASS
OR13C8	138802	broad.mit.edu	37	9	107331952	107331952	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107331952C>G	uc011lvo.1	+	1	504	c.504C>G	c.(502-504)TTC>TTG	p.F168L		NM_001004483	NP_001004483	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C,	168	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						AGTTACCATTCTGTGCTAATA	0.448													17	49	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107550224	107550224	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107550224C>T	uc004bcl.2	-	46	6494	c.6181G>A	c.(6181-6183)GGC>AGC	p.G2061S	NIPSNAP3B_uc004bcj.1_RNA	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	2061	ABC transporter 2.				Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	GGAGGCCCGCCGATCAAAGCC	0.478													19	46	---	---	---	---	PASS
C9orf6	54942	broad.mit.edu	37	9	111698726	111698726	+	Intron	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111698726C>A	uc004bdn.2	+						IKBKAP_uc004bdm.3_5'Flank|IKBKAP_uc011lwc.1_5'Flank|IKBKAP_uc010mtq.2_5'Flank|C9orf6_uc010mtr.2_Intron	NM_017832	NP_060302	Q9NX38	CI006_HUMAN	hypothetical protein LOC54942						glycine catabolic process	glycine cleavage complex				pancreas(1)	1		Myeloproliferative disorder(63;0.0511)		OV - Ovarian serous cystadenocarcinoma(323;9.58e-07)		GGGTATGTTCCTGTAATTCTG	0.363													6	113	---	---	---	---	PASS
SVEP1	79987	broad.mit.edu	37	9	113241915	113241915	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113241915C>T	uc010mtz.2	-	13	2824	c.2487G>A	c.(2485-2487)ATG>ATA	p.M829I	SVEP1_uc010mua.1_Missense_Mutation_p.M829I|SVEP1_uc004beu.2_Missense_Mutation_p.M829I	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	829					cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						ATTGATGTACCATTTTTCCCA	0.388													56	154	---	---	---	---	PASS
ZFP37	7539	broad.mit.edu	37	9	115806333	115806333	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115806333C>A	uc004bgm.1	-	4	593	c.565G>T	c.(565-567)GAT>TAT	p.D189Y	ZFP37_uc011lwz.1_Missense_Mutation_p.D204Y|ZFP37_uc011lxa.1_Missense_Mutation_p.D190Y	NM_003408	NP_003399	Q9Y6Q3	ZFP37_HUMAN	zinc finger protein 37 homolog	189						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2						TCAGGTAAATCTAAATTCTGT	0.318													34	51	---	---	---	---	PASS
FKBP15	23307	broad.mit.edu	37	9	115956357	115956357	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115956357G>T	uc004bgs.2	-	10	1075	c.957C>A	c.(955-957)CTC>CTA	p.L319L	FKBP15_uc010muu.1_Silent_p.L383L|FKBP15_uc011lxd.1_Silent_p.L251L|FKBP15_uc010mut.1_Silent_p.L187L|FKBP15_uc004bgt.2_Silent_p.L319L	NM_015258	NP_056073	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	319					endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3						GATCAGCAGAGAGGTTGTCAG	0.463													6	81	---	---	---	---	PASS
COL27A1	85301	broad.mit.edu	37	9	116984503	116984503	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116984503G>T	uc011lxl.1	+	14	2422	c.2422G>T	c.(2422-2424)GGA>TGA	p.G808*	COL27A1_uc004bii.2_RNA	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor	808	Pro-rich.|Triple-helical region.|Collagen-like 4.				cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4						CTATCTGCAGGGAGAACTGGG	0.607													5	52	---	---	---	---	PASS
GSN	2934	broad.mit.edu	37	9	124083615	124083615	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124083615G>T	uc004blf.1	+	10	1475	c.1414G>T	c.(1414-1416)GAC>TAC	p.D472Y	GSN_uc004bld.1_Missense_Mutation_p.D421Y|GSN_uc010mvq.1_Missense_Mutation_p.D432Y|GSN_uc010mvr.1_Missense_Mutation_p.D432Y|GSN_uc010mvu.1_Missense_Mutation_p.D421Y|GSN_uc010mvt.1_Missense_Mutation_p.D421Y|GSN_uc010mvs.1_Missense_Mutation_p.D421Y|GSN_uc004ble.1_Missense_Mutation_p.D421Y|GSN_uc010mvv.1_Missense_Mutation_p.D421Y|GSN_uc011lyh.1_Missense_Mutation_p.D438Y|GSN_uc011lyi.1_Missense_Mutation_p.D421Y|GSN_uc011lyj.1_Missense_Mutation_p.D445Y|GSN_uc004blg.1_Missense_Mutation_p.D203Y	NM_000177	NP_000168	P06396	GELS_HUMAN	gelsolin isoform a precursor	472	Actin-binding, Ca-sensitive (Potential).|Gelsolin-like 4.				actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3						CTATGGAGGCGACAGCTACAT	0.547													12	19	---	---	---	---	PASS
DENND1A	57706	broad.mit.edu	37	9	126144461	126144461	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126144461G>A	uc004bnz.1	-	22	2513	c.2280C>T	c.(2278-2280)GGC>GGT	p.G760G	DENND1A_uc011lzl.1_Silent_p.G578G|DENND1A_uc004bny.1_Silent_p.G542G|DENND1A_uc011lzm.1_Silent_p.G771G|DENND1A_uc010mwh.1_Silent_p.G181G	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1	760	Pro-rich.					cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						GTTCAGTGGGGCCTTGGGGGA	0.706													4	4	---	---	---	---	PASS
FAM129B	64855	broad.mit.edu	37	9	130287409	130287409	+	Missense_Mutation	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130287409T>C	uc004brh.2	-	4	551	c.349A>G	c.(349-351)ATC>GTC	p.I117V	FAM129B_uc004bri.2_Missense_Mutation_p.I104V|FAM129B_uc004brj.3_Missense_Mutation_p.I117V	NM_022833	NP_073744	Q96TA1	NIBL1_HUMAN	hypothetical protein LOC64855 isoform 1	117	PH.						protein binding				0						GCACTGTTGATGACGGCTCGT	0.582													8	22	---	---	---	---	PASS
GLE1	2733	broad.mit.edu	37	9	131287581	131287581	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131287581G>C	uc004bvj.2	+	7	1122	c.1008G>C	c.(1006-1008)AAG>AAC	p.K336N	GLE1_uc004bvi.2_Missense_Mutation_p.K336N|GLE1_uc010myd.2_Missense_Mutation_p.K82N	NM_001003722	NP_001003722	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator homolog isoform 1	336	Potential.				poly(A)+ mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear pore	protein binding				0						GCGAAGACAAGAGGAGGCAGG	0.612													18	30	---	---	---	---	PASS
SETX	23064	broad.mit.edu	37	9	135202449	135202449	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135202449C>A	uc004cbk.2	-	10	4719	c.4536G>T	c.(4534-4536)ATG>ATT	p.M1512I	SETX_uc004cbj.2_Missense_Mutation_p.M1131I|SETX_uc010mzt.2_Missense_Mutation_p.M1131I	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	1512					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TGTCATTCTCCATTTGTGAAC	0.368													23	61	---	---	---	---	PASS
TTF1	7270	broad.mit.edu	37	9	135273606	135273606	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135273606G>T	uc004cbl.2	-	4	1751	c.1699C>A	c.(1699-1701)CTG>ATG	p.L567M	TTF1_uc011mcp.1_RNA|TTF1_uc004cbm.2_Missense_Mutation_p.L52M	NM_007344	NP_031370	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase	567					negative regulation of DNA replication|regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription	nucleolus|nucleoplasm	DNA binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		TCCGTGTACAGCAGCTTGTCT	0.378													5	42	---	---	---	---	PASS
C9orf96	169436	broad.mit.edu	37	9	136263095	136263095	+	Intron	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136263095G>T	uc004cdk.2	+						C9orf96_uc004cdl.2_Intron	NM_153710	NP_714921	Q8NE28	SGK71_HUMAN	hypothetical protein LOC169436								ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TCCTGTCCCTGCAGAGGTCAT	0.507													8	13	---	---	---	---	PASS
GTPBP4	23560	broad.mit.edu	37	10	1053023	1053023	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1053023G>T	uc001ift.2	+	10	1139	c.1068G>T	c.(1066-1068)GTG>GTT	p.V356V	GTPBP4_uc010qac.1_Silent_p.V147V|GTPBP4_uc001ifu.2_RNA|GTPBP4_uc010qad.1_Silent_p.V240V|GTPBP4_uc010qae.1_Silent_p.V309V	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG	356					negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		TGAATGAGGTGCTGAATAGAC	0.502													17	53	---	---	---	---	PASS
C10orf140	387640	broad.mit.edu	37	10	21805197	21805197	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21805197C>G	uc009xkd.2	-	4	3808	c.1555G>C	c.(1555-1557)GAG>CAG	p.E519Q	uc001iqp.1_RNA	NM_207371	NP_997254	Q1XH10	DLN1_HUMAN	hypothetical protein LOC387640	438						nucleus	nucleotide binding			ovary(1)	1						AGATTCCACTCCGCCGGCGAC	0.612													14	15	---	---	---	---	PASS
THNSL1	79896	broad.mit.edu	37	10	25312955	25312955	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25312955C>A	uc001isi.3	+	3	1132	c.803C>A	c.(802-804)CCT>CAT	p.P268H	ENKUR_uc001ish.1_Intron	NM_024838	NP_079114	Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1	268					threonine biosynthetic process		ATP binding|pyridoxal phosphate binding|shikimate kinase activity|threonine synthase activity			pancreas(1)	1					L-Threonine(DB00156)|Pyridoxal Phosphate(DB00114)	CTCTTTGTTCCTGCAAAGGAG	0.448													5	43	---	---	---	---	PASS
BMS1	9790	broad.mit.edu	37	10	43288396	43288396	+	Intron	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43288396G>C	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						TTTGGGTTCTGTCTTCCAGGG	0.468													34	70	---	---	---	---	PASS
ZNF239	8187	broad.mit.edu	37	10	44053470	44053470	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44053470C>A	uc001jaw.3	-	2	711	c.58G>T	c.(58-60)GAT>TAT	p.D20Y	ZNF239_uc001jax.3_Missense_Mutation_p.D20Y|ZNF239_uc009xmj.2_Missense_Mutation_p.D20Y|ZNF239_uc009xmk.2_Missense_Mutation_p.D20Y	NM_005674	NP_005665	Q16600	ZN239_HUMAN	zinc finger protein 239	20					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|RNA binding|zinc ion binding				0						GGCTCCCCATCCACTTCCCCT	0.468													10	18	---	---	---	---	PASS
OR13A1	79290	broad.mit.edu	37	10	45799862	45799862	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45799862C>A	uc001jcc.1	-	4	318	c.9G>T	c.(7-9)CTG>CTT	p.L3L	OR13A1_uc001jcd.1_5'UTR	NM_001004297	NP_001004297	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A,	3	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TCTCCATCCACAGCTTCATGT	0.502													12	41	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55616991	55616991	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55616991G>A	uc001jju.1	-	28	4145	c.3750C>T	c.(3748-3750)GTC>GTT	p.V1250V	PCDH15_uc010qhq.1_Silent_p.V1255V|PCDH15_uc010qhr.1_Silent_p.V1250V|PCDH15_uc010qhs.1_Silent_p.V1262V|PCDH15_uc010qht.1_Silent_p.V1257V|PCDH15_uc010qhu.1_Silent_p.V1250V|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Silent_p.V1250V|PCDH15_uc010qhw.1_Silent_p.V1213V|PCDH15_uc010qhx.1_Silent_p.V1179V|PCDH15_uc010qhy.1_Silent_p.V1255V|PCDH15_uc010qhz.1_Silent_p.V1250V|PCDH15_uc010qia.1_Silent_p.V1228V|PCDH15_uc010qib.1_Silent_p.V1228V	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1250	Cadherin 11.|Extracellular (Potential).				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)				TGGAAACAATGACTTGCATAT	0.328										HNSCC(58;0.16)			14	65	---	---	---	---	PASS
FAM13C	220965	broad.mit.edu	37	10	61029736	61029736	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61029736G>T	uc001jkn.2	-	8	860	c.726C>A	c.(724-726)TCC>TCA	p.S242S	FAM13C_uc001jko.2_Silent_p.S242S|FAM13C_uc010qid.1_Silent_p.S159S|FAM13C_uc010qie.1_Silent_p.S159S|FAM13C_uc010qif.1_Silent_p.S264S|FAM13C_uc001jkp.2_Silent_p.S159S	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1	242										ovary(2)	2						GGCTGAAGATGGAGCATCGTG	0.522													4	27	---	---	---	---	PASS
HERC4	26091	broad.mit.edu	37	10	69804216	69804216	+	Missense_Mutation	SNP	C	G	G	rs148764489		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69804216C>G	uc001jng.3	-	4	642	c.331G>C	c.(331-333)GAT>CAT	p.D111H	HERC4_uc001jnf.3_RNA|HERC4_uc001jnh.3_Missense_Mutation_p.D111H|HERC4_uc009xpr.2_Missense_Mutation_p.D111H|HERC4_uc001jni.3_Intron|HERC4_uc001jnj.2_Missense_Mutation_p.D111H	NM_022079	NP_071362	Q5GLZ8	HERC4_HUMAN	hect domain and RLD 4 isoform a	111	RCC1 3.				cell differentiation|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	cytosol	ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3						CCATCAGAATCGAGACCCCAA	0.458													8	44	---	---	---	---	PASS
HK1	3098	broad.mit.edu	37	10	71129353	71129353	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71129353G>T	uc001jpl.3	+	7	949	c.848G>T	c.(847-849)CGG>CTG	p.R283L	HK1_uc001jpg.3_Missense_Mutation_p.R271L|HK1_uc001jph.3_Missense_Mutation_p.R287L|HK1_uc001jpi.3_Missense_Mutation_p.R287L|HK1_uc001jpj.3_Missense_Mutation_p.R318L|HK1_uc001jpk.3_Missense_Mutation_p.R282L|HK1_uc009xqd.2_Missense_Mutation_p.R161L	NM_000188	NP_000179	P19367	HXK1_HUMAN	hexokinase 1 isoform HKI	283	Regulatory.				glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1						GAGATAGACCGGGGATCCCTC	0.483													4	20	---	---	---	---	PASS
TACR2	6865	broad.mit.edu	37	10	71175996	71175996	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71175996C>A	uc001jpn.2	-	1	679	c.84G>T	c.(82-84)ATG>ATT	p.M28I		NM_001057	NP_001048	P21452	NK2R_HUMAN	tachykinin receptor 2	28	Extracellular (Potential).				excretion|muscle contraction	integral to plasma membrane	tachykinin receptor activity			prostate(1)	1					Clonidine(DB00575)|Octreotide(DB00104)	GCCAGCTGGGCATGGAGAAGG	0.597													14	34	---	---	---	---	PASS
SGPL1	8879	broad.mit.edu	37	10	72604314	72604314	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72604314G>C	uc001jrm.2	+	3	334	c.112G>C	c.(112-114)GAG>CAG	p.E38Q		NM_003901	NP_003892	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	38	Lumenal (Potential).				apoptosis|carboxylic acid metabolic process|ceramide metabolic process|sphingolipid catabolic process	integral to endoplasmic reticulum membrane	carboxy-lyase activity|pyridoxal phosphate binding|sphinganine-1-phosphate aldolase activity				0					Pyridoxal Phosphate(DB00114)	CACCAAGTATGAGCCCTGGCA	0.448													11	22	---	---	---	---	PASS
SFTPA2	729238	broad.mit.edu	37	10	81317816	81317816	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81317816G>T	uc001kal.3	-	5	459	c.362C>A	c.(361-363)ACA>AAA	p.T121K	SFTPA2_uc001kan.3_Missense_Mutation_p.T121K	NM_006926	NP_008857	Q8IWL1	SFPA2_HUMAN	RecName: Full=Pulmonary surfactant-associated protein A2;          Short=SP-A2;          Short=SP-A;          Short=PSP-A;          Short=PSPA; AltName: Full=Alveolar proteinosis protein; AltName: Full=35 kDa pulmonary surfactant-associated protein; Flags: Precursor;	121					cell junction assembly|respiratory gaseous exchange	collagen|extracellular space	sugar binding				0	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			ACCTCCCCTTGTCTGCAGGAT	0.547									Pulmonary_Fibrosis_Idiopathic				13	104	---	---	---	---	PASS
LRIT1	26103	broad.mit.edu	37	10	85992387	85992387	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85992387C>T	uc001kcz.1	-	4	1190	c.1168G>A	c.(1168-1170)GCT>ACT	p.A390T		NM_015613	NP_056428	Q9P2V4	LRIT1_HUMAN	retina specific protein PAL	390	Lumenal (Potential).					integral to endoplasmic reticulum membrane					0						GCCAGGACAGCGGGTTTGGGA	0.622													7	4	---	---	---	---	PASS
TNKS2	80351	broad.mit.edu	37	10	93588172	93588172	+	Intron	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93588172T>A	uc001khp.2	+							NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related						positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)				TGGTAATGTTTCAGATTTAAG	0.313													10	23	---	---	---	---	PASS
PLCE1	51196	broad.mit.edu	37	10	96005734	96005734	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96005734A>G	uc001kjk.2	+	8	3086	c.2452A>G	c.(2452-2454)AAT>GAT	p.N818D	PLCE1_uc010qnx.1_Missense_Mutation_p.N818D|PLCE1_uc001kjm.2_Missense_Mutation_p.N510D	NM_016341	NP_057425	Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1 isoform 1	818					activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)				GGATTCAGACAATGACATCTT	0.413													23	37	---	---	---	---	PASS
CYP2C19	1557	broad.mit.edu	37	10	96609752	96609752	+	Missense_Mutation	SNP	C	T	T	rs17879685	byFrequency	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96609752C>T	uc010qnz.1	+	8	1228	c.1228C>T	c.(1228-1230)CGT>TGT	p.R410C	CYP2C19_uc010qny.1_Missense_Mutation_p.R388C	NM_000769	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C,	410					exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding|steroid hydroxylase activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Adinazolam(DB00546)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Arformoterol(DB01274)|Bortezomib(DB00188)|Carisoprodol(DB00395)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Desipramine(DB01151)|Desloratadine(DB00967)|Diclofenac(DB00586)|Diltiazem(DB00343)|Efavirenz(DB00625)|Esomeprazole(DB00736)|Famotidine(DB00927)|Felbamate(DB00949)|Finasteride(DB01216)|Flunitrazepam(DB01544)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Guanfacine(DB01018)|Imipramine(DB00458)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Loratadine(DB00455)|Melatonin(DB01065)|Mephenytoin(DB00532)|Methadone(DB00333)|Methylphenobarbital(DB00849)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nilutamide(DB00665)|Norgestrel(DB00506)|Omeprazole(DB00338)|Oxcarbazepine(DB00776)|Pantoprazole(DB00213)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Quinidine(DB00908)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ritonavir(DB00503)|Selegiline(DB01037)|Sertraline(DB01104)|Temazepam(DB00231)|Teniposide(DB00444)|Terfenadine(DB00342)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tolbutamide(DB01124)|Topiramate(DB00273)|Tranylcypromine(DB00752)|Troglitazone(DB00197)|Troleandomycin(DB01361)|Voriconazole(DB00582)	GTTTGACCCTCGTCACTTTCT	0.393													28	101	---	---	---	---	PASS
TCTN3	26123	broad.mit.edu	37	10	97440243	97440243	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97440243A>T	uc001klb.3	-	13	1820	c.1576T>A	c.(1576-1578)TGC>AGC	p.C526S	TCTN3_uc001kla.3_Missense_Mutation_p.C370S|TCTN3_uc010qoi.1_Missense_Mutation_p.C378S	NM_015631	NP_056446	Q6NUS6	TECT3_HUMAN	tectonic 3 isoform a precursor	526	Extracellular (Potential).				apoptosis	integral to membrane					0		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		ATAGACTGGCACTGGTATAGG	0.423													48	143	---	---	---	---	PASS
ABCC2	1244	broad.mit.edu	37	10	101603605	101603605	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101603605C>T	uc001kqf.2	+	27	3930	c.3791C>T	c.(3790-3792)ACC>ATC	p.T1264I		NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),	1264	ABC transmembrane type-1 2.|Cytoplasmic (By similarity).					apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	GAAATAGAGACCAACATTGTG	0.418													112	199	---	---	---	---	PASS
FAM178A	55719	broad.mit.edu	37	10	102676494	102676494	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102676494G>T	uc001krt.3	+	3	894	c.352G>T	c.(352-354)GGT>TGT	p.G118C	FAM178A_uc001krr.1_Missense_Mutation_p.G118C|FAM178A_uc001krs.2_Missense_Mutation_p.G118C|FAM178A_uc001kru.1_Missense_Mutation_p.G54C	NM_018121	NP_060591	Q8IX21	F178A_HUMAN	hypothetical protein LOC55719 isoform 1	118											0						TTTCATGAAAGGTGTTAAAGA	0.413													5	52	---	---	---	---	PASS
CCDC147	159686	broad.mit.edu	37	10	106160462	106160462	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106160462G>C	uc001kyh.2	+	13	1974	c.1840G>C	c.(1840-1842)GGG>CGG	p.G614R		NM_001008723	NP_001008723	Q5T655	CC147_HUMAN	coiled-coil domain containing 147	614										ovary(2)|central_nervous_system(2)|skin(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		AGATATCCTGGGGTCTCAGCT	0.478													22	39	---	---	---	---	PASS
PNLIP	5406	broad.mit.edu	37	10	118315626	118315626	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118315626C>A	uc001lcm.2	+	9	969	c.926C>A	c.(925-927)ACT>AAT	p.T309N		NM_000936	NP_000927	P16233	LIPP_HUMAN	pancreatic lipase precursor	309					lipid catabolic process|retinoid metabolic process|steroid metabolic process	extracellular region	retinyl-palmitate esterase activity|triglyceride lipase activity			ovary(1)|central_nervous_system(1)|skin(1)	3				all cancers(201;0.0131)	Bentiromide(DB00522)|Orlistat(DB01083)	AACGTCTTCACTGCAGTAAGT	0.428													20	64	---	---	---	---	PASS
PDZD8	118987	broad.mit.edu	37	10	119043185	119043185	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119043185C>A	uc001lde.1	-	5	3258	c.3059G>T	c.(3058-3060)GGT>GTT	p.G1020V		NM_173791	NP_776152	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	1020					intracellular signal transduction		metal ion binding				0		Colorectal(252;0.19)		all cancers(201;0.0121)		CAGATCACGACCAATTTCTTT	0.428													25	69	---	---	---	---	PASS
FAM24A	118670	broad.mit.edu	37	10	124671179	124671179	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124671179A>G	uc001lgv.2	+	2	150	c.29A>G	c.(28-30)AAG>AGG	p.K10R		NM_001029888	NP_001025059	A6NFZ4	FA24A_HUMAN	family with sequence similarity 24, member A	10						extracellular region				ovary(2)	2		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.124)|COAD - Colon adenocarcinoma(40;0.141)		CTCAGGACGAAGATCATGATC	0.488													42	117	---	---	---	---	PASS
BCCIP	56647	broad.mit.edu	37	10	127529887	127529887	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127529887A>G	uc001ljd.3	+	7	861	c.838A>G	c.(838-840)ATA>GTA	p.I280V	DHX32_uc001lje.1_Intron|DHX32_uc001ljf.1_Intron|DHX32_uc001ljg.1_Intron|BCCIP_uc010qui.1_Missense_Mutation_p.I278V|BCCIP_uc001ljc.3_Missense_Mutation_p.I280V|BCCIP_uc010quj.1_Missense_Mutation_p.I250V	NM_016567	NP_057651	Q9P287	BCCIP_HUMAN	BRCA2 and CDKN1A-interacting protein isoform	Error:Variant_position_missing_in_Q9P287_after_alignment					cell cycle|DNA repair|neuroendocrine cell differentiation|regulation of cyclin-dependent protein kinase activity	nuclear cyclin-dependent protein kinase holoenzyme complex	kinase regulator activity|protein binding			ovary(1)|breast(1)	2		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				ACCAGTTCCGATACAGCACAA	0.428													7	27	---	---	---	---	PASS
MKI67	4288	broad.mit.edu	37	10	129907439	129907439	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129907439C>T	uc001lke.2	-	13	2860	c.2665G>A	c.(2665-2667)GTG>ATG	p.V889M	MKI67_uc001lkf.2_Missense_Mutation_p.V529M|MKI67_uc009yav.1_Missense_Mutation_p.V464M|MKI67_uc009yaw.1_Missense_Mutation_p.V39M	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	889					cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTACTTTCCACAGGTAGCTTC	0.403													19	73	---	---	---	---	PASS
TUBGCP2	10844	broad.mit.edu	37	10	135106682	135106682	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135106682G>T	uc001lmg.1	-	7	1242	c.885C>A	c.(883-885)GCC>GCA	p.A295A	TUBGCP2_uc001lmf.1_5'Flank|TUBGCP2_uc010qvc.1_Silent_p.A323A|TUBGCP2_uc009ybk.1_Silent_p.A295A|TUBGCP2_uc010qvd.1_Silent_p.A165A|TUBGCP2_uc001lmh.1_RNA	NM_006659	NP_006650	Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	295					G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		GGGTGCGCATGGCGGCCGCCA	0.567													4	14	---	---	---	---	PASS
FRG2B	441581	broad.mit.edu	37	10	135440117	135440117	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135440117C>A	uc010qvg.1	-	1	183	c.130G>T	c.(130-132)GGC>TGC	p.G44C		NM_001080998	NP_001074467	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	44						nucleus					0		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		GCGGTCTTGCCTTTTTCTTTG	0.517													8	47	---	---	---	---	PASS
OR51G2	81282	broad.mit.edu	37	11	4936671	4936671	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4936671C>A	uc001lzr.1	-	1	223	c.223G>T	c.(223-225)GAC>TAC	p.D75Y		NM_001005238	NP_001005238	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G,	75	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		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)		AGACCCAGGTCAATCAGAGCC	0.478													22	19	---	---	---	---	PASS
OR56A3	390083	broad.mit.edu	37	11	5969056	5969056	+	Silent	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5969056T>A	uc010qzt.1	+	1	480	c.480T>A	c.(478-480)ACT>ACA	p.T160T		NM_001003443	NP_001003443	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A,	160	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCTTATGACTCTGCCCATCC	0.448													24	33	---	---	---	---	PASS
OR56B4	196335	broad.mit.edu	37	11	6129644	6129644	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6129644G>T	uc010qzx.1	+	1	636	c.636G>T	c.(634-636)TTG>TTT	p.L212F		NM_001005181	NP_001005181	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B,	212	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATGGGTCTTGGTTGGGAGTG	0.473													7	105	---	---	---	---	PASS
DCHS1	8642	broad.mit.edu	37	11	6651379	6651379	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6651379G>A	uc001mem.1	-	10	5056	c.4646C>T	c.(4645-4647)CCG>CTG	p.P1549L		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	1549	Cadherin 15.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACGCGTGACGGCGAGGCGAA	0.716													4	5	---	---	---	---	PASS
C11orf41	25758	broad.mit.edu	37	11	33689492	33689492	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33689492G>A	uc001mup.3	+	20	5484	c.5360G>A	c.(5359-5361)CGT>CAT	p.R1787H		NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	1781						integral to membrane				ovary(2)	2						AGGCTTCCTCGTCAGTACAGC	0.682													11	21	---	---	---	---	PASS
NUP160	23279	broad.mit.edu	37	11	47843340	47843340	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47843340C>A	uc001ngm.2	-	9	1298	c.1213G>T	c.(1213-1215)GAT>TAT	p.D405Y	NUP160_uc009ylw.2_RNA	NM_015231	NP_056046	Q12769	NU160_HUMAN	nucleoporin 160kDa	405					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7						GCCCAGATATCCGTGGAAGTT	0.418													7	44	---	---	---	---	PASS
PTPRJ	5795	broad.mit.edu	37	11	48146592	48146592	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48146592C>T	uc001ngp.3	+	6	1302	c.947C>T	c.(946-948)CCT>CTT	p.P316L	PTPRJ_uc001ngo.3_Missense_Mutation_p.P316L	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	316	Extracellular (Potential).|Fibronectin type-III 3.				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						CTCGTGGGACCTGTGGACCCA	0.587													21	43	---	---	---	---	PASS
OR4X1	390113	broad.mit.edu	37	11	48285947	48285947	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48285947G>A	uc010rht.1	+	1	535	c.535G>A	c.(535-537)GTC>ATC	p.V179I		NM_001004726	NP_001004726	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X,	179	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3						CTTCTGTGATGTCCACCCAGT	0.562													14	16	---	---	---	---	PASS
OR4A15	81328	broad.mit.edu	37	11	55135842	55135842	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55135842G>A	uc010rif.1	+	1	483	c.483G>A	c.(481-483)TTG>TTA	p.L161L		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	161	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						TTCATGAATTGATCACCATGA	0.418													47	131	---	---	---	---	PASS
OR4S2	219431	broad.mit.edu	37	11	55418457	55418457	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55418457T>G	uc001nhs.1	+	1	78	c.78T>G	c.(76-78)TTT>TTG	p.F26L		NM_001004059	NP_001004059	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S,	26	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.0748)				AAGTTTGTTTTGTGGTGTTTT	0.388													7	50	---	---	---	---	PASS
OR5D13	390142	broad.mit.edu	37	11	55541730	55541730	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55541730G>A	uc010ril.1	+	1	817	c.817G>A	c.(817-819)GTT>ATT	p.V273I		NM_001001967	NP_001001967	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D,	273	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3		all_epithelial(135;0.196)				TAGCCTCATAGTTACAGTGGC	0.408													22	48	---	---	---	---	PASS
OR8H3	390152	broad.mit.edu	37	11	55890051	55890051	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55890051C>A	uc001nii.1	+	1	203	c.203C>A	c.(202-204)TCA>TAA	p.S68*		NM_001005201	NP_001005201	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H,	68	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00693)					ACTCACCTGTCATTTATTGAC	0.438													8	255	---	---	---	---	PASS
LRRC55	219527	broad.mit.edu	37	11	56954786	56954786	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56954786G>T	uc001njl.1	+	2	1005	c.858G>T	c.(856-858)GAG>GAT	p.E286D	LRRC55_uc001njm.1_5'Flank	NM_001005210	NP_001005210	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	256	LRRCT.					integral to membrane					0						CACTCACTGAGGAGAGCTTCA	0.587													11	47	---	---	---	---	PASS
P2RX3	5024	broad.mit.edu	37	11	57135888	57135888	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57135888C>A	uc001nju.2	+	10	1056	c.980C>A	c.(979-981)GCG>GAG	p.A327E		NM_002559	NP_002550	P56373	P2RX3_HUMAN	purinergic receptor P2X3	327	Helical; Name=2; (Potential).				positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0						AGCTCTGTGGCGGCCTTTACT	0.622													18	78	---	---	---	---	PASS
CPSF7	79869	broad.mit.edu	37	11	61183967	61183967	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61183967C>A	uc001nrq.2	-	6	709	c.575G>T	c.(574-576)CGA>CTA	p.R192L	CPSF7_uc001nro.2_Missense_Mutation_p.R183L|CPSF7_uc001nrp.2_Missense_Mutation_p.R235L|CPSF7_uc001nrr.2_Missense_Mutation_p.R183L|CPSF7_uc001nrs.1_Missense_Mutation_p.R93L	NM_001136040	NP_001129512	Q8N684	CPSF7_HUMAN	pre-mRNA cleavage factor I, 59 kDa subunit	192					mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	mRNA cleavage factor complex	nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1						ACTAGAATCTCGGGAATGGGC	0.522													5	87	---	---	---	---	PASS
SYT7	9066	broad.mit.edu	37	11	61323677	61323677	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61323677C>G	uc001nrv.2	-	2	40	c.34G>C	c.(34-36)GCG>CCG	p.A12P	SYT7_uc009ynr.2_Missense_Mutation_p.A12P|SYT7_uc001nrx.1_RNA	NM_004200	NP_004191	O43581	SYT7_HUMAN	synaptotagmin VII	12	Vesicular (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			ovary(3)|pancreas(1)	4						CGCGAGGGCGCCCCTGGGGAG	0.652													4	9	---	---	---	---	PASS
FLRT1	23769	broad.mit.edu	37	11	63885079	63885079	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63885079C>T	uc001nyi.1	+	2	1681	c.1340C>T	c.(1339-1341)ACG>ATG	p.T447M	MACROD1_uc001nyh.2_Intron	NM_013280	NP_037412	Q9NZU1	FLRT1_HUMAN	fibronectin leucine rich transmembrane protein	419	Fibronectin type-III.|Extracellular (Potential).				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity				0						AAGGCCCTGACGGCAGACTCC	0.672													5	9	---	---	---	---	PASS
PLCB3	5331	broad.mit.edu	37	11	64027528	64027528	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64027528G>T	uc001nzb.2	+	14	1553	c.1553G>T	c.(1552-1554)GGC>GTC	p.G518V	PLCB3_uc009ypg.1_Missense_Mutation_p.G518V|PLCB3_uc009yph.1_Missense_Mutation_p.G451V|PLCB3_uc009ypi.2_Missense_Mutation_p.G518V	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	518					intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2						AGCTGCCCAGGCCTGAGCAAT	0.617													8	5	---	---	---	---	PASS
PPFIA1	8500	broad.mit.edu	37	11	70170596	70170596	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70170596G>T	uc001opo.2	+	3	551	c.353G>T	c.(352-354)AGG>ATG	p.R118M	PPFIA1_uc001opn.1_Missense_Mutation_p.R118M|PPFIA1_uc001opp.2_RNA|PPFIA1_uc001opq.1_5'Flank	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b	118	Potential.				cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			AAAGCAGAAAGGAATAACACC	0.493													16	686	---	---	---	---	PASS
PPFIA1	8500	broad.mit.edu	37	11	70172786	70172786	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70172786G>T	uc001opo.2	+	7	990	c.792G>T	c.(790-792)AGG>AGT	p.R264S	PPFIA1_uc001opn.1_Missense_Mutation_p.R264S|PPFIA1_uc001opp.2_RNA|PPFIA1_uc001opq.1_RNA	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b	264	Potential.				cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			AGCAGTCAAGGGAACAGAGCC	0.438													17	897	---	---	---	---	PASS
P4HA3	283208	broad.mit.edu	37	11	73978304	73978304	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73978304G>T	uc001ouz.2	-	13	1667	c.1624C>A	c.(1624-1626)CCT>ACT	p.P542T	P4HA3_uc001ouy.3_RNA|P4HA3_uc010rrj.1_Silent_p.A539A	NM_182904	NP_878907	Q7Z4N8	P4HA3_HUMAN	prolyl 4-hydroxylase, alpha III subunit	542						endoplasmic reticulum lumen	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity			skin(1)	1	Breast(11;2.31e-05)					CAGTCTTCAGGGCTGGAGCTG	0.557													9	13	---	---	---	---	PASS
C11orf30	56946	broad.mit.edu	37	11	76207466	76207466	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76207466C>A	uc001oxl.2	+	9	1459	c.1316C>A	c.(1315-1317)CCT>CAT	p.P439H	C11orf30_uc009yuj.1_Missense_Mutation_p.P454H|C11orf30_uc010rsa.1_Missense_Mutation_p.P389H|C11orf30_uc001oxm.2_Intron|C11orf30_uc010rsb.1_Missense_Mutation_p.P454H|C11orf30_uc010rsc.1_Missense_Mutation_p.P454H|C11orf30_uc001oxn.2_Missense_Mutation_p.P440H|C11orf30_uc010rsd.1_Missense_Mutation_p.P453H	NM_020193	NP_064578	Q7Z589	EMSY_HUMAN	EMSY protein	439	Interaction with BRCA2.|Gln-rich.				chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6						CAGCAGTCTCCTTTGCCACCT	0.428													6	72	---	---	---	---	PASS
INTS4	92105	broad.mit.edu	37	11	77705659	77705659	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77705659C>A	uc001oys.2	-	1	59	c.31G>T	c.(31-33)GAG>TAG	p.E11*	INTS4_uc001oyt.2_RNA|INTS4_uc001oyu.1_Nonsense_Mutation_p.E11*|INTS4_uc001oyv.1_RNA	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4	11					snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			GTGAATTCCTCATAAACCCGC	0.572													4	23	---	---	---	---	PASS
SYTL2	54843	broad.mit.edu	37	11	85435813	85435813	+	Intron	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85435813C>A	uc010rth.1	-						SYTL2_uc010rtg.1_Intron|SYTL2_uc010rti.1_Intron|SYTL2_uc010rtj.1_Intron|SYTL2_uc009yvj.2_RNA|SYTL2_uc001pbd.2_Missense_Mutation_p.G563C|SYTL2_uc001pbb.2_Missense_Mutation_p.G563C|SYTL2_uc001pbc.2_Missense_Mutation_p.G563C|SYTL2_uc010rtf.1_Intron	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g						intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TCTGTACTACCTATTAACTTT	0.428													4	23	---	---	---	---	PASS
SLC36A4	120103	broad.mit.edu	37	11	92881960	92881960	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92881960C>A	uc001pdn.2	-	11	1355	c.1258G>T	c.(1258-1260)GGA>TGA	p.G420*	uc001pdl.1_5'Flank|SLC36A4_uc001pdm.2_Nonsense_Mutation_p.G285*	NM_152313	NP_689526	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid	420	Helical; (Potential).				L-alanine transport|proline transport|tryptophan transport	integral to membrane	symporter activity			ovary(2)|upper_aerodigestive_tract(1)	3		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CTCACAGCTCCAACGAAGGAA	0.353													5	58	---	---	---	---	PASS
KDM4D	55693	broad.mit.edu	37	11	94731244	94731244	+	Silent	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94731244G>C	uc001pfe.2	+	3	1540	c.708G>C	c.(706-708)CGG>CGC	p.R236R		NM_018039	NP_060509	Q6B0I6	KDM4D_HUMAN	jumonji domain containing 2D	236	JmjC.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						GCAGTTCCCGGGGTTGTGGGG	0.602													13	16	---	---	---	---	PASS
SESN3	143686	broad.mit.edu	37	11	94922999	94922999	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94922999C>T	uc001pfk.1	-	4	691	c.469G>A	c.(469-471)GAA>AAA	p.E157K	SESN3_uc010rug.1_Intron|SESN3_uc001pfl.2_Missense_Mutation_p.E157K	NM_144665	NP_653266	P58005	SESN3_HUMAN	sestrin 3	157					cell cycle arrest	nucleus					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.234)		TTATTAATTTCATTAAGATTT	0.353													11	21	---	---	---	---	PASS
KIAA1377	57562	broad.mit.edu	37	11	101815132	101815132	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101815132A>T	uc001pgm.2	+	3	655	c.385A>T	c.(385-387)AGG>TGG	p.R129W	KIAA1377_uc001pgn.2_Missense_Mutation_p.R85W|KIAA1377_uc009yxa.1_5'UTR	NM_020802	NP_065853	Q9P2H0	K1377_HUMAN	hypothetical protein LOC57562	129							protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		TTCACAGCGGAGGAAAGCAGG	0.343													15	11	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108175517	108175517	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108175517C>T	uc001pkb.1	+	37	5997	c.5612C>T	c.(5611-5613)ACC>ATC	p.T1871I	ATM_uc009yxr.1_Missense_Mutation_p.T1871I|ATM_uc001pke.1_Missense_Mutation_p.T523I|ATM_uc001pkg.1_Missense_Mutation_p.T228I|ATM_uc009yxt.1_Silent_p.H14H	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	1871					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		GGATTTTTCACCAGCTGTCTT	0.373			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			12	14	---	---	---	---	PASS
DSCAML1	57453	broad.mit.edu	37	11	117310040	117310040	+	Silent	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117310040C>G	uc001prh.1	-	23	4268	c.4266G>C	c.(4264-4266)ACG>ACC	p.T1422T		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1362	Extracellular (Potential).|Ig-like C2-type 10.				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)		TGGCCGTGCACGTGTAGTAGC	0.597													10	30	---	---	---	---	PASS
HINFP	25988	broad.mit.edu	37	11	119001518	119001518	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119001518C>A	uc001pvp.2	+	4	454	c.265C>A	c.(265-267)CAC>AAC	p.H89N	HINFP_uc010rzb.1_Missense_Mutation_p.H89N|HINFP_uc001pvq.2_Missense_Mutation_p.H89N|HINFP_uc001pvr.2_5'Flank	NM_015517	NP_056332	Q9BQA5	HINFP_HUMAN	MBD2 (methyl-CpG-binding protein)-interacting	89					DNA damage checkpoint|DNA repair|establishment of protein localization|in utero embryonic development|myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	enzyme binding|histone binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4						TGTCTACTTCCACTGCTACCA	0.542													5	56	---	---	---	---	PASS
GRAMD1B	57476	broad.mit.edu	37	11	123464819	123464819	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123464819T>A	uc001pyx.2	+	4	614	c.285T>A	c.(283-285)AAT>AAA	p.N95K	GRAMD1B_uc001pyw.2_Missense_Mutation_p.N102K|GRAMD1B_uc010rzw.1_Missense_Mutation_p.N55K|GRAMD1B_uc010rzx.1_Missense_Mutation_p.N55K|GRAMD1B_uc009zbe.1_Missense_Mutation_p.N91K	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	95						integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		AGCAGAGAAATGAAGACTTCA	0.527													22	24	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	124135591	124135591	+	IGR	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124135591C>A								OR8G2 (39281 upstream) : OR8D1 (44146 downstream)																							TTTGGGTCTGCAGCATTCATG	0.522													55	31	---	---	---	---	PASS
FAM118B	79607	broad.mit.edu	37	11	126126696	126126696	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126126696C>A	uc001qdf.2	+	7	1114	c.931C>A	c.(931-933)CCA>ACA	p.P311T	FAM118B_uc009zca.2_Missense_Mutation_p.P315T|FAM118B_uc001qdg.2_Missense_Mutation_p.P311T	NM_024556	NP_078832	Q9BPY3	F118B_HUMAN	hypothetical protein LOC79607	311											0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		TGCCGATCTTCCAGAATATTT	0.448													103	108	---	---	---	---	PASS
RAD52	5893	broad.mit.edu	37	12	1039000	1039000	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1039000C>A	uc001qis.1	-	5	447	c.333G>T	c.(331-333)GTG>GTT	p.V111V	RAD52_uc001qit.1_RNA|RAD52_uc010sdt.1_Silent_p.V34V|RAD52_uc001qiu.1_Silent_p.V111V|RAD52_uc001qiv.1_RNA|RAD52_uc001qiw.1_Intron|RAD52_uc010sdu.1_Silent_p.V111V|RAD52_uc001qix.1_Silent_p.V111V	NM_134424	NP_602296	P43351	RAD52_HUMAN	RAD52 homolog	111					DNA recombinase assembly|mitotic recombination|reciprocal meiotic recombination	nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)			GCTGGACCCTCACAAATGCAC	0.542								Homologous_recombination					8	253	---	---	---	---	PASS
DCP1B	196513	broad.mit.edu	37	12	2058392	2058392	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2058392G>A	uc001qjx.1	-	8	1713	c.1633C>T	c.(1633-1635)CTC>TTC	p.L545F	DCP1B_uc010sdy.1_Missense_Mutation_p.L443F	NM_152640	NP_689853	Q8IZD4	DCP1B_HUMAN	decapping enzyme Dcp1b	545					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	hydrolase activity|protein binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			ACAGGCAAGAGGCCGCTCTCC	0.647													6	15	---	---	---	---	PASS
PRMT8	56341	broad.mit.edu	37	12	3692386	3692386	+	Intron	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3692386G>A	uc001qmf.2	+						PRMT8_uc009zed.2_Intron|PRMT8_uc001qmg.2_Intron	NM_019854	NP_062828	Q9NR22	ANM8_HUMAN	HMT1 hnRNP methyltransferase-like 4						regulation of protein binding	cytoplasm|plasma membrane	histone-arginine N-methyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity			ovary(3)|central_nervous_system(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			TGAGCTGTTTGTTGCTTCCCA	0.522													4	11	---	---	---	---	PASS
NANOG	79923	broad.mit.edu	37	12	7942325	7942325	+	Nonsense_Mutation	SNP	C	T	T	rs140243232	byFrequency	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7942325C>T	uc009zfy.1	+	1	331	c.115C>T	c.(115-117)CAA>TAA	p.Q39*		NM_024865	NP_079141	Q9H9S0	NANOG_HUMAN	Nanog homeobox	39					cell proliferation|embryo development|somatic stem cell maintenance	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				Kidney(36;0.0872)		TCCATCCTTGCAAATGTCTTC	0.453													19	114	---	---	---	---	PASS
SLC2A3	6515	broad.mit.edu	37	12	8082312	8082312	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8082312G>T	uc001qtr.2	-	6	1091	c.829C>A	c.(829-831)CAG>AAG	p.Q277K	SLC2A3_uc001qts.2_3'UTR	NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose	277	Defines substrate specificity (By similarity).|Helical; Name=7; (Potential).				carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		TGAGAGAGCTGGAGCACAATG	0.413													4	28	---	---	---	---	PASS
DUSP16	80824	broad.mit.edu	37	12	12630882	12630882	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12630882C>T	uc001rao.1	-	7	1515	c.883G>A	c.(883-885)GAG>AAG	p.E295K	DUSP16_uc001ram.1_5'Flank|DUSP16_uc001ran.1_Missense_Mutation_p.E147K	NM_030640	NP_085143	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	295					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)		ATCTTCTTCTCATAGTCCAGG	0.438													26	99	---	---	---	---	PASS
PDE6H	5149	broad.mit.edu	37	12	15132142	15132142	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15132142G>T	uc001rcr.2	+	3	248	c.164G>T	c.(163-165)GGG>GTG	p.G55V		NM_006205	NP_006196	Q13956	CNCG_HUMAN	phosphodiesterase 6H	55					visual perception		3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|enzyme inhibitor activity			ovary(1)|skin(1)	2						GGAATGGAGGGGCTAGGAACA	0.413													10	21	---	---	---	---	PASS
STRAP	11171	broad.mit.edu	37	12	16047010	16047010	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16047010G>T	uc001rdc.3	+	5	787	c.433G>T	c.(433-435)GGT>TGT	p.G145C	STRAP_uc010shw.1_Missense_Mutation_p.G158C|STRAP_uc001rdd.3_Missense_Mutation_p.G51C	NM_007178	NP_009109	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated	145	WD 4.				mRNA processing|RNA splicing	cell junction|mitochondrion|spliceosomal complex	identical protein binding			skin(1)	1		Hepatocellular(102;0.121)				TCATACTTCTGGTATAAAAAA	0.279													5	86	---	---	---	---	PASS
PLEKHA5	54477	broad.mit.edu	37	12	19413942	19413942	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19413942C>A	uc001reb.2	+	7	683	c.597C>A	c.(595-597)CTC>CTA	p.L199L	PLEKHA5_uc010sie.1_Silent_p.L199L|PLEKHA5_uc001rea.2_Silent_p.L199L|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Silent_p.L91L|PLEKHA5_uc010sig.1_Silent_p.L91L|PLEKHA5_uc010sih.1_Silent_p.L91L	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A	199	PH.						1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					ACCTTTGCCTCTTTTATTATA	0.303													7	192	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32138194	32138194	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32138194G>T	uc001rks.2	+	4	4719	c.4305G>T	c.(4303-4305)GCG>GCT	p.A1435A	C12orf35_uc001rkt.2_5'Flank	NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	1435										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			ACACGAAAGCGAGTTCATCTA	0.353													5	120	---	---	---	---	PASS
LRRK2	120892	broad.mit.edu	37	12	40692163	40692163	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40692163C>A	uc001rmg.3	+	24	3336	c.3215C>A	c.(3214-3216)CCC>CAC	p.P1072H	LRRK2_uc001rmh.1_Missense_Mutation_p.P694H|LRRK2_uc009zjw.2_5'UTR	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1072	LRR 4.				activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GACATTGGACCCTCAGTGGTT	0.368													9	45	---	---	---	---	PASS
TMEM117	84216	broad.mit.edu	37	12	44338016	44338016	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44338016A>T	uc001rod.2	+	3	347	c.281A>T	c.(280-282)CAG>CTG	p.Q94L	TMEM117_uc001roe.2_Silent_p.S23S|TMEM117_uc009zkc.2_Missense_Mutation_p.Q94L	NM_032256	NP_115632	Q9H0C3	TM117_HUMAN	transmembrane protein 117	94						endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)		ATTTCAGGTCAGTTGCTCCGA	0.299													16	21	---	---	---	---	PASS
SFRS2IP	9169	broad.mit.edu	37	12	46320689	46320689	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46320689C>A	uc001rox.2	-	11	3082	c.2795G>T	c.(2794-2796)TGG>TTG	p.W932L	SFRS2IP_uc001row.2_Missense_Mutation_p.W617L|SFRS2IP_uc001roy.1_Missense_Mutation_p.W1006L	NM_004719	NP_004710	Q99590	SCAFB_HUMAN	splicing factor, arginine/serine-rich 2,	932	Arg-rich.				spliceosome assembly	nucleus	protein binding|zinc ion binding				0	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.209)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.1)		GGACCTAGACCACTTTCTGGT	0.453													6	92	---	---	---	---	PASS
SFRS2IP	9169	broad.mit.edu	37	12	46321720	46321720	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46321720G>T	uc001rox.2	-	11	2051	c.1764C>A	c.(1762-1764)TCC>TCA	p.S588S	SFRS2IP_uc001row.2_Silent_p.S273S|SFRS2IP_uc001roy.1_Silent_p.S662S	NM_004719	NP_004710	Q99590	SCAFB_HUMAN	splicing factor, arginine/serine-rich 2,	588					spliceosome assembly	nucleus	protein binding|zinc ion binding				0	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.209)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.1)		TTTCTACTAGGGAACTCTCTG	0.368													6	65	---	---	---	---	PASS
SLC38A2	54407	broad.mit.edu	37	12	46761131	46761131	+	Intron	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46761131G>T	uc001rpg.2	-						SLC38A2_uc010sli.1_5'Flank|SLC38A2_uc001rph.2_Intron	NM_018976	NP_061849	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2						cellular nitrogen compound metabolic process|glutamate secretion|neurotransmitter secretion|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			urinary_tract(1)|skin(1)	2	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		ATTCTGGTGAGAGAAGGAAAA	0.348													6	118	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49442950	49442950	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49442950C>A	uc001rta.3	-	12	3958	c.3958G>T	c.(3958-3960)GGA>TGA	p.G1320*		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1320	Arg-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						CCACGTCCTCCATGGGCTCCT	0.572			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			8	7	---	---	---	---	PASS
ESPL1	9700	broad.mit.edu	37	12	53662832	53662832	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53662832G>T	uc001sck.2	+	3	197	c.106G>T	c.(106-108)GGT>TGT	p.G36C	ESPL1_uc001scj.2_5'UTR	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	36					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						CCCTCCAGCTGGTTTTCCCAG	0.502													4	23	---	---	---	---	PASS
OR6C65	403282	broad.mit.edu	37	12	55794584	55794584	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55794584C>T	uc010spl.1	+	1	272	c.272C>T	c.(271-273)TCC>TTC	p.S91F		NM_001005518	NP_001005518	A6NJZ3	O6C65_HUMAN	olfactory receptor, family 6, subfamily C,	91	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						ACAACCATTTCCTATAATGCT	0.353													21	32	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78444760	78444760	+	Silent	SNP	G	C	C	rs35997153	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78444760G>C	uc001syp.2	+	11	2522	c.2349G>C	c.(2347-2349)ACG>ACC	p.T783T	NAV3_uc001syo.2_Silent_p.T783T|NAV3_uc010sub.1_Silent_p.T283T	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	783						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						TGTATACCACGCCTCTCCGTC	0.552										HNSCC(70;0.22)			5	19	---	---	---	---	PASS
PAWR	5074	broad.mit.edu	37	12	80014853	80014853	+	Intron	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80014853C>A	uc001syx.2	-							NM_002583	NP_002574	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator						actin filament bundle assembly|apoptosis|induction of apoptosis|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	actin binding|enzyme binding|leucine zipper domain binding|transcription corepressor activity				0						TTTAAATACTCACCTGTAGCA	0.363													8	126	---	---	---	---	PASS
PLEKHG7	440107	broad.mit.edu	37	12	93147929	93147929	+	Nonsense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93147929C>T	uc001tcj.2	+	6	609	c.379C>T	c.(379-381)CAG>TAG	p.Q127*		NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G	127	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1						GGCCCCACTACAGAGGCTCAC	0.493													19	30	---	---	---	---	PASS
SLC17A8	246213	broad.mit.edu	37	12	100806558	100806558	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100806558G>T	uc010svi.1	+	10	1510	c.1197G>T	c.(1195-1197)ATG>ATT	p.M399I	SLC17A8_uc009ztx.2_Missense_Mutation_p.M349I	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent	399	Helical; (Potential).				neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						GTTTTGGCATGGAGGCAACCT	0.408													5	67	---	---	---	---	PASS
ANO4	121601	broad.mit.edu	37	12	101488070	101488070	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101488070G>T	uc010svm.1	+	18	2310	c.1738G>T	c.(1738-1740)GAA>TAA	p.E580*	ANO4_uc001thw.2_Nonsense_Mutation_p.E545*|ANO4_uc001thx.2_Nonsense_Mutation_p.E580*|ANO4_uc001thy.2_Nonsense_Mutation_p.E100*	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4	580	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						GACGAATTTAGGTGAGTGGAA	0.338										HNSCC(74;0.22)			6	38	---	---	---	---	PASS
UTP20	27340	broad.mit.edu	37	12	101685795	101685795	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101685795G>T	uc001tia.1	+	10	1242	c.1086G>T	c.(1084-1086)TGG>TGT	p.W362C		NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	362					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4						CATCTTGCTGGGAGACCCTCT	0.393													7	141	---	---	---	---	PASS
UTP20	27340	broad.mit.edu	37	12	101763508	101763508	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101763508G>T	uc001tia.1	+	49	6550	c.6394G>T	c.(6394-6396)GGT>TGT	p.G2132C		NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	2132					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4						GGTGATCACAGGTGCTTTACA	0.448													6	74	---	---	---	---	PASS
RFX4	5992	broad.mit.edu	37	12	107103163	107103163	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107103163G>A	uc001tlr.2	+	9	955	c.889G>A	c.(889-891)GCT>ACT	p.A297T	RFX4_uc010swv.1_RNA|RFX4_uc001tls.2_Missense_Mutation_p.A306T|RFX4_uc001tlt.2_Missense_Mutation_p.A306T|RFX4_uc001tlv.2_Missense_Mutation_p.A203T	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c	297					transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1						GCTAAAAGTGGCTCTCCACGA	0.418													8	35	---	---	---	---	PASS
WSCD2	9671	broad.mit.edu	37	12	108589946	108589946	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108589946C>G	uc001tms.2	+	2	1081	c.337C>G	c.(337-339)CGA>GGA	p.R113G	WSCD2_uc001tmt.2_Missense_Mutation_p.R113G	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	113						integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3						AGCCTGGAGCCGAGCCCTCAA	0.597													8	28	---	---	---	---	PASS
SSH1	54434	broad.mit.edu	37	12	109210857	109210857	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109210857C>A	uc001tnm.2	-	5	445	c.358G>T	c.(358-360)GAG>TAG	p.E120*	SSH1_uc010sxg.1_Nonsense_Mutation_p.E131*|SSH1_uc001tnn.3_Nonsense_Mutation_p.E120*|SSH1_uc001tno.1_Nonsense_Mutation_p.E47*	NM_018984	NP_061857	Q8WYL5	SSH1_HUMAN	slingshot 1 isoform 1	120					actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(4)	4						ATATTCTCCTCGGTGTCCTGG	0.602													6	106	---	---	---	---	PASS
ACACB	32	broad.mit.edu	37	12	109639514	109639514	+	Intron	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109639514G>T	uc001tob.2	+						ACACB_uc001toc.2_Intron	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	CCGGTATGTGGCTCCACGGCC	0.582													13	12	---	---	---	---	PASS
UBE3B	89910	broad.mit.edu	37	12	109962291	109962291	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109962291G>T	uc001top.2	+	23	3154	c.2551G>T	c.(2551-2553)GAG>TAG	p.E851*	UBE3B_uc001toq.2_Nonsense_Mutation_p.E851*|UBE3B_uc001tos.2_Nonsense_Mutation_p.E278*|UBE3B_uc001too.1_RNA|UBE3B_uc009zvj.1_Nonsense_Mutation_p.E851*	NM_130466	NP_569733	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	851	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			ovary(2)|lung(2)	4						GTCTTACGACGAGGACGTCAT	0.547													17	20	---	---	---	---	PASS
PXN	5829	broad.mit.edu	37	12	120653417	120653417	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120653417G>A	uc001txt.2	-	7	1010	c.879C>T	c.(877-879)GCC>GCT	p.A293A	PXN_uc001txu.2_Silent_p.A57A|PXN_uc001txv.2_Intron|PXN_uc001txx.2_Intron|PXN_uc001txy.2_Intron|PXN_uc001txz.2_RNA	NM_001080855	NP_001074324	P49023	PAXI_HUMAN	paxillin isoform 1	293					cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)|breast(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GAGGCCAGCCGGCCGCCCAGC	0.622													9	13	---	---	---	---	PASS
P2RX7	5027	broad.mit.edu	37	12	121615214	121615214	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121615214A>T	uc001tzm.2	+	11	1249	c.1153A>T	c.(1153-1155)AGG>TGG	p.R385W	P2RX7_uc001tzn.2_Missense_Mutation_p.R295W|P2RX7_uc001tzo.2_RNA|P2RX7_uc001tzp.2_Missense_Mutation_p.R96W|P2RX7_uc001tzq.2_Missense_Mutation_p.R215W	NM_002562	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X7	385						integral to membrane	ATP binding|ion channel activity|receptor activity			large_intestine(2)|lung(1)|breast(1)|skin(1)	5	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ATACTACTACAGGAAGAAGTG	0.507													22	22	---	---	---	---	PASS
WDR66	144406	broad.mit.edu	37	12	122437833	122437833	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122437833G>C	uc009zxk.2	+	20	3360	c.3218G>C	c.(3217-3219)AGA>ACA	p.R1073T		NM_144668	NP_653269	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	1073							calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		GACTTCCTGAGACTGCTCGTT	0.498													12	49	---	---	---	---	PASS
FLT1	2321	broad.mit.edu	37	13	29008091	29008091	+	Silent	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29008091G>C	uc001usb.3	-	6	963	c.678C>G	c.(676-678)ACC>ACG	p.T226T	FLT1_uc010aar.1_Silent_p.T226T|FLT1_uc001usc.3_Silent_p.T226T|FLT1_uc010tdp.1_Silent_p.T226T	NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1	226	Extracellular (Potential).				cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)	TGATTGTATTGGCTGCAAGCA	0.378													25	36	---	---	---	---	PASS
FAM48A	55578	broad.mit.edu	37	13	37593482	37593482	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37593482G>T	uc001uwg.2	-	22	2117	c.1869C>A	c.(1867-1869)CTC>CTA	p.L623L	FAM48A_uc010abt.2_Silent_p.L624L|FAM48A_uc001uwh.2_Silent_p.L624L|FAM48A_uc001uwi.2_Silent_p.L623L|FAM48A_uc001uwj.2_Silent_p.L624L|FAM48A_uc001uwk.2_Silent_p.L702L|FAM48A_uc001uwd.2_Silent_p.L110L|FAM48A_uc001uwe.2_Silent_p.L107L|FAM48A_uc001uwf.2_Silent_p.L201L	NM_001014286	NP_001014308	Q8NEM7	FA48A_HUMAN	family with sequence similarity 48, member A	623					autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)		GGTTTACCTGGAGTAGATTTA	0.294													5	38	---	---	---	---	PASS
PCDH8	5100	broad.mit.edu	37	13	53419021	53419021	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53419021G>A	uc001vhi.2	-	3	3090	c.2887C>T	c.(2887-2889)CGC>TGC	p.R963C	PCDH8_uc001vhj.2_Missense_Mutation_p.R866C	NM_002590	NP_002581	O95206	PCDH8_HUMAN	protocadherin 8 isoform 1 precursor	963	Cytoplasmic (Potential).				cell-cell signaling|homophilic cell adhesion	cell junction|dendrite|integral to plasma membrane|postsynaptic membrane|presynaptic membrane	calcium ion binding			breast(1)	1		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		CTCCAGCAGCGGTCAGAGTGG	0.557													7	14	---	---	---	---	PASS
PCDH20	64881	broad.mit.edu	37	13	61987742	61987742	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61987742C>T	uc001vid.3	-	2	854	c.490G>A	c.(490-492)GGC>AGC	p.G164S	PCDH20_uc010thj.1_Missense_Mutation_p.G164S	NM_022843	NP_073754	Q8N6Y1	PCD20_HUMAN	protocadherin 20	137	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|breast(1)|central_nervous_system(1)	6		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		GAAACGCTGCCGCTCCACGCA	0.562													18	13	---	---	---	---	PASS
KLF5	688	broad.mit.edu	37	13	73636323	73636323	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73636323C>A	uc001vje.2	+	2	910	c.586C>A	c.(586-588)CAC>AAC	p.H196N	KLF5_uc001vjd.2_Missense_Mutation_p.H105N	NM_001730	NP_001721	Q13887	KLF5_HUMAN	Kruppel-like factor 5	196					transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|pancreas(1)	3		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		ATTCAGCTCACACCAGACCGC	0.532													18	25	---	---	---	---	PASS
HS6ST3	266722	broad.mit.edu	37	13	97485376	97485376	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97485376A>T	uc001vmw.2	+	2	1364	c.1340A>T	c.(1339-1341)CAC>CTC	p.H447L		NM_153456	NP_703157	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	447	Lumenal (Potential).					integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					CACAGGGACCACCAGTGGCCC	0.632													9	9	---	---	---	---	PASS
POTEG	404785	broad.mit.edu	37	14	19553744	19553744	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19553744A>T	uc001vuz.1	+	1	380	c.328A>T	c.(328-330)AGG>TGG	p.R110W	POTEG_uc001vva.1_RNA|POTEG_uc010ahc.1_RNA	NM_001005356	NP_001005356	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	110										ovary(1)	1						CCCCTGCTGCAGGGGGAGCGG	0.592													17	188	---	---	---	---	PASS
OR4N2	390429	broad.mit.edu	37	14	20295680	20295680	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20295680C>A	uc010tkv.1	+	1	73	c.73C>A	c.(73-75)CTC>ATC	p.L25I		NM_001004723	NP_001004723	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N,	25	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.L25L(1)		ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		AGATATTCAGCTCCTGGTCTT	0.438													39	94	---	---	---	---	PASS
RNASE4	6038	broad.mit.edu	37	14	21167824	21167824	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21167824C>A	uc001vxy.3	+	2	857	c.294C>A	c.(292-294)AAC>AAA	p.N98K	RNASE4_uc001vxx.3_RNA|RNASE4_uc001vya.2_Missense_Mutation_p.N98K	NM_002937	NP_002928	P34096	RNAS4_HUMAN	ribonuclease, RNase A family, 4 precursor	98					mRNA cleavage	extracellular region	nucleic acid binding|pancreatic ribonuclease activity			central_nervous_system(1)	1	all_cancers(95;0.00304)		Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	GBM - Glioblastoma multiforme(265;0.0133)		GCAAGATGAACTGCCATGAGG	0.498													16	62	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44975152	44975152	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44975152G>T	uc001wvn.2	-	1	1348	c.1039C>A	c.(1039-1041)CTG>ATG	p.L347M		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	347	Pro-rich.					cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		ATTTCAGCCAGAAGCTCTACA	0.502													39	64	---	---	---	---	PASS
FRMD6	122786	broad.mit.edu	37	14	52171516	52171516	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52171516C>G	uc001wzd.2	+	6	706	c.421C>G	c.(421-423)CTT>GTT	p.L141V	FRMD6_uc001wzb.2_Missense_Mutation_p.L133V|FRMD6_uc001wzc.2_Missense_Mutation_p.L133V|FRMD6_uc001wze.2_Missense_Mutation_p.L64V	NM_152330	NP_689543	Q96NE9	FRMD6_HUMAN	FERM domain containing 6	141	FERM.					cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)					AAAACAAGTTCTTCATTCTCA	0.428													10	42	---	---	---	---	PASS
ARID4A	5926	broad.mit.edu	37	14	58796253	58796253	+	Missense_Mutation	SNP	A	G	G	rs138296226	byFrequency	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58796253A>G	uc001xdp.2	+	10	924	c.670A>G	c.(670-672)ATA>GTA	p.I224V	ARID4A_uc001xdo.2_Missense_Mutation_p.I224V|ARID4A_uc001xdq.2_Missense_Mutation_p.I224V|ARID4A_uc010apg.1_5'Flank	NM_002892	NP_002883	P29374	ARI4A_HUMAN	retinoblastoma-binding protein 1 isoform I	224					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	transcriptional repressor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|lung(1)	6						TAGTTACTCTATAGCAAGAAA	0.299													14	26	---	---	---	---	PASS
TOMM20L	387990	broad.mit.edu	37	14	58869446	58869446	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58869446G>T	uc001xdr.1	+	3	261	c.229G>T	c.(229-231)GAG>TAG	p.E77*	TOMM20L_uc010trq.1_Intron	NM_207377	NP_997260	Q6UXN7	TO20L_HUMAN	translocase of outer mitochondrial membrane 20	77	Cytoplasmic (Potential).				protein targeting	integral to membrane|mitochondrial outer membrane translocase complex					0						TTTCTTGCAAGAGGTACGGAT	0.313													6	98	---	---	---	---	PASS
RAB15	376267	broad.mit.edu	37	14	65417054	65417054	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65417054G>T	uc001xhz.2	-	5	615	c.534C>A	c.(532-534)AGC>AGA	p.S178R	FNTB_uc010tsl.1_Intron|FNTB_uc010tsm.1_Intron|RAB15_uc010aqk.2_RNA	NM_198686	NP_941959	P59190	RAB15_HUMAN	RAB15, member RAS onocogene family	Error:Variant_position_missing_in_P59190_after_alignment					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)	1				all cancers(60;0.00136)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.0102)		TGCTGCCCTTGCTCTCTTCCC	0.587													67	104	---	---	---	---	PASS
ADAM20	8748	broad.mit.edu	37	14	70989667	70989667	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70989667G>T	uc001xme.2	-	2	2203	c.1958C>A	c.(1957-1959)CCT>CAT	p.P653H		NM_003814	NP_003805	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20 preproprotein	603	Cys-rich.|Extracellular (Potential).				proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		ACCAATATCAGGTATAGCCAT	0.458													6	103	---	---	---	---	PASS
TTLL5	23093	broad.mit.edu	37	14	76232418	76232418	+	Silent	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76232418A>G	uc001xrx.2	+	20	1927	c.1722A>G	c.(1720-1722)CCA>CCG	p.P574P	TTLL5_uc010ask.1_Silent_p.P588P|TTLL5_uc001xrz.2_Silent_p.P149P|TTLL5_uc001xry.1_RNA	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	574					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)		TTACCCAACCAGCTGAAATGA	0.388													15	35	---	---	---	---	PASS
ASB2	51676	broad.mit.edu	37	14	94419793	94419793	+	Missense_Mutation	SNP	G	C	C	rs113529772		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94419793G>C	uc001ycc.1	-	3	884	c.395C>G	c.(394-396)ACG>AGG	p.T132R	ASB2_uc001ycd.2_Missense_Mutation_p.T180R|ASB2_uc001yce.1_Missense_Mutation_p.T78R	NM_016150	NP_057234	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box-containing protein	132	ANK 3.				intracellular signal transduction					ovary(1)|pancreas(1)	2		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		GCCCCTGCACGTTGCCAAGTA	0.587													6	24	---	---	---	---	PASS
DICER1	23405	broad.mit.edu	37	14	95570126	95570126	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95570126T>A	uc001ydw.2	-	22	3789	c.3607A>T	c.(3607-3609)AAT>TAT	p.N1203Y	DICER1_uc010avh.1_Missense_Mutation_p.N101Y|DICER1_uc001ydv.2_Missense_Mutation_p.N1193Y|DICER1_uc001ydx.2_Missense_Mutation_p.N1203Y|DICER1_uc001ydy.1_Missense_Mutation_p.N55Y	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	1203					negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		TTGTAGTAATTTAGCTGATTT	0.403			Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				28	54	---	---	---	---	PASS
EVL	51466	broad.mit.edu	37	14	100602237	100602237	+	Intron	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100602237T>C	uc001ygt.2	+						EVL_uc001ygv.2_Intron|EVL_uc001ygu.2_Intron|EVL_uc010avu.2_Intron	NM_016337	NP_057421	Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)				TCTTCTCCATTTTAGGAAGAT	0.567													29	39	---	---	---	---	PASS
MIR329-1	574408	broad.mit.edu	37	14	101493134	101493134	+	RNA	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101493134G>T	hsa-mir-329-1|MI0001725	+			c.13G>T			MIR329-2_hsa-mir-329-2|MI0001726_5'Flank|MIR494_hsa-mir-494|MI0003134_5'Flank|uc010txm.1_5'Flank																	0						TACCTGAAGAGAGGTTTTCTG	0.443													20	36	---	---	---	---	PASS
SIVA1	10572	broad.mit.edu	37	14	105222016	105222016	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105222016C>G	uc001yph.2	+	2	237	c.168C>G	c.(166-168)CAC>CAG	p.H56Q	INF2_uc010tyi.1_Intron|SIVA1_uc010tyj.1_Missense_Mutation_p.H56Q|SIVA1_uc001ypg.1_Missense_Mutation_p.H56Q|SIVA1_uc001ypi.2_Intron	NM_006427	NP_006418	O15304	SIVA_HUMAN	CD27-binding (Siva) protein isoform 1	56					activation of caspase activity by cytochrome c|activation-induced cell death of T cells|apoptosis|induction of apoptosis|interspecies interaction between organisms|negative regulation of anti-apoptosis|negative regulation of NF-kappaB transcription factor activity	cytoplasm|mitochondrion|nucleoplasm|nucleus	caspase activator activity|CD27 receptor binding|metal ion binding|viral receptor activity|zinc ion binding				0		all_cancers(154;0.14)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.173)		ACCTGGACCACGTGTGGGATG	0.607													8	15	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105413877	105413877	+	Silent	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105413877G>C	uc010axc.1	-	7	8031	c.7911C>G	c.(7909-7911)GCC>GCG	p.A2637A	AHNAK2_uc001ypx.2_Silent_p.A2537A	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2637						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CACCCTTGTCGGCCAGGGACA	0.607													28	171	---	---	---	---	PASS
NDN	4692	broad.mit.edu	37	15	23931540	23931540	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23931540G>T	uc001ywk.2	-	1	911	c.825C>A	c.(823-825)ATC>ATA	p.I275I		NM_002487	NP_002478	Q99608	NECD_HUMAN	necdin	275	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)		GGAACTCCATGATTTGCATCT	0.582									Prader-Willi_syndrome				6	11	---	---	---	---	PASS
ATP10A	57194	broad.mit.edu	37	15	25925069	25925069	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25925069C>A	uc010ayu.2	-	21	4025	c.3919G>T	c.(3919-3921)GCA>TCA	p.A1307S		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1307	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		AACTGACGTGCCAGCTGAAGT	0.507													32	30	---	---	---	---	PASS
FSIP1	161835	broad.mit.edu	37	15	39910398	39910398	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39910398C>A	uc001zki.2	-	11	1455	c.1237G>T	c.(1237-1239)GAT>TAT	p.D413Y		NM_152597	NP_689810	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	413										ovary(2)|skin(1)	3		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		ATGCATTCATCCAGAAGACAC	0.368													20	22	---	---	---	---	PASS
CHP	11261	broad.mit.edu	37	15	41570972	41570972	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41570972G>T	uc001znl.2	+	6	563	c.419G>T	c.(418-420)CGC>CTC	p.R140L	CHP_uc010bcd.1_5'Flank	NM_007236	NP_009167	Q99653	CHP1_HUMAN	calcium binding protein P22	140	EF-hand 3.				potassium ion transport|small GTPase mediated signal transduction		potassium channel regulator activity			ovary(1)	1		all_cancers(109;1.19e-18)|all_epithelial(112;5.87e-16)|Lung NSC(122;8.86e-12)|all_lung(180;2.47e-10)|Melanoma(134;0.0574)|Colorectal(260;0.0946)|Ovarian(310;0.143)		GBM - Glioblastoma multiforme(113;1.68e-06)|LUSC - Lung squamous cell carcinoma(244;0.008)|Lung(196;0.00802)|BRCA - Breast invasive adenocarcinoma(123;0.169)		CAGGTGCTACGCATGATGGTC	0.478													16	11	---	---	---	---	PASS
TYRO3	7301	broad.mit.edu	37	15	41862286	41862286	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41862286G>A	uc001zof.1	+	10	1538	c.1314G>A	c.(1312-1314)ACG>ACA	p.T438T		NM_006293	NP_006284	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase precursor	438	Helical; (Potential).					integral to plasma membrane	ATP binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			ovary(3)|lung(2)|central_nervous_system(1)	6		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GTGTGCTAACGGCCCTGGTGA	0.627													16	5	---	---	---	---	PASS
VPS39	23339	broad.mit.edu	37	15	42483764	42483764	+	Intron	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42483764G>C	uc001zpd.2	-						VPS39_uc001zpc.2_Intron	NM_015289	NP_056104	Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39						protein transport	HOPS complex|late endosome membrane|lysosomal membrane	small GTPase regulator activity			ovary(1)|pancreas(1)|skin(1)	3		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		GCAACCTATGGAAAACAAATA	0.363													11	18	---	---	---	---	PASS
GANC	2595	broad.mit.edu	37	15	42632878	42632878	+	Intron	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42632878C>G	uc001zpi.2	+							NM_198141	NP_937784	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C						carbohydrate metabolic process		carbohydrate binding|maltose alpha-glucosidase activity			central_nervous_system(2)	2		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)		AATTTTTTTTCTTTCCCCAGG	0.239													23	30	---	---	---	---	PASS
CAPN3	825	broad.mit.edu	37	15	42702687	42702687	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42702687C>T	uc001zpn.1	+	20	2483	c.2177C>T	c.(2176-2178)GCC>GTC	p.A726V	CAPN3_uc001zpk.1_Missense_Mutation_p.A493V|CAPN3_uc001zpl.1_Missense_Mutation_p.A633V|CAPN3_uc010udf.1_Missense_Mutation_p.A639V|CAPN3_uc010udg.1_Missense_Mutation_p.A591V|CAPN3_uc001zpo.1_Missense_Mutation_p.A720V|CAPN3_uc001zpp.1_Missense_Mutation_p.A634V|CAPN3_uc001zpq.1_Missense_Mutation_p.A214V|CAPN3_uc010bcv.1_Missense_Mutation_p.A61V|CAPN3_uc001zpr.1_Missense_Mutation_p.A61V|CAPN3_uc001zps.1_Missense_Mutation_p.A61V|CAPN3_uc001zpt.1_Missense_Mutation_p.A61V	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a	726	EF-hand 3.|Domain IV.				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)		AAGATTAAGGCCTGGCAGGTG	0.502													18	26	---	---	---	---	PASS
CEP152	22995	broad.mit.edu	37	15	49064722	49064722	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49064722G>T	uc001zwy.2	-	13	1778	c.1744C>A	c.(1744-1746)CAC>AAC	p.H582N	CEP152_uc001zwz.2_Missense_Mutation_p.H582N|CEP152_uc001zxa.1_Missense_Mutation_p.H489N	NM_014985	NP_055800	O94986	CE152_HUMAN	centrosomal protein 152kDa	582					centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding			lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TTCACTTGGTGGAGATCTTCA	0.363													5	68	---	---	---	---	PASS
ATP8B4	79895	broad.mit.edu	37	15	50152498	50152498	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50152498C>T	uc001zxu.2	-	28	3614	c.3472G>A	c.(3472-3474)GGG>AGG	p.G1158R	ATP8B4_uc010ber.2_Missense_Mutation_p.G1031R|ATP8B4_uc010ufd.1_Missense_Mutation_p.G968R|ATP8B4_uc010ufe.1_RNA|ATP8B4_uc001zxt.2_Missense_Mutation_p.G161R	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4	1158	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		TTTTCCAGCCCTGATGTTGGG	0.418													30	23	---	---	---	---	PASS
RORA	6095	broad.mit.edu	37	15	60919479	60919479	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60919479C>G	uc002agv.2	-	1	251	c.95G>C	c.(94-96)AGA>ACA	p.R32T	RORA_uc002agw.2_Missense_Mutation_p.R32T|RORA_uc002agx.2_Intron	NM_134260	NP_599022	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform b	32	Modulating.				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						GGCAGACATTCTGGCCTGTCC	0.373													11	16	---	---	---	---	PASS
NEIL1	79661	broad.mit.edu	37	15	75644693	75644693	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75644693C>T	uc002bad.2	+	4	1089	c.583C>T	c.(583-585)CGC>TGC	p.R195C	NEIL1_uc002bae.2_Missense_Mutation_p.R281C	NM_024608	NP_078884	Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1	195					base-excision repair|negative regulation of nuclease activity|nucleotide-excision repair|response to oxidative stress	cytoplasm|nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|protein C-terminus binding|zinc ion binding			ovary(1)	1						TGAGAAGGCCCGCTCGGTCCT	0.657								BER_DNA_glycosylases					9	13	---	---	---	---	PASS
ALPK3	57538	broad.mit.edu	37	15	85400738	85400738	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85400738C>G	uc002ble.2	+	6	3542	c.3375C>G	c.(3373-3375)CAC>CAG	p.H1125Q		NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1125					heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CTCAGAGTCACCCACCAGAAA	0.662													8	17	---	---	---	---	PASS
PRC1	9055	broad.mit.edu	37	15	91528042	91528042	+	Nonsense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91528042C>A	uc002bqm.2	-	2	182	c.25G>T	c.(25-27)GAG>TAG	p.E9*	PRC1_uc002bqn.2_Nonsense_Mutation_p.E9*|PRC1_uc002bqo.2_Nonsense_Mutation_p.E9*|PRC1_uc010uqs.1_Nonsense_Mutation_p.E9*|PRC1_uc010uqt.1_Intron	NM_003981	NP_003972	O43663	PRC1_HUMAN	protein regulator of cytokinesis 1 isoform 1	9	Dimerization.				cytokinesis|mitotic spindle elongation	cytoplasm|nucleus|spindle microtubule|spindle pole	protein binding			ovary(1)|skin(1)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)					ATGGACTCCTCCGCCAGCACC	0.453													34	58	---	---	---	---	PASS
CACNA1H	8912	broad.mit.edu	37	16	1250520	1250520	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1250520C>T	uc002cks.2	+	7	1316	c.1068C>T	c.(1066-1068)AAC>AAT	p.N356N	CACNA1H_uc002ckt.2_Silent_p.N356N	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	356	Extracellular (Potential).|I.				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	ACCCCCACAACGGTGCCATCA	0.657													10	30	---	---	---	---	PASS
ABCA3	21	broad.mit.edu	37	16	2331210	2331210	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2331210G>T	uc002cpy.1	-	28	4889	c.4177C>A	c.(4177-4179)CGG>AGG	p.R1393R	ABCA3_uc010bsk.1_Silent_p.R1335R	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3	1393	ABC transporter 2.				response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)				AGGGGCACCCGCTGCTCGTAC	0.632													17	11	---	---	---	---	PASS
NDUFAB1	4706	broad.mit.edu	37	16	23607476	23607476	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23607476C>G	uc002dlw.2	-	1	164	c.136G>C	c.(136-138)GGG>CGG	p.G46R		NM_005003	NP_004994	O14561	ACPM_HUMAN	NADH dehydrogenase (ubiquinone) 1, alpha/beta	46					fatty acid biosynthetic process|mitochondrial electron transport, NADH to ubiquinone	mitochondrial matrix|mitochondrial respiratory chain complex I	acyl carrier activity|calcium ion binding|cofactor binding|fatty acid binding|NADH dehydrogenase (ubiquinone) activity|phosphopantetheine binding				0				GBM - Glioblastoma multiforme(48;0.0339)	NADH(DB00157)	TGCAAAGTCCCGAGCCTCGTC	0.726													3	10	---	---	---	---	PASS
GSG1L	146395	broad.mit.edu	37	16	27818807	27818807	+	Splice_Site	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27818807C>T	uc002doz.2	-	6	983	c.898_splice	c.e6+1	p.R300_splice	GSG1L_uc010bya.1_Splice_Site_p.R249_splice|GSG1L_uc010bxz.1_Splice_Site_p.R163_splice|GSG1L_uc002doy.2_Splice_Site_p.R145_splice	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						AGGCCACTTACGGGCAGGGTA	0.532													4	19	---	---	---	---	PASS
NOD2	64127	broad.mit.edu	37	16	50744691	50744691	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50744691A>T	uc002egm.1	+	4	974	c.869A>T	c.(868-870)GAC>GTC	p.D290V	NOD2_uc010cbk.1_Missense_Mutation_p.D263V|NOD2_uc002egl.1_Missense_Mutation_p.D68V|NOD2_uc010cbl.1_Missense_Mutation_p.D68V|NOD2_uc010cbm.1_Missense_Mutation_p.D68V|NOD2_uc010cbn.1_RNA|NOD2_uc010cbo.1_RNA|NOD2_uc010cbp.1_5'Flank|NOD2_uc010cbq.1_5'Flank|NOD2_uc010cbr.1_5'Flank	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain	290					activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)|skin(1)	4		all_cancers(37;0.0156)				CACCTCAATGACGATGCGGAC	0.662													7	9	---	---	---	---	PASS
C16orf57	79650	broad.mit.edu	37	16	58036523	58036523	+	Missense_Mutation	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58036523A>G	uc002emz.2	+	2	322	c.239A>G	c.(238-240)AAC>AGC	p.N80S	ZNF319_uc002emx.1_5'Flank|C16orf57_uc010via.1_Missense_Mutation_p.N80S|C16orf57_uc002emy.2_RNA|C16orf57_uc010vib.1_Missense_Mutation_p.N80S|C16orf57_uc010vic.1_Missense_Mutation_p.N29S	NM_024598	NP_078874	Q9BQ65	CP057_HUMAN	hypothetical protein LOC79650	80											0						GAGCGAGGCAACTGGGCCACC	0.592													8	11	---	---	---	---	PASS
ZNF23	7571	broad.mit.edu	37	16	71487152	71487152	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71487152G>T	uc002faf.2	-	5	950	c.136C>A	c.(136-138)CAG>AAG	p.Q46K	ZNF23_uc002fad.2_5'UTR|ZNF23_uc002fae.2_5'UTR|ZNF23_uc010vmf.1_Intron|ZNF23_uc002fag.2_5'UTR|ZNF23_uc002fah.2_Missense_Mutation_p.Q46K|ZNF23_uc002fai.2_Missense_Mutation_p.Q84K	NM_145911	NP_666016	P17027	ZNF23_HUMAN	zinc finger protein 23	46					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		TTACCAGTCTGGAGGCCCTGG	0.488													4	8	---	---	---	---	PASS
CDYL2	124359	broad.mit.edu	37	16	80718954	80718954	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80718954C>G	uc002ffs.2	-	2	202	c.97G>C	c.(97-99)GGG>CGG	p.G33R		NM_152342	NP_689555	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	33	Chromo.					nucleus	catalytic activity|protein binding			central_nervous_system(1)	1						TCGGTGCTCCCGTAGCCTTTC	0.478													34	21	---	---	---	---	PASS
POLR2A	5430	broad.mit.edu	37	17	7415644	7415644	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7415644C>T	uc002ghf.3	+	26	4707	c.4473C>T	c.(4471-4473)CCC>CCT	p.P1491P		NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	1491					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)				CCAATATCCCCGGCCTGGGGG	0.652													11	6	---	---	---	---	PASS
SLC25A35	399512	broad.mit.edu	37	17	8193298	8193298	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8193298C>A	uc002gku.1	-	5	779	c.734G>T	c.(733-735)CGA>CTA	p.R245L	SLC25A35_uc002gkt.2_Missense_Mutation_p.R245L|RANGRF_uc002gkv.2_3'UTR|RANGRF_uc002gkw.2_3'UTR|RANGRF_uc002gky.2_3'UTR|RANGRF_uc002gkx.2_3'UTR|SLC25A35_uc002gkz.1_RNA	NM_201520	NP_958928	Q3KQZ1	S2535_HUMAN	solute carrier family 25, member 35	Error:Variant_position_missing_in_Q3KQZ1_after_alignment					transport	integral to membrane|mitochondrial inner membrane					0						CTTGGGGACTCGGTTCTGTGA	0.468													5	135	---	---	---	---	PASS
MYH13	8735	broad.mit.edu	37	17	10215277	10215277	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10215277C>T	uc002gmk.1	-	32	4572	c.4482G>A	c.(4480-4482)GAG>GAA	p.E1494E		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1494	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						GGTCCACCACCTCCTCATAGG	0.532													9	42	---	---	---	---	PASS
ZNF624	57547	broad.mit.edu	37	17	16526040	16526040	+	Silent	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16526040T>C	uc010cpi.1	-	6	2243	c.2160A>G	c.(2158-2160)GGA>GGG	p.G720G		NM_020787	NP_065838	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	720					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		ATGGTTTCTCTCCAGTATGTG	0.388													34	23	---	---	---	---	PASS
EVI2B	2124	broad.mit.edu	37	17	29632186	29632186	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29632186G>T	uc002hgk.2	-	2	597	c.442C>A	c.(442-444)CAA>AAA	p.Q148K	NF1_uc002hgg.2_Intron|NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron|NF1_uc010cso.2_Intron|EVI2B_uc010csq.2_Missense_Mutation_p.Q163K	NM_006495	NP_006486	P34910	EVI2B_HUMAN	ecotropic viral integration site 2B precursor	148	Extracellular (Potential).					cytoplasm|integral to plasma membrane				ovary(2)	2		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;6.88e-13)|Epithelial(4;8.95e-12)|OV - Ovarian serous cystadenocarcinoma(4;1.01e-11)|GBM - Glioblastoma multiforme(4;0.184)		GATGATTGTTGAGTAAAAGTA	0.433													6	131	---	---	---	---	PASS
KRTAP3-1	83896	broad.mit.edu	37	17	39165091	39165091	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39165091C>G	uc002hvt.1	-	1	276	c.236G>C	c.(235-237)GGG>GCG	p.G79A		NM_031958	NP_114164	Q9BYR8	KRA31_HUMAN	keratin associated protein 3.1	79						keratin filament	structural molecule activity				0		Breast(137;0.00043)				CAGGTTGATCCCACTCAGTCC	0.597													3	7	---	---	---	---	PASS
KRTAP4-5	85289	broad.mit.edu	37	17	39305582	39305582	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39305582G>T	uc002hwb.2	-	1	473	c.438C>A	c.(436-438)TGC>TGA	p.C146*		NM_033188	NP_149445	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	151	27 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].|27.					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CTGGACGCACgcagcagcagg	0.378													3	9	---	---	---	---	PASS
WNK4	65266	broad.mit.edu	37	17	40934960	40934960	+	Intron	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40934960G>C	uc002ibj.2	+						WNK4_uc010wgx.1_Intron|WNK4_uc002ibk.1_5'Flank|WNK4_uc010wgy.1_5'Flank	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4						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)		TGAGCTCTGCGCATGAGTGGG	0.478													5	6	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45219285	45219285	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45219285G>C	uc002ild.3	-	12	1612	c.1485C>G	c.(1483-1485)CAC>CAG	p.H495Q	CDC27_uc002ile.3_Missense_Mutation_p.H501Q|CDC27_uc002ilf.3_Missense_Mutation_p.H494Q|CDC27_uc010wkp.1_Missense_Mutation_p.H434Q|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	495					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|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	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						CAGTATTGTAGTGGTGAGAAG	0.373													7	188	---	---	---	---	PASS
CACNA1G	8913	broad.mit.edu	37	17	48704077	48704077	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48704077G>A	uc002irk.1	+	38	7471	c.7099G>A	c.(7099-7101)GGT>AGT	p.G2367S	CACNA1G_uc002irj.1_Missense_Mutation_p.G2161S|CACNA1G_uc002irl.1_Missense_Mutation_p.G2251S|CACNA1G_uc002irm.1_Missense_Mutation_p.G2288S|CACNA1G_uc002irn.1_Missense_Mutation_p.G2233S|CACNA1G_uc002iro.1_Missense_Mutation_p.G2240S|CACNA1G_uc002irp.1_Missense_Mutation_p.G2322S|CACNA1G_uc002irq.1_Missense_Mutation_p.G2344S|CACNA1G_uc002irr.1_Missense_Mutation_p.G2274S|CACNA1G_uc002irs.1_Missense_Mutation_p.G2311S|CACNA1G_uc002irt.1_Missense_Mutation_p.G2256S|CACNA1G_uc002irv.1_Missense_Mutation_p.G2263S|CACNA1G_uc002irw.1_Missense_Mutation_p.G2296S|CACNA1G_uc002iru.1_Missense_Mutation_p.G2333S|CACNA1G_uc002irx.1_Missense_Mutation_p.G2108S|CACNA1G_uc002iry.1_Missense_Mutation_p.G2097S|CACNA1G_uc002irz.1_Missense_Mutation_p.G2180S|CACNA1G_uc002isa.1_Missense_Mutation_p.G2153S|CACNA1G_uc002isb.1_Missense_Mutation_p.G2194S|CACNA1G_uc002isc.1_Missense_Mutation_p.G2269S|CACNA1G_uc002isd.1_Missense_Mutation_p.G2162S|CACNA1G_uc002ise.1_Missense_Mutation_p.G2190S|CACNA1G_uc002isf.1_Missense_Mutation_p.G2217S|CACNA1G_uc002isg.1_Missense_Mutation_p.G2135S|CACNA1G_uc002ish.1_Missense_Mutation_p.G2142S|CACNA1G_uc002isi.1_Missense_Mutation_p.G2130S	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	2367	Cytoplasmic (Potential).				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GAGTCTCTCCGGTTTATCCTC	0.622											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	15	99	---	---	---	---	PASS
ANKFN1	162282	broad.mit.edu	37	17	54451996	54451996	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54451996G>T	uc002iun.1	+	7	875	c.840G>T	c.(838-840)ATG>ATT	p.M280I		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	280	Fibronectin type-III.									large_intestine(1)|ovary(1)	2						TCTGTCTCATGGTAACCAGCA	0.468													8	192	---	---	---	---	PASS
MPO	4353	broad.mit.edu	37	17	56350171	56350171	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56350171A>T	uc002ivu.1	-	10	1907	c.1730T>A	c.(1729-1731)ATG>AAG	p.M577K		NM_000250	NP_000241	P05164	PERM_HUMAN	myeloperoxidase	577					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)	CCCAATCCTCATGACCTGCTC	0.617													29	61	---	---	---	---	PASS
STRADA	92335	broad.mit.edu	37	17	61788144	61788144	+	Missense_Mutation	SNP	C	A	A	rs141081057		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61788144C>A	uc002jbm.2	-	7	560	c.401G>T	c.(400-402)CGA>CTA	p.R134L	STRADA_uc002jbn.2_Missense_Mutation_p.R76L|STRADA_uc002jbo.2_Missense_Mutation_p.R97L|STRADA_uc002jbp.2_Missense_Mutation_p.R97L|STRADA_uc002jbq.2_Missense_Mutation_p.R76L|STRADA_uc010wpq.1_Missense_Mutation_p.R90L|STRADA_uc010wpr.1_Missense_Mutation_p.R105L|STRADA_uc010ddw.2_Missense_Mutation_p.R105L|STRADA_uc002jbr.2_Missense_Mutation_p.R76L	NM_001003787	NP_001003787	Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha isoform 1	134	Protein kinase.				activation of protein kinase activity|cell cycle arrest|insulin receptor signaling pathway|protein export from nucleus|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|kinase binding|protein kinase activity			ovary(1)	1						AAAAGTGGCTCGATATGGCAC	0.478													4	59	---	---	---	---	PASS
DDX42	11325	broad.mit.edu	37	17	61885120	61885120	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61885120G>T	uc002jbu.2	+	10	1140	c.883G>T	c.(883-885)GGT>TGT	p.G295C	DDX42_uc002jbv.2_Missense_Mutation_p.G295C|DDX42_uc002jbw.1_Missense_Mutation_p.G31C|DDX42_uc002jbx.2_Missense_Mutation_p.G31C	NM_007372	NP_031398	Q86XP3	DDX42_HUMAN	DEAD box polypeptide 42 protein	295	Helicase ATP-binding.				protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5						AGACATGATTGGTATTGCCAA	0.403													7	157	---	---	---	---	PASS
BPTF	2186	broad.mit.edu	37	17	65918974	65918974	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65918974G>T	uc002jgf.2	+	14	5637	c.5576G>T	c.(5575-5577)AGG>ATG	p.R1859M	BPTF_uc002jge.2_Missense_Mutation_p.R1985M	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1985					brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			ACACCTCAGAGGAAAGGCCTT	0.413													6	113	---	---	---	---	PASS
KCNJ2	3759	broad.mit.edu	37	17	68171272	68171272	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68171272G>T	uc010dfg.2	+	2	493	c.92G>T	c.(91-93)GGG>GTG	p.G31V	KCNJ2_uc002jir.2_Missense_Mutation_p.G31V	NM_000891	NP_000882	P63252	IRK2_HUMAN	potassium inwardly-rectifying channel J2	31	Cytoplasmic (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity|protein binding				0	Breast(10;1.64e-08)					AATGGCTTTGGGAACGGGAAG	0.512													5	60	---	---	---	---	PASS
AATK	9625	broad.mit.edu	37	17	79094857	79094857	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79094857G>T	uc010dia.2	-	11	2959	c.2879C>A	c.(2878-2880)CCC>CAC	p.P960H	AATK_uc010dhz.2_Intron	NM_001080395	NP_001073864	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	960						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)			AAAGGCCTGGGGCTCACACCC	0.647													8	3	---	---	---	---	PASS
AZI1	22994	broad.mit.edu	37	17	79163715	79163715	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79163715C>A	uc002jzp.1	-	25	3377	c.3177G>T	c.(3175-3177)GAG>GAT	p.E1059D	AZI1_uc002jzm.1_Missense_Mutation_p.E491D|AZI1_uc002jzn.1_Missense_Mutation_p.E1056D|AZI1_uc002jzo.1_Missense_Mutation_p.E1020D|AZI1_uc010wum.1_Missense_Mutation_p.E1023D|AZI1_uc002jzq.2_Missense_Mutation_p.E207D	NM_014984	NP_055799	Q9UPN4	AZI1_HUMAN	5-azacytidine induced 1 isoform a	1059					cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centrosome|cytosol|intracellular membrane-bounded organelle				central_nervous_system(2)|large_intestine(1)|ovary(1)	4	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			AGGGACTCACCTCATGTTGTG	0.672													18	9	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3215013	3215013	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3215013T>A	uc002klp.2	-	2	543	c.209A>T	c.(208-210)CAG>CTG	p.Q70L	MYOM1_uc002klq.2_Missense_Mutation_p.Q70L	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	70						striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						GGCCTGCTGCTGGGAGGAGGA	0.692													12	12	---	---	---	---	PASS
ATP5A1	498	broad.mit.edu	37	18	43666187	43666187	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43666187G>T	uc002lbr.1	-	10	1411	c.1321C>A	c.(1321-1323)CGT>AGT	p.R441S	ATP5A1_uc010dnl.1_Missense_Mutation_p.R391S|ATP5A1_uc002lbs.1_Missense_Mutation_p.R391S|ATP5A1_uc002lbt.1_Missense_Mutation_p.R441S	NM_004046	NP_004037	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1	441					ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism				0						GCAACCTCACGATACTGAGCC	0.458													4	56	---	---	---	---	PASS
KATNAL2	83473	broad.mit.edu	37	18	44595926	44595926	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44595926C>A	uc002lco.2	+	10	941	c.747C>A	c.(745-747)TCC>TCA	p.S249S	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lcp.3_Silent_p.S176S	NM_031303	NP_112593	Q8IYT4	KATL2_HUMAN	katanin p60 subunit A-like 2	321						cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4						TTTCTGCATCCACCATTGTCA	0.373													5	48	---	---	---	---	PASS
MBD1	4152	broad.mit.edu	37	18	47799296	47799296	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47799296C>T	uc010dow.1	-	14	2051	c.1614G>A	c.(1612-1614)AAG>AAA	p.K538K	MBD1_uc002lef.2_Silent_p.K243K|MBD1_uc002leg.2_Silent_p.K488K|MBD1_uc010xdi.1_Silent_p.K589K|MBD1_uc002leh.3_Silent_p.K482K|MBD1_uc002len.2_Silent_p.K492K|MBD1_uc002lei.3_Silent_p.K538K|MBD1_uc002lej.3_Silent_p.K436K|MBD1_uc002lek.3_Silent_p.K489K|MBD1_uc002lel.3_Silent_p.K469K|MBD1_uc002lem.3_Silent_p.K538K|MBD1_uc010xdj.1_Silent_p.K436K|MBD1_uc010xdk.1_Silent_p.K563K|MBD1_uc010dox.1_Silent_p.K469K|MBD1_uc002leo.2_Silent_p.K492K	NM_015846	NP_056671	Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1 isoform 1	538	TRD.			K->A: Abolishes sumoylation; when associated with A-499.	negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|nuclear speck	methyl-CpG binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						GTGGCTCTTGCTTCACAGAAG	0.562													19	32	---	---	---	---	PASS
ZNF236	7776	broad.mit.edu	37	18	74649197	74649197	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74649197G>T	uc002lmi.2	+	26	4872	c.4674G>T	c.(4672-4674)TCG>TCT	p.S1558S	ZNF236_uc002lmj.2_RNA	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1558					cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		TCATGTCCTCGTCGGGCGTGG	0.542													31	23	---	---	---	---	PASS
SF3A2	8175	broad.mit.edu	37	19	2246873	2246873	+	Intron	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2246873C>T	uc002lvg.2	+						AMH_uc002lvh.2_5'Flank	NM_007165	NP_009096	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2						nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex	nucleic acid binding|zinc ion binding				0		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)		CCGGCCGTGTCCCTGCAGATT	0.657													3	9	---	---	---	---	PASS
PIAS4	51588	broad.mit.edu	37	19	4012940	4012940	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4012940G>T	uc002lzg.2	+	2	57	c.47G>T	c.(46-48)CGA>CTA	p.R16L		NM_015897	NP_056981	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	16	SAP.				positive regulation of protein sumoylation|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|PML body	DNA binding|SUMO ligase activity|ubiquitin protein ligase binding|zinc ion binding			pancreas(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGAGTTTTCGAGTCTCCGAC	0.597													5	68	---	---	---	---	PASS
SEMA6B	10501	broad.mit.edu	37	19	4552448	4552448	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4552448G>T	uc010duc.1	-	9	1013	c.975C>A	c.(973-975)TCC>TCA	p.S325S	SEMA6B_uc010dud.2_Silent_p.S325S|SEMA6B_uc010xih.1_Silent_p.S325S	NM_032108	NP_115484	Q9H3T3	SEM6B_HUMAN	semaphorin 6B precursor	325	Extracellular (Potential).|Sema.				cell differentiation|nervous system development	integral to membrane	receptor activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCTGGGCGTGGAAAAAACGG	0.617													3	6	---	---	---	---	PASS
MLLT1	4298	broad.mit.edu	37	19	6222149	6222149	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6222149C>A	uc002mek.2	-	6	1257	c.1093G>T	c.(1093-1095)GCC>TCC	p.A365S		NM_005934	NP_005925	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	365					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|protein binding			skin(1)	1						TTGAAGGAGGCCTCGTCCTCT	0.587			T	MLL	AL								6	6	---	---	---	---	PASS
EMR1	2015	broad.mit.edu	37	19	6906479	6906479	+	Missense_Mutation	SNP	G	T	T	rs151096072		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6906479G>T	uc002mfw.2	+	9	1023	c.985G>T	c.(985-987)GAT>TAT	p.D329Y	EMR1_uc010dvc.2_Missense_Mutation_p.D329Y|EMR1_uc010dvb.2_Missense_Mutation_p.D277Y|EMR1_uc010xji.1_Missense_Mutation_p.D188Y|EMR1_uc010xjj.1_Missense_Mutation_p.D152Y	NM_001974	NP_001965	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone	329	Ser/Thr-rich.|Extracellular (Potential).				cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(3)|lung(1)|skin(1)	5	all_hematologic(4;0.166)					TGTGATACCCGATAATAAGCA	0.393													27	45	---	---	---	---	PASS
ELAVL1	1994	broad.mit.edu	37	19	8045966	8045966	+	Splice_Site	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8045966C>A	uc002mjb.2	-	3	443	c.276_splice	c.e3+1	p.K92_splice		NM_001419	NP_001410	Q15717	ELAV1_HUMAN	ELAV-like 1						3'-UTR-mediated mRNA stabilization|multicellular organismal development	cytoplasm|nucleoplasm	identical protein binding|mRNA binding|nucleotide binding				0						GATCCCTTTACCTTAATGGTT	0.557													16	16	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8156451	8156451	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8156451G>A	uc002mjf.2	-	47	5950	c.5929C>T	c.(5929-5931)CCC>TCC	p.P1977S	FBN3_uc002mje.2_5'Flank	NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1977	EGF-like 32; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						CAGAGGTTGGGCTCCTCTGAG	0.592													25	43	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8161784	8161784	+	Silent	SNP	C	G	G	rs80293030	byFrequency	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8161784C>G	uc002mjf.2	-	42	5415	c.5394G>C	c.(5392-5394)TCG>TCC	p.S1798S		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1798	EGF-like 27; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						CCCCGCCTGGCGACAGTTTGT	0.617													12	37	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9061578	9061578	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9061578G>T	uc002mkp.2	-	3	26072	c.25868C>A	c.(25867-25869)TCA>TAA	p.S8623*		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8625	Ser-rich.|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						TATTTCAGCTGAGGTGCTGCT	0.458													5	79	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9089069	9089069	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9089069G>C	uc002mkp.2	-	1	2950	c.2746C>G	c.(2746-2748)CTA>GTA	p.L916V		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	916	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						TCACTCACTAGGTGGGATGAA	0.522													6	28	---	---	---	---	PASS
OR7D2	162998	broad.mit.edu	37	19	9297407	9297407	+	3'UTR	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9297407G>T	uc002mkz.1	+	1						NM_175883	NP_787079	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D,						regulation of transcription, DNA-dependent|sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|upper_aerodigestive_tract(1)	3						TGGATCCCTTGGCCCCAGGAC	0.398													13	16	---	---	---	---	PASS
ZNF823	55552	broad.mit.edu	37	19	11833187	11833187	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11833187G>T	uc002msm.2	-	4	1288	c.1162C>A	c.(1162-1164)CAG>AAG	p.Q388K	ZNF823_uc010xmd.1_Missense_Mutation_p.Q206K|ZNF823_uc010dyi.1_Missense_Mutation_p.Q344K	NM_001080493	NP_001073962	P16415	ZN823_HUMAN	ZFP-36 for a zinc finger protein	388	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						TTGCATTTCTGGGGTCCATCT	0.428										HNSCC(68;0.2)			14	60	---	---	---	---	PASS
ZNF443	10224	broad.mit.edu	37	19	12541030	12541030	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12541030C>A	uc002mtu.2	-	4	2154	c.1956G>T	c.(1954-1956)AAG>AAT	p.K652N		NM_005815	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	652	C2H2-type 19.				induction of apoptosis|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1						TCCCACATTCCTTACATTCAT	0.383													5	63	---	---	---	---	PASS
TNPO2	30000	broad.mit.edu	37	19	12830132	12830132	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12830132G>C	uc002muo.2	-	3	303	c.118C>G	c.(118-120)CAG>GAG	p.Q40E	TNPO2_uc002mup.2_Missense_Mutation_p.Q132E|TNPO2_uc002muq.2_Missense_Mutation_p.Q40E|TNPO2_uc002mur.2_Missense_Mutation_p.Q40E	NM_001136196	NP_001129668	O14787	TNPO2_HUMAN	transportin 2 (importin 3, karyopherin beta 2b)	40	Importin N-terminal.				intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1						TCAGGAAACTGATTGAGTTGT	0.512													7	27	---	---	---	---	PASS
CACNA1A	773	broad.mit.edu	37	19	13397689	13397689	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13397689G>C	uc010dze.2	-	20	3420	c.3184C>G	c.(3184-3186)CTG>GTG	p.L1062V	CACNA1A_uc010dzc.2_Missense_Mutation_p.L587V|CACNA1A_uc002mwy.3_Missense_Mutation_p.L1061V|CACNA1A_uc010xne.1_Missense_Mutation_p.L590V	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3	1062	Cytoplasmic (Potential).				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	TCCTCTGCCAGGGGTGGGTCT	0.672													8	11	---	---	---	---	PASS
EPS15L1	58513	broad.mit.edu	37	19	16506271	16506271	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16506271G>C	uc002ndz.1	-	17	1805	c.1799C>G	c.(1798-1800)CCT>CGT	p.P600R	EPS15L1_uc002ndx.2_Missense_Mutation_p.P600R|EPS15L1_uc002ndy.2_RNA|EPS15L1_uc010xpe.1_Missense_Mutation_p.P490R|EPS15L1_uc010xpf.1_Missense_Mutation_p.P503R|EPS15L1_uc002nea.1_Missense_Mutation_p.P600R|EPS15L1_uc010eah.1_Missense_Mutation_p.P602R	NM_021235	NP_067058	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway	600					endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|nucleus|plasma membrane	calcium ion binding			ovary(3)|skin(2)	5						ATTTTTGAAAGGATCATCCTA	0.373													22	100	---	---	---	---	PASS
JAK3	3718	broad.mit.edu	37	19	17949144	17949144	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17949144C>A	uc002nhn.3	-	11	1597	c.1497G>T	c.(1495-1497)TTG>TTT	p.L499F	JAK3_uc010ebh.2_RNA|JAK3_uc002nho.2_Missense_Mutation_p.L499F|JAK3_uc010xpx.1_3'UTR	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	499					B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	56						GGGGCTGAACCAAGGATGATG	0.517		2	Mis		acute megakaryocytic leukemia|								6	102	---	---	---	---	PASS
ZNF486	90649	broad.mit.edu	37	19	20308008	20308008	+	Silent	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20308008T>C	uc002nou.2	+	4	546	c.489T>C	c.(487-489)TTT>TTC	p.F163F		NM_052852	NP_443084	Q96H40	ZN486_HUMAN	zinc finger protein 486	163	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						TGAAAGTCTTTCATCAATTTT	0.313													17	64	---	---	---	---	PASS
ZNF208	7757	broad.mit.edu	37	19	22154698	22154698	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22154698T>A	uc002nqp.2	-	6	2903	c.2754A>T	c.(2752-2754)GAA>GAT	p.E918D	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTGCCTTATGTTCAGTAAGGC	0.438													42	62	---	---	---	---	PASS
ZNF98	148198	broad.mit.edu	37	19	22575785	22575785	+	Intron	SNP	T	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22575785T>C	uc002nqt.2	-							NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				AATATACAACTGAAAGAAATA	0.289													4	12	---	---	---	---	PASS
ZNF99	7652	broad.mit.edu	37	19	22939259	22939259	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22939259G>C	uc010xrh.1	-	7	2912	c.2912C>G	c.(2911-2913)CCC>CGC	p.P971R		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				ACATTTGTAGGGTTTCTTTCC	0.373													10	22	---	---	---	---	PASS
SPTBN4	57731	broad.mit.edu	37	19	41066342	41066342	+	Intron	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41066342C>T	uc002ony.2	+						SPTBN4_uc002onx.2_Missense_Mutation_p.S1983F|SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron|SPTBN4_uc002ooa.2_Missense_Mutation_p.S659F	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CTTCCTGCCTCCCCCTGGTGG	0.527													17	4	---	---	---	---	PASS
ZNF114	163071	broad.mit.edu	37	19	48789340	48789340	+	Silent	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48789340T>A	uc002pil.1	+	6	956	c.459T>A	c.(457-459)CGT>CGA	p.R153R	ZNF114_uc010elv.1_Silent_p.R153R|ZNF114_uc002pim.1_Silent_p.R153R|ZNF114_uc002pin.2_Silent_p.R119R	NM_153608	NP_705836	Q8NC26	ZN114_HUMAN	zinc finger protein 114	153					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_epithelial(76;8.01e-05)|all_lung(116;0.000112)|Lung NSC(112;0.000192)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;7.56e-05)|all cancers(93;0.000113)|Epithelial(262;0.00962)|GBM - Glioblastoma multiforme(486;0.0153)		TCCTAACACGTGACTCAAGTA	0.408													29	29	---	---	---	---	PASS
LHB	3972	broad.mit.edu	37	19	49520350	49520350	+	5'Flank	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49520350C>A	uc002plt.2	-							NM_000894	NP_000885	P01229	LSHB_HUMAN	luteinizing hormone beta subunit precursor						cell-cell signaling|cellular nitrogen compound metabolic process|male gonad development|peptide hormone processing|progesterone biosynthetic process|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Lutropin alfa(DB00044)|Menotropins(DB00032)	CTTGGTGCATCCCCTGCCTCG	0.607													11	42	---	---	---	---	PASS
TEAD2	8463	broad.mit.edu	37	19	49854628	49854628	+	Intron	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49854628G>T	uc002pnj.2	-						TEAD2_uc002png.2_Intron|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		TCACACTGAGGGAAAAAGGAA	0.413													6	9	---	---	---	---	PASS
GPR32	2854	broad.mit.edu	37	19	51274370	51274370	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51274370C>T	uc010ycf.1	+	1	513	c.513C>T	c.(511-513)GCC>GCT	p.A171A		NM_001506	NP_001497	O75388	GPR32_HUMAN	G protein-coupled receptor 32	171	Helical; Name=4; (Potential).					integral to plasma membrane	N-formyl peptide receptor activity			upper_aerodigestive_tract(1)	1		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		TGGCCGCCGCCTTGTGCTCTG	0.592													12	18	---	---	---	---	PASS
KLK6	5653	broad.mit.edu	37	19	51470440	51470440	+	Missense_Mutation	SNP	G	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51470440G>C	uc002pui.2	-	4	442	c.182C>G	c.(181-183)GCC>GGC	p.A61G	KLK6_uc010eoj.2_Missense_Mutation_p.A61G|KLK6_uc002puh.2_Missense_Mutation_p.A70G|KLK6_uc002puj.2_5'UTR|KLK6_uc010ycn.1_Intron|KLK6_uc002pul.2_Missense_Mutation_p.A61G|KLK6_uc002pum.2_Intron	NM_001012964	NP_001012982	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6 isoform A	61	Peptidase S1.				amyloid precursor protein metabolic process|central nervous system development|collagen catabolic process|hormone metabolic process|myelination|positive regulation of G-protein coupled receptor protein signaling pathway|protein autoprocessing|proteolysis|regulation of cell differentiation|tissue regeneration	endoplasmic reticulum|extracellular region|microsome|mitochondrion|nucleolus	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		TTTGCAGTGGGCAGCTGTGAG	0.537													15	12	---	---	---	---	PASS
ETFB	2109	broad.mit.edu	37	19	51857763	51857763	+	Intron	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51857763C>G	uc002pwh.2	-						ETFB_uc002pwg.2_Missense_Mutation_p.E44Q	NM_001985	NP_001976	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		CTCCTTCTCTCATCCAGCCAT	0.318													16	19	---	---	---	---	PASS
ZNF813	126017	broad.mit.edu	37	19	53994668	53994668	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53994668G>A	uc002qbu.2	+	4	1310	c.1182G>A	c.(1180-1182)CAG>CAA	p.Q394Q	ZNF813_uc010eqq.1_Intron	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	394	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		CCTTCAGTCAGGAGTTAACCC	0.418													12	52	---	---	---	---	PASS
ZNF667	63934	broad.mit.edu	37	19	56952833	56952833	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56952833T>A	uc002qnd.2	-	5	1693	c.1531A>T	c.(1531-1533)AGT>TGT	p.S511C	ZNF667_uc010etl.2_Missense_Mutation_p.S293C|ZNF667_uc002qne.2_Missense_Mutation_p.S511C|ZNF667_uc010etm.2_Missense_Mutation_p.S454C	NM_022103	NP_071386	Q5HYK9	ZN667_HUMAN	zinc finger protein 667	511	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		AGGTGTGCACTCTGGCTGAAG	0.448													19	13	---	---	---	---	PASS
ZSCAN4	201516	broad.mit.edu	37	19	58187556	58187556	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58187556G>T	uc002qpu.2	+	3	740	c.43G>T	c.(43-45)GAG>TAG	p.E15*		NM_152677	NP_689890	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	15					telomere maintenance via telomere lengthening|viral reproduction	nuclear chromosome, telomeric region	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TGAACCATCCGAGAATAATCT	0.393													4	53	---	---	---	---	PASS
TMC2	117532	broad.mit.edu	37	20	2597739	2597739	+	Silent	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2597739A>T	uc002wgf.1	+	16	1977	c.1962A>T	c.(1960-1962)CCA>CCT	p.P654P	TMC2_uc002wgg.1_Silent_p.P638P	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2	654	Cytoplasmic (Potential).					integral to membrane				ovary(3)	3						TCTATGCTCCAGGCCTGGTGG	0.567													18	16	---	---	---	---	PASS
BMP2	650	broad.mit.edu	37	20	6759229	6759229	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6759229G>T	uc002wmu.1	+	3	1469	c.684G>T	c.(682-684)GTG>GTT	p.V228V		NM_001200	NP_001191	P12643	BMP2_HUMAN	bone morphogenetic protein 2 preproprotein	228					BMP signaling pathway involved in heart induction|bone mineralization involved in bone maturation|cardiac cell differentiation|cardiac epithelial to mesenchymal transition|cartilage development|growth|negative regulation of cell cycle|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|pathway-restricted SMAD protein phosphorylation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cartilage development|positive regulation of endothelial cell proliferation|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of phosphatase activity|positive regulation of transcription from RNA polymerase II promoter|SMAD protein signal transduction	extracellular space	activin receptor activity, type II|BMP receptor binding|cytokine activity|growth factor activity|phosphatase activator activity|protein heterodimerization activity|SMAD binding|transforming growth factor beta receptor binding			ovary(1)|breast(1)	2					Simvastatin(DB00641)	GATTCGTGGTGGAAGTGGCCC	0.522													4	18	---	---	---	---	PASS
DTD1	92675	broad.mit.edu	37	20	18576691	18576691	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18576691G>T	uc002wrf.3	+	3	337	c.176G>T	c.(175-177)AGT>ATT	p.S59I		NM_080820	NP_543010	Q8TEA8	DTD1_HUMAN	D-tyrosyl-tRNA deacylase 1	59					D-amino acid catabolic process	cytoplasm	hydrolase activity, acting on ester bonds			ovary(2)	2						GAGGATGAGAGTGGGAAGCAC	0.498													29	17	---	---	---	---	PASS
C20orf26	26074	broad.mit.edu	37	20	20269413	20269413	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20269413G>A	uc002wru.2	+	23	3033	c.2957G>A	c.(2956-2958)AGA>AAA	p.R986K	C20orf26_uc002wrw.2_Intron	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	986										ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		TTCTCCAATAGATACTACTCA	0.458													28	19	---	---	---	---	PASS
CSTL1	128817	broad.mit.edu	37	20	23424661	23424661	+	Missense_Mutation	SNP	C	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23424661C>G	uc002wte.2	+	3	556	c.310C>G	c.(310-312)CAA>GAA	p.Q104E	CSTL1_uc010zsu.1_RNA|CSTL1_uc010zsv.1_RNA	NM_138283	NP_612140	Q9H114	CST1L_HUMAN	cystatin-like 1 precursor	104						extracellular region	cysteine-type endopeptidase inhibitor activity				0	Colorectal(13;0.0993)|Lung NSC(19;0.235)					CTGCCCCCTGCAAAGCAAGAA	0.468													31	15	---	---	---	---	PASS
MYLK2	85366	broad.mit.edu	37	20	30409459	30409459	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30409459C>A	uc002wwq.2	+	4	793	c.691C>A	c.(691-693)CAG>AAG	p.Q231K		NM_033118	NP_149109	Q9H1R3	MYLK2_HUMAN	skeletal myosin light chain kinase	231					cardiac muscle tissue morphogenesis|regulation of muscle filament sliding		ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			lung(2)|skin(2)|ovary(1)|central_nervous_system(1)	6			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GATTGAGTTCCAGGCTGTTCC	0.607													5	52	---	---	---	---	PASS
CEP250	11190	broad.mit.edu	37	20	34078459	34078459	+	Intron	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34078459C>A	uc002xcm.2	+						CEP250_uc010zve.1_Intron	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2						centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			CTTCATGTGGCCAGGAGAAGG	0.338													3	12	---	---	---	---	PASS
KIAA1755	85449	broad.mit.edu	37	20	36874360	36874360	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36874360G>T	uc002xhy.1	-	2	444	c.172C>A	c.(172-174)CTG>ATG	p.L58M	KIAA1755_uc002xhz.1_Missense_Mutation_p.L58M	NM_001029864	NP_001025035	Q5JYT7	K1755_HUMAN	hypothetical protein LOC85449	58										ovary(4)|pancreas(1)	5		Myeloproliferative disorder(115;0.00874)				TGCTCACACAGGCGCTTGGCA	0.587													5	29	---	---	---	---	PASS
ARFGEF2	10564	broad.mit.edu	37	20	47601934	47601934	+	Intron	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47601934G>A	uc002xtx.3	+						ARFGEF2_uc010zyf.1_Intron	NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine						exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			AAGTGAGTGTGTATGTTTCAG	0.463													18	11	---	---	---	---	PASS
FAM65C	140876	broad.mit.edu	37	20	49219090	49219090	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49219090C>A	uc002xvm.2	-	13	1484	c.1166G>T	c.(1165-1167)CGG>CTG	p.R389L	FAM65C_uc010zyt.1_Missense_Mutation_p.R393L|FAM65C_uc010zyu.1_RNA|FAM65C_uc002xvn.1_Missense_Mutation_p.R389L	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876	389										ovary(2)	2						GCTGGGACCCCGGAGGTCGCT	0.637													3	14	---	---	---	---	PASS
TH1L	51497	broad.mit.edu	37	20	57564617	57564617	+	Silent	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57564617G>T	uc002yag.2	+	6	633	c.606G>T	c.(604-606)TCG>TCT	p.S202S	TH1L_uc010zzu.1_Silent_p.S202S|TH1L_uc002yaf.1_RNA|TH1L_uc002yah.2_Silent_p.S202S	NM_198976	NP_945327	Q8IXH7	NELFD_HUMAN	TH1-like protein	202					negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	all_lung(29;0.00711)		Colorectal(105;0.109)			AAGTGTTCTCGAGAGTGCTCC	0.463													8	155	---	---	---	---	PASS
CDH26	60437	broad.mit.edu	37	20	58564203	58564203	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58564203C>A	uc002ybe.2	+	9	1568	c.1268C>A	c.(1267-1269)CCA>CAA	p.P423Q	CDH26_uc002ybf.1_Missense_Mutation_p.P3Q|CDH26_uc010zzy.1_RNA	NM_177980	NP_817089	Q8IXH8	CAD26_HUMAN	cadherin-like 26 isoform a	423	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			GCCATGGATCCAGACAGCCAG	0.522													6	144	---	---	---	---	PASS
PRPF6	24148	broad.mit.edu	37	20	62655899	62655899	+	Intron	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62655899A>G	uc002yho.2	+						PRPF6_uc002yhp.2_Intron	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog						assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)					GTGGCCTCTTATCTTGCAGGG	0.592													7	14	---	---	---	---	PASS
PRPF6	24148	broad.mit.edu	37	20	62660759	62660759	+	Nonsense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62660759G>T	uc002yho.2	+	19	2629	c.2461G>T	c.(2461-2463)GAG>TAG	p.E821*	PRPF6_uc002yhp.2_Nonsense_Mutation_p.E781*	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog	821					assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)					CATCTTCCTCGAGGCAAGGCC	0.572													4	47	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	10944758	10944758	+	Missense_Mutation	SNP	T	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10944758T>A	uc002yip.1	-	11	844	c.476A>T	c.(475-477)AAC>ATC	p.N159I	TPTE_uc002yis.1_RNA|TPTE_uc002yiq.1_Missense_Mutation_p.N141I|TPTE_uc002yir.1_Missense_Mutation_p.N121I|TPTE_uc010gkv.1_Missense_Mutation_p.N21I	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	159					signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ATCTAAAATGTTAAATAAGTC	0.318													14	68	---	---	---	---	PASS
HUNK	30811	broad.mit.edu	37	21	33371371	33371371	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33371371G>T	uc002yph.2	+	11	2379	c.2019G>T	c.(2017-2019)AGG>AGT	p.R673S		NM_014586	NP_055401	P57058	HUNK_HUMAN	hormonally upregulated Neu-associated kinase	673					multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity			stomach(1)|skin(1)	2						AGATGTTAAGGAAGCGCCATC	0.612													13	27	---	---	---	---	PASS
IFNAR1	3454	broad.mit.edu	37	21	34715845	34715845	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34715845G>T	uc002yrn.2	+	5	683	c.536G>T	c.(535-537)AGG>ATG	p.R179M	IFNAR1_uc011adv.1_Missense_Mutation_p.R110M	NM_000629	NP_000620	P17181	INAR1_HUMAN	interferon-alpha receptor 1 precursor	179	Fibronectin type-III 1.|Extracellular (Potential).				JAK-STAT cascade|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	integral to plasma membrane	type I interferon receptor activity			central_nervous_system(1)|skin(1)	2					Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)	TTATAGGAAAGGATTGAAAAT	0.284													5	30	---	---	---	---	PASS
MX2	4600	broad.mit.edu	37	21	42771143	42771143	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42771143G>T	uc002yzf.1	+	10	1397	c.1293G>T	c.(1291-1293)CAG>CAT	p.Q431H	MX2_uc002yzg.1_Missense_Mutation_p.Q154H|MX2_uc010gop.1_Intron	NM_002463	NP_002454	P20592	MX2_HUMAN	myxovirus resistance protein 2	431					response to virus|type I interferon-mediated signaling pathway	cytoplasm|nucleus	GTP binding|GTPase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				TGTTTAATCAGGACATCGAAA	0.383													5	63	---	---	---	---	PASS
TPST2	8459	broad.mit.edu	37	22	26937263	26937263	+	Missense_Mutation	SNP	C	A	A	rs142901851	byFrequency	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26937263C>A	uc003acv.2	-	2	502	c.334G>T	c.(334-336)GCC>TCC	p.A112S	TPST2_uc003acw.2_Missense_Mutation_p.A112S|TPST2_uc003acx.2_Missense_Mutation_p.A112S|TPST2_uc011akf.1_Missense_Mutation_p.A112S	NM_003595	NP_003586	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	112	Lumenal (Potential).				peptidyl-tyrosine sulfation	endoplasmic reticulum|Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity			central_nervous_system(1)	1						TTGGACCAGGCCTGGCGCATG	0.687													5	9	---	---	---	---	PASS
NF2	4771	broad.mit.edu	37	22	30035117	30035117	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30035117C>A	uc003age.3	+	3	722	c.279C>A	c.(277-279)ACC>ACA	p.T93T	NF2_uc003afy.3_Silent_p.T93T|NF2_uc003afz.3_Intron|NF2_uc003agf.3_Silent_p.T93T|NF2_uc003agb.3_Silent_p.T16T|NF2_uc003agc.3_Silent_p.T55T|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Silent_p.T93T|NF2_uc003aga.3_Silent_p.T51T|NF2_uc003agh.3_Intron|NF2_uc003agi.3_Intron|NF2_uc003agj.3_Silent_p.T93T|NF2_uc003agk.3_Silent_p.T55T	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1	93	FERM.				actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.H84_F100del(1)|p.V86_Q111>E(1)|p.F94fs*27(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						AACCAGTCACCTTTCACTTCT	0.433			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				5	58	---	---	---	---	PASS
C22orf33	339669	broad.mit.edu	37	22	37397983	37397983	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37397983C>T	uc003aqf.2	-	3	530	c.384G>A	c.(382-384)CAG>CAA	p.Q128Q	C22orf33_uc003aqe.2_Silent_p.Q43Q	NM_001163857	NP_001157329	O43247	EAN57_HUMAN	hypothetical protein LOC339669 isoform 1	128											0						TCCTCTGGTCCTGAGCCCCCA	0.622													4	8	---	---	---	---	PASS
SMCR7L	54471	broad.mit.edu	37	22	39908363	39908363	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39908363C>A	uc003axx.2	+	5	947	c.449C>A	c.(448-450)CCT>CAT	p.P150H	SMCR7L_uc003axw.2_Missense_Mutation_p.P150H|SMCR7L_uc010gxz.1_Translation_Start_Site|SMCR7L_uc003axy.2_Translation_Start_Site	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	150						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)					GCAGCCATCCCTGCTGGAGAG	0.607													5	22	---	---	---	---	PASS
MEI1	150365	broad.mit.edu	37	22	42172170	42172170	+	Missense_Mutation	SNP	T	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42172170T>G	uc003baz.1	+	21	2634	c.2609T>G	c.(2608-2610)CTG>CGG	p.L870R	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|MEI1_uc011apd.1_RNA|MEI1_uc003bbb.1_Missense_Mutation_p.L256R|MEI1_uc003bbc.1_Missense_Mutation_p.L238R|MEI1_uc010gym.1_Missense_Mutation_p.L238R|MEI1_uc003bbd.1_Missense_Mutation_p.L113R|MEI1_uc010gyn.1_RNA|MEI1_uc003bbe.1_RNA	NM_152513	NP_689726	Q5TIA1	MEI1_HUMAN	meiosis defective 1	870							binding			central_nervous_system(1)|skin(1)	2						AGGACCTTCCTGAGGAGGAAT	0.552													12	48	---	---	---	---	PASS
WNT7B	7477	broad.mit.edu	37	22	46327162	46327162	+	Missense_Mutation	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46327162C>T	uc003bgo.2	-	3	760	c.386G>A	c.(385-387)AGC>AAC	p.S129N	WNT7B_uc010haa.2_Missense_Mutation_p.S133N	NM_058238	NP_478679	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family,	129					activation of JUN kinase activity|anterior/posterior pattern formation|axis specification|axonogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|central nervous system vasculogenesis|chorio-allantoic fusion|developmental growth involved in morphogenesis|embryonic placenta morphogenesis|establishment or maintenance of polarity of embryonic epithelium|fibroblast proliferation|forebrain regionalization|inner medullary collecting duct development|lens fiber cell development|lobar bronchus development|lung epithelium development|lung morphogenesis|lung-associated mesenchyme development|mammary gland epithelium development|metanephric collecting duct development|metanephric loop of Henle development|metanephros morphogenesis|negative regulation of smoothened signaling pathway|outer medullary collecting duct development|oxygen homeostasis|positive regulation of JNK cascade|positive regulation of osteoblast differentiation|renal inner medulla development|renal outer medulla development|stem cell proliferation|synapse organization|trachea cartilage morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled binding|signal transducer activity			lung(1)	1		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)		GCCGCAGTTGCTCAGGTTCCC	0.682													4	16	---	---	---	---	PASS
TUBGCP6	85378	broad.mit.edu	37	22	50678788	50678788	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50678788C>A	uc003bkb.1	-	2	1262	c.750G>T	c.(748-750)CCG>CCT	p.P250P	TUBGCP6_uc010har.1_Silent_p.P250P|TUBGCP6_uc010has.1_RNA|TUBGCP6_uc010hau.1_Silent_p.P250P	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	250					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-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)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GATCCACACTCGGTGGGACCT	0.547													3	16	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	229423	229423	+	5'Flank	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:229423G>A	uc004cpd.1	-						uc004cpe.1_Intron|uc011mgy.1_Missense_Mutation_p.A60V	NM_012227	NP_036359			pseudoautosomal GTP-binding protein-like																		TCCCCTGGGCGCGTGCTCACC	0.701													4	9	---	---	---	---	PASS
TMEM27	57393	broad.mit.edu	37	X	15657828	15657828	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15657828C>A	uc004cxc.1	-	5	625	c.369G>T	c.(367-369)CTG>CTT	p.L123L		NM_020665	NP_065716	Q9HBJ8	TMM27_HUMAN	transmembrane protein 27 precursor	123	Extracellular (Potential).				proteolysis	integral to membrane	metallopeptidase activity|peptidyl-dipeptidase activity			ovary(1)	1	Hepatocellular(33;0.183)					TTAAAAATTCCAGAGTTTGGT	0.333													5	82	---	---	---	---	PASS
DCAF8L1	139425	broad.mit.edu	37	X	27998521	27998521	+	Missense_Mutation	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27998521C>A	uc004dbx.1	-	1	1046	c.931G>T	c.(931-933)GTG>TTG	p.V311L		NM_001017930	NP_001017930	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	311	WD 3.									ovary(3)|skin(1)	4						ATGGTGAACACAACGGCATCT	0.483													22	16	---	---	---	---	PASS
FAM47B	170062	broad.mit.edu	37	X	34961693	34961693	+	Missense_Mutation	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34961693G>A	uc004ddi.1	+	1	763	c.745G>A	c.(745-747)GTG>ATG	p.V249M		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	249	Pro-rich.									ovary(3)|breast(1)	4						TCATCTCCGCGTGGATCCTCC	0.627													27	17	---	---	---	---	PASS
AKAP4	8852	broad.mit.edu	37	X	49957417	49957417	+	Silent	SNP	G	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49957417G>A	uc004dow.1	-	5	2071	c.1947C>T	c.(1945-1947)TGC>TGT	p.C649C	AKAP4_uc004dov.1_Silent_p.C266C|AKAP4_uc010njp.1_Silent_p.C471C|AKAP4_uc004dou.1_Silent_p.C640C	NM_003886	NP_003877	Q5JQC9	AKAP4_HUMAN	A-kinase anchor protein 4 isoform 1	649					cell projection organization|single fertilization|sperm motility	cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum	protein kinase A binding			kidney(3)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	8	Ovarian(276;0.236)					TCTCACCTTCGCATGGATCCT	0.463													29	13	---	---	---	---	PASS
POU3F4	5456	broad.mit.edu	37	X	82763671	82763671	+	Silent	SNP	C	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82763671C>T	uc004eeg.2	+	1	403	c.339C>T	c.(337-339)GCC>GCT	p.A113A		NM_000307	NP_000298	P49335	PO3F4_HUMAN	POU domain, class 3, transcription factor 4	113					sensory perception of sound	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1						ACCCCAACGCCTGGGGGGCCA	0.652													7	3	---	---	---	---	PASS
NXF3	56000	broad.mit.edu	37	X	102335086	102335086	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102335086G>T	uc004eju.2	-	11	1057	c.986C>A	c.(985-987)CCA>CAA	p.P329Q	NXF3_uc010noi.1_Missense_Mutation_p.P179Q	NM_022052	NP_071335	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	329						cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3						CTTACAGGTTGGTAACCTCTT	0.537													8	198	---	---	---	---	PASS
IL1RAPL2	26280	broad.mit.edu	37	X	105011289	105011289	+	Silent	SNP	C	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105011289C>A	uc004elz.1	+	11	2452	c.1696C>A	c.(1696-1698)CGG>AGG	p.R566R		NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	566	Cytoplasmic (Potential).				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3						AATGCTACCTCGGTGCCATGT	0.438													5	127	---	---	---	---	PASS
PLS3	5358	broad.mit.edu	37	X	114864285	114864285	+	Intron	SNP	A	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114864285A>G	uc004eqd.2	+						PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron	NM_005032	NP_005023	P13797	PLST_HUMAN	plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2						CTTTGGTAAGATGTTAGCTTG	0.363													4	80	---	---	---	---	PASS
LONRF3	79836	broad.mit.edu	37	X	118116786	118116786	+	Silent	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118116786A>T	uc004eqw.2	+	3	970	c.939A>T	c.(937-939)GCA>GCT	p.A313A	LONRF3_uc004eqx.2_Intron|LONRF3_uc004eqy.2_RNA|LONRF3_uc004eqz.2_Silent_p.A5A	NM_001031855	NP_001027026	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger	313	TPR 4.				proteolysis		ATP-dependent peptidase activity|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)	2						CCTTCCAGGCACATTTCAGAA	0.423													42	22	---	---	---	---	PASS
DCAF12L1	139170	broad.mit.edu	37	X	125685298	125685298	+	Missense_Mutation	SNP	A	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125685298A>T	uc004eul.2	-	1	1545	c.1294T>A	c.(1294-1296)TAC>AAC	p.Y432N		NM_178470	NP_848565	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	432										skin(3)|ovary(1)	4						CAGTGGGTGTAGAGCGCATTG	0.557													44	28	---	---	---	---	PASS
F8	2157	broad.mit.edu	37	X	154182254	154182254	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154182254G>T	uc004fmt.2	-	12	1987	c.1816C>A	c.(1816-1818)CTC>ATC	p.L606I		NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	606	F5/8 type A 2.|Plastocyanin-like 4.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TTCTCTGTGAGGTACCAGCTT	0.428													7	123	---	---	---	---	PASS
IL9R	3581	broad.mit.edu	37	X	155232571	155232571	+	Missense_Mutation	SNP	G	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155232571G>T	uc004fnv.1	+	2	208	c.29G>T	c.(28-30)GGC>GTC	p.G10V	IL9R_uc010nvn.2_5'UTR|IL9R_uc004fnu.1_Missense_Mutation_p.G57V	NM_002186	NP_002177	Q01113	IL9R_HUMAN	interleukin 9 receptor precursor	10					cell proliferation	extracellular space|integral to plasma membrane	interleukin-9 receptor activity				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TCCCTTGCAGGCTGGACCTTG	0.622													11	54	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	1061691	1061692	+	IGR	INS	-	TT	TT	rs71578303		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1061691_1061692insTT								C1orf159 (9955 upstream) : MIR200B (40792 downstream)																							AAttctctctgttttttttttt	0.312													6	3	---	---	---	---	
CDK11B	984	broad.mit.edu	37	1	1649371	1649375	+	Intron	DEL	TAGAG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1649371_1649375delTAGAG	uc001agv.1	-						CDK11B_uc001ags.1_5'Flank|CDK11B_uc001agt.1_5'Flank|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc009vkr.2_Intron|CDK11A_uc009vks.2_Intron|CDK11A_uc010nys.1_Intron|CDK11A_uc010nyt.1_Intron|CDK11A_uc010nyu.1_Intron|CDK11A_uc009vkt.1_Intron|CDK11A_uc009vku.1_Intron|CDK11A_uc009vkv.1_Intron|CDK11A_uc001aht.1_Intron|CDK11B_uc001ahu.1_Intron|CDK11B_uc001ahv.1_Intron|CDK11B_uc001ahw.1_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						TGCTTTCAGCTAGAGTATTCTCTCT	0.483													5	3	---	---	---	---	
GNB1	2782	broad.mit.edu	37	1	1771979	1771980	+	Intron	DEL	CA	-	-	rs111435979		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1771979_1771980delCA	uc001aif.2	-						GNB1_uc009vky.2_Intron	NM_002074	NP_002065	P62873	GBB1_HUMAN	guanine nucleotide-binding protein, beta-1						cellular response to glucagon stimulus|energy reserve metabolic process|muscarinic acetylcholine receptor signaling pathway|platelet activation|Ras protein signal transduction|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|GTPase binding|signal transducer activity				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		aacacacacgcacacacacaca	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	1884029	1884030	+	IGR	INS	-	AAAG	AAAG	rs151085750	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1884029_1884030insAAAG								TMEM52 (33289 upstream) : KIAA1751 (722 downstream)																							gaagcaaagaaaaagaaagaaa	0.030													3	3	---	---	---	---	
KIAA1751	85452	broad.mit.edu	37	1	1893928	1893929	+	Intron	INS	-	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1893928_1893929insG	uc001aim.1	-						KIAA1751_uc009vkz.1_Intron	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452											pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		aaaaaaaaaaaaaaaagtaagt	0.000													4	2	---	---	---	---	
PRKCZ	5590	broad.mit.edu	37	1	2053116	2053117	+	Intron	INS	-	TTAT	TTAT	rs150842965	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2053116_2053117insTTAT	uc001aiq.2	+						PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron|PRKCZ_uc001ais.2_Intron	NM_002744	NP_002735	Q05513	KPCZ_HUMAN	protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)		cgtggtggtggttagggtcacg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5386478	5386479	+	IGR	INS	-	GCC	GCC	rs146867562	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5386478_5386479insGCC								AJAP1 (542628 upstream) : NPHP4 (536391 downstream)																							CCAGAGCTGTGGCCGCCTCCTC	0.411													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5818083	5818084	+	IGR	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5818083_5818084delCA								AJAP1 (974233 upstream) : NPHP4 (104786 downstream)																							agcactcatgcacacacacaca	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	9283494	9283496	+	IGR	DEL	CTT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9283494_9283496delCTT								MIR34A (71658 upstream) : H6PD (11367 downstream)																							cttcttcttccttcttcttcttc	0.000													4	3	---	---	---	---	
UBE4B	10277	broad.mit.edu	37	1	10132493	10132494	+	Intron	INS	-	T	T	rs34652791		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10132493_10132494insT	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1						apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		TAACTTCCATCTTTTTTTTTTT	0.297													9	4	---	---	---	---	
CASZ1	54897	broad.mit.edu	37	1	10771643	10771643	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10771643delA	uc001aro.2	-						CASZ1_uc001arp.1_Intron	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		acaggtactcaaaaaaaaaaa	0.104													4	3	---	---	---	---	
CASZ1	54897	broad.mit.edu	37	1	10845103	10845104	+	Intron	INS	-	CTTT	CTTT			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10845103_10845104insCTTT	uc001aro.2	-						CASZ1_uc001arp.1_Intron	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		ttgcttgcttgctttctttctg	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	12215063	12215063	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12215063delT								TNFRSF8 (10801 upstream) : TNFRSF1B (11997 downstream)																							CTGGAGGGCGTTAAGGAGGCA	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	16834947	16834947	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16834947delG								CROCCL2 (15751 upstream) : NBPF1 (55465 downstream)																							TGGGCTCAAAGGTTTCAACAG	0.373													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17005732	17005732	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17005732delA								MST1P2 (28818 upstream) : ESPNP (11981 downstream)																							TCAAGCTGAGAAGCCAAGCTA	0.463													4	2	---	---	---	---	
PADI2	11240	broad.mit.edu	37	1	17433273	17433274	+	Intron	INS	-	GAG	GAG	rs140393879	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17433273_17433274insGAG	uc001baf.2	-						PADI2_uc010ocm.1_Intron|PADI2_uc001bag.1_Intron	NM_007365	NP_031391	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity			ovary(3)|pancreas(1)|central_nervous_system(1)|skin(1)	6		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	gaaagatgagagaggaggagga	0.000													2	6	---	---	---	---	
UBR4	23352	broad.mit.edu	37	1	19465779	19465779	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19465779delA	uc001bbi.2	-						UBR4_uc001bbk.1_Intron	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600						interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		aacaaaaaacaaaaaaaACCC	0.378													10	5	---	---	---	---	
PLA2G5	5322	broad.mit.edu	37	1	20403078	20403079	+	Intron	DEL	CT	-	-	rs77411181		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20403078_20403079delCT	uc001bcy.2	+						PLA2G5_uc001bcw.2_Intron|PLA2G5_uc001bcx.2_Intron	NM_000929	NP_000920	P39877	PA2G5_HUMAN	phospholipase A2, group V precursor						lipid catabolic process	extracellular region	calcium ion binding|calcium-dependent phospholipase A2 activity			skin(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)		acatctgcccctctgtttcctt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20817008	20817021	+	IGR	DEL	CACACACACACACA	-	-	rs71772616		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20817008_20817021delCACACACACACACA								CAMK2N1 (4280 upstream) : MUL1 (8922 downstream)																							CCGCCTCGTCcacacacacacacacacacacaca	0.463													4	2	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21465335	21465336	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21465335_21465336insA	uc001bef.2	-						EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		CTTCCTCATGGAAAAAAAATAG	0.089													4	2	---	---	---	---	
C1QC	714	broad.mit.edu	37	1	22967698	22967699	+	5'Flank	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22967698_22967699delCA	uc001bgc.3	+						C1QC_uc001bga.3_5'Flank|C1QC_uc001bgb.2_5'Flank	NM_172369	NP_758957	P02747	C1QC_HUMAN	complement component 1, q subcomponent, C chain						complement activation, classical pathway|innate immune response|negative regulation of granulocyte differentiation|negative regulation of macrophage differentiation	collagen					0		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.21e-27)|Colorectal(126;1.5e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.61e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000538)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.196)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTTTGTGCTGcacacacacaca	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	26256130	26256131	+	IGR	INS	-	AAA	AAA	rs139540066	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26256130_26256131insAAA								STMN1 (22762 upstream) : PAFAH2 (30129 downstream)																							gcgactctctcaaaaaaaaaag	0.188													4	3	---	---	---	---	
WASF2	10163	broad.mit.edu	37	1	27755512	27755513	+	Intron	DEL	TT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27755512_27755513delTT	uc001bof.1	-						WASF2_uc010ofl.1_Intron	NM_006990	NP_008921	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2						actin cytoskeleton organization|G-protein signaling, coupled to cAMP nucleotide second messenger	actin cytoskeleton|lamellipodium	actin binding			skin(2)|ovary(1)	3		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;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		TGTGTGAATCTTTTTTTTTTTT	0.317													5	3	---	---	---	---	
ZBTB8OS	339487	broad.mit.edu	37	1	33083912	33083912	+	Intron	DEL	T	-	-	rs66920845		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33083912delT	uc001bvo.1	-									Q8IWT0	ARCH_HUMAN	Homo sapiens cDNA FLJ75987 complete cds, highly similar to Homo sapiens zinc finger and BTB domain containing 8 opposite strand (ZBTB8OS), mRNA.												0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				tttttctttcttttttttttt	0.144													4	2	---	---	---	---	
FNDC5	252995	broad.mit.edu	37	1	33332284	33332289	+	Intron	DEL	AGTTTA	-	-	rs4045535		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33332284_33332289delAGTTTA	uc001bwg.2	-						FNDC5_uc001bwe.2_5'Flank|FNDC5_uc001bwf.1_Intron	NM_153756	NP_715637	Q8NAU1	FNDC5_HUMAN	fibronectin type III domain containing 5							integral to membrane|peroxisomal membrane				ovary(1)	1		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				actggattatagttTAAGTTCAGCCC	0.136													4	2	---	---	---	---	
AK2	204	broad.mit.edu	37	1	33476167	33476168	+	3'UTR	INS	-	TCTG	TCTG	rs145424098	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33476167_33476168insTCTG	uc001bwo.1	-	7					uc001bwn.2_Intron|AK2_uc010ohq.1_3'UTR|AK2_uc009vud.1_3'UTR	NM_013411	NP_037543	P54819	KAD2_HUMAN	adenylate kinase 2 isoform b						nucleobase, nucleoside and nucleotide interconversion	mitochondrial intermembrane space	adenylate kinase activity|ATP binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				AATATTGTGTCTATTTCTACCC	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	36252158	36252158	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36252158delA								CLSPN (16607 upstream) : EIF2C4 (21670 downstream)																							accttgtctcaaaaaaaaaaa	0.184													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	36592067	36592068	+	IGR	DEL	GT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36592067_36592068delGT								COL8A2 (26217 upstream) : TRAPPC3 (10107 downstream)																							GGATTTTGGGgtgtgtgtgtgt	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	36795305	36795306	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36795305_36795306insA								C1orf113 (4821 upstream) : STK40 (9919 downstream)																							tgaacacaatgaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38975951	38975951	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38975951delT								POU3F1 (463501 upstream) : RRAGC (329064 downstream)																							TCTTTCACCATTTTTAATACC	0.114													4	2	---	---	---	---	
RHBDL2	54933	broad.mit.edu	37	1	39377646	39377646	+	Intron	DEL	T	-	-	rs78403353		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39377646delT	uc001ccu.1	-						RHBDL2_uc010oin.1_Intron|RHBDL2_uc010oio.1_Intron	NM_017821	NP_060291	Q9NX52	RHBL2_HUMAN	rhomboid protease 2						proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity				0	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			gcccagctaattttttttttt	0.000													3	3	---	---	---	---	
PTPRF	5792	broad.mit.edu	37	1	44088117	44088118	+	3'UTR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44088117_44088118insT	uc001cjr.2	+	34					PTPRF_uc001cjs.2_3'UTR|PTPRF_uc001cju.2_3'UTR|PTPRF_uc009vwt.2_3'UTR|PTPRF_uc001cjv.2_3'UTR|PTPRF_uc001cjw.2_3'UTR	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ATTTTGTTTTGTTTTTTTTTTT	0.455													4	2	---	---	---	---	
SLC6A9	6536	broad.mit.edu	37	1	44477877	44477877	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44477877delG	uc001cll.2	-						SLC6A9_uc009vxe.2_Intron|SLC6A9_uc010okm.1_Intron|SLC6A9_uc001clm.2_Intron|SLC6A9_uc009vxd.2_Intron|SLC6A9_uc010okn.1_Intron|SLC6A9_uc001cln.2_Intron|SLC6A9_uc010oko.1_Intron|SLC6A9_uc010okp.1_Intron	NM_201649	NP_964012	P48067	SC6A9_HUMAN	solute carrier family 6 member 9 isoform 2							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)	AAGGCAGCCTGGTGCAGGTGA	0.542													4	2	---	---	---	---	
RNF220	55182	broad.mit.edu	37	1	44902524	44902524	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44902524delC	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						CGTCTGTTTACCCCTGGCACC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	51529373	51529376	+	IGR	DEL	TGTG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51529373_51529376delTGTG								CDKN2C (89066 upstream) : C1orf185 (38530 downstream)																							tgtatatatatgtgtgtgtgtgtg	0.034													2	4	---	---	---	---	
USP24	23358	broad.mit.edu	37	1	55619646	55619646	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55619646delT	uc001cyg.3	-							NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						ATACCTATAATTTCCCGATCT	0.348													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59441645	59441646	+	IGR	DEL	GT	-	-	rs113592069		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59441645_59441646delGT								JUN (191860 upstream) : LOC729467 (155964 downstream)																							ataaaGAGCAgtgtgtgtgtgt	0.084													4	2	---	---	---	---	
C1orf87	127795	broad.mit.edu	37	1	60535174	60535174	+	Intron	DEL	G	-	-	rs66496666		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60535174delG	uc001czs.1	-							NM_152377	NP_689590	Q8N0U7	CA087_HUMAN	hypothetical protein LOC127795								calcium ion binding			ovary(1)|breast(1)	2						gcacaaataagggGAAACCTG	0.149													2	4	---	---	---	---	
DOCK7	85440	broad.mit.edu	37	1	62954372	62954373	+	Intron	INS	-	A	A	rs145774892	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62954372_62954373insA	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc001dam.2_Intron|DOCK7_uc010oov.1_Intron	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2						ATTCAAAAATGAAAAAAAAAAG	0.262													4	5	---	---	---	---	
AK3L1	205	broad.mit.edu	37	1	65639545	65639546	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65639545_65639546insA	uc001dby.2	+						AK3L1_uc009wan.2_Intron|AK3L1_uc001dbz.2_Intron|AK3L1_uc001dca.2_Intron	NM_203464	NP_982289	P27144	KAD4_HUMAN	adenylate kinase 3-like 1 isoform 7							mitochondrial matrix	adenylate kinase activity|ATP binding|GTP binding				0						gaccctgtctcaaaaaaaaaaa	0.000													5	3	---	---	---	---	
NEGR1	257194	broad.mit.edu	37	1	72171541	72171544	+	Intron	DEL	AGGA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72171541_72171544delAGGA	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		gaaggaagagaggaaggaaggaag	0.039													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	78349933	78349933	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78349933delA								FAM73A (5856 upstream) : NEXN (4267 downstream)																							attcagttacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	84159820	84159820	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84159820delG	uc001diz.3	-											Homo sapiens cDNA clone IMAGE:4815396.																		GGATTTTTCAGAGGTGAATTA	0.348													4	2	---	---	---	---	
COL24A1	255631	broad.mit.edu	37	1	86324304	86324305	+	Intron	INS	-	TCCTTCCTTCATTCCTTCCT	TCCTTCCTTCATTCCTTCCT	rs61785060		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86324304_86324305insTCCTTCCTTCATTCCTTCCT	uc001dlj.2	-						COL24A1_uc001dli.2_Intron|COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		TATTTTCtccctccttccttcc	0.025													6	3	---	---	---	---	
FNBP1L	54874	broad.mit.edu	37	1	93925498	93925499	+	Intron	INS	-	TG	TG	rs34705153		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93925498_93925499insTG	uc001dpw.2	+						FNBP1L_uc001dpv.2_Intron	NM_001024948	NP_001020119	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like isoform 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	lipid binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		tggatttcagatgtgtgtgtgt	0.000													3	3	---	---	---	---	
BCAR3	8412	broad.mit.edu	37	1	94246126	94246127	+	Intron	INS	-	A	A	rs68137511		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94246126_94246127insA	uc001dqb.2	-							NM_003567	NP_003558	O75815	BCAR3_HUMAN	breast cancer antiestrogen resistance 3						response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		AAGAGGAGAGGAAAAAAAAAAA	0.450													4	2	---	---	---	---	
RWDD3	25950	broad.mit.edu	37	1	95706143	95706143	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95706143delA	uc009wdu.2	+						RWDD3_uc001drd.3_Intron|RWDD3_uc010oty.1_Intron|RWDD3_uc009wdt.2_Intron|RWDD3_uc001drf.3_Intron|RWDD3_uc001drh.3_Intron|RWDD3_uc009wdv.2_Intron|RWDD3_uc001drg.3_Intron|RWDD3_uc001dri.3_Intron	NM_015485	NP_056300	Q9Y3V2	RWDD3_HUMAN	RWD domain containing 3 isoform a							cytoplasm|nucleus	protein binding			ovary(1)	1		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)		GACATGGTATAAAATGGGTAG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96818060	96818061	+	IGR	INS	-	T	T	rs148969793	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96818060_96818061insT								None (None upstream) : PTBP2 (369114 downstream)																							catttgctgtgttttttttccc	0.000													3	3	---	---	---	---	
AKNAD1	254268	broad.mit.edu	37	1	109369062	109369062	+	Intron	DEL	A	-	-	rs34954897		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109369062delA	uc001dwa.2	-						AKNAD1_uc010ovb.1_Intron|AKNAD1_uc001dwb.2_Intron	NM_152763	NP_689976	Q5T1N1	AKND1_HUMAN	hypothetical protein LOC254268											ovary(3)	3						ACTATCTTTGAAAAAAAGGAT	0.448													4	5	---	---	---	---	
RAP1A	5906	broad.mit.edu	37	1	112137216	112137217	+	Intron	INS	-	AGGA	AGGA	rs138889267	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112137216_112137217insAGGA	uc001ebi.2	+							NM_002884	NP_002875	P62834	RAP1A_HUMAN	RAP1A, member of RAS oncogene family precursor						activation of MAPKK activity|blood coagulation|energy reserve metabolic process|nerve growth factor receptor signaling pathway|regulation of insulin secretion	cytosol|plasma membrane	GTP binding|GTPase activity				0		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)		ggaagggagggaggaaggaagc	0.149													6	3	---	---	---	---	
KCND3	3752	broad.mit.edu	37	1	112502665	112502665	+	Intron	DEL	A	-	-	rs67327865		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112502665delA	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)		ggaaaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	112624400	112624400	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112624400delT								KCND3 (92623 upstream) : CTTNBP2NL (314400 downstream)																							AAATATTGCAtttttttttta	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	114717471	114717471	+	IGR	DEL	A	-	-	rs34702296		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114717471delA								SYT6 (20999 upstream) : TRIM33 (217930 downstream)																							TGTGGCTCAGAAAAGTTACAG	0.378													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	115767073	115767074	+	IGR	DEL	AC	-	-	rs67836434		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115767073_115767074delAC								TSPAN2 (134958 upstream) : NGF (61463 downstream)																							ATacacacatacacacacacac	0.361													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120144994	120144994	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120144994delG								HSD3B1 (87313 upstream) : ZNF697 (17006 downstream)																							ACTGGACAATGAACTATCAag	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142608175	142608176	+	IGR	DEL	TG	-	-	rs141317539		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142608175_142608176delTG								None (None upstream) : None (None downstream)																							tgacaaaaactgcatgattatc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142617860	142617861	+	5'Flank	INS	-	TTGA	TTGA	rs79194507	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142617860_142617861insTTGA	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		GATAGGGAGATTTGATTGATGG	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143423460	143423461	+	IGR	INS	-	G	G	rs113197697		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143423460_143423461insG								None (None upstream) : LOC100286793 (224178 downstream)																							ccagtgcaacacacacacagca	0.000													3	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144928113	144928113	+	Intron	DEL	A	-	-	rs67719372		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144928113delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_Intron|PDE4DIP_uc001emf.1_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		agaaggaaagaaaaaaaagag	0.219			T	PDGFRB	MPD								1	5	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145054268	145054269	+	Intron	INS	-	G	G	rs149978567		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145054268_145054269insG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						TGTGGTTACCTTCATTCATTTA	0.386													7	4	---	---	---	---	
OTUD7B	56957	broad.mit.edu	37	1	149922309	149922309	+	Intron	DEL	T	-	-	rs111618537		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149922309delT	uc001etn.2	-							NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne						negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			TCTACCTCCGTTTTCACAGAT	0.393													2	5	---	---	---	---	
SNX27	81609	broad.mit.edu	37	1	151591876	151591876	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151591876delT	uc001eyn.1	+							NM_030918	NP_112180	Q96L92	SNX27_HUMAN	sorting nexin family member 27						cell communication|protein transport|signal transduction	cytosol|early endosome	phosphatidylinositol binding|protein binding			ovary(2)|central_nervous_system(1)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			TTTTGGTTTCTTTTTtcctct	0.090													4	2	---	---	---	---	
SMCP	4184	broad.mit.edu	37	1	152855136	152855137	+	Intron	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152855136_152855137delCA	uc001fat.2	+							NM_030663	NP_109588	P49901	MCSP_HUMAN	sperm mitochondria-associated cysteine-rich						penetration of zona pellucida|sperm motility	mitochondrial membrane					0	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CACTTAGGTGcacacacacaca	0.371													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	155095347	155095347	+	IGR	DEL	T	-	-	rs144448235		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155095347delT								EFNA3 (35341 upstream) : EFNA1 (5002 downstream)																							TGCAGGGttcttttttttttt	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	156003648	156003649	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156003648_156003649insA								SSR2 (12890 upstream) : UBQLN4 (1444 downstream)																							aaaaaaaaaccaaaaaaaaaaa	0.168													4	2	---	---	---	---	
SMG5	23381	broad.mit.edu	37	1	156248169	156248169	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156248169delT	uc001foc.3	-							NM_015327	NP_056142	Q9UPR3	SMG5_HUMAN	SMG5 homolog nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|nucleus	protein phosphatase 2A binding			ovary(2)|skin(2)|pancreas(1)	5	Hepatocellular(266;0.158)					TAtttttgggttttttttttt	0.184													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159717642	159717643	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159717642_159717643insT								CRP (33263 upstream) : DUSP23 (33116 downstream)																							TCTTCAAATTAttttttttttg	0.183													4	2	---	---	---	---	
C1orf204	284677	broad.mit.edu	37	1	159821951	159821954	+	Intron	DEL	AGAC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159821951_159821954delAGAC	uc001fug.1	-						C1orf204_uc001fuf.1_Intron	NM_001134233	NP_001127705	Q5VU13	VSIG8_HUMAN	hypothetical protein LOC284677							integral to membrane					0						AAAAAATCAAagacagacagacag	0.260													4	2	---	---	---	---	
PBX1	5087	broad.mit.edu	37	1	164655666	164655667	+	Intron	DEL	AG	-	-	rs144926339		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164655666_164655667delAG	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron	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						GGAATCAAACAGAGTGAAAACA	0.455			T	TCF3|EWSR1	pre B-ALL|myoepithelioma								3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165440277	165440277	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165440277delA								RXRG (25847 upstream) : LOC400794 (5802 downstream)																							aggctcaggcaggtggatcac	0.100													4	2	---	---	---	---	
LOC400794	400794	broad.mit.edu	37	1	165451256	165451259	+	Intron	DEL	GAAG	-	-	rs113568027		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165451256_165451259delGAAG	uc001gdc.2	-						LOC400794_uc001gdd.2_Intron	NR_026744				Homo sapiens cDNA FLJ35813 fis, clone TESTI2006067.												0						aagaaagaaagaaggaaggaagga	0.093													4	3	---	---	---	---	
TADA1	117143	broad.mit.edu	37	1	166829916	166829916	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166829916delT	uc001gdw.2	-						TADA1_uc001gdv.2_Intron	NM_053053	NP_444281	Q96BN2	TADA1_HUMAN	transcriptional adaptor 1-like						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(1)	1						CAAAAATGACtttttttttta	0.154													4	3	---	---	---	---	
CREG1	8804	broad.mit.edu	37	1	167515717	167515717	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167515717delA	uc001gel.2	-							NM_003851	NP_003842	O75629	CREG1_HUMAN	cellular repressor of E1A-stimulated genes						cell proliferation|multicellular organismal development|regulation of growth|regulation of transcription from RNA polymerase II promoter	extracellular region	FMN binding|transcription corepressor activity				0						catctctactaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168181054	168181054	+	IGR	DEL	A	-	-	rs34941532		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168181054delA								TIPRL (9705 upstream) : SFT2D2 (14201 downstream)																							aaaaagattgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	172176251	172176252	+	Intron	INS	-	G	G	rs147287017	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172176251_172176252insG	uc001gie.2	+						DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						AGTCTAACACAGGTCAGAAGGA	0.446													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	173364959	173364960	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173364959_173364960insT	uc001gix.1	-											Homo sapiens cDNA FLJ45305 fis, clone BRHIP3004193.																		aattctagtagttttttttgcc	0.000													4	2	---	---	---	---	
KIAA0040	9674	broad.mit.edu	37	1	175140003	175140022	+	Intron	DEL	ACTAGAAGTATGACATCTAA	-	-	rs67512742		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175140003_175140022delACTAGAAGTATGACATCTAA	uc009wws.2	-						KIAA0040_uc001gkn.3_Intron|KIAA0040_uc010pmy.1_Intron|KIAA0040_uc001gko.3_Intron	NM_014656	NP_055471	Q15053	K0040_HUMAN	hypothetical protein LOC9674												0						gcttcccgtcactagaagtatgacatctaaactagaagta	0.000													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175620037	175620037	+	Intron	DEL	T	-	-	rs112456733		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175620037delT	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)					ACTACCCCTCTCCCACCTCAT	0.065													4	3	---	---	---	---	
PAPPA2	60676	broad.mit.edu	37	1	176533118	176533118	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176533118delT	uc001gkz.2	+						PAPPA2_uc001gky.1_Intron|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						tccttccctcttttttttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177691561	177691561	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177691561delA								FAM5B (440004 upstream) : SEC16B (205928 downstream)																							tccaggtactaaaaattctga	0.000													4	2	---	---	---	---	
C1orf125	126859	broad.mit.edu	37	1	179397089	179397090	+	Intron	DEL	AA	-	-	rs10548259		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179397089_179397090delAA	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmn.1_Intron|C1orf125_uc010pnl.1_Intron|C1orf125_uc001gmp.2_Intron	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1												0						CAATCCATGTAAAAAAAAAAAA	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181360677	181360677	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181360677delG								IER5 (300700 upstream) : CACNA1E (92039 downstream)																							ggggctgtctgggggggaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181938648	181938648	+	IGR	DEL	A	-	-	rs34558966		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181938648delA								CACNA1E (167935 upstream) : ZNF648 (85059 downstream)																							ctctggagggaaaaaaagaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	184636383	184636384	+	IGR	INS	-	TG	TG	rs146693469	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184636383_184636384insTG								C1orf21 (38228 upstream) : EDEM3 (23243 downstream)																							acagaagtatttgtgtgtgtgt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193341320	193341320	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193341320delC								CDC73 (117380 upstream) : None (None downstream)																							AATTATTTCGCCCCCCCCAGA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	196991064	196991065	+	IGR	DEL	CT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196991064_196991065delCT								CFHR5 (12263 upstream) : F13B (17256 downstream)																							ctctctctccctctctctctct	0.000													4	3	---	---	---	---	
PTPN7	5778	broad.mit.edu	37	1	202117975	202117976	+	Intron	INS	-	TTT	TTT	rs35165620		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202117975_202117976insTTT	uc001gxm.1	-						PTPN7_uc001gxl.1_Intron|PTPN7_uc001gxn.1_Intron|PTPN7_uc010ppv.1_Intron|PTPN7_uc010ppw.1_Intron|PTPN7_uc010ppx.1_Intron|PTPN7_uc010ppy.1_Intron	NM_002832	NP_002823	P35236	PTN7_HUMAN	protein tyrosine phosphatase, non-receptor type							cytosol|internal side of plasma membrane	protein binding|protein tyrosine phosphatase activity			skin(1)	1						CATCTTTTCACttttttttttt	0.228													5	3	---	---	---	---	
SYT2	127833	broad.mit.edu	37	1	202593970	202593986	+	Intron	DEL	GTGTGGTGTGTAGTAGG	-	-	rs147837245		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202593970_202593986delGTGTGGTGTGTAGTAGG	uc001gye.2	-						SYT2_uc010pqb.1_Intron|SYT2_uc009xaf.2_Intron	NM_001136504	NP_001129976	Q8N9I0	SYT2_HUMAN	synaptotagmin II						neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	agtagggtgtgtgtggtgtgtagtagggtgtgtggtg	0.000													3	3	---	---	---	---	
SYT2	127833	broad.mit.edu	37	1	202678220	202678220	+	Intron	DEL	G	-	-	rs138891625		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202678220delG	uc010pqb.1	-						SYT2_uc009xaf.2_Intron	NM_177402	NP_796376	Q8N9I0	SYT2_HUMAN	synaptotagmin II						neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	CTGGCTTCCTGGGCGCCCCCA	0.622													3	3	---	---	---	---	
MYBPH	4608	broad.mit.edu	37	1	203137416	203137416	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203137416delG	uc001gzh.1	-						FMOD_uc010pqi.1_Intron	NM_004997	NP_004988	Q13203	MYBPH_HUMAN	myosin binding protein H						cell adhesion|regulation of striated muscle contraction	myosin filament	structural constituent of muscle				0			BRCA - Breast invasive adenocarcinoma(75;0.153)	Colorectal(1306;0.0306)		agaaccaccaggggaaggaag	0.269													4	2	---	---	---	---	
KISS1	3814	broad.mit.edu	37	1	204164398	204164401	+	Intron	DEL	ACAT	-	-	rs60254480		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204164398_204164401delACAT	uc001har.2	-							NM_002256	NP_002247	Q15726	KISS1_HUMAN	KiSS-1 metastasis-suppressor						cytoskeleton organization	extracellular region	protein binding			ovary(1)	1	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)	Breast(1374;9.42e-05)	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.069)|Kidney(21;0.0934)|Epithelial(59;0.239)	Colorectal(1306;0.0129)		atacacacacacatacaccacaca	0.000													4	2	---	---	---	---	
LRRN2	10446	broad.mit.edu	37	1	204624740	204624740	+	Intron	DEL	T	-	-	rs72273884		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204624740delT	uc001hbe.1	-						MDM4_uc001hbd.1_Intron|LRRN2_uc001hbf.1_Intron|LRRN2_uc009xbf.1_Intron	NM_006338	NP_006329	O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2 precursor						cell adhesion	integral to membrane	receptor activity			central_nervous_system(2)	2	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			GGTTTTTTTGTTTTTTTTTTT	0.095													4	2	---	---	---	---	
CR1L	1379	broad.mit.edu	37	1	207820368	207820369	+	Intron	DEL	AC	-	-	rs140725822		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207820368_207820369delAC	uc001hga.3	+						CR1L_uc001hfz.2_Intron	NM_175710	NP_783641	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like							cytoplasm|extracellular region|membrane					0						ctatttgtttacacacacgtac	0.124													3	3	---	---	---	---	
CR1L	1379	broad.mit.edu	37	1	207821933	207821934	+	Intron	DEL	AT	-	-	rs35272095		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207821933_207821934delAT	uc001hga.3	+						CR1L_uc001hfz.2_Intron	NM_175710	NP_783641	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like							cytoplasm|extracellular region|membrane					0						AGAAGGAAACATGTGTCAAATT	0.475													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	211783335	211783336	+	IGR	INS	-	C	C	rs139058475	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211783335_211783336insC								SLC30A1 (31236 upstream) : NEK2 (52779 downstream)																							tctaaatcagacttcctggaca	0.000													4	3	---	---	---	---	
PTPN14	5784	broad.mit.edu	37	1	214546902	214546911	+	Intron	DEL	ACACACACAC	-	-	rs150857818		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214546902_214546911delACACACACAC	uc001hkk.1	-							NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		tttcattgaaacacacacacacacacacac	0.024													6	3	---	---	---	---	
KCNK2	3776	broad.mit.edu	37	1	215387728	215387728	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215387728delC	uc001hkq.2	+						KCNK2_uc001hko.2_Intron|KCNK2_uc009xdm.2_Intron|KCNK2_uc001hkp.2_Intron|KCNK2_uc001hkr.3_Intron	NM_001017425	NP_001017425	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2 isoform								outward rectifier potassium channel activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)	ctaatcagctcccaccaggtc	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	215427621	215427621	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215427621delT								KCNK2 (17186 upstream) : KCTD3 (313114 downstream)																							AATACAGCACTTTTTTTTTTC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222301801	222301802	+	IGR	INS	-	GTGT	GTGT	rs148592805	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222301801_222301802insGTGT								DUSP10 (386340 upstream) : HHIPL2 (393800 downstream)																							tgcgtgtgtgcgtgtgtgtgtg	0.257													3	4	---	---	---	---	
CAPN8	388743	broad.mit.edu	37	1	223811778	223811779	+	Intron	INS	-	TATT	TATT	rs150358210	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223811778_223811779insTATT	uc009xee.2	-							NM_001143962	NP_001137434	A6NHC0	CAN8_HUMAN	calpain 8						proteolysis	Golgi apparatus	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity				0						TCATTTAACTCTAtttatttat	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	226223750	226223750	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226223750delA								C1orf55 (36684 upstream) : H3F3A (26671 downstream)																							TGCCAATAGGAAAAACTCCTC	0.443													4	2	---	---	---	---	
C1orf95	375057	broad.mit.edu	37	1	226765200	226765201	+	Intron	INS	-	CACA	CACA	rs141418780	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226765200_226765201insCACA	uc010pvn.1	+							NM_001003665	NP_001003665	Q69YW2	CA095_HUMAN	hypothetical protein LOC375057							integral to membrane				ovary(1)	1	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)		AAACAGTTTCTcacacacacac	0.431													4	2	---	---	---	---	
CABC1	56997	broad.mit.edu	37	1	227148244	227148246	+	Intron	DEL	TGG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227148244_227148246delTGG	uc001hqm.1	+						CABC1_uc010pvp.1_Intron|CABC1_uc001hqn.1_Intron|CABC1_uc009xeq.1_Intron|CABC1_uc010pvq.1_Intron	NM_020247	NP_064632	Q8NI60	ADCK3_HUMAN	chaperone, ABC1 activity of bc1 complex like						cell death	mitochondrion	ATP binding|protein serine/threonine kinase activity				0		Prostate(94;0.0771)				tggttgtacttggtggtggtgtc	0.000													4	3	---	---	---	---	
CDC42BPA	8476	broad.mit.edu	37	1	227400857	227400857	+	Frame_Shift_Del	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227400857delC	uc001hqr.2	-	3	1277	c.334delG	c.(334-336)GAAfs	p.E112fs	CDC42BPA_uc001hqs.2_Frame_Shift_Del_p.E112fs|CDC42BPA_uc009xes.2_Frame_Shift_Del_p.E112fs|CDC42BPA_uc010pvs.1_Frame_Shift_Del_p.E112fs	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	112	Protein kinase.				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)				TTCAGCATTTCCCATTTATTC	0.239													36	16	---	---	---	---	
RHOU	58480	broad.mit.edu	37	1	228873094	228873094	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228873094delT	uc001htf.2	+							NM_021205	NP_067028	Q7L0Q8	RHOU_HUMAN	ras homolog gene family, member U						regulation of small GTPase mediated signal transduction	cell projection|cytosol|focal adhesion|Golgi membrane|podosome	GTP binding|metal ion binding|protein binding				0	Breast(184;0.162)	Prostate(94;0.183)				CCCAGTGTTGTTTTTAGGTCC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228917698	228917701	+	IGR	DEL	GTGT	-	-	rs142063466		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228917698_228917701delGTGT								RHOU (35289 upstream) : RAB4A (489178 downstream)																							tgtgtgtgtggtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
GALNT2	2590	broad.mit.edu	37	1	230401944	230401947	+	Intron	DEL	AAAC	-	-	rs72325196		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230401944_230401947delAAAC	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron|GALNT2_uc001htu.2_Intron	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				ctgtctcaaaaaacaaacaaacaa	0.186													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232468965	232468965	+	IGR	DEL	C	-	-	rs113707890		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232468965delC								DISC1 (291949 upstream) : SIPA1L2 (64749 downstream)																							TGCCTCCCCACCCCCACAGaa	0.284													3	4	---	---	---	---	
SLC35F3	148641	broad.mit.edu	37	1	234234302	234234304	+	Intron	DEL	TGG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234234302_234234304delTGG	uc001hvy.1	+							NM_173508	NP_775779	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			tggtgattattggtggtggtggt	0.138													4	2	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	241090918	241090918	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241090918delA	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			AAAATCGTAGAAAATGAAGCA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244388595	244388595	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244388595delT								ZNF238 (167819 upstream) : C1orf100 (127342 downstream)																							tgcccagctattttttttttg	0.000													4	2	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245766448	245766448	+	Intron	DEL	A	-	-	rs5782358		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245766448delA	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron|KIF26B_uc001ibg.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)			GTACGAAGGGAAAAAAAAAAG	0.493													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4518009	4518011	+	IGR	DEL	AAG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4518009_4518011delAAG								ALLC (767751 upstream) : None (None downstream)																							ggaggagaacaaggaggaggagg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8990306	8990307	+	IGR	INS	-	AAT	AAT	rs146083951	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8990306_8990307insAAT								KIDINS220 (12551 upstream) : MBOAT2 (6394 downstream)																							gtagccagggaaataataatta	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	9854406	9854406	+	IGR	DEL	A	-	-	rs5829233		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9854406delA								YWHAQ (83300 upstream) : TAF1B (129165 downstream)																							gaatctctacaaaaattaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	9879582	9879583	+	IGR	INS	-	T	T	rs150030572		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9879582_9879583insT								YWHAQ (108476 upstream) : TAF1B (103988 downstream)																							TTTGTTTTttcttttttttttt	0.267													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10397396	10397397	+	IGR	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10397396_10397397delCA								C2orf48 (45540 upstream) : HPCAL1 (45643 downstream)																							AGTGTGCGGTCACCACCCCTGC	0.589													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	13235514	13235515	+	IGR	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13235514_13235515delCA								TRIB2 (352658 upstream) : None (None downstream)																							GATTCAGCAGCACACACACACA	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20013193	20013194	+	IGR	DEL	GT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20013193_20013194delGT								OSR1 (454821 upstream) : TTC32 (83324 downstream)																							AATCATCAACgtgtgtgtgtgt	0.084													4	2	---	---	---	---	
UBXN2A	165324	broad.mit.edu	37	2	24151048	24151048	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24151048delA	uc010exy.2	+						ATAD2B_uc002rek.3_5'Flank|ATAD2B_uc010yki.1_5'Flank|ATAD2B_uc010exx.1_5'Flank|UBXN2A_uc002rem.2_Intron	NM_181713	NP_859064	P68543	UBX2A_HUMAN	UBX domain containing 4												0						cctgtctcagaaaaaaaaaaa	0.055													6	3	---	---	---	---	
C2orf18	54978	broad.mit.edu	37	2	26986988	26986988	+	5'Flank	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26986988delA	uc002rhp.1	+						C2orf18_uc002rhq.1_5'Flank|C2orf18_uc010eyo.1_5'Flank|C2orf18_uc010ylc.1_5'Flank	NM_017877	NP_060347	Q8N357	CB018_HUMAN	ANT2-binding protein precursor							integral to membrane|lysosomal membrane					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGAAGAAAAGAAAAAAAAAAC	0.393													4	2	---	---	---	---	
ZNF512	84450	broad.mit.edu	37	2	27824511	27824512	+	Intron	INS	-	TTTTG	TTTTG	rs143396334	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27824511_27824512insTTTTG	uc002rla.2	+						ZNF512_uc010ylv.1_Intron|ZNF512_uc010ylw.1_Intron|ZNF512_uc002rlb.2_Intron|ZNF512_uc010ylx.1_Intron|ZNF512_uc002rlc.2_Intron|ZNF512_uc010yly.1_Intron|ZNF512_uc010ylz.1_Intron	NM_032434	NP_115810	Q96ME7	ZN512_HUMAN	zinc finger protein 512						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					tggctaattttttttgttttgt	0.000													4	2	---	---	---	---	
BIRC6	57448	broad.mit.edu	37	2	32600812	32600812	+	Intron	DEL	T	-	-	rs111860420		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32600812delT	uc010ezu.2	+							NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					tttctctctcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34462678	34462678	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34462678delC								MYADML (509394 upstream) : None (None downstream)																							ggaacctctgcctagatttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	36523675	36523675	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36523675delG								None (None upstream) : CRIM1 (59722 downstream)																							agatttaggtggggacacaga	0.154													4	2	---	---	---	---	
VIT	5212	broad.mit.edu	37	2	36990151	36990152	+	Intron	INS	-	T	T	rs141287942	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36990151_36990152insT	uc002rpl.2	+						VIT_uc010ynf.1_Intron|VIT_uc002rpm.2_Intron|VIT_uc010ezv.2_Intron|VIT_uc010ezw.2_Intron	NM_053276	NP_444506	Q6UXI7	VITRN_HUMAN	vitrin							proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)				CTTTGTAGAAGTTTTTTTAAAA	0.421													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37986321	37986322	+	IGR	INS	-	AATA	AATA	rs146587638	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37986321_37986322insAATA								CDC42EP3 (86995 upstream) : FAM82A1 (166140 downstream)																							gtctcagagggaataatcagcc	0.035													4	2	---	---	---	---	
EML4	27436	broad.mit.edu	37	2	42482784	42482784	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42482784delA	uc002rsi.2	+						EML4_uc002rsh.3_Intron|EML4_uc010fap.2_Intron	NM_019063	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4						microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250						ACTTATATGTAAAAAAAAAAT	0.299			T	ALK	NSCLC								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43060890	43060894	+	IGR	DEL	TGAGG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43060890_43060894delTGAGG								HAAO (41139 upstream) : ZFP36L2 (388648 downstream)																							tttgggaggctgaggtgggcggatc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43130038	43130040	+	IGR	DEL	AAC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43130038_43130040delAAC								HAAO (110287 upstream) : ZFP36L2 (319502 downstream)																							ctcTATTAAAaacaacaacaaca	0.207													4	2	---	---	---	---	
THADA	63892	broad.mit.edu	37	2	43533111	43533112	+	Intron	DEL	TC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43533111_43533112delTC	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				ctccctcccttctctctctctc	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45095516	45095517	+	IGR	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45095516_45095517delCA								C2orf34 (95787 upstream) : SIX3 (73520 downstream)																							gacacacatgcacacacacagt	0.000													4	2	---	---	---	---	
EPAS1	2034	broad.mit.edu	37	2	46555398	46555398	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46555398delG	uc002ruv.2	+							NM_001430	NP_001421	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1						angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia	transcription factor complex	histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding			ovary(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			GAGCTTGAGTGGGTCTTGAAG	0.537													4	2	---	---	---	---	
TTC7A	57217	broad.mit.edu	37	2	47198747	47198748	+	Intron	INS	-	AGG	AGG	rs142516201	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47198747_47198748insAGG	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron	NM_020458	NP_065191	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			ggaggccagttaggccgatgta	0.218													4	3	---	---	---	---	
MSH2	4436	broad.mit.edu	37	2	47678418	47678430	+	Intron	DEL	TACATGGTGTCAG	-	-	rs145759337		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47678418_47678430delTACATGGTGTCAG	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron|MSH2_uc010fbh.1_Intron|MSH2_uc010fbi.1_Intron	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding	p.?(1)		large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			aggcacatattacatggtgtcaggcaagagagt	0.000			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				3	3	---	---	---	---	
FBXO11	80204	broad.mit.edu	37	2	48070571	48070571	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48070571delT	uc010fbl.2	-						FBXO11_uc002rwe.2_Intron|FBXO11_uc002rwf.2_Intron|FBXO11_uc002rwg.1_Intron	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1						ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			gtagttaatcttttttttttt	0.000													6	4	---	---	---	---	
FOXN2	3344	broad.mit.edu	37	2	48583578	48583578	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48583578delA	uc002rwh.1	+							NM_002158	NP_002149	P32314	FOXN2_HUMAN	T-cell leukemia virus enhancer factor						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)			agactgtctcaaaaaaaaaaa	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	61042902	61042905	+	IGR	DEL	TTTG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61042902_61042905delTTTG								PAPOLG (16806 upstream) : REL (65847 downstream)																							GGATTCtttttttgtttgtttgtt	0.039													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62519588	62519589	+	IGR	INS	-	TA	TA			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62519588_62519589insTA								B3GNT2 (67724 upstream) : TMEM17 (207767 downstream)																							GCTGTCTCCTCTATATTCCCAG	0.515													4	2	---	---	---	---	
AFTPH	54812	broad.mit.edu	37	2	64818460	64818460	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64818460delT	uc002sdc.2	+						AFTPH_uc002scz.2_Intron|AFTPH_uc002sda.2_Intron|AFTPH_uc002sdb.2_Intron	NM_203437	NP_982261	Q6ULP2	AFTIN_HUMAN	aftiphilin protein isoform a						protein transport	AP-1 adaptor complex|cytosol|nucleus	clathrin binding			ovary(2)	2						GTGCTGCTGCTTTTGGACCTG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65093445	65093446	+	5'Flank	INS	-	G	G	rs145714054	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65093445_65093446insG	uc002sdf.1	-											Homo sapiens cDNA FLJ40633 fis, clone THYMU2015439.																		CCGCCCGCAGTGGCCAGACCCT	0.441													3	3	---	---	---	---	
SPRED2	200734	broad.mit.edu	37	2	65599219	65599220	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65599219_65599220insA	uc002sdr.3	-						SPRED2_uc010fcx.1_Intron	NM_181784	NP_861449	Q7Z698	SPRE2_HUMAN	sprouty-related protein with EVH-1 domain 2						inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			ovary(1)|lung(1)|central_nervous_system(1)	3						aagaaagaaagaaaaaaaaaaG	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	68164644	68164645	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68164644_68164645insA								ETAA1 (527111 upstream) : C1D (104688 downstream)																							AATGTCAGGGCAAGAGCTAGAC	0.465													4	2	---	---	---	---	
PNO1	56902	broad.mit.edu	37	2	68394618	68394618	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68394618delG	uc002seh.2	+							NM_020143	NP_064528	Q9NRX1	PNO1_HUMAN	partner of NOB1							nucleolus	RNA binding				0						ttcaaggatcggggttagcag	0.000													4	2	---	---	---	---	
ASPRV1	151516	broad.mit.edu	37	2	70190669	70190669	+	5'Flank	DEL	C	-	-	rs115072048	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70190669delC	uc002sfz.3	-						ASPRV1_uc002sga.2_Intron|ASPRV1_uc010fdn.1_Intron	NM_152792	NP_690005	Q53RT3	APRV1_HUMAN	aspartic peptidase, retroviral-like 1 precursor						protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1						TAGCATGCGACCAAGGGAGGA	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	70422450	70422450	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70422450delT								C2orf42 (4299 upstream) : TIA1 (14127 downstream)																							TAAATCACTAttttttttttt	0.010													4	2	---	---	---	---	
ADD2	119	broad.mit.edu	37	2	70947529	70947530	+	Intron	INS	-	C	C	rs143033989	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70947529_70947530insC	uc002sgz.2	-						ADD2_uc010fds.1_Intron|ADD2_uc002sgy.2_Intron|ADD2_uc002sha.2_Intron|ADD2_uc002shc.1_Intron|ADD2_uc002shd.1_Intron|ADD2_uc010fdu.1_Intron	NM_001617	NP_001608	P35612	ADDB_HUMAN	adducin 2 isoform a						actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3						CATCTCAAAAGCTGAGCAGTGA	0.515													3	3	---	---	---	---	
FIGLA	344018	broad.mit.edu	37	2	71010833	71010833	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71010833delT	uc002she.1	-							NM_001004311	NP_001004311	Q6QHK4	FIGLA_HUMAN	factor in the germline alpha						multicellular organismal development|oocyte development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcription factor complex	DNA binding|transcription factor binding				0						GCTCAGGTCAttttttttttt	0.199													4	2	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71811300	71811301	+	Intron	DEL	GT	-	-	rs71402996		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71811300_71811301delGT	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	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						CTGGGCAAGAGTGTGTGTGTGT	0.629													2	4	---	---	---	---	
EXOC6B	23233	broad.mit.edu	37	2	72674232	72674232	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72674232delA	uc010fep.2	-							NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						acttcgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73162211	73162212	+	IGR	INS	-	T	T	rs141259224	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73162211_73162212insT								EMX1 (191 upstream) : SFXN5 (6954 downstream)																							CATGAAACCTCTGCTCTTTGGC	0.510													3	3	---	---	---	---	
SFXN5	94097	broad.mit.edu	37	2	73184232	73184232	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73184232delC	uc002siq.2	-						SFXN5_uc002sio.2_Intron|SFXN5_uc010yrc.1_Intron|SFXN5_uc002sip.2_Intron|SFXN5_uc010fet.2_Intron|SFXN5_uc010fer.2_Intron|SFXN5_uc010feq.2_Intron|SFXN5_uc010fes.2_Frame_Shift_Del_p.E98fs	NM_144579	NP_653180	Q8TD22	SFXN5_HUMAN	sideroflexin 5						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity			ovary(1)	1						ttttcttcctcctatagtgga	0.144													4	2	---	---	---	---	
SFXN5	94097	broad.mit.edu	37	2	73278386	73278387	+	Intron	INS	-	TT	TT	rs61003143		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73278386_73278387insTT	uc002siq.2	-						SFXN5_uc002sio.2_Intron|SFXN5_uc010yrc.1_Intron|SFXN5_uc002sip.2_Intron|SFXN5_uc010fet.2_Intron|SFXN5_uc002sir.1_Intron	NM_144579	NP_653180	Q8TD22	SFXN5_HUMAN	sideroflexin 5						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity			ovary(1)	1						ttttccagcacttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73978518	73978518	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73978518delT								TPRKB (14001 upstream) : DUSP11 (10808 downstream)																							AAGAGGGCCCTTTTGGGGGAG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	75020341	75020342	+	IGR	DEL	AA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75020341_75020342delAA								SEMA4F (111156 upstream) : HK2 (39440 downstream)																							CACCACCACCAAAAAAAAAAAA	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	75045869	75045870	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75045869_75045870insA								SEMA4F (136684 upstream) : HK2 (13912 downstream)																							acaaaaatcacaaaaaaatctc	0.000													4	2	---	---	---	---	
REG1A	5967	broad.mit.edu	37	2	79350205	79350205	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79350205delG	uc002snz.2	+						REG1A_uc010ysd.1_Intron	NM_002909	NP_002900	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha precursor						positive regulation of cell proliferation	extracellular region	growth factor activity|sugar binding				0						TTTTTGTCCTGAGTCCTAAAG	0.458													11	7	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	80764722	80764722	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80764722delT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysi.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						gtttcctgacttttttttttt	0.000													4	2	---	---	---	---	
TCF7L1	83439	broad.mit.edu	37	2	85383255	85383255	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85383255delG	uc002soy.2	+							NM_031283	NP_112573	Q9HCS4	TF7L1_HUMAN	HMG-box transcription factor TCF-3						chromatin organization|regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|breast(1)|central_nervous_system(1)	3						GTCCCTCTTTGGAACTTCTGT	0.448													4	2	---	---	---	---	
USP39	10713	broad.mit.edu	37	2	85865962	85865962	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85865962delT	uc002sqe.2	+						USP39_uc002sqb.2_Intron|USP39_uc010ysu.1_Intron|USP39_uc010ysv.1_Intron|USP39_uc010fgn.1_Intron|USP39_uc002sqf.2_Intron|USP39_uc002sqg.2_Intron|USP39_uc010fgo.2_Intron	NM_006590	NP_006581	Q53GS9	SNUT2_HUMAN	ubiquitin specific protease 39						spliceosome assembly|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)	1						gcccggccaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	86160903	86160906	+	IGR	DEL	GTGT	-	-	rs150590836		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86160903_86160906delGTGT								ST3GAL5 (44746 upstream) : LOC90784 (86433 downstream)																							atgtgagttggtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
POLR1A	25885	broad.mit.edu	37	2	86311789	86311789	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86311789delT	uc002sqs.2	-						POLR1A_uc002sqv.2_Intron	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						TGCCttttccttttttttttt	0.174													2	4	---	---	---	---	
PTCD3	55037	broad.mit.edu	37	2	86365337	86365337	+	3'UTR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86365337delT	uc002sqw.2	+	24					PTCD3_uc002sqx.1_3'UTR	NM_017952	NP_060422	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3 precursor							mitochondrion	protein binding			ovary(1)	1						CATGTCTCCCTTTTTTTTTGT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	86721997	86722000	+	IGR	DEL	TGTC	-	-	rs140068726		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86721997_86722000delTGTC								KDM3A (2159 upstream) : VPS24 (8554 downstream)																							ctctaatctttgtctgtccttcgg	0.000													5	4	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	86951210	86951210	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86951210delT	uc010ytm.1	+						RMND5A_uc002srs.3_Intron|VPS24_uc010ytl.1_5'Flank|RMND5A_uc002srr.2_Intron	NM_022780	NP_073617	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog											ovary(1)|skin(1)	2						CAGGAATATCTTTTTTTTTTT	0.448													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87593176	87593177	+	Intron	DEL	GA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87593176_87593177delGA	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						gaaaaatgatgagatgaaatgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	88810887	88810888	+	IGR	INS	-	T	T	rs71863495		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88810887_88810888insT								FOXI3 (58834 upstream) : C2orf51 (13281 downstream)																							CTCACCCTCACttttttttttt	0.208													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91599246	91599248	+	IGR	DEL	ATG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91599246_91599248delATG								None (None upstream) : LOC654342 (205944 downstream)																							attgcattcaatgatgattgcat	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91765186	91765187	+	IGR	INS	-	A	A	rs146244002		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91765186_91765187insA								None (None upstream) : LOC654342 (40005 downstream)																							gacttcgttattttatactcaa	0.040													4	2	---	---	---	---	
SNRNP200	23020	broad.mit.edu	37	2	96959871	96959871	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96959871delA	uc002svu.2	-							NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10						GCTCCATCTCaaaaaaaaaaa	0.100													4	2	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97812185	97812187	+	Intron	DEL	TTG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97812185_97812187delTTG	uc010yva.1	+						ANKRD36_uc010yuz.1_Intron|ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						TAGGTTCCTATTGTTGATTTAAA	0.158													4	2	---	---	---	---	
INPP4A	3631	broad.mit.edu	37	2	99167414	99167414	+	Intron	DEL	T	-	-	rs71865393		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99167414delT	uc002syy.2	+						INPP4A_uc010yvj.1_Intron|INPP4A_uc010yvk.1_Intron|INPP4A_uc002syx.2_Intron|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696	Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type 1						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1						GGAAGAATCCttttttttttt	0.204													4	2	---	---	---	---	
FBLN7	129804	broad.mit.edu	37	2	112928111	112928113	+	Intron	DEL	AAA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112928111_112928113delAAA	uc002tho.1	+						FBLN7_uc002thn.2_Intron|FBLN7_uc010fki.1_Intron|FBLN7_uc010fkj.1_Intron	NM_153214	NP_694946	Q53RD9	FBLN7_HUMAN	fibulin 7 isoform 1						cell adhesion	proteinaceous extracellular matrix	calcium ion binding|heparin binding			ovary(1)|central_nervous_system(1)	2						ctcgaaagtgaaaaaaaaaaaaa	0.148													4	2	---	---	---	---	
GLI2	2736	broad.mit.edu	37	2	121506430	121506433	+	Intron	DEL	TCCA	-	-	rs71671803		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121506430_121506433delTCCA	uc010yyu.1	+						GLI2_uc002tmp.1_Intron			P10070	GLI2_HUMAN	SubName: Full=cDNA FLJ60878, highly similar to Homo sapiens GLI-Kruppel family member GLI2, mRNA;						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				TCTTGCATTCtccatccatccatc	0.196													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122716729	122716732	+	IGR	DEL	TCTT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122716729_122716732delTCTT								TSN (191303 upstream) : None (None downstream)																							cctttctccctctttctttctttc	0.098													4	2	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	125397207	125397212	+	Intron	DEL	TTATAC	-	-	rs67949152		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125397207_125397212delTTATAC	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)		ACAAGTACTATTATACTTATACTATT	0.388													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	127125059	127125060	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127125059_127125060insT								None (None upstream) : GYPC (288624 downstream)																							gtctgtaattgtttttctgtat	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	128205230	128205231	+	IGR	DEL	TG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128205230_128205231delTG								PROC (18414 upstream) : IWS1 (33152 downstream)																							cttttcaggttgtgtgtgtgtg	0.000													5	3	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	133889859	133889859	+	Intron	DEL	A	-	-	rs72322344		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133889859delA	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						actccatctcaaaaaaaaaaa	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	158497631	158497631	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158497631delA								ACVR1C (12232 upstream) : ACVR1 (95327 downstream)																							ctgggaaaagaaaaaagatgt	0.000													4	2	---	---	---	---	
FIGN	55137	broad.mit.edu	37	2	164490599	164490600	+	Intron	INS	-	GTGT	GTGT	rs143945217	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164490599_164490600insGTGT	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						cgtatgtatgcgtgtgtgtgtg	0.262													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	164630253	164630258	+	IGR	DEL	ACACAC	-	-	rs67060477		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164630253_164630258delACACAC								FIGN (37740 upstream) : GRB14 (719075 downstream)																							acaaacaaaAacacacacacacacac	0.000											OREG0004896	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	3	3	---	---	---	---	
NOSTRIN	115677	broad.mit.edu	37	2	169685811	169685811	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169685811delT	uc002ueg.2	+						NOSTRIN_uc002uef.2_Intron|NOSTRIN_uc002uei.2_Intron|NOSTRIN_uc010fpu.2_Intron|NOSTRIN_uc002ueh.2_Intron|NOSTRIN_uc002uej.2_Intron	NM_001039724	NP_001034813	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficker isoform 2						endocytosis|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	protein binding				0						cttccttcTCTTTCTtttttt	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	171622974	171622975	+	Intron	INS	-	TGTG	TGTG	rs139014869	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171622974_171622975insTGTG	uc002ugf.1	-											Homo sapiens cDNA FLJ13453 fis, clone PLACE1003205.																		atgtgtgtgtttgtgtgtgtgt	0.109													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174602923	174602934	+	IGR	DEL	GAAGGAAACAAT	-	-	rs148236674	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174602923_174602934delGAAGGAAACAAT								CDCA7 (369205 upstream) : SP3 (170325 downstream)																							aataagaaaggaaggaaacaatgaaggaagga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177462522	177462523	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177462522_177462523insT								MTX2 (259771 upstream) : MIR1246 (3185 downstream)																							TCAAGCTTGGGTTGGGGGAGAG	0.455													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	183778218	183778219	+	IGR	INS	-	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183778218_183778219insC								FRZB (46720 upstream) : NCKAP1 (11387 downstream)																							ggtgaatcccacccccacacca	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	190974081	190974081	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190974081delT								MSTN (46626 upstream) : C2orf88 (28405 downstream)																							TTTTCTCAGCTTTTTTTTTTC	0.453													4	2	---	---	---	---	
HECW2	57520	broad.mit.edu	37	2	197224172	197224175	+	Intron	DEL	AAAC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197224172_197224175delAAAC	uc002utm.1	-						HECW2_uc002utl.1_Intron	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						ctccatcttaaaacaaacaaacaa	0.108													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	198186781	198186781	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198186781delA								ANKRD44 (11286 upstream) : SF3B1 (69919 downstream)																							ctcaaaaaagaaaaaaaaaaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201961114	201961114	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201961114delT								NDUFB3 (10643 upstream) : CFLAR (19702 downstream)																							ATCATCATTCTTTTTTTTTTT	0.090													4	2	---	---	---	---	
ALS2	57679	broad.mit.edu	37	2	202579678	202579678	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202579678delA	uc002uyo.2	-						ALS2_uc010ftl.2_Intron	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1						cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						tcctctggccaaaaactgccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	203044992	203044993	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203044992_203044993insA	uc002uyy.1	+											RecName: Full=Uncharacterized protein KIAA2012;																		gaaactcctccaaaaaaaaaaa	0.119													6	3	---	---	---	---	
RAPH1	65059	broad.mit.edu	37	2	204320732	204320743	+	Intron	DEL	AAAACAAAAACA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204320732_204320743delAAAACAAAAACA	uc002vad.2	-						RAPH1_uc002vae.2_Intron|RAPH1_uc002vaf.2_Intron	NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains						cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10						actctgtctcaaaacaaaaacaaaaacaaaaa	0.090													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	207741011	207741013	+	IGR	DEL	CCC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207741011_207741013delCCC								FASTKD2 (80102 upstream) : CPO (63265 downstream)																							AACATTCCTTCCCCTGGGGTGTT	0.241													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	207941077	207941077	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207941077delG								CPO (106879 upstream) : KLF7 (4452 downstream)																							TATCTTGTTTGGGATATTTGT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	208121758	208121758	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208121758delG								KLF7 (90187 upstream) : MIR1302-4 (12241 downstream)																							GCAGGGGGAAGGGGAGAGCAG	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	210251061	210251062	+	IGR	INS	-	T	T	rs148372308	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210251061_210251062insT								PTH2R (546243 upstream) : MAP2 (37709 downstream)																							CAGTGTATTCAttttttttctt	0.193													1	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	210254674	210254677	+	IGR	DEL	AAAC	-	-	rs72216812		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210254674_210254677delAAAC								PTH2R (549856 upstream) : MAP2 (34094 downstream)																							TCTACATTAAAAACAAACAAACAA	0.176													1	8	---	---	---	---	
UNC80	285175	broad.mit.edu	37	2	210635710	210635721	+	5'Flank	DEL	GAAGGAGGAGGG	-	-	rs146937164	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210635710_210635721delGAAGGAGGAGGG	uc010zjc.1	+						UNC80_uc002vdj.1_5'Flank	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1							integral to membrane					0						ggaagaaggagaaggaggagggggaggaggag	0.193													9	6	---	---	---	---	
C2orf67	151050	broad.mit.edu	37	2	210911825	210911826	+	Intron	INS	-	TCTTCTATTG	TCTTCTATTG	rs140954498	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210911825_210911826insTCTTCTATTG	uc002vds.2	-						C2orf67_uc002vdt.2_Intron|C2orf67_uc002vdw.2_Intron|uc002vdu.1_Intron|C2orf67_uc002vdv.2_Intron|C2orf67_uc002vdx.1_Intron	NM_152519	NP_689732	A0AUZ9	CB067_HUMAN	hypothetical protein LOC151050											ovary(3)	3		Renal(323;0.202)		Epithelial(149;0.00435)|Lung(261;0.0529)|LUSC - Lung squamous cell carcinoma(261;0.0551)|all cancers(144;0.0696)		ttcagggccattcttctattgt	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	211104598	211104601	+	IGR	DEL	TTTT	-	-	rs67407753	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211104598_211104601delTTTT								ACADL (14383 upstream) : MYL1 (50268 downstream)																							tctttctttcttttttctttttct	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	224616574	224616574	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224616574delA								SCG2 (149453 upstream) : AP1S3 (3474 downstream)																							ccatttcaagaaaaaaaaaaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	226807086	226807087	+	IGR	DEL	AG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226807086_226807087delAG								KIAA1486 (211615 upstream) : IRS1 (788947 downstream)																							ggagggaggcagagagagagag	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	226939770	226939770	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226939770delA								KIAA1486 (344299 upstream) : IRS1 (656264 downstream)																							cctgtcctataaagaccacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	229760329	229760329	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229760329delT								SPHKAP (713968 upstream) : PID1 (128361 downstream)																							TCTATGTTTCTTTTTTTTTTT	0.448													4	2	---	---	---	---	
INPP5D	3635	broad.mit.edu	37	2	233940309	233940310	+	Intron	INS	-	TG	TG	rs150497378	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233940309_233940310insTG	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		gcacatgtatatgtgtgtgtgt	0.277													3	3	---	---	---	---	
UGT1A5	54579	broad.mit.edu	37	2	234654875	234654875	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234654875delA	uc002vuw.2	+						UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Intron|UGT1A4_uc010zna.1_Intron|UGT1A4_uc002vux.2_Intron|UGT1A3_uc010znb.1_Intron|UGT1A3_uc002vuy.2_Intron|DNAJB3_uc002vuz.2_5'Flank|UGT1A9_uc002vva.2_5'Flank	NM_019078	NP_061951	P35504	UD15_HUMAN	UDP glycosyltransferase 1 family, polypeptide A5						xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		ACAGATATGCAAACTGCTAAA	0.433													4	2	---	---	---	---	
UGT1A5	54579	broad.mit.edu	37	2	234663433	234663433	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234663433delA	uc002vuw.2	+						UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Intron|UGT1A4_uc010zna.1_Intron|UGT1A4_uc002vux.2_Intron|UGT1A3_uc010znb.1_Intron|UGT1A3_uc002vuy.2_Intron|UGT1A9_uc002vva.2_Intron	NM_019078	NP_061951	P35504	UD15_HUMAN	UDP glycosyltransferase 1 family, polypeptide A5						xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		CAAAGGAACGAAATCCTGTAT	0.512													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	236711655	236711660	+	Intron	DEL	TTGTGA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236711655_236711660delTTGTGA	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						atggttgtggttgtgatggtggtgat	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238872687	238872687	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238872687delC								RAMP1 (51934 upstream) : UBE2F (3013 downstream)																							tcctgcctttccagactgaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239593943	239593943	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239593943delT								ASB1 (233053 upstream) : TWIST2 (162730 downstream)																							CAGAAGAATCTTATTTCTACC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	1687408	1687409	+	IGR	DEL	GT	-	-	rs72072047		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1687408_1687409delGT								CNTN6 (242131 upstream) : CNTN4 (453141 downstream)																							CAAGTGGAGGgtgtgtgtgtgt	0.238													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	5124705	5124706	+	IGR	DEL	TT	-	-	rs72175262		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5124705_5124706delTT								BHLHE40 (97842 upstream) : ARL8B (39224 downstream)																							CATTTCAGCCtttttttttttt	0.460													4	2	---	---	---	---	
C3orf10	55845	broad.mit.edu	37	3	10156194	10156195	+	5'Flank	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10156194_10156195insA	uc003bvb.2	+							NM_018462	NP_060932	Q8WUW1	BRK1_HUMAN	chromosome 3 open reading frame 10							cytoplasm|cytoskeleton					0						aactctgtcttaaaaaaaaaaa	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	15403654	15403654	+	IGR	DEL	T	-	-	rs80117601		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15403654delT								SH3BP5 (20753 upstream) : METTL6 (19130 downstream)																							ctctcttccctgtctcacttc	0.000													0	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	28717589	28717589	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28717589delC								ZCWPW2 (150959 upstream) : RBMS3 (605354 downstream)																							gaccataccacctgttctttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	33191192	33191192	+	IGR	DEL	G	-	-	rs78178282		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33191192delG								CRTAP (1928 upstream) : SUSD5 (345 downstream)																							ttttttttttgaatggagcct	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	34194589	34194589	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34194589delG								PDCD6IP (283395 upstream) : None (None downstream)																							CACAGTGGGAGGGGATGGTAG	0.547													4	2	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41499216	41499216	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41499216delA	uc003ckv.3	-							NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CATCTTGTACAGGGCCCGTGT	0.537													4	2	---	---	---	---	
LYZL4	131375	broad.mit.edu	37	3	42453855	42453856	+	5'Flank	DEL	AA	-	-	rs71709754		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42453855_42453856delAA	uc003cle.2	-							NM_144634	NP_653235	Q96KX0	LYZL4_HUMAN	lysozyme-like 4 precursor						cell wall macromolecule catabolic process	extracellular region	lysozyme activity			central_nervous_system(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.222)		AGACAGTTTGAAAAAAAAAAaa	0.208													3	4	---	---	---	---	
CCR1	1230	broad.mit.edu	37	3	46244274	46244274	+	3'UTR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46244274delG	uc003cph.1	-	2					CCR3_uc003cpg.1_Intron	NM_001295	NP_001286	P32246	CCR1_HUMAN	chemokine (C-C motif) receptor 1						cell adhesion|cell-cell signaling|cytokine-mediated signaling pathway|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cyclic nucleotide second messenger|immune response|inflammatory response	integral to plasma membrane	C-C chemokine receptor activity			skin(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		GGAGGGTGGCGGGGGGGGGGA	0.537													4	2	---	---	---	---	
MAP4	4134	broad.mit.edu	37	3	47961092	47961095	+	Intron	DEL	CCGG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47961092_47961095delCCGG	uc003csb.2	-						MAP4_uc003csc.3_Intron|MAP4_uc011bbf.1_Intron|MAP4_uc003csf.3_Intron	NM_002375	NP_002366	P27816	MAP4_HUMAN	microtubule-associated protein 4 isoform 1						negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)		gacaccgcgcccggccGACAACGC	0.181													4	2	---	---	---	---	
VPRBP	9730	broad.mit.edu	37	3	51456814	51456814	+	Intron	DEL	A	-	-	rs72108687		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51456814delA	uc003dbe.1	-						VPRBP_uc003dbf.1_Intron	NM_014703	NP_055518	Q9Y4B6	VPRBP_HUMAN	HIV-1 Vpr binding protein						interspecies interaction between organisms	cytoplasm|nucleus	protein binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		ctccgtctccaaaaaaaaaaa	0.174													4	2	---	---	---	---	
ARHGEF3	50650	broad.mit.edu	37	3	56989210	56989211	+	Intron	DEL	TT	-	-	rs139033208		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56989210_56989211delTT	uc003dih.2	-							NM_001128615	NP_001122087	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		ATCCTTTTTCTTtttttttttt	0.233													4	3	---	---	---	---	
SUCLG2	8801	broad.mit.edu	37	3	67436978	67436978	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67436978delA	uc003dna.3	-						SUCLG2_uc010hob.2_Intron	NM_003848	NP_003839	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming beta subunit						succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	aggaggcctcacaatcgtggt	0.000													4	2	---	---	---	---	
FAM19A1	407738	broad.mit.edu	37	3	68283137	68283137	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68283137delA	uc003dnd.2	+						FAM19A1_uc003dne.2_Intron|FAM19A1_uc003dng.2_Intron	NM_213609	NP_998774	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine							endoplasmic reticulum|extracellular region				ovary(1)	1		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)		AAGCAATGGTAATTGTGGAGT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	69616506	69616506	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69616506delG								FRMD4B (24773 upstream) : MITF (172127 downstream)																							ttttccttttggaagaattcc	0.000													4	2	---	---	---	---	
PDZRN3	23024	broad.mit.edu	37	3	73609546	73609546	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73609546delC	uc003dpl.1	-						PDZRN3_uc011bgh.1_Intron|PDZRN3_uc010hoe.1_Intron	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3								ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TGCTCCTCATCCCCCAACTAT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90352597	90352598	+	IGR	INS	-	GC	GC	rs112057672		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90352597_90352598insGC								EPHA3 (821315 upstream) : None (None downstream)																							ctacaaaaagagtttcaaaact	0.000													16	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90498940	90498940	+	IGR	DEL	A	-	-	rs141646871	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90498940delA								EPHA3 (967658 upstream) : None (None downstream)																							atgtgaagatatttccttttc	0.000													8	4	---	---	---	---	
COL8A1	1295	broad.mit.edu	37	3	99464677	99464677	+	Intron	DEL	A	-	-	rs141514291		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99464677delA	uc003dtg.1	+						COL8A1_uc003dth.1_Intron|COL8A1_uc003dti.1_Intron	NM_001850	NP_001841	P27658	CO8A1_HUMAN	alpha 1 type VIII collagen precursor						angiogenesis|cell adhesion	basement membrane|collagen type VIII					0						ACCTTGATGGAAAAAAAAAAA	0.338													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	110611537	110611538	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110611537_110611538insT	uc003dxs.1	-											RecName: Full=Putative uncharacterized protein LOC151760;																		TGAGCCAAGCCttttttttttt	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127280340	127280340	+	IGR	DEL	A	-	-	rs76568741		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127280340delA								PLXNA1 (524112 upstream) : TPRA1 (11568 downstream)																							agactctgtcaaaaaaaaaaa	0.184													4	2	---	---	---	---	
ACPP	55	broad.mit.edu	37	3	132042015	132042015	+	Intron	DEL	A	-	-	rs71881183		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132042015delA	uc010htp.2	+						ACPP_uc003eon.3_Intron|ACPP_uc003eop.3_Intron	NM_001099	NP_001090	P15309	PPAP_HUMAN	acid phosphatase, prostate short isoform							extracellular region|lysosomal membrane	5'-nucleotidase activity|acid phosphatase activity			ovary(1)	1						GAAAGAAAGGAAAAAAAAAAA	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137479321	137479321	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137479321delC								IL20RB (749401 upstream) : SOX14 (4258 downstream)																							CCCCAAGCATCCCAGGCCCTC	0.612													4	2	---	---	---	---	
RASA2	5922	broad.mit.edu	37	3	141241974	141241975	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141241974_141241975insT	uc003etz.1	+						RASA2_uc010huq.1_Intron|RASA2_uc003eua.1_Intron|RASA2_uc011bnc.1_Intron	NM_006506	NP_006497	Q15283	RASA2_HUMAN	RAS p21 protein activator 2						intracellular signal transduction|negative regulation of Ras protein signal transduction	intracellular membrane-bounded organelle|intrinsic to internal side of plasma membrane|perinuclear region of cytoplasm	metal ion binding|Ras GTPase activator activity			ovary(2)|lung(2)|breast(1)|skin(1)	6						AGATAATCCCAttttttttttt	0.149													4	2	---	---	---	---	
XRN1	54464	broad.mit.edu	37	3	142159587	142159588	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142159587_142159588insA	uc003eus.2	-						XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron|XRN1_uc003euw.2_Intron|XRN1_uc011bnh.1_Intron	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3						tctgctttcccaaataccagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	142897208	142897210	+	IGR	DEL	TTG	-	-	rs71140427		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142897208_142897210delTTG								CHST2 (55398 upstream) : SLC9A9 (86855 downstream)																							gttgttgtttttgttgttgttgt	0.227													2	5	---	---	---	---	
C3orf58	205428	broad.mit.edu	37	3	143699113	143699114	+	Intron	INS	-	TGTC	TGTC	rs141818947	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143699113_143699114insTGTC	uc003evo.2	+						C3orf58_uc011bnl.1_Intron	NM_173552	NP_775823	Q8NDZ4	CC058_HUMAN	hypothetical protein LOC205428 isoform a							COPI vesicle coat|extracellular region				ovary(1)	1						TCTTTCTTATGTGTCTGTCTGT	0.158													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145403257	145403258	+	IGR	INS	-	T	T	rs111771423		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145403257_145403258insT								None (None upstream) : PLOD2 (383970 downstream)																							TCTTCTCACTCTTTTTTTTTTT	0.396													2	5	---	---	---	---	
HPS3	84343	broad.mit.edu	37	3	148847336	148847336	+	5'Flank	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148847336delG	uc003ewu.1	+						HPS3_uc003ewt.1_5'Flank|HPS3_uc011bnq.1_5'Flank	NM_032383	NP_115759	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3 protein							cytoplasm				ovary(5)|large_intestine(1)	6			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CCCGACGCCTGCCACGCCCCG	0.716									Hermansky-Pudlak_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149446306	149446307	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149446306_149446307insT								WWTR1 (25191 upstream) : COMMD2 (9953 downstream)																							AGGAAGGGGACttttttttttt	0.203													5	7	---	---	---	---	
MED12L	116931	broad.mit.edu	37	3	150956469	150956470	+	Intron	INS	-	A	A	rs142013922	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150956469_150956470insA	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|P2RY14_uc003eys.1_Intron|P2RY14_uc003eyr.1_Intron	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			cttactgacatacaatcttaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151200696	151200696	+	IGR	DEL	T	-	-	rs111951165		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151200696delT								IGSF10 (24199 upstream) : AADACL2 (251008 downstream)																							tgtttttttgttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151311781	151311781	+	IGR	DEL	G	-	-	rs75273785		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151311781delG								IGSF10 (135284 upstream) : AADACL2 (139923 downstream)																							GAATGAATACGGCAGATCAGA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151342151	151342152	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151342151_151342152insT								IGSF10 (165654 upstream) : AADACL2 (109552 downstream)																							cctggccACACTTTTTTTTTTT	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151645264	151645264	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151645264delT								SUCNR1 (45614 upstream) : LOC401093 (335149 downstream)																							TTGTTTGGCCTTTTTTTTTTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152764819	152764828	+	IGR	DEL	TTCTTTTCTT	-	-	rs63218061		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152764819_152764828delTTCTTTTCTT								P2RY1 (208978 upstream) : RAP2B (115201 downstream)																							GTTTCCTGTCttcttttcttttcttttctt	0.205													5	4	---	---	---	---	
PLCH1	23007	broad.mit.edu	37	3	155247548	155247549	+	Intron	INS	-	TTTTGTTTTG	TTTTGTTTTG	rs143259903	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155247548_155247549insTTTTGTTTTG	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			atttgcttcttttttgttttgt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	158515692	158515693	+	IGR	INS	-	TT	TT	rs147488583	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158515692_158515693insTT								RARRES1 (65417 upstream) : MFSD1 (4219 downstream)																							ACCTTTTTACCTTTTTTTTTTC	0.386													4	2	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	159038397	159038397	+	Intron	DEL	T	-	-	rs5853859		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159038397delT	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.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)			GGTAAGTTCCTTTTTTTTTTC	0.368													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	159701545	159701546	+	Intron	INS	-	A	A	rs140898242	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159701545_159701546insA	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		caaaacaaaacaaaaAACTACC	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	159815988	159815989	+	Intron	INS	-	A	A	rs146428136		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159815988_159815989insA	uc003fcw.1	-						uc003fcz.1_5'Flank					Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		gaccccgtctcaaaaaaaaaaa	0.079													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161521091	161521092	+	IGR	DEL	GT	-	-	rs112580712		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161521091_161521092delGT								OTOL1 (299363 upstream) : None (None downstream)																							CTTGAGAGGGgtgtgtgtgtgt	0.287													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163875816	163875817	+	IGR	INS	-	A	A	rs139791896	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163875816_163875817insA								None (None upstream) : MIR1263 (13442 downstream)																							ctagatccttgggaatcaccac	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165841862	165841863	+	IGR	DEL	AC	-	-	rs77362053		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165841862_165841863delAC								BCHE (286609 upstream) : None (None downstream)																							atacagacatacacacacacac	0.000													5	3	---	---	---	---	
LRRC34	151827	broad.mit.edu	37	3	169520767	169520767	+	Intron	DEL	A	-	-	rs79186799		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169520767delA	uc003ffx.2	-						LRRC34_uc003ffy.2_Intron|LRRC34_uc011bpn.1_Intron|LRRC34_uc003ffz.2_Intron|LRRC34_uc003fga.3_Intron	NM_153353	NP_699184	Q8IZ02	LRC34_HUMAN	leucine rich repeat containing 34												0	all_cancers(22;4.12e-22)|all_epithelial(15;7.54e-27)|all_lung(20;1.63e-16)|Lung NSC(18;6.92e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			ctctgtctccaaaaaaaaaaa	0.179													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	169922764	169922764	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169922764delT								PHC3 (23227 upstream) : PRKCI (17456 downstream)																							TGTTTTTTacttttttttttt	0.025													3	5	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170162510	170162510	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170162510delA	uc011bpt.1	+							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)			actccgtctcaaaaaaaaaaa	0.179													2	7	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170424123	170424123	+	Intron	DEL	T	-	-	rs113251908		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170424123delT	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)			gctcagctaattttttttttt	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	170759519	170759520	+	IGR	INS	-	T	T	rs113893881		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170759519_170759520insT								SLC2A2 (14751 upstream) : TNIK (20772 downstream)																							ttctttgttacttttttttttt	0.124													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	171198462	171198465	+	IGR	DEL	TGAG	-	-	rs72231722		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171198462_171198465delTGAG								TNIK (20265 upstream) : PLD1 (120155 downstream)																							CAAAACTTCCTGAGTATTTCTTTT	0.304													2	4	---	---	---	---	
PLD1	5337	broad.mit.edu	37	3	171383495	171383496	+	Intron	INS	-	A	A	rs113461455		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171383495_171383496insA	uc003fhs.2	-						PLD1_uc003fht.2_Intron|PLD1_uc003fhu.3_Intron|PLD1_uc003fhv.1_Intron	NM_002662	NP_002653	Q13393	PLD1_HUMAN	phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	cgtctcaaaagaaaaaaaaaaa	0.203													3	3	---	---	---	---	
PLD1	5337	broad.mit.edu	37	3	171424055	171424056	+	Intron	INS	-	T	T	rs11456818		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171424055_171424056insT	uc003fhs.2	-						PLD1_uc003fht.2_Intron	NM_002662	NP_002653	Q13393	PLD1_HUMAN	phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	ctatgccattcttttttttttt	0.005													4	8	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173483879	173483879	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173483879delT	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)			ATGttttgtcttttttttttt	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	175780675	175780675	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175780675delT								NAALADL2 (257249 upstream) : TBL1XR1 (957868 downstream)																							atgcaacccctcccaaatctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177684204	177684205	+	IGR	INS	-	AA	AA	rs143362319	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177684204_177684205insAA								TBL1XR1 (769156 upstream) : KCNMB2 (570019 downstream)																							aaagcaaaaacaaaaaaaaatg	0.005													3	3	---	---	---	---	
ZMAT3	64393	broad.mit.edu	37	3	178774119	178774120	+	Intron	INS	-	G	G	rs145326075	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178774119_178774120insG	uc003fjg.2	-						ZMAT3_uc010hxa.2_Intron|ZMAT3_uc003fji.2_Intron	NM_022470	NP_071915	Q9HA38	ZMAT3_HUMAN	p53 target zinc finger protein isoform 1						apoptosis|protein transport|regulation of growth|response to DNA damage stimulus|transmembrane transport	nucleolus	RNA binding|zinc ion binding			ovary(2)	2	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			taaaaaaaaaagggggggtcca	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	179921173	179921173	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179921173delG								PEX5L (166656 upstream) : TTC14 (398745 downstream)																							cgccaaccccgggcagtgcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180622510	180622510	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180622510delT								CCDC39 (166848 upstream) : FXR1 (7942 downstream)																							TTTTCTTTCCTTTTTTTTTTT	0.184													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180872347	180872348	+	IGR	INS	-	T	T	rs145498160	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180872347_180872348insT								DNAJC19 (164817 upstream) : SOX2OT (409161 downstream)																							aataaagaatcttgagatgtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	182258874	182258874	+	IGR	DEL	A	-	-	rs76092909		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182258874delA								SOX2OT (799871 upstream) : ATP11B (252417 downstream)																							AAATATGAGCAAGCTATCATT	0.328													0	11	---	---	---	---	
MCF2L2	23101	broad.mit.edu	37	3	183053490	183053491	+	Intron	INS	-	A	A	rs150434373	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183053490_183053491insA	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc003flp.1_Intron	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			accccctctctaaaaaaaatta	0.000													2	4	---	---	---	---	
MCF2L2	23101	broad.mit.edu	37	3	183067658	183067658	+	Intron	DEL	T	-	-	rs74937608		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183067658delT	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc003flp.1_Intron	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TTGCTGCTCCTTTTTTTTTTC	0.358													2	5	---	---	---	---	
MCF2L2	23101	broad.mit.edu	37	3	183083436	183083437	+	Intron	INS	-	A	A	rs147286564	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183083436_183083437insA	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc003flp.1_Intron	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			atagaaagcatactacattaca	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	183341344	183341346	+	IGR	DEL	AAC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183341344_183341346delAAC								KLHL6 (67845 upstream) : KLHL24 (12065 downstream)																							gactgtctcaaacaacaacaaca	0.128													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	183619001	183619002	+	IGR	INS	-	AA	AA	rs147299870	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183619001_183619002insAA								PARL (16308 upstream) : ABCC5 (18724 downstream)																							gattctgtctcaaaaaaaaaga	0.000													3	5	---	---	---	---	
POLR2H	5437	broad.mit.edu	37	3	184084934	184084935	+	Intron	DEL	TG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184084934_184084935delTG	uc003fok.1	+						POLR2H_uc003foj.1_Intron	NM_006232	NP_006223	P52434	RPAB3_HUMAN	RNA polymerase II, polypeptide H						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|termination of RNA polymerase I transcription|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription elongation from RNA polymerase III promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex|nucleolus	DNA-directed RNA polymerase activity|protein binding|zinc ion binding				0	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			tgtaaaaggctgtgtgtgtgtg	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184495794	184495795	+	IGR	INS	-	TAT	TAT	rs148600199	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184495794_184495795insTAT								MAGEF1 (65958 upstream) : VPS8 (34136 downstream)																							tatcaaagatgtattgagcccc	0.188											OREG0015957	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187592010	187592011	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187592010_187592011insA								BCL6 (128535 upstream) : LPP (279708 downstream)																							TTTTCTGAAACAAAAAAAAAAA	0.351													4	2	---	---	---	---	
TPRG1	285386	broad.mit.edu	37	3	188937307	188937308	+	Intron	INS	-	A	A	rs112033944		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188937307_188937308insA	uc003frv.1	+						TPRG1_uc003frw.1_Intron	NM_198485	NP_940887	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		TGGCCCTTCTGaaaaaaaaaaa	0.347													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190498251	190498251	+	IGR	DEL	T	-	-	rs139559806		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190498251delT								IL1RAP (122408 upstream) : LOC647309 (72275 downstream)																							agtttgttcatttttttacaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193850459	193850459	+	IGR	DEL	A	-	-	rs10707992		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193850459delA								LOC100128023 (138432 upstream) : HES1 (3475 downstream)																							AACATTTTTTAAAAAAAATCT	0.448													2	4	---	---	---	---	
C3orf21	152002	broad.mit.edu	37	3	194836485	194836486	+	Intron	INS	-	AGG	AGG	rs143493553	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194836485_194836486insAGG	uc003fum.3	-						C3orf21_uc003ful.2_Intron|C3orf21_uc003fuk.2_Intron	NM_152531	NP_689744	Q8NBI6	CC021_HUMAN	hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)		AGGAGGGCGGCAGGTGCAGGCC	0.599													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195434536	195434537	+	Intron	INS	-	AG	AG	rs138424469	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195434536_195434537insAG	uc011btd.1	+						uc003fux.1_Intron					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		ttagtagagacgggtttcacca	0.000													1	7	---	---	---	---	
ZDHHC19	131540	broad.mit.edu	37	3	195929201	195929201	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195929201delA	uc003fwc.2	-						ZDHHC19_uc010hzz.2_Intron|ZDHHC19_uc010iaa.2_Intron|ZDHHC19_uc010iab.2_Intron	NM_001039617	NP_001034706	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC domain containing 19							integral to membrane	acyltransferase activity|zinc ion binding			ovary(3)	3	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		ctcaaaaaggaaaaaaaaaaa	0.020													4	2	---	---	---	---	
DLG1	1739	broad.mit.edu	37	3	196852844	196852845	+	Intron	INS	-	A	A	rs147089664	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196852844_196852845insA	uc003fxo.3	-						DLG1_uc011bub.1_Intron|DLG1_uc011buc.1_Intron|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_Intron|DLG1_uc010iam.1_Intron|DLG1_uc010ian.2_Intron	NM_001098424	NP_001091894	Q12959	DLG1_HUMAN	discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		CTCACTTATGTAAAAAAAATTT	0.267													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197165594	197165594	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197165594delA								DLG1 (139451 upstream) : BDH1 (71061 downstream)																							TGAAGCTGGGAAAAGGGGAGG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49345	49345	+	IGR	DEL	T	-	-	rs56012841		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49345delT								None (None upstream) : ZNF595 (3882 downstream)																							TAAATGCAGGTGATGTGGCCA	0.338													4	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	1555398	1555398	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1555398delT								CRIPAK (165616 upstream) : FAM53A (86211 downstream)																							GCCCGGGGGATGCAGGGAAGA	0.597													4	2	---	---	---	---	
POLN	353497	broad.mit.edu	37	4	2192204	2192204	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2192204delT	uc003ger.2	-						POLN_uc010ich.1_Intron|POLN_uc011bvi.1_Intron	NM_181808	NP_861524	Q7Z5Q5	DPOLN_HUMAN	DNA-directed DNA polymerase nu						DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			tgggcaatgattttttttttt	0.000								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3608344	3608359	+	IGR	DEL	TGAATGAGTGAGTGAA	-	-	rs62274273	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3608344_3608359delTGAATGAGTGAGTGAA								LRPAP1 (74120 upstream) : ADRA2C (159716 downstream)																							agtgaatgagtgaatgagtgagtgaatgagtgaatg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3619807	3619808	+	IGR	INS	-	A	A	rs150577781	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3619807_3619808insA								LRPAP1 (85583 upstream) : ADRA2C (148267 downstream)																							TTTCTTCTTTTAAAAAATCTGT	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3620071	3620072	+	IGR	INS	-	A	A	rs142732704	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3620071_3620072insA								LRPAP1 (85847 upstream) : ADRA2C (148003 downstream)																							GGCATTGTTATAACTGTATTTT	0.347													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3738043	3738043	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3738043delC								LRPAP1 (203819 upstream) : ADRA2C (30032 downstream)																							TCCATTCTGTCCCACCCCCTG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4831020	4831020	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4831020delC								STX18 (287245 upstream) : MSX1 (30372 downstream)																							TGAGTGTTCACCCTCACCTAC	0.527													4	2	---	---	---	---	
PPP2R2C	5522	broad.mit.edu	37	4	6513848	6513850	+	Intron	DEL	GGT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6513848_6513850delGGT	uc011bwd.1	-						PPP2R2C_uc011bwe.1_Intron	NM_181876	NP_870991	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein						signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4						tgatggtgggggtggtggtggtg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	9586101	9586102	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9586101_9586102insA								MIR548I2 (28164 upstream) : DRD5 (197156 downstream)																							GAAAGAGAAGCAAGGGCATAAA	0.406													4	2	---	---	---	---	
CCKAR	886	broad.mit.edu	37	4	26493958	26493959	+	5'Flank	INS	-	TC	TC			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26493958_26493959insTC	uc003gse.1	-							NM_000730	NP_000721	P32238	CCKAR_HUMAN	cholecystokinin A receptor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|elevation of cytosolic calcium ion concentration|response to nutrient	integral to plasma membrane	cholecystokinin receptor activity			lung(3)|pancreas(1)	4		Breast(46;0.0503)			Ceruletide(DB00403)	cctcctttctttctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	27177414	27177415	+	IGR	DEL	TC	-	-	rs146652824	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27177414_27177415delTC								STIM2 (151606 upstream) : None (None downstream)																							cttccttccttcttttcttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	37877670	37877671	+	IGR	DEL	TG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37877670_37877671delTG								PGM2 (13111 upstream) : TBC1D1 (15049 downstream)																							ttgacagatttgtgtgtgtgtg	0.000													3	3	---	---	---	---	
FRYL	285527	broad.mit.edu	37	4	48751916	48751916	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48751916delA	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gym.1_Intron|FRYL_uc003gyn.3_Intron	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						ttgggaggtcaaagcaggagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49560708	49560708	+	5'Flank	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49560708delA	uc011bzm.1	+						uc003gza.1_5'Flank					DQ582260																		AGGAAAGGCCATGTCCCAAAA	0.577													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49651084	49651084	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49651084delT								CWH43 (586991 upstream) : None (None downstream)																							tggaatcaactcgagtggaaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55822809	55822810	+	IGR	INS	-	T	T	rs150062917	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55822809_55822810insT								KIT (215930 upstream) : KDR (121617 downstream)																							GTCTTTCAGGATGTGGAAATCA	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55822811	55822812	+	IGR	INS	-	A	A	rs66487449		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55822811_55822812insA								KIT (215932 upstream) : KDR (121615 downstream)																							CTTTCAGGATGTGGAAATCAGG	0.411													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63028698	63028699	+	IGR	INS	-	T	T	rs143830582	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63028698_63028699insT								LPHN3 (90531 upstream) : None (None downstream)																							aggatatgagaaatggtagaag	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	67999021	67999021	+	IGR	DEL	A	-	-	rs35789654		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67999021delA								MIR1269 (856375 upstream) : CENPC1 (338968 downstream)																							aggttgtgggaaaaaaaatgc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	70691298	70691299	+	IGR	DEL	GT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70691298_70691299delGT								SULT1B1 (64868 upstream) : SULT1E1 (15632 downstream)																							ttctgggaaagtgttctctaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	71941339	71941339	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71941339delC								DCK (44712 upstream) : SLC4A4 (111664 downstream)																							atggctcactccagctcttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	89166032	89166032	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89166032delG								ABCG2 (13558 upstream) : PPM1K (15502 downstream)																							cctggaagcaggacaagaacc	0.000													4	2	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91290594	91290595	+	Intron	DEL	AG	-	-	rs35993765		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91290594_91290595delAG	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						GTATAAAAAAAGAGAATTGAAG	0.243													4	3	---	---	---	---	
UNC5C	8633	broad.mit.edu	37	4	96248333	96248333	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96248333delC	uc003htp.1	-						UNC5C_uc010ilc.1_Intron|UNC5C_uc003htq.2_Intron	NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor						apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		TCAGGGAAAACCCCCCAACCT	0.398													4	2	---	---	---	---	
NHEDC1	150159	broad.mit.edu	37	4	103869482	103869483	+	Intron	INS	-	AC	AC			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103869482_103869483insAC	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		ggcaaagccatacacacacaca	0.000													3	3	---	---	---	---	
GSTCD	79807	broad.mit.edu	37	4	106718203	106718204	+	Intron	INS	-	TG	TG	rs28533186		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106718203_106718204insTG	uc003hxz.3	+						GSTCD_uc003hxx.2_Intron|GSTCD_uc003hxy.3_Intron|GSTCD_uc011cfb.1_Intron	NM_001031720	NP_001026890	Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain							cytoplasm	rRNA methyltransferase activity			breast(1)|central_nervous_system(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)		ACAGAGATACAtgtgtgtgtgt	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111772464	111772465	+	IGR	DEL	GT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111772464_111772465delGT								PITX2 (209347 upstream) : MIR297 (9273 downstream)																							gtgtgtgtgcgtgtgtgtgtgt	0.431													4	2	---	---	---	---	
ANK2	287	broad.mit.edu	37	4	113871806	113871806	+	Intron	DEL	A	-	-	rs147062967		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113871806delA	uc003ibd.3	+						ANK2_uc003ibc.2_Intron	NM_001127493	NP_001120965	Q01484	ANK2_HUMAN	ankyrin 2 isoform 3						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		tctcaaaaagaaaaaaaaaaa	0.065													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	119492265	119492265	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119492265delG								CEP170L (16908 upstream) : METTL14 (114309 downstream)																							ggtttcatctgctcgaagctg	0.114													4	2	---	---	---	---	
FGF2	2247	broad.mit.edu	37	4	123776123	123776124	+	Intron	DEL	CC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123776123_123776124delCC	uc003iev.1	+							NM_002006	NP_001997	P09038	FGF2_HUMAN	fibroblast growth factor 2						activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing	extracellular space	fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|lung(1)|central_nervous_system(1)	3					Pentosan Polysulfate(DB00686)	ACTTGCCTTTCCCCCAAAGCTC	0.480													4	2	---	---	---	---	
LARP1B	55132	broad.mit.edu	37	4	129093978	129093980	+	Intron	DEL	TTG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129093978_129093980delTTG	uc003iga.2	+						LARP1B_uc003igc.2_Intron|LARP1B_uc003igb.1_Intron	NM_018078	NP_060548	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family member 2								RNA binding				0						atgctctgttttgttgttgttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	129595730	129595730	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129595730delT								PGRMC2 (386782 upstream) : PHF17 (135049 downstream)																							CTCCTGATTCTTTTTTTTTTC	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	140517252	140517252	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140517252delA								SETD7 (39675 upstream) : MGST2 (69670 downstream)																							CCTGGGGGAGAAAAAAAAGGG	0.512													4	2	---	---	---	---	
MAML3	55534	broad.mit.edu	37	4	140954579	140954579	+	Intron	DEL	G	-	-	rs10713599		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140954579delG	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187	Q96JK9	MAML3_HUMAN	mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)					GAAGAGGTACGGTATGGGAAA	0.468													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	144574671	144574672	+	IGR	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144574671_144574672delCA								LOC441046 (85358 upstream) : GYPE (217348 downstream)																							gacagagatgcacacacacaca	0.000													4	2	---	---	---	---	
EDNRA	1909	broad.mit.edu	37	4	148464977	148464978	+	3'UTR	INS	-	A	A	rs145292318	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148464977_148464978insA	uc003iky.2	+	8					EDNRA_uc011cid.1_3'UTR|EDNRA_uc010ipf.1_RNA|EDNRA_uc010ipg.1_3'UTR	NM_001957	NP_001948	P25101	EDNRA_HUMAN	endothelin receptor type A isoform a precursor						activation of adenylate cyclase activity|artery smooth muscle contraction|cell proliferation|glucose transport|respiratory gaseous exchange	integral to plasma membrane	endothelin-A receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|breast(1)	2	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Bosentan(DB00559)	CACCAGAACTTACGATTCTTCA	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	152745409	152745409	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152745409delT								PET112L (63263 upstream) : FBXW7 (497002 downstream)																							AATGCCAGGAttttttttttt	0.229													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	152853222	152853222	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152853222delT								PET112L (171076 upstream) : FBXW7 (389189 downstream)																							aaaccttaccTTACCtttgtt	0.020													4	2	---	---	---	---	
TRIM2	23321	broad.mit.edu	37	4	154142937	154142940	+	Intron	DEL	AAGG	-	-	rs35003062		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154142937_154142940delAAGG	uc003ing.2	+						TRIM2_uc003inh.2_Intron	NM_001130067	NP_001123539	Q9C040	TRIM2_HUMAN	tripartite motif-containing 2 isoform 2							cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		gaaagaagaaaaggaaggaaagag	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	155677384	155677384	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155677384delT								LRAT (3114 upstream) : RBM46 (25043 downstream)																							tatgaagaacttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	157197026	157197026	+	IGR	DEL	T	-	-	rs111413903		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157197026delT								CTSO (321978 upstream) : PDGFC (485738 downstream)																							ttgaggtaagttttttacaaa	0.000													3	3	---	---	---	---	
PDGFC	56034	broad.mit.edu	37	4	157818503	157818504	+	Intron	DEL	TG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157818503_157818504delTG	uc003iph.1	-						PDGFC_uc003ipi.1_Intron|PDGFC_uc011cis.1_Intron	NM_016205	NP_057289	Q9NRA1	PDGFC_HUMAN	platelet-derived growth factor C precursor						central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		tgagagtgtatgtgtgtgtgtg	0.257													4	2	---	---	---	---	
CPE	1363	broad.mit.edu	37	4	166360449	166360449	+	Intron	DEL	T	-	-	rs75616476		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166360449delT	uc003irg.3	+							NM_001873	NP_001864	P16870	CBPE_HUMAN	carboxypeptidase E preproprotein						cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AACTTTAAAATTTTAGTAAGG	0.378													4	2	---	---	---	---	
PALLD	23022	broad.mit.edu	37	4	169698255	169698256	+	Intron	DEL	AC	-	-	rs112829388		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169698255_169698256delAC	uc011cjx.1	+						PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron	NM_016081	NP_057165	Q8WX93	PALLD_HUMAN	palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		acacacatatacacacacacac	0.322									Pancreatic_Cancer_Familial_Clustering_of				3	3	---	---	---	---	
NEK1	4750	broad.mit.edu	37	4	170456608	170456609	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170456608_170456609insA	uc003isb.1	-						NEK1_uc003isc.1_Intron|NEK1_uc003isd.1_Intron|NEK1_uc003ise.1_Intron|NEK1_uc003isf.1_Intron	NM_012224	NP_036356	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1						cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		aacacacagagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189448692	189448693	+	Intron	INS	-	AAAGA	AAAGA	rs143660089	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189448692_189448693insAAAGA	uc003izp.1	+											Homo sapiens cDNA FLJ38649 fis, clone HHDPC2007302.																		aaaggaaagggaaagaaaagaa	0.119													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190619768	190619777	+	IGR	DEL	AAAACAAAAC	-	-	rs36202645		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190619768_190619777delAAAACAAAAC								None (None upstream) : FRG1 (242197 downstream)																							TGTTCTCTTTaaaacaaaacaaaacaaaac	0.295													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190815465	190815466	+	Intron	DEL	AT	-	-	rs62346083		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190815465_190815466delAT	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		ttgaggaaccatatgttttcca	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190817143	190817144	+	Intron	INS	-	TCAAA	TCAAA	rs146980504		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190817143_190817144insTCAAA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		TTTCAATTTGCTCAAACTATTC	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190835506	190835507	+	Intron	DEL	TT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190835506_190835507delTT	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		agtccaagactttgcctttgtg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190840895	190840895	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190840895delG	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		tttttgcattgaaaaggagaa	0.085													2	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2001019	2001019	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2001019delC								IRX4 (118139 upstream) : IRX2 (745262 downstream)																							GACATCAGGTCCGCCTTCACC	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5989913	5989914	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5989913_5989914insT								KIAA0947 (499576 upstream) : FLJ33360 (320640 downstream)																							CACCCACAGCATTTCAGCAAGT	0.480													4	2	---	---	---	---	
MTRR	4552	broad.mit.edu	37	5	7885676	7885676	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7885676delT	uc003jed.2	+						MTRR_uc010itn.1_Intron|MTRR_uc003jee.3_Intron|MTRR_uc003jef.3_Intron|MTRR_uc003jeg.3_Intron|MTRR_uc010ito.2_Intron	NM_024010	NP_076915	Q9UBK8	MTRR_HUMAN	methionine synthase reductase isoform 2						methionine biosynthetic process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	CAATTGTGTGTTTTTTTTTTT	0.254													4	2	---	---	---	---	
DAP	1611	broad.mit.edu	37	5	10705369	10705369	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10705369delA	uc003jez.3	-						DAP_uc011cmw.1_Intron	NM_004394	NP_004385	P51397	DAP1_HUMAN	death-associated protein						activation of caspase activity|cellular response to amino acid starvation|induction of apoptosis by extracellular signals|negative regulation of autophagy|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent		death domain binding				0		Ovarian(839;1.34e-05)|Breast(839;0.0634)|Lung NSC(810;0.0804)				CACATGTATTAAAGGCTGAGT	0.333													4	2	---	---	---	---	
CTNND2	1501	broad.mit.edu	37	5	11110699	11110699	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11110699delA	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						GCGCCTGCTCAGAGGTGGAAT	0.473													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	18129372	18129372	+	IGR	DEL	T	-	-	rs78547581		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18129372delT								BASP1 (852437 upstream) : None (None downstream)																							agcaataatattgctttctta	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	25438417	25438418	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25438417_25438418insT								CDH10 (793506 upstream) : None (None downstream)																							gtttgtttttggttttttttga	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36576475	36576475	+	IGR	DEL	G	-	-	rs147818348		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36576475delG								RANBP3L (274464 upstream) : SLC1A3 (29982 downstream)																							caggagaattgcttgaagctg	0.000													2	4	---	---	---	---	
HEATR7B2	133558	broad.mit.edu	37	5	41011775	41011775	+	Intron	DEL	T	-	-	rs112390740		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41011775delT	uc003jmj.3	-						HEATR7B2_uc003jmi.3_Intron	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2								binding			ovary(6)|central_nervous_system(2)	8						ttcctttttcttttttttttt	0.149													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42745817	42745818	+	IGR	INS	-	A	A	rs140946194	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42745817_42745818insA								GHR (23892 upstream) : CCDC152 (11102 downstream)																							TAGAAAAAGGTAAAAAATTGTC	0.317													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	46340126	46340126	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46340126delA								HCN1 (643906 upstream) : None (None downstream)																							gcttctgtctagtttttatgt	0.000													4	2	---	---	---	---	
SKIV2L2	23517	broad.mit.edu	37	5	54603687	54603687	+	5'UTR	DEL	A	-	-	rs77094835		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54603687delA	uc003jpy.3	+	1					SKIV2L2_uc011cqi.1_5'UTR|DHX29_uc003jpx.2_5'Flank|DHX29_uc010ivw.2_5'Flank	NM_015360	NP_056175	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2						maturation of 5.8S rRNA	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)|skin(1)	2		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				gaaaagcaggaaaaaaaaaaa	0.473													4	2	---	---	---	---	
GUSBP3	653188	broad.mit.edu	37	5	69391976	69391977	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69391976_69391977insA	uc003jxm.2	-						uc003jxp.3_Intron|uc011crh.1_Intron|uc011crl.1_Intron|uc003jyj.1_Intron					Homo sapiens cDNA FLJ36702 fis, clone UTERU2009206.												0						aaagagaaaacaaaaaaaaaaa	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	73444081	73444082	+	IGR	DEL	CA	-	-	rs35390617		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73444081_73444082delCA								RGNEF (206668 upstream) : ENC1 (479153 downstream)																							CTCCTGCCTCCACACACACACA	0.406													2	4	---	---	---	---	
ANKRD31	256006	broad.mit.edu	37	5	74491716	74491718	+	In_Frame_Del	DEL	TCA	-	-	rs143148927		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74491716_74491718delTCA	uc003kdo.1	-	7	947_949	c.755_757delTGA	c.(754-759)ATGAAC>AAC	p.M252del				Q8N7Z5	ANR31_HUMAN	Homo sapiens cDNA FLJ40191 fis, clone TESTI2019280, weakly similar to Homo sapiens nasopharyngeal carcinoma susceptibility protein LZ16 mRNA.	252											0						CTCAATGGGTTCATCAATTCTTT	0.379													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	76218344	76218345	+	IGR	INS	-	TTGTTTGT	TTGTTTGT	rs138741059	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76218344_76218345insTTGTTTGT								S100Z (1289 upstream) : CRHBP (30335 downstream)																							tttttttgttgttgtttgtttg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	85988458	85988459	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85988458_85988459insT								COX7C (71877 upstream) : RASA1 (575692 downstream)																							tgtacactgtattttttttttt	0.000													4	2	---	---	---	---	
RASA1	5921	broad.mit.edu	37	5	86630707	86630707	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86630707delT	uc003kiw.2	+						RASA1_uc010jav.2_Intron|RASA1_uc003kix.2_Intron|RASA1_uc011ctv.1_Intron|RASA1_uc011ctw.1_Intron|RASA1_uc010jaw.2_Intron	NM_002890	NP_002881	P20936	RASA1_HUMAN	RAS p21 protein activator 1 isoform 1						cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		agtttgttccttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87077554	87077554	+	IGR	DEL	T	-	-	rs35183323		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87077554delT								CCNH (368718 upstream) : TMEM161B (413470 downstream)																							TTTTTCCTGATTTTTTTTTCA	0.368											OREG0016696	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	5	87760402	87760403	+	IGR	INS	-	A	A	rs36086186		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87760402_87760403insA								TMEM161B (195737 upstream) : LOC645323 (76194 downstream)																							GTCTTCTGTAGAAAAAAAAAAA	0.312													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	95978714	95978715	+	IGR	INS	-	GCCCTAGGTTACACA	GCCCTAGGTTACACA	rs140277760	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95978714_95978715insGCCCTAGGTTACACA								PCSK1 (209762 upstream) : CAST (19062 downstream)																							ttgagtaatttgctgctaaggg	0.025													4	2	---	---	---	---	
APC	324	broad.mit.edu	37	5	112154530	112154531	+	Intron	DEL	TG	-	-	rs141013063	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112154530_112154531delTG	uc010jby.2	+						APC_uc011cvt.1_Intron|APC_uc003kpz.3_Intron|APC_uc003kpy.3_Intron|APC_uc010jbz.2_Intron	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli						canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity			large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCCGGTTTTTTGTTTTTTTTTT	0.317		12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	120070033	120070034	+	IGR	DEL	TG	-	-	rs77357878	byFrequency	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120070033_120070034delTG								PRR16 (47071 upstream) : None (None downstream)																							TCTCTCTCTCtgtgtgtgtgtg	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134869299	134869300	+	IGR	INS	-	GT	GT	rs140591870	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134869299_134869300insGT								TIFAB (81210 upstream) : NEUROG1 (680 downstream)																							GCGGGTGTTAAgtgtgtgtgtg	0.554													4	2	---	---	---	---	
BRD8	10902	broad.mit.edu	37	5	137514309	137514309	+	5'UTR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137514309delC	uc003lcf.1	-	1					BRD8_uc003lcc.1_5'Flank|BRD8_uc003lcg.2_5'UTR|BRD8_uc003lci.2_5'UTR|BRD8_uc003lch.2_5'UTR|BRD8_uc011cym.1_5'UTR|BRD8_uc010jer.1_5'Flank|BRD8_uc011cyn.1_5'UTR|BRD8_uc010jes.1_5'UTR|KIF20A_uc003lcj.2_5'Flank|KIF20A_uc011cyo.1_5'Flank	NM_139199	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8 isoform 2						cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GCCATCTTGGCCCCGAAGTCT	0.557													50	45	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	138540782	138540782	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138540782delA								SIL1 (6717 upstream) : SNHG4 (68996 downstream)																							actctgtctcaaaaaaaaaaa	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151197324	151197324	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151197324delT								G3BP1 (12411 upstream) : GLRA1 (4751 downstream)																							ATAGGGAGGGttttttttttt	0.214													4	2	---	---	---	---	
CCDC99	54908	broad.mit.edu	37	5	169024237	169024244	+	Intron	DEL	TGTGTGTG	-	-	rs112150263		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169024237_169024244delTGTGTGTG	uc003mae.3	+						CCDC99_uc010jjj.2_Intron|CCDC99_uc011deq.1_Intron|CCDC99_uc010jjk.2_Intron	NM_017785	NP_060255	Q96EA4	SPDLY_HUMAN	coiled-coil domain containing 99						cell division|establishment of mitotic spindle orientation|mitotic metaphase plate congression|mitotic prometaphase|protein localization to kinetochore	condensed chromosome outer kinetochore|cytosol|microtubule organizing center|nucleus|spindle pole	kinetochore binding|protein binding			ovary(1)|liver(1)	2	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGTAAGCATTtgtgtgtgtgtgtgtgtg	0.048													2	4	---	---	---	---	
DUSP22	56940	broad.mit.edu	37	6	345224	345225	+	Intron	INS	-	T	T	rs5873745		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:345224_345225insT	uc003msx.2	+						DUSP22_uc011dhn.1_Intron|DUSP22_uc003msy.1_Intron	NM_020185	NP_064570	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22						apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		tggtttctttcttttttttttt	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	17730943	17730943	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17730943delT								NUP153 (24125 upstream) : KIF13A (29642 downstream)																							tagttctttgttttcacacta	0.000													4	2	---	---	---	---	
CDKAL1	54901	broad.mit.edu	37	6	20981385	20981385	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20981385delG	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244	Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			GTTCATTTTTGAACTTCTTTT	0.353													1	5	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34039096	34039097	+	Intron	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34039096_34039097delCA	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	agatacacaccacacacacaca	0.000													4	2	---	---	---	---	
KIF6	221458	broad.mit.edu	37	6	39348419	39348419	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39348419delA	uc003oot.2	-						KIF6_uc003oos.2_Intron|KIF6_uc010jwz.1_Intron|KIF6_uc010jxa.1_Intron|KIF6_uc011dua.1_Intron|KIF6_uc010jxb.1_Intron	NM_145027	NP_659464	Q6ZMV9	KIF6_HUMAN	kinesin family member 6						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3						cactctttggaaaaaaaaaaa	0.085													4	2	---	---	---	---	
TRERF1	55809	broad.mit.edu	37	6	42318741	42318742	+	Intron	DEL	AC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42318741_42318742delAC	uc003osd.2	-						TRERF1_uc003osb.2_Intron|TRERF1_uc003osc.2_Intron|TRERF1_uc003ose.2_Intron|TRERF1_uc010jxu.1_Intron	NM_033502	NP_277037	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1						cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			acacacacaaacacacacacac	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	44472018	44472019	+	IGR	INS	-	TG	TG	rs138676695	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44472018_44472019insTG								CDC5L (57239 upstream) : SUPT3H (305035 downstream)																							Ttgtgtgtgtatgtgtgtgtgt	0.337													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	52720028	52720028	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52720028delG								GSTA5 (9135 upstream) : GSTA3 (41413 downstream)																							catatgtcttggaggctttgt	0.000													4	2	---	---	---	---	
COL21A1	81578	broad.mit.edu	37	6	56180475	56180476	+	Intron	INS	-	T	T	rs143965787	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56180475_56180476insT	uc003pcu.1	-							NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			ctccctcttcctcctcatctcc	0.282													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57255016	57255017	+	Intron	INS	-	C	C	rs140410891	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57255016_57255017insC	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)		ctaaTAACAGAAAAAAAATCAT	0.218													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57324849	57324849	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57324849delT	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)		GAGGTCATGCTTCACCTAGTC	0.463													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57390643	57390644	+	Intron	DEL	CA	-	-	rs141634742		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57390643_57390644delCA	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)		TTTAATGCTCCACACATTGCCT	0.401													8	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57402022	57402023	+	Intron	INS	-	G	G	rs144916181		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57402022_57402023insG	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)		actttgttaatttttttttctc	0.000													5	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57404370	57404371	+	Intron	INS	-	A	A	rs139203387		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57404370_57404371insA	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)		aaagaaacacgaaaagcagctc	0.104													5	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57414398	57414399	+	Intron	INS	-	A	A	rs151258963		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57414398_57414399insA	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)		ATTGTGCCTTGAGGCCTCTTAC	0.287													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57419782	57419782	+	Intron	DEL	A	-	-	rs112636436		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57419782delA	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)		TCAGGTCAAGATTCCATCTGA	0.328													4	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57432660	57432669	+	Intron	DEL	GTTTTGTTAA	-	-	rs111697583		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57432660_57432669delGTTTTGTTAA	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)		TGAAGTCTCTGTTTTGTTAAGTTCTTCAAC	0.195													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57538130	57538131	+	IGR	DEL	TG	-	-	rs67422833		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57538130_57538131delTG								PRIM2 (24755 upstream) : GUSBL2 (708028 downstream)																							CGAGTTTGACTGTTTTGGTTAG	0.386													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57557095	57557095	+	IGR	DEL	T	-	-	rs79478192		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57557095delT								PRIM2 (43720 upstream) : GUSBL2 (689064 downstream)																							atttacaaagtaaagaggttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	72455568	72455568	+	IGR	DEL	A	-	-	rs34822559		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72455568delA								C6orf155 (325120 upstream) : RIMS1 (141082 downstream)																							CTATTTTCAGATATTTGCTTG	0.448													1	5	---	---	---	---	
DDX43	55510	broad.mit.edu	37	6	74104496	74104497	+	5'UTR	INS	-	T	T	rs66566509		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74104496_74104497insT	uc003pgw.2	+	1					OOEP_uc003pgv.3_5'UTR|DDX43_uc011dyn.1_RNA	NM_018665	NP_061135	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43							intracellular	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4						GAGCGTGGGCGGGGGGGCTAGC	0.619											OREG0003901	type=REGULATORY REGION|Gene=DDX43|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	80004817	80004817	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80004817delA								HMGN3 (60362 upstream) : LCA5 (189892 downstream)																							cagaaatgctagcaatttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	87171298	87171303	+	IGR	DEL	AGGAGG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87171298_87171303delAGGAGG								SNHG5 (782847 upstream) : HTR1E (475721 downstream)																							gaggaggagaaggaggaggaggagga	0.000													4	2	---	---	---	---	
CDK19	23097	broad.mit.edu	37	6	111091496	111091496	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111091496delA	uc003puh.1	-						CDK19_uc003pui.1_Intron	NM_015076	NP_055891	Q9BWU1	CDK19_HUMAN	cell division cycle 2-like 6 (CDK8-like)								ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4						gattgggaagaaaaagaggtt	0.065													3	4	---	---	---	---	
LAMA4	3910	broad.mit.edu	37	6	112492418	112492418	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112492418delT	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		ctgtctctccttttttttttt	0.100													2	4	---	---	---	---	
GOPC	57120	broad.mit.edu	37	6	117789544	117789544	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117789544delT	uc003pxq.1	-							NM_001017408	NP_001017408	Q9HD26	GOPC_HUMAN	golgi associated PDZ and coiled-coil motif						apical protein localization|cytoplasmic sequestering of CFTR protein|ER to Golgi vesicle-mediated transport|Golgi to plasma membrane transport|protein homooligomerization|protein transport	cell junction|dendrite|Golgi membrane|postsynaptic density|postsynaptic membrane|trans-Golgi network transport vesicle	cystic fibrosis transmembrane conductance regulator binding			ovary(1)	1		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		agataagttatttggtggtga	0.070			O	ROS1	glioblastoma								4	2	---	---	---	---	
SLC35F1	222553	broad.mit.edu	37	6	118356066	118356066	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118356066delA	uc003pxx.3	+							NM_001029858	NP_001025029	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)		ctggccttgtaaaactagttg	0.085													4	2	---	---	---	---	
C6orf204	387119	broad.mit.edu	37	6	118797447	118797448	+	Intron	DEL	TT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118797447_118797448delTT	uc003pxz.1	-							NM_001042475	NP_001035940	Q5SZL2	CF204_HUMAN	chromosome 6 open reading frame 204 isoform a							centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)		AGTGTGTGCGTTTTTTTTTTTT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	119067563	119067564	+	IGR	INS	-	GT	GT	rs58914769		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119067563_119067564insGT								C6orf204 (36325 upstream) : ASF1A (147677 downstream)																							GGCTTAGAAACgtgtgtgtgtg	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	121360028	121360029	+	IGR	INS	-	AGG	AGG	rs143646626	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121360028_121360029insAGG								None (None upstream) : C6orf170 (40598 downstream)																							tgtccatcaatagaatggataa	0.000													0	6	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	124167989	124167990	+	Intron	INS	-	CACA	CACA	rs141897220	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124167989_124167990insCACA	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010kep.1_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		acgcacgcgcgcacacacacac	0.213													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	130076917	130076920	+	IGR	DEL	ATAG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130076917_130076920delATAG								ARHGAP18 (45547 upstream) : C6orf191 (75471 downstream)																							aaacatgggaatagagatatcttt	0.000													4	2	---	---	---	---	
EPB41L2	2037	broad.mit.edu	37	6	131166525	131166525	+	Intron	DEL	T	-	-	rs11288907		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131166525delT	uc003qch.2	-						EPB41L2_uc003qce.1_Intron|EPB41L2_uc003qcf.1_Intron|EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc003qcd.1_Intron	NM_001431	NP_001422	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		aaccttattctttttttttta	0.000													3	5	---	---	---	---	
EPB41L2	2037	broad.mit.edu	37	6	131299517	131299517	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131299517delG	uc003qch.2	-						EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron	NM_001431	NP_001422	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		TACATGATCTGCAATGGTGTG	0.493													4	2	---	---	---	---	
MAP3K5	4217	broad.mit.edu	37	6	137051860	137051864	+	Intron	DEL	AAAAA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137051860_137051864delAAAAA	uc003qhc.2	-						MAP3K5_uc011edk.1_Intron|MAP3K5_uc010kgw.1_Intron	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		actctgcctcaaaaaaaaaaaaaaa	0.176													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138391180	138391181	+	IGR	INS	-	ACT	ACT			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138391180_138391181insACT								TNFAIP3 (186735 upstream) : PERP (18461 downstream)																							aataaatatGAACTACGTTTCT	0.188													4	2	---	---	---	---	
NHSL1	57224	broad.mit.edu	37	6	138785853	138785853	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138785853delT	uc003qhx.2	-						NHSL1_uc011edp.1_Intron|NHSL1_uc003qhy.2_Intron	NM_020464	NP_065197	Q5SYE7	NHSL1_HUMAN	NHS-like 1 isoform 1												0						ttttcttttcttttttttttt	0.134													4	2	---	---	---	---	
NHSL1	57224	broad.mit.edu	37	6	138826958	138826958	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138826958delT	uc003qhx.2	-							NM_020464	NP_065197	Q5SYE7	NHSL1_HUMAN	NHS-like 1 isoform 1												0						AATTTAGCTCTTCAAACAGAA	0.328													4	2	---	---	---	---	
LOC285740	285740	broad.mit.edu	37	6	143887969	143887969	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143887969delA	uc003qjp.2	-							NR_027113				Homo sapiens cDNA FLJ35832 fis, clone TESTI2006523.												0						aggacttttcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	144453321	144453324	+	IGR	DEL	TTCC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144453321_144453324delTTCC								SF3B5 (36567 upstream) : STX11 (18330 downstream)																							ccttccttctttccttccttcctt	0.098													4	2	---	---	---	---	
UTRN	7402	broad.mit.edu	37	6	145165407	145165407	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145165407delT	uc003qkt.2	+							NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		tttctctctcttttttttttt	0.169													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145516354	145516355	+	IGR	DEL	AA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145516354_145516355delAA								UTRN (342186 upstream) : EPM2A (430091 downstream)																							actccatctgaaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	147495783	147495783	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147495783delA	uc003qlt.1	-						uc003qlu.1_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																		AGAAGCCAAGAAAAGCAGACA	0.423													4	2	---	---	---	---	
SASH1	23328	broad.mit.edu	37	6	148830091	148830091	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148830091delG	uc003qme.1	+						SASH1_uc011eeb.1_Intron	NM_015278	NP_056093	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1								protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		TGCTGCTCCTGCCTATGATGT	0.423													4	2	---	---	---	---	
C6orf97	80129	broad.mit.edu	37	6	151917439	151917439	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151917439delA	uc003qol.2	+							NM_025059	NP_079335	Q8IYT3	CF097_HUMAN	hypothetical protein LOC80129												0		Ovarian(120;0.126)	BRCA - Breast invasive adenocarcinoma(37;0.111)	OV - Ovarian serous cystadenocarcinoma(155;1.48e-10)		TTCAATTATTAAAAAAAAAAT	0.343													20	29	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156714174	156714175	+	IGR	DEL	CT	-	-	rs72217589		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156714174_156714175delCT								MIR1202 (446161 upstream) : ARID1B (384911 downstream)																							ccctccctccctctctctctct	0.183													3	5	---	---	---	---	
PACRG	135138	broad.mit.edu	37	6	163731622	163731622	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163731622delG	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron|LOC285796_uc011egh.1_RNA	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		GGAGTGACGTGGGAAGACCTC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164111856	164111856	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164111856delG	uc003quk.1	+											Homo sapiens cDNA FLJ35795 fis, clone TESTI2005827.																		agggagaggtggggaaggcag	0.154													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165239492	165239492	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165239492delA								None (None upstream) : C6orf118 (453663 downstream)																							AAATGACTGGAAAATTGTCTA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166621596	166621597	+	IGR	INS	-	TG	TG	rs145182781	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166621596_166621597insTG								T (39465 upstream) : PRR18 (97571 downstream)																							gtgtgtgtctatgtgtgtgtgt	0.124													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168052408	168052419	+	IGR	DEL	GTGTATGTGTGA	-	-	rs138307437		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168052408_168052419delGTGTATGTGTGA								TCP10 (254410 upstream) : C6orf123 (132802 downstream)																							ggtatgtgtggtgtatgtgtgagtgtatgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	189355	189355	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:189355delG								None (None upstream) : FAM20C (3614 downstream)																							GTCACCACCTGGCGCTCACCT	0.602													4	2	---	---	---	---	
PRKAR1B	5575	broad.mit.edu	37	7	621806	621807	+	Intron	INS	-	A	A	rs35955005		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:621806_621807insA	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron|PRKAR1B_uc003six.1_Intron	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		GCCCAGGGGGGAACCCATCGTC	0.604													2	4	---	---	---	---	
PRKAR1B	5575	broad.mit.edu	37	7	679801	679801	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:679801delA	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		ctccgtctcgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
PRKAR1B	5575	broad.mit.edu	37	7	751203	751204	+	Intron	INS	-	C	C			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:751203_751204insC	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CCTGAGAGCTGCCCGGGGCTGC	0.614													4	8	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945040	945041	+	Intron	INS	-	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945040_945041insG	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						gaaaggagaaaggagaaaggga	0.168													4	2	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945728	945728	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945728delG	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						aaaggagaaagggagaaagga	0.000													8	4	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	970615	970616	+	Intron	INS	-	A	A	rs78848668		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:970615_970616insA	uc003sjo.3	-						ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						gactgtgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
GNA12	2768	broad.mit.edu	37	7	2853262	2853262	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2853262delG	uc003smu.2	-						GNA12_uc011jwb.1_Intron|GNA12_uc003smt.2_Intron	NM_007353	NP_031379	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein)						G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|Rho protein signal transduction	brush border membrane|heterotrimeric G-protein complex	D5 dopamine receptor binding|G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		AATCTGTGAAGGAAATGAAAA	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	5312997	5313010	+	IGR	DEL	TCTCTCCCTCCCTC	-	-	rs62441106		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5312997_5313010delTCTCTCCCTCCCTC								WIPI2 (39512 upstream) : SLC29A4 (9551 downstream)																							tcttttcctgtctctccctccctctctctccctc	0.042													4	2	---	---	---	---	
USP42	84132	broad.mit.edu	37	7	6164639	6164640	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6164639_6164640insT	uc011jwo.1	+						USP42_uc011jwn.1_Intron|USP42_uc010kth.1_Intron|USP42_uc011jwp.1_Intron|USP42_uc011jwq.1_Intron|USP42_uc011jwr.1_Intron	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42						cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		tagcaaaaccccgtctctactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	9064312	9064315	+	IGR	DEL	CCTT	-	-	rs34803648		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9064312_9064315delCCTT								NXPH1 (271720 upstream) : PER4 (609585 downstream)																							CTTCTTCCTCCCTTAATGTTCCAC	0.333													4	2	---	---	---	---	
PHF14	9678	broad.mit.edu	37	7	11204559	11204560	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11204559_11204560insT	uc003srz.2	+						PHF14_uc011jxj.1_Intron|PHF14_uc003ssa.2_Intron	NM_001007157	NP_001007158	O94880	PHF14_HUMAN	PHD finger protein 14 isoform 1								zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		ccttgacattcttttttttttg	0.000													4	2	---	---	---	---	
ISPD	729920	broad.mit.edu	37	7	16157067	16157067	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16157067delG	uc010ktx.2	-						ISPD_uc010kty.2_Intron	NM_001101426	NP_001094896	A4D126	ISPD_HUMAN	notch1-induced protein isoform a						isoprenoid biosynthetic process		nucleotidyltransferase activity			ovary(1)	1						GGCTGAGTGAGGCAGGAGTTC	0.517										Multiple Myeloma(15;0.18)			4	2	---	---	---	---	
HDAC9	9734	broad.mit.edu	37	7	18824567	18824574	+	Intron	DEL	TGTGTGTG	-	-	rs71553933		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18824567_18824574delTGTGTGTG	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc011jyd.1_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003sua.1_Intron	NM_058176	NP_478056	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 1						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|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)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)	AGCAATTGCTtgtgtgtgtgtgtgtgtg	0.274													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	21439971	21439976	+	IGR	DEL	AGACTT	-	-	rs141270884		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21439971_21439976delAGACTT								RPL23P8 (572532 upstream) : SP4 (27713 downstream)																							aagaggaaacagacttagaACaactc	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	22051482	22051483	+	IGR	INS	-	TT	TT	rs10645283		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22051482_22051483insTT								CDCA7L (65940 upstream) : RAPGEF5 (106426 downstream)																							GGCCTGGGAACttttttttttt	0.218													4	4	---	---	---	---	
RAPGEF5	9771	broad.mit.edu	37	7	22193724	22193724	+	Intron	DEL	T	-	-	rs35254223		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22193724delT	uc003svg.2	-						RAPGEF5_uc011jyl.1_Intron	NM_012294	NP_036426	Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1						CCATCTTTCCTTTTTTTTTTC	0.343													8	4	---	---	---	---	
MGC87042	256227	broad.mit.edu	37	7	22484043	22484044	+	Intron	INS	-	A	A	rs138315804		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22484043_22484044insA	uc003svh.2	-						MGC87042_uc010kum.1_Intron			Q6NZ63	STEAL_HUMAN	SubName: Full=cDNA FLJ60218, highly similar to Six transmembrane epithelial antigen ofprostate 1;							integral to membrane	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0						TTCCCTGttttaaaaaaaaaaa	0.371													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	23124782	23124784	+	IGR	DEL	AAC	-	-	rs34243434		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23124782_23124784delAAC								FAM126A (71012 upstream) : KLHL7 (20569 downstream)																							cttaaaaaaaaacaacacaaaac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	23244675	23244676	+	5'Flank	INS	-	A	A	rs112084815		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23244675_23244676insA	uc003svz.1	+											Homo sapiens cDNA FLJ25144 fis, clone CBR07272.																		aTATGTGACTTAAAAAAAAAAA	0.059													7	6	---	---	---	---	
C7orf30	115416	broad.mit.edu	37	7	23338847	23338847	+	5'Flank	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23338847delG	uc003swd.1	+							NM_138446	NP_612455	Q96EH3	CG030_HUMAN	hypothetical protein LOC115416							mitochondrion					0			GBM - Glioblastoma multiforme(13;0.154)			CAGTCTTCACGGGCTCCAGAC	0.592													0	7	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23747889	23747894	+	5'Flank	DEL	TGTGTG	-	-	rs71552251		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23747889_23747894delTGTGTG	uc003sws.3	+						STK31_uc003swt.3_5'Flank|STK31_uc011jze.1_5'Flank|STK31_uc010kuq.2_5'Flank	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						cagcaggctctgtgtgtgtgtgtgtg	0.000													6	4	---	---	---	---	
OSBPL3	26031	broad.mit.edu	37	7	25012139	25012139	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25012139delA	uc003sxf.2	-						OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1						tctagtctgtaagctccttga	0.000													4	2	---	---	---	---	
OSBPL3	26031	broad.mit.edu	37	7	25018908	25018909	+	Intron	INS	-	A	A	rs73691291		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25018908_25018909insA	uc003sxf.2	-						OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1						TGGAAACTAACAAAAAAAAAAA	0.490													1	5	---	---	---	---	
PLEKHA8	84725	broad.mit.edu	37	7	30152331	30152331	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30152331delA	uc003tap.1	+						PLEKHA8_uc003tao.2_Intron	NM_032639	NP_116028	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A						protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4						acccagtctgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	34087970	34087971	+	Intron	DEL	AC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34087970_34087971delAC	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						acacacacgtacacacacacac	0.277													6	3	---	---	---	---	
POU6F2	11281	broad.mit.edu	37	7	39417335	39417335	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39417335delC	uc003thb.1	+							NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1						GTAGGTTTAACCCCAGAAATT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	44782856	44782859	+	IGR	DEL	TTTC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44782856_44782859delTTTC								OGDH (34188 upstream) : ZMIZ2 (5321 downstream)																							CTGTGCCATGTTTCTTTATTTCTG	0.240													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	45436798	45436799	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45436798_45436799insT								RAMP3 (212951 upstream) : ADCY1 (176940 downstream)																							ctttttctttcttctttctttt	0.010													4	2	---	---	---	---	
ABCA13	154664	broad.mit.edu	37	7	48348630	48348631	+	Intron	INS	-	CACA	CACA	rs140477467	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48348630_48348631insCACA	uc003toq.2	+						ABCA13_uc010kys.1_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						acacatgactgcacacacacac	0.035													3	3	---	---	---	---	
COBL	23242	broad.mit.edu	37	7	51149079	51149079	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51149079delC	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron|COBL_uc003tpp.3_Intron|COBL_uc003tpq.3_Intron	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)					AATGGAGCCACAAGGCAAGAC	0.562													4	2	---	---	---	---	
COBL	23242	broad.mit.edu	37	7	51296612	51296612	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51296612delA	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)					TATCTCCTTCAAAAAAAAAAG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54816113	54816113	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54816113delT								VSTM2A (177926 upstream) : SEC61G (3828 downstream)																							CCAGCTGGGCTTTAGCTGAAA	0.313													4	2	---	---	---	---	
EGFR	1956	broad.mit.edu	37	7	55238563	55238563	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55238563delG	uc003tqk.2	+						EGFR_uc003tqj.2_3'UTR|EGFR_uc010kzg.1_Intron|EGFR_uc011kco.1_Intron|EGFR_uc011kcp.1_Intron|EGFR_uc011kcq.1_Intron	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	AGCCAGCTGTGGGACAATTAT	0.358		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57768888	57768888	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57768888delC								ZNF716 (235623 upstream) : None (None downstream)																							ttctttttttctgagacggag	0.124													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57989291	57989291	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57989291delA								ZNF716 (456026 upstream) : None (None downstream)																							ctgctcaatcaaaagaaaggt	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61513863	61513864	+	IGR	DEL	AA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61513863_61513864delAA								None (None upstream) : None (None downstream)																							atcttcacataaaaagtagaca	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68726769	68726769	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68726769delT								None (None upstream) : AUTS2 (337136 downstream)																							ctgccctgccttgtactaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68992122	68992123	+	IGR	INS	-	T	T	rs143721378		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68992122_68992123insT								None (None upstream) : AUTS2 (71782 downstream)																							ccttcttcttcttttttttttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	70283039	70283040	+	IGR	DEL	GA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70283039_70283040delGA								AUTS2 (25155 upstream) : WBSCR17 (314749 downstream)																							aggggggtgggagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	74455444	74455444	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74455444delC								GATSL1 (16641 upstream) : WBSCR16 (841 downstream)																							tctcatttttcccgtttccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	80722030	80722030	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80722030delT								SEMA3C (170355 upstream) : HGF (609415 downstream)																							ggctgtgtcctagtctttcct	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	82874546	82874546	+	IGR	DEL	T	-	-	rs34715607		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82874546delT								PCLO (82349 upstream) : SEMA3E (118676 downstream)																							atattctctctgctttttgat	0.000													2	5	---	---	---	---	
SEMA3D	223117	broad.mit.edu	37	7	84657700	84657700	+	Intron	DEL	C	-	-	rs73713927		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84657700delC	uc003uic.2	-						SEMA3D_uc010led.2_Intron|SEMA3D_uc003uib.2_Intron	NM_152754	NP_689967	O95025	SEM3D_HUMAN	semaphorin 3D precursor						cell differentiation|nervous system development	extracellular region|membrane	receptor activity			ovary(3)|large_intestine(2)	5						ACAGTTTAGACAAAAAAAAAA	0.393													3	3	---	---	---	---	
GRM3	2913	broad.mit.edu	37	7	86408739	86408740	+	Intron	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86408739_86408740delCA	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)	CACACGTGCGCACACACACACA	0.381													4	2	---	---	---	---	
MTERF	7978	broad.mit.edu	37	7	91446831	91446831	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91446831delA	uc010let.1	-									Q99551	MTERF_HUMAN	Synthetic construct DNA, clone: pF1KB8286, Homo sapiens MTERF gene for mitochondrial transcription termination factor, without stop codon, in Flexi system.						DNA geometric change|regulation of transcription, DNA-dependent|termination of mitochondrial transcription	mitochondrial nucleoid	double-stranded DNA binding				0	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)			TAATTAAGAGAAGGGTCAGGT	0.428													4	2	---	---	---	---	
COL1A2	1278	broad.mit.edu	37	7	94031073	94031073	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94031073delC	uc003ung.1	+						COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor						axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TTTTTGTTTTCAAATTTATGA	0.239										HNSCC(75;0.22)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	95348428	95348429	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95348428_95348429insT								PDK4 (122503 upstream) : DYNC1I1 (53389 downstream)																							GTCCAAAGAGATTTTTTTTTTT	0.342													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	96959322	96959322	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96959322delC								ACN9 (148249 upstream) : TAC1 (401949 downstream)																							acaggaaactcccgcccatat	0.000													4	2	---	---	---	---	
LMTK2	22853	broad.mit.edu	37	7	97830911	97830912	+	Intron	INS	-	TGTTT	TGTTT	rs150011134	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97830911_97830912insTGTTT	uc003upd.1	+							NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor						early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					cttcgtgtgtgtgttttgtttt	0.000													3	3	---	---	---	---	
EMID2	136227	broad.mit.edu	37	7	101011268	101011268	+	Intron	DEL	G	-	-	rs34227918		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101011268delG	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)					CTCCTCCACTGTCTCCcttct	0.194													3	3	---	---	---	---	
EMID2	136227	broad.mit.edu	37	7	101042621	101042622	+	Intron	INS	-	CTTT	CTTT	rs143309560	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101042621_101042622insCTTT	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)					TTTCTAATGAGctttctttccc	0.025													4	2	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101822162	101822162	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101822162delG	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						Ctttttttttggagtcggagt	0.239													4	2	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103546221	103546221	+	Intron	DEL	C	-	-	rs76674502		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103546221delC	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GGTTTTTAAACAAGCAAATTT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	119852527	119852528	+	IGR	INS	-	T	T	rs141506643	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119852527_119852528insT								None (None upstream) : KCND2 (61194 downstream)																							ggtactgttacaaaaatagaca	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	121273560	121273560	+	IGR	DEL	T	-	-	rs11337019		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121273560delT								FAM3C (237138 upstream) : PTPRZ1 (239599 downstream)																							GGAGTGGGAGTGATTCGTGAA	0.259													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	129796107	129796110	+	IGR	DEL	CTTT	-	-	rs71527949		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129796107_129796110delCTTT								KLHDC10 (22514 upstream) : TMEM209 (8445 downstream)																							cctcttcttcctttgtgttagatt	0.230													4	3	---	---	---	---	
TRIM24	8805	broad.mit.edu	37	7	138142249	138142249	+	5'Flank	DEL	T	-	-	rs111877065		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138142249delT	uc003vuc.2	+						TRIM24_uc003vub.2_5'Flank	NM_015905	NP_056989	O15164	TIF1A_HUMAN	transcriptional intermediary factor 1 alpha						cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1)	8						CATCTAATGCttttttttttt	0.194													4	2	---	---	---	---	
SVOPL	136306	broad.mit.edu	37	7	138288584	138288584	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138288584delA	uc011kqh.1	-						SVOPL_uc003vue.2_Intron	NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1							integral to membrane	transmembrane transporter activity				0						aaactttcttataaaaacctt	0.000													4	2	---	---	---	---	
ZC3HAV1	56829	broad.mit.edu	37	7	138779727	138779727	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138779727delT	uc003vun.2	-						ZC3HAV1_uc003vup.2_Intron	NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1						response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1						AACCCGAGTCTTTTTTTTTTT	0.428													4	2	---	---	---	---	
HIPK2	28996	broad.mit.edu	37	7	139259122	139259122	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139259122delA	uc003vvf.3	-						HIPK2_uc003vvd.3_Intron	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)					accctgtcttaaaaaaaaaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	140217323	140217323	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140217323delG								MKRN1 (37954 upstream) : DENND2A (904 downstream)																							GCTGAGGGCAGGGGTCACCTG	0.532											OREG0018369	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
KIAA1147	57189	broad.mit.edu	37	7	141390191	141390193	+	Intron	DEL	TCC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141390191_141390193delTCC	uc003vwk.2	-							NM_001080392	NP_001073861	A4D1U4	LCHN_HUMAN	hypothetical protein LOC57189											ovary(1)	1	Melanoma(164;0.0171)					ctcttccttttcctcctcctcct	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142110900	142110901	+	Intron	INS	-	CT	CT			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142110900_142110901insCT	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		GCTCTGACTTACTGACCAGGAT	0.426											OREG0018389	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
ZYX	7791	broad.mit.edu	37	7	143064924	143064925	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143064924_143064925insA	uc011ktd.1	+							NM_003461	NP_003452	Q15942	ZYX_HUMAN	zyxin						cell adhesion|cell-cell signaling|interspecies interaction between organisms|signal transduction	cell-cell adherens junction|cytoplasm|focal adhesion|integral to plasma membrane|nucleus|stress fiber	protein binding|zinc ion binding				0	Melanoma(164;0.205)					TCAACGTCCCCAAATCACGTTC	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149731732	149731732	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149731732delC								ATP6V0E2 (153946 upstream) : ACTR3C (212570 downstream)																							tgccttcggacccgtcggatc	0.030													4	2	---	---	---	---	
KCNH2	3757	broad.mit.edu	37	7	150649386	150649387	+	Intron	INS	-	TCTTTCTC	TCTTTCTC	rs142675575	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150649386_150649387insTCTTTCTC	uc003wic.2	-						KCNH2_uc003wib.2_Intron|KCNH2_uc011kux.1_Intron|KCNH2_uc003wid.2_Intron|KCNH2_uc003wie.2_Intron	NM_000238	NP_000229	Q12809	KCNH2_HUMAN	voltage-gated potassium channel, subfamily H,						blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|two-component sensor activity			skin(3)|ovary(1)	4	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661)	ctctcccactgtctttctctct	0.465													3	4	---	---	---	---	
GALNTL5	168391	broad.mit.edu	37	7	151678767	151678767	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151678767delT	uc003wkp.2	+						GALNTL5_uc003wkq.2_Intron|GALNTL5_uc003wkr.2_Intron|GALNTL5_uc003wks.2_Intron|GALNTL5_uc010lqf.2_Intron	NM_145292	NP_660335	Q7Z4T8	GLTL5_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		tctttctttctttTTTTTTTT	0.000													4	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152105101	152105101	+	Intron	DEL	G	-	-	rs5888473		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152105101delG	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)		GTggccgggtggggtggctca	0.144			N		medulloblastoma								6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152181963	152181964	+	IGR	INS	-	T	T	rs71198786		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152181963_152181964insT								LOC100128822 (19335 upstream) : XRCC2 (161625 downstream)																							tccttctttccaccctccttcc	0.168													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157229119	157229120	+	IGR	DEL	TT	-	-	rs145924096		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157229119_157229120delTT								DNAJB6 (18987 upstream) : PTPRN2 (102631 downstream)																							AAAAAGTAAATTGTGGTTTTTG	0.312													4	5	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158014659	158014659	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158014659delA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		caagaaacgtaggaaaaatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	158387856	158387858	+	IGR	DEL	ATA	-	-	rs141952618		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158387856_158387858delATA								PTPRN2 (7374 upstream) : NCAPG2 (36145 downstream)																							agagatggtgataatggtggtca	0.000													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	4327391	4327391	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4327391delT	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ttggttttccttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	9068162	9068162	+	IGR	DEL	A	-	-	rs78476917		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9068162delA								PPP1R3B (59078 upstream) : TNKS (345283 downstream)																							CACAGTCTACAAAAAAAAAAG	0.353													4	2	---	---	---	---	
C8orf48	157773	broad.mit.edu	37	8	13423209	13423210	+	5'Flank	DEL	AG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13423209_13423210delAG	uc003wwp.2	+							NM_001007090	NP_001007091	Q96LL4	CH048_HUMAN	hypothetical protein LOC157773								protein binding				0						ACAGGAAGAAAGAGAGAGAGAG	0.381													4	2	---	---	---	---	
RBPMS	11030	broad.mit.edu	37	8	30251040	30251041	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30251040_30251041insT	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc011lba.1_Intron|RBPMS_uc003xib.2_Intron	NM_006867	NP_006858	Q93062	RBPMS_HUMAN	RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)		ttttcattttcttttttttttt	0.183													4	2	---	---	---	---	
UBXN8	7993	broad.mit.edu	37	8	30600408	30600408	+	5'Flank	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30600408delT	uc003xii.2	+						UBXN8_uc010lvi.2_5'Flank|UBXN8_uc011lbb.1_5'Flank	NM_005671	NP_005662	O00124	UBXN8_HUMAN	reproduction 8						single fertilization						0						tctttcccaGTTTTTTTTTTT	0.164													4	2	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32328318	32328318	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32328318delT	uc003xip.2	+							NM_013962	NP_039256	Q02297	NRG1_HUMAN	neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TCGTTGGGTCttttttttttt	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37090510	37090511	+	IGR	DEL	TC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37090510_37090511delTC								KCNU1 (296869 upstream) : ZNF703 (462790 downstream)																							ACAGAACAGAtctctctctctc	0.366													4	2	---	---	---	---	
STAR	6770	broad.mit.edu	37	8	38004140	38004140	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38004140delA	uc003xkv.1	-						STAR_uc010lwc.1_Intron	NM_001007243	NP_001007244	P49675	STAR_HUMAN	steroidogenic acute regulatory protein isoform						C21-steroid hormone biosynthetic process	mitochondrial intermembrane space	cholesterol transporter activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.0151)|Lung NSC(58;0.0295)		READ - Rectum adenocarcinoma(644;0.188)		ctaaaactacaaaattagcca	0.000													4	2	---	---	---	---	
PLEKHA2	59339	broad.mit.edu	37	8	38772476	38772478	+	Intron	DEL	TCT	-	-	rs67487782		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38772476_38772478delTCT	uc003xmi.3	+						PLEKHA2_uc011lce.1_Intron	NM_021623	NP_067636	Q9HB19	PKHA2_HUMAN	pleckstrin homology domain containing, family A						positive regulation of cell-matrix adhesion	cytoplasm|nucleus|plasma membrane|protein complex	fibronectin binding|laminin binding				0		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)			cctttattcctcttcttctgaca	0.143													3	4	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40716976	40716977	+	Intron	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40716976_40716977delCA	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)			TCTAGCAacgcacacacacaca	0.401													4	2	---	---	---	---	
SLC20A2	6575	broad.mit.edu	37	8	42359678	42359678	+	5'Flank	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42359678delT	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron	NM_006749	NP_006740	Q08357	S20A2_HUMAN	solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			CATTTTCCTCTTTTTTTTTTT	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	50318776	50318776	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50318776delT								C8orf22 (330135 upstream) : SNTG1 (503573 downstream)																							cttttaggcattttttttttt	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	53725334	53725334	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53725334delA								RB1CC1 (98308 upstream) : NPBWR1 (127134 downstream)																							attcagggtcaagtagtagaa	0.000													4	2	---	---	---	---	
LYN	4067	broad.mit.edu	37	8	56852022	56852023	+	Intron	DEL	AG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56852022_56852023delAG	uc003xsk.3	+						LYN_uc003xsl.3_Intron	NM_002350	NP_002341	P07948	LYN_HUMAN	Yamaguchi sarcoma viral (v-yes-1) oncogene						erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation	cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)			TCCCAagagaagagagagagag	0.490													5	3	---	---	---	---	
NSMAF	8439	broad.mit.edu	37	8	59551846	59551846	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59551846delA	uc003xtt.2	-						NSMAF_uc011lee.1_Intron|NSMAF_uc003xtu.2_Intron	NM_003580	NP_003571	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation						ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)				ccgtctcaataaaaaaaaaaa	0.000													4	2	---	---	---	---	
CLVS1	157807	broad.mit.edu	37	8	62251524	62251525	+	Intron	DEL	TG	-	-	rs71689192		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62251524_62251525delTG	uc003xuh.2	+						CLVS1_uc003xug.2_Intron|CLVS1_uc003xui.2_Intron|CLVS1_uc010lyp.2_Intron	NM_173519	NP_775790	Q8IUQ0	CLVS1_HUMAN	retinaldehyde binding protein 1-like 1						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5						AAGGGAACACtgtgtgtgtgtg	0.381													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65793242	65793242	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65793242delG								CYP7B1 (81894 upstream) : ARMC1 (721830 downstream)																							tataaacattgggtaatttta	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	66899588	66899588	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66899588delT								PDE7A (145833 upstream) : DNAJC5B (34203 downstream)																							ataaaaacaattttttttttt	0.000													4	2	---	---	---	---	
ARFGEF1	10565	broad.mit.edu	37	8	68240700	68240703	+	Intron	DEL	TCTC	-	-	rs143593738		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68240700_68240703delTCTC	uc003xxo.1	-							NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			ttctccagcatctctctgattatt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70771737	70771737	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70771737delG								SLCO5A1 (24438 upstream) : PRDM14 (192288 downstream)																							TTTAATATTCGGAGGAGTACT	0.388													24	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	72921729	72921730	+	Intron	DEL	AC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72921729_72921730delAC	uc011lff.1	+						uc003xyy.2_Intron					Homo sapiens cDNA FLJ41321 fis, clone BRAMY2045299.																		acgcacagggacacacacacac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79410156	79410157	+	IGR	INS	-	TG	TG	rs141603345	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79410156_79410157insTG								None (None upstream) : PKIA (18179 downstream)																							gtgtgtgtgcatgtgtgtgtgt	0.223													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	83684828	83684828	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83684828delA								SNX16 (930307 upstream) : None (None downstream)																							atgatggaggaaaaaaaaaag	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	87859835	87859836	+	IGR	INS	-	AGGA	AGGA			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87859835_87859836insAGGA								CNGB3 (103934 upstream) : CNBD1 (18840 downstream)																							gggagggagggaggaaggaagg	0.000													3	3	---	---	---	---	
C8orf38	137682	broad.mit.edu	37	8	95964626	95964626	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95964626delA	uc003yhf.2	+						C8orf38_uc003yhe.1_Intron			Q330K2	CH038_HUMAN	RecName: Full=UPF0551 protein C8orf38, mitochondrial; AltName: Full=Putative phytoene synthase; Flags: Precursor;						biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)					TGGCAAAGTGAAGTCCACTTA	0.468													4	2	---	---	---	---	
C8orf38	137682	broad.mit.edu	37	8	96030988	96030988	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96030988delG	uc003yhi.2	+						C8orf38_uc003yhe.1_Intron|C8orf38_uc003yhf.2_Intron	NM_152416	NP_689629	Q330K2	CH038_HUMAN	hypothetical protein LOC137682 precursor						biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)					agaaggaacaggacaagatga	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103692235	103692236	+	IGR	INS	-	CACA	CACA	rs142499302	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103692235_103692236insCACA								KLF10 (24252 upstream) : AZIN1 (146301 downstream)																							CCCAAGCACTTcacacacacac	0.233													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103738873	103738873	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103738873delT								KLF10 (70890 upstream) : AZIN1 (99664 downstream)																							GTGCCAAGCATTAGGCCCAGG	0.527													4	2	---	---	---	---	
OXR1	55074	broad.mit.edu	37	8	107314814	107314814	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107314814delA	uc003ymf.2	+							NM_018002	NP_060472	Q8N573	OXR1_HUMAN	oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			atgctgtctcaaaaaaaaaaa	0.109													2	4	---	---	---	---	
RSPO2	340419	broad.mit.edu	37	8	109080307	109080307	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109080307delA	uc003yms.2	-						RSPO2_uc003ymq.2_Intron|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660	Q6UXX9	RSPO2_HUMAN	R-spondin family, member 2 precursor						Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			aaaaacaaacaaaaaaaaaaC	0.159													3	4	---	---	---	---	
EXT1	2131	broad.mit.edu	37	8	118974373	118974374	+	Intron	INS	-	TCAT	TCAT	rs10657425		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118974373_118974374insTCAT	uc003yok.1	-							NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			TGATTTCTTCCTCAGTCACCAG	0.411			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120012149	120012149	+	IGR	DEL	T	-	-	rs146342686		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120012149delT								TNFRSF11B (47766 upstream) : COLEC10 (67275 downstream)																							ctttaaagagtttttttgtaa	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125908109	125908110	+	IGR	INS	-	A	A	rs147050745	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125908109_125908110insA								MTSS1 (167379 upstream) : LOC157381 (43774 downstream)																							AGGAAGTCCTTAAGACACAACT	0.421													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	133579936	133579937	+	IGR	INS	-	CTT	CTT	rs149494266	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133579936_133579937insCTT								HPYR1 (6210 upstream) : LRRC6 (4511 downstream)																							tgcagttctaacttcttggtgt	0.010													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136016733	136016733	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136016733delG								MIR30D (199545 upstream) : LOC286094 (229641 downstream)																							GGACTCCTTTGAACAGAAAGT	0.299													4	2	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139635985	139635985	+	Frame_Shift_Del	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139635985delG	uc003yvd.2	-	52	4208	c.3761delC	c.(3760-3762)CCTfs	p.P1254fs	COL22A1_uc011ljo.1_Frame_Shift_Del_p.P534fs	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1254	Pro-rich.|Gly-rich.|Collagen-like 12.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CGGCTCTCCAGGGGGACCCGG	0.378										HNSCC(7;0.00092)			149	69	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140223123	140223123	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140223123delG								COL22A1 (296887 upstream) : KCNK9 (389959 downstream)																							GAAGGCGAGTGGCATGGAGAC	0.542													0	6	---	---	---	---	
KCNK9	51305	broad.mit.edu	37	8	140650004	140650005	+	Intron	DEL	AC	-	-	rs34018499		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140650004_140650005delAC	uc003yvf.1	-						KCNK9_uc003yvg.1_Intron	NM_016601	NP_057685	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9							integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)			ttcctactctacacacacacac	0.084													4	2	---	---	---	---	
PTK2	5747	broad.mit.edu	37	8	142010115	142010115	+	Intron	DEL	A	-	-	rs36146347		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142010115delA	uc003yvu.2	-						PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560	Q05397	FAK1_HUMAN	PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			AATGACTCGGAAAAAAAAAAA	0.274													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142565299	142565300	+	IGR	INS	-	C	C	rs141772575		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142565299_142565300insC								FLJ43860 (47969 upstream) : MIR1302-7 (302303 downstream)																							tggaggtgtgtcatggtgttgg	0.119													4	5	---	---	---	---	
TSNARE1	203062	broad.mit.edu	37	8	143294169	143294171	+	Intron	DEL	CCC	-	-	rs78538097		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143294169_143294171delCCC	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)					tccaatccttcccccccctgtcc	0.187													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144492889	144492891	+	IGR	DEL	GTA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144492889_144492891delGTA								RHPN1 (26500 upstream) : MAFA (18624 downstream)																							ggtggtggtggtagtgatggtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	145933064	145933068	+	IGR	DEL	AAAAG	-	-	rs149692414		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145933064_145933068delAAAAG								ARHGAP39 (21870 upstream) : ZNF251 (13227 downstream)																							actccatctcaaaagaaaagaaaag	0.166													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	1152682	1152683	+	IGR	INS	-	T	T	rs112708676		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1152682_1152683insT								DMRT2 (95129 upstream) : SMARCA2 (862659 downstream)																							atcaagaacaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	2255278	2255278	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2255278delT								SMARCA2 (61657 upstream) : FLJ35024 (167424 downstream)																							CAACTCCTTCTTTCCAGTTCG	0.274													4	2	---	---	---	---	
RFX3	5991	broad.mit.edu	37	9	3525942	3525943	+	5'UTR	DEL	GA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3525942_3525943delGA	uc003zhr.2	-	1					RFX3_uc010mhd.2_5'UTR|RFX3_uc003zhs.1_5'UTR|RFX3_uc010mhe.1_5'UTR	NM_134428	NP_602304	P48380	RFX3_HUMAN	regulatory factor X3 isoform b						cell maturation|ciliary cell motility|cilium assembly|cilium movement involved in determination of left/right asymmetry|endocrine pancreas development|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|regulation of insulin secretion	nuclear chromatin	protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		gagagagagggagagagagaga	0.465													4	2	---	---	---	---	
GLDC	2731	broad.mit.edu	37	9	6646315	6646316	+	5'Flank	INS	-	CTCCTCCTC	CTCCTCCTC	rs140387597	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6646315_6646316insCTCCTCCTC	uc003zkc.2	-							NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)						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)	cttccttctttctcctcctcct	0.099													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	7554555	7554555	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7554555delT								KDM4C (378908 upstream) : C9orf123 (241938 downstream)																							ttctcactcataagtgggata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	7720409	7720409	+	IGR	DEL	T	-	-	rs111564342		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7720409delT								KDM4C (544762 upstream) : C9orf123 (76084 downstream)																							ATAAACTACGTTTTTTTTTCC	0.373													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16068433	16068434	+	IGR	INS	-	TC	TC			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16068433_16068434insTC								C9orf93 (96538 upstream) : BNC2 (341068 downstream)																							aatgactttcttcTTCCTCTTT	0.124													6	3	---	---	---	---	
SH3GL2	6456	broad.mit.edu	37	9	17771889	17771892	+	Intron	DEL	GTAA	-	-	rs149472560		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17771889_17771892delGTAA	uc003zna.2	+						SH3GL2_uc011lmx.1_Intron|SH3GL2_uc011lmy.1_Intron	NM_003026	NP_003017	Q99962	SH3G2_HUMAN	SH3-domain GRB2-like 2						axon guidance|central nervous system development|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	cytosol|Golgi membrane|plasma membrane	identical protein binding|lipid binding			skin(1)	1				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)		GTCTATTTGTGTAAGTCAGTAGGC	0.377													3	3	---	---	---	---	
TEK	7010	broad.mit.edu	37	9	27155818	27155818	+	Intron	DEL	T	-	-	rs113843351		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27155818delT	uc003zqi.3	+						TEK_uc010mjc.1_Intron|TEK_uc011lnn.1_Intron|TEK_uc011lno.1_Intron|TEK_uc011lnp.1_Intron|TEK_uc003zqj.1_5'Flank	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor						angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)		AGCACttttgttttttttttt	0.194													3	3	---	---	---	---	
LINGO2	158038	broad.mit.edu	37	9	28078845	28078845	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28078845delA	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)		aaactctgtcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	32007935	32007936	+	IGR	INS	-	T	T	rs142659663	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32007935_32007936insT								None (None upstream) : ACO1 (376665 downstream)																							gtttgccagtattttttttttg	0.000													2	4	---	---	---	---	
SUGT1P1	441394	broad.mit.edu	37	9	33439148	33439148	+	Intron	DEL	G	-	-	rs58969990		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33439148delG	uc010mjq.1	-							NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0						GTGCTTCTTTGCCCTGCATCC	0.612													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33728811	33728811	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33728811delC								PTENP1 (51393 upstream) : PRSS3 (21704 downstream)																							ccaggcaataccatactgtcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44084399	44084400	+	IGR	INS	-	TAATC	TAATC			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44084399_44084400insTAATC								FAM75A6 (453669 upstream) : FAM27C (905836 downstream)																							GATAAAGACTATATATAAAAAT	0.277													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44230574	44230574	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44230574delC								FAM75A6 (599844 upstream) : FAM27C (759662 downstream)																							AGTCTTCAGTCCCCTACCATG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66486005	66486005	+	IGR	DEL	G	-	-	rs75683706		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66486005delG								FAM74A4 (991619 upstream) : LOC442421 (10465 downstream)																							acacaaaaaaggtatgaagat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66487249	66487252	+	IGR	DEL	ACAG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66487249_66487252delACAG								FAM74A4 (992863 upstream) : LOC442421 (9218 downstream)																							TCAGTAAGATACAGAGAGATTTTA	0.240													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66491022	66491022	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66491022delA								FAM74A4 (996636 upstream) : LOC442421 (5448 downstream)																							agaaagacacaaactaccaaa	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66529520	66529521	+	Intron	INS	-	A	A	rs148013875	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66529520_66529521insA	uc010mnh.1	-						uc004aef.2_Intron					Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																		CTGATACTGCCAAAAAAAAGAA	0.317													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66797636	66797636	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66797636delT								LOC442421 (294609 upstream) : AQP7P1 (456631 downstream)																							gatttgaacattcctcttcat	0.000													3	6	---	---	---	---	
AQP7P1	375719	broad.mit.edu	37	9	67282933	67282933	+	5'Flank	DEL	T	-	-	rs5898015		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67282933delT	uc004aem.1	-						AQP7P1_uc004aen.1_Intron|AQP7P1_uc004aeo.1_Intron|AQP7P1_uc004aep.1_Intron					Homo sapiens aquaporin 7 pseudogene 1, mRNA (cDNA clone IMAGE:6191443).												0						tagccaggcatggtggcgcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67331359	67331359	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67331359delT								AQP7P1 (41867 upstream) : FAM27B (461571 downstream)																							CATGATGGGGTTGGGGGGGAA	0.393													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	70126408	70126408	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70126408delA								LOC100133920 (461459 upstream) : FOXD4L5 (49301 downstream)																							ggtcttacgcaaaaaaatctt	0.000													6	3	---	---	---	---	
RORB	6096	broad.mit.edu	37	9	77207727	77207728	+	Intron	DEL	TC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77207727_77207728delTC	uc004ajh.2	+							NM_006914	NP_008845	Q92753	RORB_HUMAN	RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4						tctctttcaatctctctctctc	0.193													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	84702323	84702324	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84702323_84702324insT								FLJ46321 (92153 upstream) : RASEF (894993 downstream)																							AAAGATTCCAATTTTTTCTGGA	0.327													25	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	87713991	87713991	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87713991delC								NTRK2 (75486 upstream) : AGTPBP1 (447464 downstream)																							ccatttttttcctccattgtt	0.000													4	2	---	---	---	---	
SEMA4D	10507	broad.mit.edu	37	9	92023580	92023581	+	Intron	INS	-	GAG	GAG	rs150917526	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92023580_92023581insGAG	uc004aqo.1	-						SEMA4D_uc011ltm.1_Intron|SEMA4D_uc011ltn.1_Intron|SEMA4D_uc011lto.1_Intron|SEMA4D_uc004aqp.1_Intron	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1						anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2						CCGCGCCACTAGAGGAGGAGGA	0.599													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	96183635	96183636	+	IGR	INS	-	TCTT	TCTT	rs71511662		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96183635_96183636insTCTT								C9orf129 (74939 upstream) : FAM120AOS (15260 downstream)																							acaaccgctgctctattgtctg	0.000													4	2	---	---	---	---	
ZNF169	169841	broad.mit.edu	37	9	97039146	97039146	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97039146delT	uc004aum.1	+						ZNF169_uc004aun.2_5'Flank|ZNF169_uc004auo.2_5'Flank	NM_194320	NP_919301	Q14929	ZN169_HUMAN	zinc finger protein 169							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)				TTAATGACTGTTTCCTCCATA	0.219													4	2	---	---	---	---	
SLC35D2	11046	broad.mit.edu	37	9	99125451	99125451	+	Intron	DEL	T	-	-	rs76091219		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99125451delT	uc004awc.2	-						SLC35D2_uc010msd.2_Intron|SLC35D2_uc010mse.2_Intron|SLC35D2_uc010msf.2_Intron|SLC35D2_uc004awd.2_Intron|SLC35D2_uc004awe.2_Intron	NM_007001	NP_008932	Q76EJ3	S35D2_HUMAN	solute carrier family 35, member D2							Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity				0		Acute lymphoblastic leukemia(62;0.0167)				acctggcTTAttttttttttt	0.000													3	3	---	---	---	---	
ZNF510	22869	broad.mit.edu	37	9	99537347	99537348	+	Intron	INS	-	T	T	rs113196824		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99537347_99537348insT	uc004awn.1	-						ZNF510_uc004awo.1_Intron	NM_014930	NP_055745	Q9Y2H8	ZN510_HUMAN	zinc finger protein 510						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)				GTGtttttttgttttttttttt	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102340481	102340481	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102340481delC								SEC61B (347581 upstream) : NR4A3 (243656 downstream)																							atcctgcagacccttgggttc	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	109012400	109012402	+	Intron	DEL	CTC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109012400_109012402delCTC	uc004bcw.2	+											Homo sapiens, clone IMAGE:5538960, mRNA.																		ccttcttcttctcctcctcctcc	0.039													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110341317	110341318	+	IGR	DEL	TG	-	-	rs71923184		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110341317_110341318delTG								KLF4 (89270 upstream) : None (None downstream)																							tttgtgtgtttgtgtgtgtgtg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	112107463	112107464	+	IGR	INS	-	G	G	rs146205108	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112107463_112107464insG								EPB41L4B (24442 upstream) : PTPN3 (30510 downstream)																							GTGGGCCAGGAGGGGCCAATGC	0.495													3	3	---	---	---	---	
DFNB31	25861	broad.mit.edu	37	9	117257149	117257149	+	Intron	DEL	G	-	-	rs34788832		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117257149delG	uc004biz.3	-						DFNB31_uc004biy.3_Intron|DFNB31_uc004bja.3_Intron|DFNB31_uc004bjb.2_Intron	NM_015404	NP_056219	Q9P202	WHRN_HUMAN	CASK-interacting protein CIP98 isoform 1						inner ear receptor stereocilium organization|retina homeostasis|sensory perception of light stimulus|sensory perception of sound	cytoplasm|growth cone|stereocilium				ovary(4)|central_nervous_system(1)|pancreas(1)	6						ACAAAGAAAAGAAAACACCAA	0.299													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	121308786	121308786	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121308786delC								TLR4 (829022 upstream) : DBC1 (620122 downstream)																							tgtttaggaacaacacctcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122269464	122269465	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122269464_122269465insA								DBC1 (137725 upstream) : MIR147 (737792 downstream)																							aaaaacatatgaaaaaaaagct	0.000													4	2	---	---	---	---	
GPR144	347088	broad.mit.edu	37	9	127236165	127236165	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127236165delA	uc010mwn.2	+						GPR144_uc010mwo.1_Intron	NM_001161808	NP_001155280	Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity				0						tggtggggtcaaatggtgggg	0.050													4	2	---	---	---	---	
PPP6C	5537	broad.mit.edu	37	9	127947527	127947527	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127947527delT	uc004bpg.3	-						PPP6C_uc010mwv.2_Intron|PPP6C_uc010mww.2_Intron|PPP6C_uc011lzr.1_Intron	NM_002721	NP_002712	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2						ACATATGTCAttttttttttt	0.154													4	3	---	---	---	---	
GARNL3	84253	broad.mit.edu	37	9	130049258	130049258	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130049258delT	uc011mae.1	+						GARNL3_uc011mad.1_Intron	NM_032293	NP_115669	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3						atctgctgtcttcaacatgaa	0.015													4	2	---	---	---	---	
LRSAM1	90678	broad.mit.edu	37	9	130213972	130213973	+	Intron	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130213972_130213973delCA	uc004brb.1	+						RPL12_uc004bqx.1_5'Flank|RPL12_uc004bqy.1_5'Flank|RPL12_uc004bqz.1_5'Flank|LRSAM1_uc010mxk.1_Intron|LRSAM1_uc004brc.1_5'Flank|LRSAM1_uc004brd.1_5'Flank	NM_001005373	NP_001005373	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif						negative regulation of endocytosis|non-lytic virus budding|protein autoubiquitination|protein catabolic process|protein polyubiquitination|protein transport|ubiquitin-dependent endocytosis	cytoplasm|extracellular region|membrane part	hormone activity|ubiquitin-protein ligase activity|zinc ion binding				0						CGGTCCCCGTCACCCAATCCCA	0.629													4	2	---	---	---	---	
DPM2	8818	broad.mit.edu	37	9	130701216	130701216	+	5'Flank	DEL	T	-	-	rs111867274		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130701216delT	uc004bsv.2	-							NM_003863	NP_003854	O94777	DPM2_HUMAN	dolichyl-phosphate mannosyltransferase 2						C-terminal protein lipidation|dolichol-linked oligosaccharide biosynthetic process|preassembly of GPI anchor in ER membrane|protein N-linked glycosylation via asparagine|protein O-linked mannosylation|regulation of protein stability	dolichol-phosphate-mannose synthase complex|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex|integral to endoplasmic reticulum membrane	protein binding				0						ggtttttttgttttttttttt	0.035													4	2	---	---	---	---	
PKN3	29941	broad.mit.edu	37	9	131474747	131474747	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131474747delA	uc004bvw.2	+						PKN3_uc010myh.2_Intron|PKN3_uc011mbk.1_Intron	NM_013355	NP_037487	Q6P5Z2	PKN3_HUMAN	protein kinase PKNbeta						signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein binding|protein kinase C activity			stomach(2)|lung(2)	4						gctgggactcacctccactgt	0.264													4	2	---	---	---	---	
C9orf114	51490	broad.mit.edu	37	9	131586558	131586559	+	Intron	INS	-	GT	GT	rs141026925	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131586558_131586559insGT	uc004bwd.2	-						C9orf114_uc004bwe.2_Intron|C9orf114_uc010mym.2_Intron	NM_016390	NP_057474	Q5T280	CI114_HUMAN	hypothetical protein LOC51490												0						AGAGCtgtgtggtgtgtgtgtg	0.505													4	2	---	---	---	---	
PPP2R4	5524	broad.mit.edu	37	9	131880331	131880331	+	Intron	DEL	T	-	-	rs36010420		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131880331delT	uc004bxm.1	+						PPP2R4_uc004bxl.1_Intron|PPP2R4_uc011mbo.1_Intron|PPP2R4_uc010myr.1_Intron|PPP2R4_uc004bxn.1_Intron|PPP2R4_uc004bxo.1_Intron|PPP2R4_uc011mbp.1_Intron|PPP2R4_uc011mbq.1_Intron|PPP2R4_uc010mys.1_Intron	NM_178001	NP_821068	Q15257	PTPA_HUMAN	protein phosphatase 2A, regulatory subunit B'						ATP catabolic process|negative regulation of phosphoprotein phosphatase activity|negative regulation of protein dephosphorylation|positive regulation of apoptosis|positive regulation of phosphoprotein phosphatase activity|positive regulation of protein dephosphorylation	calcium channel complex|cytoplasm|nucleus|protein phosphatase type 2A complex|soluble fraction	ATP binding|peptidyl-prolyl cis-trans isomerase activity|protein heterodimerization activity|protein homodimerization activity|protein phosphatase 2A binding|protein phosphatase type 2A regulator activity|protein tyrosine phosphatase activator activity|receptor binding			ovary(1)|lung(1)|pancreas(1)	3		Medulloblastoma(224;0.235)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)		gagttgtttcttttttttttt	0.000													4	2	---	---	---	---	
MED27	9442	broad.mit.edu	37	9	134818559	134818559	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134818559delA	uc004cbe.1	-						MED27_uc004cbf.1_Intron|MED27_uc011mco.1_Intron|MED27_uc004cbg.3_Intron	NM_004269	NP_004260	Q6P2C8	MED27_HUMAN	mediator complex subunit 27						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleolus|transcription factor complex	protein binding|transcription coactivator activity			skin(1)	1		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		TGTATTTGCCAAAAGGGGAAA	0.348													4	2	---	---	---	---	
TSC1	7248	broad.mit.edu	37	9	135788588	135788588	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135788588delG	uc004cca.2	-						TSC1_uc004ccb.3_Intron|TSC1_uc011mcq.1_Intron|TSC1_uc011mcr.1_Intron|TSC1_uc011mcs.1_Intron|TSC1_uc004ccc.1_Intron|TSC1_uc004ccd.2_Intron|TSC1_uc004cce.1_Intron	NM_000368	NP_000359	Q92574	TSC1_HUMAN	tuberous sclerosis 1 protein isoform 1						activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus	cell cortex|lamellipodium|membrane|TSC1-TSC2 complex	chaperone binding|protein N-terminus binding	p.?(1)		lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1)	14				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		ccaaagtgctgggattacagg	0.025			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				4	2	---	---	---	---	
COL5A1	1289	broad.mit.edu	37	9	137709530	137709531	+	Intron	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137709530_137709531delCA	uc004cfe.2	+							NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCCTGCAGGCCACACACACACA	0.688													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137919555	137919556	+	IGR	INS	-	AGAC	AGAC	rs143438947	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137919555_137919556insAGAC								FCN1 (109746 upstream) : OLFM1 (47533 downstream)																							CCTTGCCGCTGacacacacaca	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	138313546	138313547	+	IGR	INS	-	TTT	TTT	rs36006169		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138313546_138313547insTTT								OLFM1 (300515 upstream) : KIAA0649 (58101 downstream)																							ttaactttcccttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	138535132	138535132	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138535132delG								GLT6D1 (3746 upstream) : LCN9 (20036 downstream)																							AACAGCCCTTGGGTTTTATCC	0.383													2	4	---	---	---	---	
NACC2	138151	broad.mit.edu	37	9	138964102	138964103	+	Intron	INS	-	T	T	rs4842098	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138964102_138964103insT	uc004cgw.2	-						NACC2_uc010nbh.2_Intron	NM_144653	NP_653254	Q96BF6	NACC2_HUMAN	BTB (POZ) domain containing 14A						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization	nuclear body					0						aaaaaaaaaaaaCCCAAAggca	0.015													4	2	---	---	---	---	
SEC16A	9919	broad.mit.edu	37	9	139337681	139337682	+	Intron	INS	-	AC	AC	rs140788545	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139337681_139337682insAC	uc004chx.2	-						SEC16A_uc004chp.2_Intron|SEC16A_uc004chq.2_Intron|SEC16A_uc011mea.1_Intron|SEC16A_uc004chr.2_Intron|SEC16A_uc004chs.2_Intron|SEC16A_uc004cht.2_Intron|SEC16A_uc004chu.2_Intron|SEC16A_uc004chv.3_Intron|SEC16A_uc004chw.2_Intron|SEC16A_uc010nbn.2_Intron	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GCCTCGTGTCGACAGAGCTCCA	0.579													3	6	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140564001	140564001	+	Intron	DEL	G	-	-	rs11289791		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140564001delG	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		AAGACGCCCCGCACAGCACgt	0.368													6	4	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140670335	140670336	+	Intron	DEL	GT	-	-	rs35694222		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140670335_140670336delGT	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		TGCATGTAGGgtgtgtgtgtgt	0.307													4	2	---	---	---	---	
DIP2C	22982	broad.mit.edu	37	10	661573	661574	+	Intron	DEL	CA	-	-	rs58771630		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:661573_661574delCA	uc001ifp.2	-							NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		acacccgccccacacacacaca	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2144601	2144601	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2144601delT								ADARB2 (364883 upstream) : PFKP (965151 downstream)																							ccccgagagcttcagggcacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2944659	2944660	+	IGR	DEL	AT	-	-	rs59600294		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2944659_2944660delAT								None (None upstream) : PFKP (165092 downstream)																							ACATGGTCACATGTTTAGCTTA	0.356													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3635375	3635375	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3635375delC	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																		ATGCGCGTTTCCATGTTGTTC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3927872	3927872	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3927872delA								KLF6 (100399 upstream) : LOC100216001 (693572 downstream)																							TATGGATGAGAAACGGGACTC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4056577	4056577	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4056577delT								KLF6 (229104 upstream) : LOC100216001 (564867 downstream)																							CTTCACTACATTTCTTTAGAA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4556318	4556319	+	IGR	DEL	AC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4556318_4556319delAC								KLF6 (728845 upstream) : LOC100216001 (65125 downstream)																							acaagcagatacacacacacac	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	6393707	6393710	+	IGR	DEL	CAGG	-	-	rs78813584		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6393707_6393710delCAGG								PFKFB3 (116202 upstream) : PRKCQ (75395 downstream)																							gagagggagacaggcaggcaggca	0.147													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	6696145	6696146	+	IGR	INS	-	T	T	rs149485389	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6696145_6696146insT								PRKCQ (73907 upstream) : SFMBT2 (508103 downstream)																							ctttcttcttcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	6992541	6992542	+	IGR	INS	-	T	T	rs141964059	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6992541_6992542insT								PRKCQ (370303 upstream) : SFMBT2 (211707 downstream)																							attatgggagctacaattcaag	0.000													1	6	---	---	---	---	
SFMBT2	57713	broad.mit.edu	37	10	7359680	7359680	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7359680delT	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron|SFMBT2_uc001ijo.1_Intron	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8						GAGGAGAAGGTAAAAGATCTG	0.308													4	2	---	---	---	---	
ATP5C1	509	broad.mit.edu	37	10	7843145	7843145	+	Intron	DEL	T	-	-	rs145159592		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7843145delT	uc001iju.2	+						ATP5C1_uc009xiq.1_Intron|ATP5C1_uc010qbc.1_Intron|ATP5C1_uc001ijv.2_Intron	NM_001001973	NP_001001973	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1						oxidative phosphorylation|respiratory electron transport chain	mitochondrial matrix|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)	hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism				0						ATACCATCTATTTTCTAAtac	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8685556	8685557	+	IGR	INS	-	T	T	rs147307262	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8685556_8685557insT								GATA3 (568394 upstream) : None (None downstream)																							CAATGACTCTCTTTTTTTTTGG	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	9369764	9369764	+	IGR	DEL	T	-	-	rs113704862		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9369764delT								None (None upstream) : None (None downstream)																							CTGTTTTACGTTTTTTTTTTT	0.348													4	3	---	---	---	---	
USP6NL	9712	broad.mit.edu	37	10	11536727	11536728	+	Intron	DEL	AG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11536727_11536728delAG	uc001ikt.3	-						USP6NL_uc001iks.1_Intron	NM_014688	NP_055503	Q92738	US6NL_HUMAN	USP6 N-terminal like isoform 1							intracellular	Rab GTPase activator activity				0						cagctgaggcagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	13412235	13412235	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13412235delT								SEPHS1 (21955 upstream) : BEND7 (68249 downstream)																							taaaacggtattttttttttt	0.000													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	13717367	13717367	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13717367delA	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						AGAAAGGGGGAAAGAAAAGCT	0.199													4	2	---	---	---	---	
ITGA8	8516	broad.mit.edu	37	10	15573282	15573283	+	Intron	DEL	TT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15573282_15573283delTT	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor						cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6						ATTTTCTCTCTTTTAACTTTTT	0.193													4	2	---	---	---	---	
ST8SIA6	338596	broad.mit.edu	37	10	17448281	17448281	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17448281delT	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron|uc001ipe.2_Intron|uc001ipf.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						ctttacaaccttttatcagct	0.000													4	2	---	---	---	---	
KIAA1217	56243	broad.mit.edu	37	10	24480821	24480821	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24480821delT	uc001irs.2	+							NM_001098500	NP_001091970	Q5T5P2	SKT_HUMAN	sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7						tagctgggactacaagtgtgc	0.000													4	2	---	---	---	---	
MYO3A	53904	broad.mit.edu	37	10	26465223	26465223	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26465223delA	uc001isn.2	+						MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA						protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						actccgtctcaaaaaaaaaaa	0.209													4	2	---	---	---	---	
ABI1	10006	broad.mit.edu	37	10	27150994	27150994	+	5'Flank	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27150994delT	uc001isx.2	-						ABI1_uc001ite.2_5'Flank|ABI1_uc010qdh.1_5'Flank|ABI1_uc010qdi.1_5'Flank|ABI1_uc001isy.2_5'Flank|ABI1_uc001ita.2_5'Flank|ABI1_uc001isz.2_5'Flank|ABI1_uc001itb.2_5'Flank|ABI1_uc001itc.2_5'Flank|ABI1_uc010qdj.1_5'Flank|ABI1_uc001itd.2_5'Flank|ABI1_uc010qdk.1_5'Flank	NM_005470	NP_005461	Q8IZP0	ABI1_HUMAN	abl-interactor 1 isoform a						actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome	cytoskeletal protein binding			central_nervous_system(1)	1						TTTTTGCTCCTGGATTTTTGT	0.219													4	2	---	---	---	---	
MAP3K8	1326	broad.mit.edu	37	10	30742800	30742801	+	Intron	INS	-	A	A	rs8177016		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30742800_30742801insA	uc001ivi.1	+						MAP3K8_uc009xlf.1_Intron|MAP3K8_uc001ivj.1_Intron	NM_005204	NP_005195	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase						cell cycle|T cell costimulation	cytosol	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			breast(3)|central_nervous_system(1)	4		Prostate(175;0.151)				catctcttttgaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42643682	42643683	+	IGR	INS	-	T	T	rs79321228		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42643682_42643683insT								None (None upstream) : LOC441666 (183632 downstream)																							tttcttgttggttttttttttt	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42660137	42660137	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42660137delA								None (None upstream) : LOC441666 (167178 downstream)																							gtagaatcacaaaaaaattca	0.144													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	43185442	43185442	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43185442delA	uc001jah.1	-											Homo sapiens cDNA FLJ41072 fis, clone 3NB692005439.																		aaagaagaacaagaagatgat	0.169													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47114221	47114222	+	Intron	INS	-	ACAC	ACAC	rs145011762	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47114221_47114222insACAC	uc001jed.3	-						uc001jef.2_Intron			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						gccaattccttacacacacaca	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	49508846	49508846	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49508846delA								FRMPD2 (26129 upstream) : MAPK8 (5844 downstream)																							TGAGGGGCTCAAAACCCTGCC	0.527													4	2	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51513947	51513947	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51513947delG	uc001jih.2	-						uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		atactggcaaggctgtggaga	0.000													4	2	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51581779	51581779	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51581779delA	uc001jih.2	-						uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Intron|NCOA4_uc010qhd.1_Intron|NCOA4_uc001jis.3_Intron|NCOA4_uc010qhe.1_Intron|NCOA4_uc010qhf.1_Intron|NCOA4_uc001jit.2_Intron|NCOA4_uc009xoo.2_Intron	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		gactccgcctaaaaaaaaaaa	0.169													4	2	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53108188	53108188	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53108188delA	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)		CTTACACCGTAAGGCAACCTG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	63391652	63391653	+	IGR	INS	-	A	A	rs141555088	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63391652_63391653insA								TMEM26 (178444 upstream) : C10orf107 (31066 downstream)																							AGGCACTGGACAAAGAAAAAGA	0.119													1	5	---	---	---	---	
ARID5B	84159	broad.mit.edu	37	10	63849288	63849288	+	Intron	DEL	T	-	-	rs111270606		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63849288delT	uc001jlt.1	+							NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)						liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)					cttctttttcttttttttttt	0.055													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64804627	64804627	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64804627delA								EGR2 (225700 upstream) : NRBF2 (88380 downstream)																							ctgtctcaggaaaaaaaaaaa	0.000													4	3	---	---	---	---	
JMJD1C	221037	broad.mit.edu	37	10	65145854	65145855	+	Intron	DEL	AC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65145854_65145855delAC	uc001jmn.2	-						JMJD1C_uc001jmr.1_Intron	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					acatacacagacacacacacac	0.153													4	2	---	---	---	---	
CCDC109A	90550	broad.mit.edu	37	10	74463649	74463651	+	Intron	DEL	AAC	-	-	rs113892377		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74463649_74463651delAAC	uc001jtc.2	+						CCDC109A_uc009xqp.1_Intron|CCDC109A_uc009xqq.1_Intron|CCDC109A_uc010qjy.1_Intron|CCDC109A_uc009xqr.2_Intron|CCDC109A_uc001jtd.2_Intron	NM_138357	NP_612366	Q8NE86	MCU_HUMAN	coiled-coil domain containing 109A						elevation of mitochondrial calcium ion concentration|mitochondrial calcium ion transport|protein complex oligomerization	integral to membrane|mitochondrial inner membrane	protein binding				0	Prostate(51;0.0198)					tctgtctcaaaacaacaacaaca	0.000													4	2	---	---	---	---	
C10orf11	83938	broad.mit.edu	37	10	77810597	77810597	+	Intron	DEL	T	-	-	rs67180803		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77810597delT	uc001jxi.2	+							NM_032024	NP_114413	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)					AACAATGGACTTGAAGGTTAA	0.408													3	4	---	---	---	---	
SH2D4B	387694	broad.mit.edu	37	10	82297661	82297661	+	5'UTR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82297661delA	uc001kck.1	+	1					SH2D4B_uc001kcl.1_5'Flank	NM_207372	NP_997255	Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B isoform 1												0			Colorectal(32;0.229)			ACCTTCCACTAACAGATCACT	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	83623575	83623576	+	IGR	INS	-	A	A	rs143440558	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83623575_83623576insA								None (None upstream) : NRG3 (11494 downstream)																							AATTATGACATAAAGATCCAAA	0.431													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	84452616	84452617	+	Intron	INS	-	A	A	rs141162660	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84452616_84452617insA	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)		GAACTGAGGGGAAAAATATATG	0.267													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85349752	85349753	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85349752_85349753insA								NRG3 (602817 upstream) : GHITM (549432 downstream)																							caaaacaaaacaaaaaaaacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	88302645	88302645	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88302645delA								WAPAL (21104 upstream) : OPN4 (111669 downstream)																							gactccatctaaaaaaaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	90813294	90813295	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90813294_90813295insT								FAS (37753 upstream) : CH25H (152401 downstream)																							CCTGATGCATATTTTTTGGTGC	0.381													4	2	---	---	---	---	
KIF20B	9585	broad.mit.edu	37	10	91488663	91488666	+	Intron	DEL	TGTG	-	-	rs10548807		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91488663_91488666delTGTG	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron|KIF20B_uc001kgt.1_Intron	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						CTTTTTTCTTtgtgtgtgtgtgtg	0.108													4	3	---	---	---	---	
TBC1D12	23232	broad.mit.edu	37	10	96286839	96286840	+	Intron	INS	-	TGTGTG	TGTGTG	rs150870230	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96286839_96286840insTGTGTG	uc001kjr.2	+							NM_015188	NP_056003	O60347	TBC12_HUMAN	TBC1 domain family, member 12							intracellular	Rab GTPase activator activity				0		Colorectal(252;0.0429)				gctggattgattgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	99168659	99168659	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99168659delG								RRP12 (7532 upstream) : PGAM1 (17368 downstream)																							tgcgtgagccggggcaggcgg	0.114													4	2	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100815877	100815878	+	Intron	INS	-	CAT	CAT	rs143260011	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100815877_100815878insCAT	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600	Q8WWQ2	HPSE2_HUMAN	heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		ataaaagcagacatcactacag	0.000													4	4	---	---	---	---	
FAM178A	55719	broad.mit.edu	37	10	102700480	102700488	+	Intron	DEL	CCTTCCCTC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102700480_102700488delCCTTCCCTC	uc001krt.3	+						FAM178A_uc001krs.2_Intron	NM_018121	NP_060591	Q8IX21	F178A_HUMAN	hypothetical protein LOC55719 isoform 1												0						tccttcccctccttccctcccttccctcc	0.081													4	2	---	---	---	---	
PCGF6	84108	broad.mit.edu	37	10	105063898	105063898	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105063898delT	uc001kwt.2	-						PCGF6_uc001kwu.2_Intron|PCGF6_uc009xxk.2_Intron|PCGF6_uc009xxl.2_Intron|PCGF6_uc009xxm.2_Intron	NM_001011663	NP_001011663	Q9BYE7	PCGF6_HUMAN	polycomb group ring finger 6 isoform a						negative regulation of transcription, DNA-dependent	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			kidney(1)	1		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)		GTGAATGTGCttttttttttt	0.134													4	3	---	---	---	---	
TACC2	10579	broad.mit.edu	37	10	123807930	123807931	+	Intron	INS	-	CCTT	CCTT	rs7905230	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123807930_123807931insCCTT	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing							microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				ctccctccctcccttccttccc	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	124110333	124110334	+	IGR	INS	-	G	G	rs140915740	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124110333_124110334insG								BTBD16 (12657 upstream) : PLEKHA1 (23886 downstream)																							ACGTATTCTGATCCACCTGGAG	0.480													3	3	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126812307	126812307	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126812307delC	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		AATTCCTGAACCCTGACCTTC	0.582													4	2	---	---	---	---	
C10orf90	118611	broad.mit.edu	37	10	128206630	128206631	+	Intron	DEL	TT	-	-	rs79691555		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128206630_128206631delTT	uc001ljq.2	-						C10orf90_uc010qum.1_Intron|C10orf90_uc009yao.2_Intron|C10orf90_uc001ljs.1_Intron	NM_001004298	NP_001004298	Q96M02	CJ090_HUMAN	hypothetical protein LOC118611											ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		ctcttgtatgtttttttttttc	0.054													1	5	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	128936649	128936649	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128936649delG	uc001ljt.2	+						DOCK1_uc010qun.1_Intron|FAM196A_uc010quo.1_Intron|FAM196A_uc001ljv.1_Intron|FAM196A_uc001lju.1_Intron|FAM196A_uc009yap.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)		AAGTATGAGTGGGCAGGGGTC	0.423													4	2	---	---	---	---	
TCERG1L	256536	broad.mit.edu	37	10	132975109	132975114	+	Intron	DEL	ATAGGA	-	-	rs141287830		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132975109_132975114delATAGGA	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		acacaggcacataggaacacacagag	0.000													4	2	---	---	---	---	
PARVA	55742	broad.mit.edu	37	11	12550876	12550876	+	3'UTR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12550876delG	uc001mki.2	+	13						NM_018222	NP_060692	Q9NVD7	PARVA_HUMAN	parvin, alpha						cell adhesion|cell junction assembly|cilium morphogenesis	actin cytoskeleton|cytosol|focal adhesion	actin binding			breast(3)	3				Epithelial(150;0.00624)		GAAGGGCGGAGGGGGGTGGGC	0.483													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	20694783	20694783	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20694783delC	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						TGAACATGAGCCCCCAGCCTC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	34851867	34851867	+	IGR	DEL	G	-	-	rs5791017		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34851867delG								EHF (168786 upstream) : APIP (44847 downstream)																							GGCAGAAGCTGGGGGGTGTAC	0.522													1	5	---	---	---	---	
PAMR1	25891	broad.mit.edu	37	11	35455015	35455015	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35455015delT	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2						TGGTCATGCCTTTTGATGGGA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	36268073	36268073	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36268073delA								LDLRAD3 (15232 upstream) : COMMD9 (23615 downstream)																							caaatacatcaaaatccctgc	0.045													4	2	---	---	---	---	
LRP4	4038	broad.mit.edu	37	11	46941815	46941815	+	5'Flank	DEL	T	-	-	rs72094166		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46941815delT	uc001ndn.3	-						LRP4_uc009ylh.1_5'Flank	NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein						endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)		AGACTTGCTCtttttttttct	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48364859	48364860	+	IGR	INS	-	C	C	rs147261683	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48364859_48364860insC								OR4C3 (17379 upstream) : OR4C45 (2042 downstream)																							TCTCACAGTGGCCCCACCAGCC	0.431													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48365579	48365579	+	IGR	DEL	G	-	-	rs67239811		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48365579delG								OR4C3 (18099 upstream) : OR4C45 (1323 downstream)																							tgaaaaaaaagacatgtaatg	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49080677	49080678	+	IGR	INS	-	A	A	rs34947092		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49080677_49080678insA								OR4A47 (569405 upstream) : FOLH1 (87510 downstream)																							TTCTTGAAATTAAAAAAAAAAA	0.381													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50173271	50173271	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50173271delT								OR4C12 (169234 upstream) : LOC441601 (65729 downstream)																							CTTTAACTTCTTTCTTCTCAA	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50725578	50725578	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50725578delA								LOC646813 (345775 upstream) : OR4A5 (685870 downstream)																							cacacatcacaaaagtttctc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	54990412	54990412	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:54990412delG								None (None upstream) : TRIM48 (39246 downstream)																							tcaaaataaaggttcaactct	0.000													2	7	---	---	---	---	
DTX4	23220	broad.mit.edu	37	11	58974560	58974560	+	3'UTR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58974560delG	uc001nns.2	+	9					DTX4_uc001nnr.2_3'UTR	NM_015177	NP_055992	Q9Y2E6	DTX4_HUMAN	deltex 4 homolog						Notch signaling pathway	cytoplasm	zinc ion binding			lung(2)|central_nervous_system(1)	3		all_epithelial(135;0.125)				TTCGCACACTGGTCAAGTATC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	63603271	63603272	+	IGR	INS	-	T	T	rs111727340		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63603271_63603272insT								C11orf84 (8082 upstream) : MARK2 (3128 downstream)																							gggcagagttgttttttttttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	63693961	63693962	+	IGR	INS	-	TT	TT	rs10666109		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63693961_63693962insTT								RCOR2 (9645 upstream) : NAA40 (12480 downstream)																							ctctctctctcttttttttttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	64259836	64259837	+	IGR	DEL	TT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64259836_64259837delTT								RPS6KA4 (120150 upstream) : SLC22A11 (63261 downstream)																							ttttcttctctttttttttttt	0.054													4	2	---	---	---	---	
PC	5091	broad.mit.edu	37	11	66695195	66695195	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66695195delA	uc001ojo.1	-						PC_uc001ojp.1_Intron	NM_001040716	NP_001035806	P11498	PYC_HUMAN	pyruvate carboxylase precursor						gluconeogenesis|lipid biosynthetic process	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|pyruvate carboxylase activity			ovary(2)|lung(1)|kidney(1)	4		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	agtccgtctcaaaaaaaaaaa	0.214													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69558258	69558258	+	IGR	DEL	T	-	-	rs35083496		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69558258delT								FGF19 (39152 upstream) : FGF4 (29539 downstream)																							TACTTATTGCTTTTTTTTTTT	0.313													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69862131	69862131	+	IGR	DEL	T	-	-	rs5792504		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69862131delT								FGF3 (227939 upstream) : ANO1 (62277 downstream)																							CCtttctttcttttttttttt	0.249													3	7	---	---	---	---	
ANO1	55107	broad.mit.edu	37	11	69967285	69967286	+	Intron	INS	-	TTCT	TTCT	rs149259914	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69967285_69967286insTTCT	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						tccctccctccttctctccccg	0.257													8	7	---	---	---	---	
PPFIA1	8500	broad.mit.edu	37	11	70177341	70177341	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70177341delA	uc001opo.2	+						PPFIA1_uc001opn.1_Intron|PPFIA1_uc001opp.2_Intron|PPFIA1_uc001opq.1_Intron	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b						cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			actccgtctcaaaaaaaaaaa	0.144													4	2	---	---	---	---	
PPME1	51400	broad.mit.edu	37	11	73962329	73962329	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73962329delC	uc001ouw.2	+						PPME1_uc009yty.2_Intron|PPME1_uc001oux.2_Intron|P4HA3_uc001ouy.3_Intron	NM_016147	NP_057231	Q9Y570	PPME1_HUMAN	protein phosphatase methylesterase 1						protein demethylation		carboxylesterase activity|protein C-terminal methylesterase activity|protein phosphatase 2A binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity				0	Breast(11;3.29e-05)					TTCTCCAATACCCCCAAAAGC	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	77374064	77374065	+	IGR	INS	-	CA	CA	rs140823768	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77374064_77374065insCA								CLNS1A (25213 upstream) : RSF1 (3210 downstream)																							GTGTGCGTGTGCACACACACAC	0.366													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	77751461	77751461	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77751461delT								KCTD14 (17141 upstream) : THRSP (23446 downstream)																							ctcttctctctttaactctgc	0.065													4	2	---	---	---	---	
CASP5	838	broad.mit.edu	37	11	104872625	104872626	+	Intron	DEL	AC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104872625_104872626delAC	uc010rva.1	-						CASP5_uc010ruz.1_Intron|CASP5_uc010rvb.1_Intron|CASP5_uc010rvc.1_Intron|CASP5_uc009yxh.2_Intron|CASP5_uc010rvd.1_Intron	NM_004347	NP_004338	P51878	CASP5_HUMAN	caspase 5 isoform a precursor						apoptosis|cellular response to mechanical stimulus|proteolysis|regulation of apoptosis	intracellular	cysteine-type endopeptidase activity|protein binding			ovary(2)|lung(1)	3		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		GTGCGCATGTacacacacacac	0.307													5	3	---	---	---	---	
CUL5	8065	broad.mit.edu	37	11	107925712	107925712	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107925712delG	uc001pjv.2	+						CUL5_uc001pju.2_Intron	NM_003478	NP_003469	Q93034	CUL5_HUMAN	Vasopressin-activated calcium-mobilizing						cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		TACATTTTATGGGATTATTTG	0.279													13	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115761249	115761249	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115761249delT								CADM1 (386008 upstream) : BUD13 (857639 downstream)																							taagggttactttgaggatat	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115802365	115802368	+	IGR	DEL	TATA	-	-	rs72365095		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115802365_115802368delTATA								CADM1 (427124 upstream) : BUD13 (816520 downstream)																							CATGAAAACTTATATCCTTTTCCT	0.431													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124071924	124071925	+	IGR	INS	-	AC	AC	rs149017281	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124071924_124071925insAC								VWA5A (54308 upstream) : OR8G2 (23473 downstream)																							aacgccctgtaacgcgcccact	0.000													4	2	---	---	---	---	
CCDC15	80071	broad.mit.edu	37	11	124824027	124824027	+	5'UTR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124824027delG	uc001qbm.3	+	1						NM_025004	NP_079280	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15							centrosome				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		ATAAGGCTACGGATGGGCGGG	0.642													4	2	---	---	---	---	
ARHGAP32	9743	broad.mit.edu	37	11	128993225	128993225	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128993225delA	uc009zcp.2	-						ARHGAP32_uc009zcq.1_Intron	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1						cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5						GACATCAATTAAAAAAAAAAC	0.279													4	2	---	---	---	---	
WNK1	65125	broad.mit.edu	37	12	971219	971220	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:971219_971220insT	uc001qio.3	+						WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TTCTCTCTCTCTTTTTTTTGGC	0.411													27	12	---	---	---	---	
PZP	5858	broad.mit.edu	37	12	9307928	9307928	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9307928delG	uc001qvl.2	-						PZP_uc009zgl.2_Intron	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5						GTCCGTTTTTGTTGTTTTGTA	0.323													4	2	---	---	---	---	
CLEC1A	51267	broad.mit.edu	37	12	10225700	10225701	+	Intron	DEL	AC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10225700_10225701delAC	uc001qxb.2	-						CLEC1A_uc009zhf.2_Intron|CLEC1A_uc001qxc.2_Intron|CLEC1A_uc001qxd.2_Intron|CLEC1A_uc010sgx.1_Intron	NM_016511	NP_057595	Q8NC01	CLC1A_HUMAN	C-type lectin-like receptor-1						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane|intracellular	sugar binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2						AAACGAACAAACACACACACAC	0.223													4	2	---	---	---	---	
ETV6	2120	broad.mit.edu	37	12	11822311	11822312	+	Intron	INS	-	CCTTCCTC	CCTTCCTC			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11822311_11822312insCCTTCCTC	uc001qzz.2	+							NM_001987	NP_001978	P41212	ETV6_HUMAN	ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				ctcccttcctccctccctccct	0.099			T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								4	4	---	---	---	---	
GRIN2B	2904	broad.mit.edu	37	12	13899583	13899583	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13899583delC	uc001rbt.2	-							NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	ggatgtttgtcccccccaaat	0.174													4	3	---	---	---	---	
ATF7IP	55729	broad.mit.edu	37	12	14555062	14555062	+	Intron	DEL	T	-	-	rs142733910		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14555062delT	uc001rbw.2	+						ATF7IP_uc010shs.1_Intron|ATF7IP_uc001rbu.2_Intron|ATF7IP_uc001rbv.1_Intron|ATF7IP_uc001rbx.2_Intron|ATF7IP_uc010sht.1_Intron|ATF7IP_uc001rby.3_Intron	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5						ttcttctttcttttttttttt	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	19986930	19986931	+	IGR	DEL	AT	-	-	rs67597436		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19986930_19986931delAT								AEBP2 (311757 upstream) : PDE3A (535266 downstream)																							ccacacacacatacacacacac	0.054													4	2	---	---	---	---	
SLCO1B1	10599	broad.mit.edu	37	12	21385474	21385474	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21385474delA	uc001req.3	+							NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|skin(3)|pancreas(1)|central_nervous_system(1)	8					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)	taggaatcctaagcctacttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	22266637	22266640	+	IGR	DEL	CTCT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22266637_22266640delCTCT								CMAS (48036 upstream) : ST8SIA1 (79686 downstream)																							TTGACCCTGCCTCTCTCTCTCTCT	0.402													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31278603	31278606	+	Intron	DEL	TGTT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31278603_31278606delTGTT	uc010sjy.1	-											RecName: Full=Ovostatin homolog 1; Flags: Precursor;																		TCCCGACCTCtgtttgtgctgaat	0.176													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	37991301	37991301	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37991301delT								None (None upstream) : ALG10B (719256 downstream)																							tatcttcacataaaaactaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38002192	38002193	+	IGR	INS	-	A	A	rs75136323		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38002192_38002193insA								None (None upstream) : ALG10B (708364 downstream)																							ttggaaacgggatatcttcaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38108817	38108817	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38108817delC								None (None upstream) : ALG10B (601740 downstream)																							atttggagggctttgtggcct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38303049	38303050	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38303049_38303050insA								None (None upstream) : ALG10B (407507 downstream)																							actgcccaatcaaaaaaaaggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	42047496	42047496	+	IGR	DEL	G	-	-	rs5797753		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42047496delG								PDZRN4 (79112 upstream) : GXYLT1 (428154 downstream)																							attacaattcggattacaatt	0.080													3	4	---	---	---	---	
DNAJC22	79962	broad.mit.edu	37	12	49745683	49745684	+	3'UTR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49745683_49745684insA	uc001rua.2	+	3					DNAJC22_uc001rub.2_3'UTR	NM_024902	NP_079178	Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22						protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			ovary(1)	1						aactccgtctcaaaaaaaaaaa	0.158													2	4	---	---	---	---	
NCKAP5L	57701	broad.mit.edu	37	12	50201030	50201031	+	Intron	DEL	GT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50201030_50201031delGT	uc009zlk.2	-							NM_001037806	NP_001032895	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like											central_nervous_system(1)	1						ATGCTTCTTCgtgtgtgtgtgt	0.391													4	2	---	---	---	---	
FAIM2	23017	broad.mit.edu	37	12	50272343	50272344	+	Intron	DEL	GT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50272343_50272344delGT	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						gcatgtgtgagtgtatatgttc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	56754296	56754296	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56754296delG								STAT2 (387 upstream) : APOF (59 downstream)																							AGGGCTCCATGGGAAGGGGTG	0.473													4	2	---	---	---	---	
ATP5B	506	broad.mit.edu	37	12	57033282	57033283	+	Intron	DEL	GC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57033282_57033283delGC	uc001slr.2	-							NM_001686	NP_001677	P06576	ATPB_HUMAN	mitochondrial ATP synthase beta subunit						angiogenesis|ATP hydrolysis coupled proton transport|regulation of intracellular pH|respiratory electron transport chain	cell surface|mitochondrial nucleoid|mitochondrial proton-transporting ATP synthase, catalytic core|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|hydrogen-exporting ATPase activity, phosphorylative mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)	1						ATTCCgccgggcgcagtggctc	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	61423676	61423676	+	IGR	DEL	T	-	-	rs74790740		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61423676delT								None (None upstream) : FAM19A2 (678367 downstream)																							cctcctcttctttttTCTTTc	0.005													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65656068	65656069	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65656068_65656069insT								LEMD3 (13961 upstream) : MSRB3 (16419 downstream)																							ttatccttttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89280596	89280596	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89280596delT								KITLG (306358 upstream) : DUSP6 (461243 downstream)																							tttgttcttgttgcacacaac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89520009	89520009	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89520009delA								KITLG (545771 upstream) : DUSP6 (221830 downstream)																							CAACGAAAACAATATCTTGTT	0.343													4	2	---	---	---	---	
SOCS2	8835	broad.mit.edu	37	12	93968379	93968379	+	Intron	DEL	T	-	-	rs35259505		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93968379delT	uc001tcw.1	+						uc001tcv.1_5'Flank|uc001tcu.2_5'Flank|SOCS2_uc001tcx.1_Intron|SOCS2_uc009zsu.2_3'UTR|SOCS2_uc001tcy.1_Intron|SOCS2_uc001tcz.2_3'UTR	NM_003877	NP_003868	O14508	SOCS2_HUMAN	suppressor of cytokine signaling-2						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						ACACACCACCTTTTTTTTTTT	0.328													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	94325588	94325592	+	IGR	DEL	AAAAG	-	-	rs71071768		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94325588_94325592delAAAAG								CRADD (36972 upstream) : PLXNC1 (216907 downstream)																							GAGAGAGAGAAaaagaaaaaaagag	0.161													4	2	---	---	---	---	
PLXNC1	10154	broad.mit.edu	37	12	94675906	94675910	+	Intron	DEL	AAAGT	-	-	rs2307570		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94675906_94675910delAAAGT	uc001tdc.2	+						PLXNC1_uc010sut.1_Intron|PLXNC1_uc009zsv.2_Intron	NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor						axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						ACAAACAAACAAAGTAAAACAGAAC	0.376													8	5	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99917815	99917815	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99917815delG	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		ACAAGAGTGTGGGTTTATGGC	0.363													4	2	---	---	---	---	
UHRF1BP1L	23074	broad.mit.edu	37	12	100449994	100449994	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100449994delA	uc001tgq.2	-						UHRF1BP1L_uc001tgp.2_Intron	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2						taagacccttaaaaaagaggc	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106555769	106555769	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106555769delA								NUAK1 (21958 upstream) : CKAP4 (75891 downstream)																							atttataggtaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106653138	106653138	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106653138delA								CKAP4 (11425 upstream) : TCP11L2 (43443 downstream)																							ggtgccccgtaatgcagattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108841303	108841304	+	IGR	INS	-	A	A	rs35818126		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108841303_108841304insA								CMKLR1 (108209 upstream) : FICD (67747 downstream)																							atcatcttatgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
GIT2	9815	broad.mit.edu	37	12	110411515	110411516	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110411515_110411516insT	uc001tps.2	-						GIT2_uc001tpq.2_Intron|GIT2_uc001tpv.2_Intron|GIT2_uc001tpu.2_Intron|GIT2_uc001tpt.2_Intron|GIT2_uc010sxu.1_Intron|GIT2_uc001tpw.2_Intron|GIT2_uc010sxv.1_Intron	NM_057169	NP_476510	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting						regulation of ARF GTPase activity|regulation of G-protein coupled receptor protein signaling pathway	nucleoplasm	ARF GTPase activator activity|protein binding|zinc ion binding			central_nervous_system(1)	1						ttattttgctcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112768574	112768574	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112768574delC								C12orf51 (24536 upstream) : RPL6 (74421 downstream)																							CACCTGGTTTCCACTGTACAT	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116060556	116060559	+	IGR	DEL	AGAG	-	-	rs61213723		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116060556_116060559delAGAG								TBX3 (938587 upstream) : MED13L (335824 downstream)																							acacacacacagagagagaatgta	0.000													4	3	---	---	---	---	
WDR66	144406	broad.mit.edu	37	12	122365095	122365095	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122365095delT	uc009zxk.2	+							NM_144668	NP_653269	Q8TBY9	WDR66_HUMAN	WD repeat domain 66								calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		GTTGTTTAGGTTTTTTTTTTT	0.383													4	2	---	---	---	---	
TMEM132B	114795	broad.mit.edu	37	12	125957072	125957072	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125957072delA	uc001uhe.1	+							NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CCTGCAGTAGAAGGACCTGCT	0.323													4	2	---	---	---	---	
TMEM132B	114795	broad.mit.edu	37	12	126012684	126012685	+	Intron	INS	-	T	T	rs111972959		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126012684_126012685insT	uc001uhe.1	+							NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		GTGTCTATTTCTTTTTTTTTTT	0.411													3	3	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129580209	129580211	+	Intron	DEL	AAG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129580209_129580211delAAG	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		gtttccttttaagaagaagagat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19596959	19596963	+	IGR	DEL	GAGGA	-	-	rs56194035		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19596959_19596963delGAGGA								LOC348021 (10185 upstream) : DKFZp686A1627 (23330 downstream)																							gagaggaggggaggagaggggaggg	0.171													4	3	---	---	---	---	
ZMYM2	7750	broad.mit.edu	37	13	20599783	20599785	+	Intron	DEL	TTG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20599783_20599785delTTG	uc001umr.2	+						ZMYM2_uc001ums.2_Intron|ZMYM2_uc001umt.2_Intron|ZMYM2_uc010tco.1_Intron|ZMYM2_uc001umv.2_5'UTR|ZMYM2_uc001umw.2_5'UTR	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		TTATCTCCTTttgttgttgttgt	0.044													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	24068329	24068332	+	IGR	DEL	GTGT	-	-	rs35298599		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24068329_24068332delGTGT								SACS (60488 upstream) : TNFRSF19 (76391 downstream)																							CACACGgtgagtgtgtgtgtgtgt	0.255													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	24128337	24128338	+	IGR	DEL	TG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24128337_24128338delTG								SACS (120496 upstream) : TNFRSF19 (16385 downstream)																							TCCCTCTCTCTGTGTCATGCTG	0.574													4	2	---	---	---	---	
MTUS2	23281	broad.mit.edu	37	13	29897392	29897393	+	Intron	INS	-	T	T	rs72070069		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29897392_29897393insT	uc001usl.3	+							NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						TATGATGTGGCttttttttttt	0.050													4	2	---	---	---	---	
SIAH3	283514	broad.mit.edu	37	13	46421758	46421759	+	Intron	DEL	GT	-	-	rs71750697		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46421758_46421759delGT	uc001vap.2	-							NM_198849	NP_942146	Q8IW03	SIAH3_HUMAN	seven in absentia homolog 3						multicellular organismal development|ubiquitin-dependent protein catabolic process	nucleus	metal ion binding			ovary(1)|skin(1)	2						CCAtgtgttcgtgtgtgtgtgt	0.391													4	2	---	---	---	---	
THSD1P1	374500	broad.mit.edu	37	13	52855276	52855277	+	Intron	DEL	TG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52855276_52855277delTG	uc001vgm.1	-											Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						ctggtgtgcttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	69610264	69610264	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69610264delT								None (None upstream) : KLHL1 (664462 downstream)																							tctttctttcttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	74011465	74011465	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74011465delT								KLF5 (359790 upstream) : KLF12 (248685 downstream)																							CCCTCTTTCCTtttttttttt	0.284													4	2	---	---	---	---	
DZIP1	22873	broad.mit.edu	37	13	96272346	96272346	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96272346delC	uc001vmk.2	-						DZIP1_uc001vml.2_Intron	NM_198968	NP_945319	Q86YF9	DZIP1_HUMAN	DAZ interacting protein 1 isoform 2						germ cell development|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			ggctctcggtccccactcaaa	0.134													3	3	---	---	---	---	
FARP1	10160	broad.mit.edu	37	13	98920941	98920942	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98920941_98920942insT	uc001vnj.2	+						FARP1_uc001vnh.2_Intron	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1						regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			aggatggtctcgaacttctgac	0.020													4	2	---	---	---	---	
COL4A2	1284	broad.mit.edu	37	13	111134090	111134090	+	Intron	DEL	T	-	-	rs63008160		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111134090delT	uc001vqx.2	+							NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein						angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			TGTCCCTCCGTTGCTGGAGAC	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112771197	112771198	+	IGR	INS	-	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112771197_112771198insG								SOX1 (45177 upstream) : C13orf28 (259471 downstream)																							ggaggaacagaggccggtaagg	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19041378	19041379	+	IGR	INS	-	CA	CA			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19041378_19041379insCA								None (None upstream) : OR11H12 (336215 downstream)																							gcagattctacaaaaagagcgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19077502	19077503	+	IGR	DEL	GT	-	-	rs111654764		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19077502_19077503delGT								None (None upstream) : OR11H12 (300091 downstream)																							GGAATGGGGAgtgtgtgtgtgt	0.183													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19672247	19672248	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19672247_19672248insT	uc001vvk.1	+						uc001vvl.3_Intron|uc001vvo.1_Intron					Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																		ATAAAACGACAttttttttttt	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	21663051	21663051	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21663051delT								OR5AU1 (38867 upstream) : HNRNPC (14247 downstream)																							TGttcttttcttttttttttt	0.015													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	23027952	23027954	+	IGR	DEL	CAA	-	-	rs71920933		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23027952_23027954delCAA								OR4E2 (893716 upstream) : DAD1 (5853 downstream)																							TGAAATTTAGCAACAACAACAAC	0.261													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	28408383	28408383	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28408383delA								None (None upstream) : FOXG1 (827904 downstream)																							tccctttcctaaccaagggaa	0.000													4	2	---	---	---	---	
SLC25A21	89874	broad.mit.edu	37	14	37437038	37437039	+	Intron	DEL	TG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37437038_37437039delTG	uc001wtz.1	-							NM_030631	NP_085134	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial						lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		CACATGCACTtgtgtgtgtgtg	0.173													4	2	---	---	---	---	
FANCM	57697	broad.mit.edu	37	14	45604569	45604569	+	5'Flank	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45604569delA	uc001wwd.3	+						FANCM_uc001wwc.2_5'Flank|FANCM_uc010anf.2_5'Flank|FKBP3_uc010tqf.1_5'Flank	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M						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						aaggagcattaAAAAAAAAAA	0.259								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	2	---	---	---	---	
NID2	22795	broad.mit.edu	37	14	52534355	52534355	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52534355delT	uc001wzo.2	-						NID2_uc010tqs.1_Intron|NID2_uc010tqt.1_Intron|NID2_uc001wzp.2_Intron	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor							basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					CCGCTAAGCATTTTTTTCCTC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57236982	57236982	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57236982delC								C14orf101 (120752 upstream) : OTX2 (30445 downstream)																							TGACTTGAGTCTAAAAGAAAA	0.373													4	2	---	---	---	---	
C14orf37	145407	broad.mit.edu	37	14	58757493	58757494	+	Intron	INS	-	T	T	rs142402683	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58757493_58757494insT	uc010tro.1	-						uc001xdl.2_Intron|uc001xdm.1_Intron|uc001xdn.1_Intron|uc010apd.1_Intron|uc010ape.1_Intron	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						gctcatccctgtaatcccagca	0.144													4	3	---	---	---	---	
RTN1	6252	broad.mit.edu	37	14	60096966	60096966	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60096966delA	uc001xen.1	-						RTN1_uc001xem.1_Intron|RTN1_uc001xek.1_Intron|RTN1_uc001xel.1_Intron|RTN1_uc010apl.1_Intron	NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A						neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		GGGTGGGGTTAAAAAAAAAAA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	61057657	61057657	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61057657delT								SIX6 (79134 upstream) : SIX1 (53761 downstream)																							ttcttactgatttttttgcct	0.000													4	2	---	---	---	---	
FAM71D	161142	broad.mit.edu	37	14	67661156	67661157	+	Intron	DEL	GT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67661156_67661157delGT	uc001xja.1	+						FAM71D_uc010tsv.1_Intron|FAM71D_uc001xiz.2_Intron|FAM71D_uc010aqn.1_Intron	NM_173526	NP_775797	Q8N9W8	FA71D_HUMAN	hypothetical protein LOC161142											ovary(1)	1		all_hematologic(31;0.0116)		all cancers(60;0.00107)|BRCA - Breast invasive adenocarcinoma(234;0.00993)|OV - Ovarian serous cystadenocarcinoma(108;0.012)		TGAGGGGGGCGTGTGTGTGTGT	0.282													5	3	---	---	---	---	
RAD51L1	5890	broad.mit.edu	37	14	68867614	68867615	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68867614_68867615insT	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)		ACCATTCAGGATTTTTTTTTTC	0.366			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	69462247	69462247	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69462247delA								ACTN1 (16164 upstream) : DCAF5 (55391 downstream)																							actccatctcaaaaaaaaaga	0.154													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	70048634	70048645	+	IGR	DEL	CACACACACACA	-	-	rs72075303		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70048634_70048645delCACACACACACA								C14orf162 (10716 upstream) : KIAA0247 (29665 downstream)																							Aacatgcacgcacacacacacacacacacaca	0.288													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	75655960	75655960	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75655960delG								TMED10 (12611 upstream) : FOS (89521 downstream)																							GAGAAGTGAAGAAGTATCAAG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	77044370	77044371	+	IGR	INS	-	AT	AT	rs10675149		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77044370_77044371insAT								ESRRB (76192 upstream) : VASH1 (183864 downstream)																							gagagagagagagagagagcga	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	78255858	78255858	+	IGR	DEL	T	-	-	rs35058509		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78255858delT								C14orf178 (19773 upstream) : ADCK1 (10568 downstream)																							GGTTTGAGCATTTTTTTTTTT	0.413													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88198745	88198746	+	IGR	INS	-	ACAC	ACAC	rs143109724	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88198745_88198746insACAC								None (None upstream) : GALC (105418 downstream)																							aatgaggaattacacacacaca	0.069													4	2	---	---	---	---	
SLC24A4	123041	broad.mit.edu	37	14	92875761	92875761	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92875761delT	uc001yak.2	+						SLC24A4_uc001yai.2_Intron|SLC24A4_uc010twm.1_Intron|SLC24A4_uc001yaj.2_Intron	NM_153646	NP_705932	Q8NFF2	NCKX4_HUMAN	solute carrier family 24 member 4 isoform 1							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			breast(2)|ovary(1)	3		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		AGGCAGCGCATTCAGTGTTAT	0.423													4	2	---	---	---	---	
C14orf142	84520	broad.mit.edu	37	14	93672349	93672350	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93672349_93672350insT	uc001ybl.1	-						UBR7_uc001ybm.3_5'Flank|UBR7_uc001ybn.3_5'Flank	NM_032490	NP_115879	Q9BXV9	CN142_HUMAN	hypothetical protein LOC84520												0		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.177)|all cancers(159;0.198)|COAD - Colon adenocarcinoma(157;0.203)		ACCACTTTCACtttttttttct	0.218													6	3	---	---	---	---	
PRIMA1	145270	broad.mit.edu	37	14	94246755	94246755	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94246755delC	uc001ybw.1	-						PRIMA1_uc001ybx.1_Intron	NM_178013	NP_821092	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1 precursor						neurotransmitter catabolic process	cell junction|integral to membrane|synapse				large_intestine(1)|skin(1)	2		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		taagggaatgcccaccatttg	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	94451637	94451638	+	IGR	DEL	AC	-	-	rs60775991		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94451637_94451638delAC								ASB2 (8561 upstream) : C14orf48 (11978 downstream)																							GTGCATTCAGacacacacacac	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98073579	98073579	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98073579delA								VRK1 (725629 upstream) : C14orf64 (318368 downstream)																							acactgtctcaaaaaaaaaaa	0.164													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99414305	99414305	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99414305delT								C14orf177 (230208 upstream) : BCL11B (221322 downstream)																							AGTTGGTGACTTATGACATAG	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	104755609	104755612	+	IGR	DEL	TGTC	-	-	rs138185678	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104755609_104755612delTGTC								KIF26A (108375 upstream) : C14orf180 (290444 downstream)																							TGCATATCTGTGTCTGTGTGCATG	0.118													5	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106434564	106434564	+	Intron	DEL	G	-	-	rs112670192		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106434564delG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						GGCACTGAGTGGGTGGGCCCT	0.672													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20038610	20038611	+	IGR	INS	-	T	T	rs138274552	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20038610_20038611insT								None (None upstream) : GOLGA6L6 (698483 downstream)																							atatgaagatattccttttcca	0.000													5	3	---	---	---	---	
NIPA2	81614	broad.mit.edu	37	15	23023780	23023783	+	Intron	DEL	AAAG	-	-	rs76737916		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23023780_23023783delAAAG	uc001yux.2	-						NIPA2_uc001yuy.2_Intron|NIPA2_uc001yuz.2_Intron|NIPA2_uc001yva.2_Intron|NIPA2_uc001yvb.2_Intron|NIPA2_uc010ayb.2_Intron	NM_030922	NP_112184	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome							early endosome|integral to membrane|plasma membrane				haematopoietic_and_lymphoid_tissue(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		ATATACATAAAAAGAAAGAAGCTG	0.402													4	2	---	---	---	---	
HERC2	8924	broad.mit.edu	37	15	28479058	28479058	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28479058delA	uc001zbj.2	-							NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		AAGCCTCGCTAGCATGTTAAC	0.423													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	35341829	35341830	+	IGR	DEL	TT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35341829_35341830delTT								ZNF770 (61375 upstream) : LOC723972 (187697 downstream)																							atttttcctcttgtcttctttt	0.173													2	6	---	---	---	---	
RASGRP1	10125	broad.mit.edu	37	15	38792549	38792549	+	Intron	DEL	G	-	-	rs12904148	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38792549delG	uc001zke.3	-						RASGRP1_uc010bbe.2_Intron|RASGRP1_uc010bbf.2_Intron|RASGRP1_uc010bbg.2_Intron|RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		GGttttttttgttttgttttt	0.179													4	2	---	---	---	---	
RASGRP1	10125	broad.mit.edu	37	15	38794760	38794760	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38794760delT	uc001zke.3	-						RASGRP1_uc010bbe.2_Intron|RASGRP1_uc010bbf.2_Intron|RASGRP1_uc010bbg.2_Intron|RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		AACCTGCTCCTTTAGCTGTGG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39085403	39085404	+	IGR	INS	-	TT	TT			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39085403_39085404insTT								C15orf53 (93164 upstream) : C15orf54 (457481 downstream)																							ATACTGTTTTGTTTTTTTTCTT	0.376													4	2	---	---	---	---	
GANC	2595	broad.mit.edu	37	15	42632869	42632870	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42632869_42632870insT	uc001zpi.2	+							NM_198141	NP_937784	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C						carbohydrate metabolic process		carbohydrate binding|maltose alpha-glucosidase activity			central_nervous_system(2)	2		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)		TAAAACAATAATTTTTTTTCTT	0.238													38	25	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	47402758	47402759	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47402758_47402759insT								None (None upstream) : SEMA6D (73644 downstream)																							aatacttgtgattttttcacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	48232539	48232542	+	IGR	DEL	AGAG	-	-	rs145234709		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48232539_48232542delAGAG								SEMA6D (166120 upstream) : SLC24A5 (180627 downstream)																							gaaagagaaaAGagagagagagag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	71117912	71117913	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71117912_71117913insT								UACA (62062 upstream) : LARP6 (5978 downstream)																							CTTTGTGAATAttttttttttt	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	74054590	74054590	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74054590delT								C15orf59 (10774 upstream) : TBC1D21 (111378 downstream)																							ctcttgactcttttttttttt	0.000													3	3	---	---	---	---	
CCDC33	80125	broad.mit.edu	37	15	74560828	74560829	+	Intron	INS	-	G	G	rs138360055	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74560828_74560829insG	uc002axo.2	+						CCDC33_uc002axp.2_Intron	NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5						TCTGGGGTGGTGGTGGGGGTGG	0.614													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	77825705	77825705	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77825705delA								HMG20A (47762 upstream) : LINGO1 (79664 downstream)																							AGAGCCTTCCAAAGGGTGCAG	0.547													4	2	---	---	---	---	
RASGRF1	5923	broad.mit.edu	37	15	79370475	79370476	+	Intron	DEL	GT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79370475_79370476delGT	uc002beq.2	-						RASGRF1_uc002bep.2_Intron|RASGRF1_uc002ber.3_Intron	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine						activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6						AGAGAACCTGgtgtgtgtgtgt	0.455													4	2	---	---	---	---	
FAM108C1	58489	broad.mit.edu	37	15	81015480	81015487	+	Intron	DEL	TGTGTGTG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81015480_81015487delTGTGTGTG	uc002bfu.2	+						FAM108C1_uc002bft.2_Intron	NM_021214	NP_067037	Q6PCB6	F108C_HUMAN	hypothetical protein LOC58489								hydrolase activity				0						tgtgtatatatgtgtgtgtgtgtgtgtg	0.130													2	4	---	---	---	---	
IL16	3603	broad.mit.edu	37	15	81559821	81559822	+	Intron	DEL	AC	-	-	rs67408576		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81559821_81559822delAC	uc002bgh.3	+						IL16_uc002bgc.2_Intron|IL16_uc010blq.1_Intron|IL16_uc002bge.3_Intron|IL16_uc010unp.1_Intron|IL16_uc002bgg.2_Intron	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2						immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4						acatacacagacacacacacac	0.059													4	2	---	---	---	---	
UBE2Q2P1	388165	broad.mit.edu	37	15	85077360	85077360	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85077360delA	uc002bkn.1	-							NR_003661				Homo sapiens cDNA FLJ43276 fis, clone KIDNE2011532, moderately similar to Homo sapiens melanoma-associated chondroitin sulfate proteoglycan 4.												0						tttttaaactaaaaaaaaaaa	0.159													4	3	---	---	---	---	
AKAP13	11214	broad.mit.edu	37	15	86111173	86111176	+	Intron	DEL	GTGT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86111173_86111176delGTGT	uc002blv.1	+						AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						GCCCAAAGAGgtgtgtgtgtgtgt	0.225													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	89460255	89460256	+	IGR	INS	-	A	A	rs74708859		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89460255_89460256insA								MFGE8 (3592 upstream) : ABHD2 (171125 downstream)																							gacttcgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
FANCI	55215	broad.mit.edu	37	15	89837871	89837872	+	Intron	INS	-	AACC	AACC	rs142174023	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89837871_89837872insAACC	uc010bnp.1	+						FANCI_uc002bnm.1_Intron|FANCI_uc002bnn.1_Intron|FANCI_uc002bnp.1_Intron|FANCI_uc002bnq.1_Intron	NM_001113378	NP_001106849	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I isoform						cell cycle|DNA repair	nucleoplasm	protein binding			ovary(2)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)					GGGACAAAAAAAAACCTAAAAG	0.248								Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				2	4	---	---	---	---	
CRTC3	64784	broad.mit.edu	37	15	91094081	91094081	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91094081delG	uc002bpp.2	+						CRTC3_uc002bpn.2_Intron|CRTC3_uc002bpo.2_Intron	NM_022769	NP_073606	Q6UUV7	CRTC3_HUMAN	transducer of regulated CREB protein 3 isoform						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus			CRTC3/MAML2(26)	salivary_gland(26)|ovary(1)	27	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			CGGGTTTGTAGGGAAGGATGA	0.542			T	MAML2	salivary gland mucoepidermoid								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	91593443	91593443	+	IGR	DEL	T	-	-	rs34442988		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91593443delT								VPS33B (27610 upstream) : SV2B (49740 downstream)																							GTCttttttcttttttttttt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94744022	94744022	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94744022delC								None (None upstream) : MCTP2 (30779 downstream)																							tgatttattaccacaaaagga	0.000													4	2	---	---	---	---	
TTC23	64927	broad.mit.edu	37	15	99775146	99775146	+	Intron	DEL	A	-	-	rs34271192		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99775146delA	uc002bur.2	-						TTC23_uc002bus.2_Intron|TTC23_uc002but.2_Intron|TTC23_uc002buu.2_Intron|TTC23_uc002buv.2_Intron|TTC23_uc002bux.2_Intron|TTC23_uc002buw.2_Intron|TTC23_uc010boq.2_Intron|TTC23_uc002buy.2_Intron|TTC23_uc010bor.2_Intron|TTC23_uc002buz.2_Intron	NM_022905	NP_075056	Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23								binding				0	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)			ggcagGGTTTAAAAAAAAAAA	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102047371	102047372	+	IGR	DEL	CA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102047371_102047372delCA								PCSK6 (17184 upstream) : TM2D3 (125808 downstream)																							actaatacttcacacacacaca	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	3180183	3180184	+	Intron	INS	-	T	T	rs71391802		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3180183_3180184insT	uc002cuc.2	-											Homo sapiens, clone IMAGE:3862054, mRNA.																		tcgcaTAtttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	10446852	10446853	+	IGR	DEL	TG	-	-	rs57588473		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10446852_10446853delTG								GRIN2A (170241 upstream) : ATF7IP2 (33059 downstream)																							CTtttttttttgttttgttttg	0.084													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12305415	12305416	+	Intron	DEL	GT	-	-	rs76518697		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12305415_12305416delGT	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						accaataggggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12403975	12403976	+	Intron	INS	-	CACACACATG	CACACACATG	rs150257908	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12403975_12403976insCACACACATG	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						atacacgtgcacgcacacatgc	0.213													2	4	---	---	---	---	
NDE1	54820	broad.mit.edu	37	16	15794298	15794298	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15794298delT	uc010uzy.1	+						NDE1_uc002dds.2_Intron	NM_001143979	NP_001137451	Q9NXR1	NDE1_HUMAN	nuclear distribution gene E homolog 1						cell differentiation|cell division|centrosome duplication|establishment of chromosome localization|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|mitotic prometaphase|nervous system development	cleavage furrow|condensed chromosome kinetochore|cytosol|microtubule|spindle pole centrosome	microtubule binding			ovary(1)	1						CTGATTGGtcttttttttttt	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20176016	20176016	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20176016delC								GPR139 (90916 upstream) : GP2 (145796 downstream)																							cctctttcttccatcctttcc	0.045													4	2	---	---	---	---	
COG7	91949	broad.mit.edu	37	16	23451758	23451758	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23451758delA	uc002dlo.2	-							NM_153603	NP_705831	P83436	COG7_HUMAN	component of oligomeric golgi complex 7						intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)		agagctaaggaaaaaaattag	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	23728294	23728294	+	IGR	DEL	A	-	-	rs145039082		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23728294delA								ERN2 (3473 upstream) : CHP2 (37654 downstream)																							actctgtctcaaaaaaaaaaa	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	24737893	24737893	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24737893delG								RBBP6 (153712 upstream) : TNRC6A (3156 downstream)																							cagttttgcaggagggatggg	0.000													4	2	---	---	---	---	
SLC5A11	115584	broad.mit.edu	37	16	24858616	24858617	+	Intron	INS	-	TTTC	TTTC	rs143879683	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24858616_24858617insTTTC	uc002dmu.2	+						SLC5A11_uc002dms.2_Intron|SLC5A11_uc010vcd.1_Intron|SLC5A11_uc002dmt.2_Intron|SLC5A11_uc010vce.1_Intron|SLC5A11_uc010bxt.2_Intron	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose						apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)		cttttcccttttttctttcttt	0.005													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26379142	26379142	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26379142delT								HS3ST4 (230134 upstream) : C16orf82 (699077 downstream)																							agtaaaggcataaaatcaagc	0.000													4	2	---	---	---	---	
SBK1	388228	broad.mit.edu	37	16	28301091	28301091	+	5'Flank	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28301091delA	uc002dpd.2	+						uc002dpc.1_Intron	NM_001024401	NP_001019572	Q52WX2	SBK1_HUMAN	SH3-binding kinase 1							cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)|kidney(1)	2						tccatctcagaaaaaaaaaaa	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28971859	28971860	+	Intron	DEL	CT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28971859_28971860delCT	uc010vct.1	-						NFATC2IP_uc002drt.2_Intron|NFATC2IP_uc002dru.2_Intron|NFATC2IP_uc002drv.2_Intron|NFATC2IP_uc010vdh.1_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		gacaaaattcctctctctctct	0.000													4	2	---	---	---	---	
CDIPT	10423	broad.mit.edu	37	16	29870379	29870379	+	3'UTR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29870379delC	uc002dum.2	-	6					uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|CDIPT_uc002duk.2_3'UTR|CDIPT_uc002dul.2_3'UTR|CDIPT_uc002dun.2_3'UTR	NM_006319	NP_006310	O14735	CDIPT_HUMAN	CDP-diacylglycerol-inositol							endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity|phosphatidylinositol transporter activity				0						GAGAGGCTGACCCCCATCCCA	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	30929989	30930013	+	IGR	DEL	CTTCTTCTCCTTCTCCTTCTTCTTC	-	-	rs71151428		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30929989_30930013delCTTCTTCTCCTTCTCCTTCTTCTTC								CTF1 (15109 upstream) : NCRNA00095 (627 downstream)																							ccGCcttcttcttcttctccttctccttcttcttccttcttctcc	0.040													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	31183235	31183236	+	IGR	DEL	AG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31183235_31183236delAG								PRSS36 (21820 upstream) : FUS (8217 downstream)																							cagccgaggcagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32296285	32296286	+	IGR	INS	-	AA	AA			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32296285_32296286insAA								HERC2P4 (132411 upstream) : TP53TG3B (388555 downstream)																							atgatgaaatgatgaaataatg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32556862	32556863	+	IGR	INS	-	T	T	rs139315292		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32556862_32556863insT								HERC2P4 (392988 upstream) : TP53TG3B (127978 downstream)																							tggaaacactgatttgtagtat	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	35260084	35260085	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35260084_35260085insT								LOC146481 (545117 upstream) : None (None downstream)																							gagacctattgggaaaaggaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46466174	46466174	+	IGR	DEL	C	-	-	rs75817075		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46466174delC								None (None upstream) : ANKRD26P1 (37075 downstream)																							ATTGGCCATACGAAAAAATTG	0.274													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	47849570	47849570	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47849570delC								PHKB (114137 upstream) : ABCC12 (267314 downstream)																							atactgttttccatggggttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51525921	51525922	+	IGR	INS	-	T	T	rs149900800		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51525921_51525922insT								SALL1 (340738 upstream) : TOX3 (945996 downstream)																							TTCTACTTTAAttttttttttt	0.144													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54816965	54816965	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54816965delC								IRX3 (496587 upstream) : IRX5 (148146 downstream)																							atgagaaataccatttgaccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55428823	55428823	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55428823delA								IRX6 (64152 upstream) : MMP2 (84258 downstream)																							tcaaaagaagaaaaaaaaaaa	0.050													4	2	---	---	---	---	
SLC38A7	55238	broad.mit.edu	37	16	58716540	58716541	+	Intron	DEL	TT	-	-	rs11292515		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58716540_58716541delTT	uc002eod.1	-						SLC38A7_uc002eob.1_Intron|SLC38A7_uc002eoc.1_Intron|SLC38A7_uc010vil.1_Intron|SLC38A7_uc002eoe.1_Intron	NM_018231	NP_060701	Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7						amino acid transport|sodium ion transport	integral to membrane				ovary(1)	1						acttttAAAAtttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58920660	58920662	+	IGR	DEL	CAA	-	-	rs74765537		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58920660_58920662delCAA								GOT2 (152414 upstream) : None (None downstream)																							acagcagcagcaacaacaacaac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59760423	59760423	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59760423delA								GOT2 (992177 upstream) : None (None downstream)																							AGAGGAAGGTAAAAAAAAAAA	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66907788	66907789	+	IGR	INS	-	TCC	TCC	rs149353229	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66907788_66907789insTCC								CA7 (19741 upstream) : PDP2 (6647 downstream)																							ctcctcctccttcctcctcctc	0.000													1	5	---	---	---	---	
CALB2	794	broad.mit.edu	37	16	71413395	71413395	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71413395delA	uc002faa.3	+						CALB2_uc010vme.1_Intron|CALB2_uc002fac.3_Intron	NM_001740	NP_001731	P22676	CALB2_HUMAN	calbindin 2 isoform 1								calcium ion binding				0		Ovarian(137;0.125)				tcaaccaaaTATATTACTAAT	0.229													2	4	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	83623549	83623549	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83623549delG	uc002fgx.2	+						CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CTTAGGAGGTGGGGGCGGGAA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86887565	86887567	+	IGR	DEL	AGA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86887565_86887567delAGA								FOXL1 (272262 upstream) : FBXO31 (475377 downstream)																							aaacaaaaacagaagaagaagaa	0.177													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88465054	88465055	+	IGR	INS	-	G	G	rs147534677	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88465054_88465055insG								BANP (354131 upstream) : ZNF469 (28824 downstream)																							CCACAGATGAAGGGGGGGTGTG	0.554													2	4	---	---	---	---	
ZC3H18	124245	broad.mit.edu	37	16	88644943	88644944	+	Intron	INS	-	T	T	rs149000114	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88644943_88644944insT	uc002fky.2	+						ZC3H18_uc010voy.1_Intron|ZC3H18_uc010voz.1_Intron|ZC3H18_uc010vpa.1_Intron	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18							nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		GGTTTTTGTTGTTTTTTTTTTG	0.480													4	2	---	---	---	---	
CBFA2T3	863	broad.mit.edu	37	16	88992308	88992308	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88992308delA	uc002fmm.1	-						CBFA2T3_uc002fml.1_Intron|CBFA2T3_uc010cif.1_Intron|CBFA2T3_uc002fmn.1_Intron	NM_005187	NP_005178	O75081	MTG16_HUMAN	myeloid translocation gene on chromosome 16						cell proliferation|granulocyte differentiation	Golgi membrane|nucleolus|nucleoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(3)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0275)		ACGCCATGTGAACGTTTTTAC	0.582			T	RUNX1	AML								4	2	---	---	---	---	
CBFA2T3	863	broad.mit.edu	37	16	89017815	89017815	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89017815delT	uc002fmm.1	-						CBFA2T3_uc002fmn.1_Intron	NM_005187	NP_005178	O75081	MTG16_HUMAN	myeloid translocation gene on chromosome 16						cell proliferation|granulocyte differentiation	Golgi membrane|nucleolus|nucleoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(3)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0275)		AGAGGTATCATTAGCTGCGTC	0.343			T	RUNX1	AML								4	2	---	---	---	---	
NXN	64359	broad.mit.edu	37	17	852066	852066	+	Intron	DEL	G	-	-	rs9747534		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:852066delG	uc002fsa.2	-							NM_022463	NP_071908	Q6DKJ4	NXN_HUMAN	nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		ctctccccgcggcctcctcct	0.249													4	2	---	---	---	---	
CRK	1398	broad.mit.edu	37	17	1362533	1362533	+	5'Flank	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1362533delA	uc002fsl.2	-						CRK_uc002fsm.2_5'Flank	NM_016823	NP_058431	P46108	CRK_HUMAN	v-crk sarcoma virus CT10 oncogene homolog						actin cytoskeleton organization|activation of MAPKK activity|blood coagulation|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of transcription from RNA polymerase II promoter	cytosol|endosome|nucleus|plasma membrane	protein binding|SH2 domain binding			lung(2)|central_nervous_system(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.083)		tccgtctcagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SCARF1	8578	broad.mit.edu	37	17	1538677	1538678	+	Frame_Shift_Ins	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1538677_1538678insT	uc002fsz.1	-	11	1917_1918	c.1867_1868insA	c.(1867-1869)GCGfs	p.A623fs	SCARF1_uc002fsy.1_3'UTR|SCARF1_uc002fta.1_RNA|SCARF1_uc010cjv.1_Frame_Shift_Ins_p.A537fs	NM_003693	NP_003684	Q14162	SREC_HUMAN	scavenger receptor class F, member 1 isoform 1	623	Gly-rich.|Cytoplasmic (Potential).				cell adhesion|neuron remodeling|positive regulation of axon regeneration|receptor-mediated endocytosis	integral to membrane	low-density lipoprotein particle binding|scavenger receptor activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ACCCGACTGCGCCCCCCGGGAG	0.668													6	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	2656110	2656111	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2656110_2656111insT								MIR1253 (4634 upstream) : RAP1GAP2 (43621 downstream)																							TTTCCttttccttttttttttt	0.025													3	3	---	---	---	---	
ATP2A3	489	broad.mit.edu	37	17	3856287	3856287	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3856287delC	uc002fxb.1	-						ATP2A3_uc002fwx.1_Intron|ATP2A3_uc002fwy.1_Intron|ATP2A3_uc002fwz.1_Intron|ATP2A3_uc002fxa.1_Intron|ATP2A3_uc002fxc.1_Intron|ATP2A3_uc002fxd.1_Intron	NM_174955	NP_777615	Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous isoform b						ATP biosynthetic process|platelet activation	integral to membrane|nuclear membrane|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			ovary(3)|breast(1)|central_nervous_system(1)	5				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		aaagcccccacccccaccccg	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6112067	6112068	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6112067_6112068insA								WSCD1 (84322 upstream) : AIPL1 (214992 downstream)																							cccaaaaaaacaaaaaaaaaaa	0.104													4	2	---	---	---	---	
TP53	7157	broad.mit.edu	37	17	7577550	7577550	+	Frame_Shift_Del	DEL	C	-	-	rs28934572		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577550delC	uc002gim.2	-	7	925	c.731delG	c.(730-732)GGCfs	p.G244fs	TP53_uc002gig.1_Frame_Shift_Del_p.G244fs|TP53_uc002gih.2_Frame_Shift_Del_p.G244fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.G112fs|TP53_uc010cng.1_Frame_Shift_Del_p.G112fs|TP53_uc002gii.1_Frame_Shift_Del_p.G112fs|TP53_uc010cnh.1_Frame_Shift_Del_p.G244fs|TP53_uc010cni.1_Frame_Shift_Del_p.G244fs|TP53_uc002gij.2_Frame_Shift_Del_p.G244fs|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Frame_Shift_Del_p.G151fs|TP53_uc002gio.2_Frame_Shift_Del_p.G112fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	244	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		G -> A (in sporadic cancers; somatic mutation).|G -> S (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|MG -> IC (in a sporadic cancer; somatic mutation).|G -> E (in a sporadic cancer; somatic mutation).|G -> C (in sporadic cancers; somatic mutation).|MG -> IS (in a sporadic cancer; somatic mutation).|G -> V (in LFS; germline mutation and in sporadic cancers; 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.G244S(35)|p.G244C(34)|p.G244D(32)|p.G244V(14)|p.G244G(13)|p.G244A(9)|p.0?(7)|p.G244fs*3(5)|p.G244R(3)|p.M243_G244>IC(1)|p.G244fs*19(1)|p.G244fs*17(1)|p.M243fs*18(1)|p.G244E(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.C242_M246>L(1)|p.G244del(1)|p.C238_M246delCNSSCMGGM(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)		GTTCATGCCGCCCATGCAGGA	0.577		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)			30	22	---	---	---	---	
USP43	124739	broad.mit.edu	37	17	9578747	9578747	+	Intron	DEL	A	-	-	rs74847054		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9578747delA	uc010cod.2	+						USP43_uc002gma.3_Intron|USP43_uc010vva.1_Intron|USP43_uc010coe.2_Intron	NM_153210	NP_694942	Q70EL4	UBP43_HUMAN	ubiquitin specific protease 43						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						GGAAGATGAGAAAAAAAAAGA	0.408													4	2	---	---	---	---	
NCOR1	9611	broad.mit.edu	37	17	16066805	16066805	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16066805delA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpp.1_Intron|NCOR1_uc002gpr.2_Intron|NCOR1_uc002gps.1_Intron|NCOR1_uc010coz.1_Intron|NCOR1_uc010cpb.1_Intron|NCOR1_uc010cpa.1_Intron	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ggatggctatatttttttaaa	0.000													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	17507540	17507540	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17507540delT								PEMT (12546 upstream) : RAI1 (77247 downstream)																							TGACCCCAGGTTCCTGAGTTA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21343818	21343819	+	IGR	INS	-	G	G	rs151017738	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21343818_21343819insG								KCNJ12 (20639 upstream) : C17orf51 (87753 downstream)																							TTGATCCTCACTGGTGTTCTTC	0.460													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21547444	21547445	+	IGR	INS	-	TT	TT			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21547444_21547445insTT								C17orf51 (69713 upstream) : FAM27L (277925 downstream)																							tttttaaaatgtttttttgctt	0.000													7	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21553751	21553752	+	IGR	INS	-	TAG	TAG			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21553751_21553752insTAG								C17orf51 (76020 upstream) : FAM27L (271618 downstream)																							gatggtaaggatggtgatgagg	0.000													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21555329	21555332	+	IGR	DEL	AAAC	-	-	rs144484861		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21555329_21555332delAAAC								C17orf51 (77598 upstream) : FAM27L (270038 downstream)																							tttaaaaaataaaCAAACTATTGG	0.338													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21558197	21558198	+	IGR	INS	-	C	C	rs112684425		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21558197_21558198insC								C17orf51 (80466 upstream) : FAM27L (267172 downstream)																							GAGGTGGATATGGGCTCCAGGT	0.599													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21563646	21563646	+	IGR	DEL	T	-	-	rs9901273	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21563646delT								C17orf51 (85915 upstream) : FAM27L (261724 downstream)																							TCCAAAAAAATAAAAGGATAG	0.358													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22210807	22210807	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22210807delT								FLJ36000 (297737 upstream) : None (None downstream)																							ggctgatatctggaaagagga	0.040													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25285874	25285875	+	IGR	INS	-	CTCCTT	CTCCTT	rs73984730	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25285874_25285875insCTCCTT								None (None upstream) : WSB1 (335231 downstream)																							tccccctcctctttacttttca	0.040													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25293950	25293951	+	IGR	INS	-	ACA	ACA			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25293950_25293951insACA								None (None upstream) : WSB1 (327155 downstream)																							gaaatgaaatgagatgaaaagg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25298950	25298950	+	IGR	DEL	A	-	-	rs77602219		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25298950delA								None (None upstream) : WSB1 (322156 downstream)																							gttgataaatatttttcttgg	0.000													13	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25319139	25319140	+	IGR	INS	-	AAG	AAG	rs144466474	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25319139_25319140insAAG								None (None upstream) : WSB1 (301966 downstream)																							CTCCACACAATAAGGTCACAGG	0.599													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	30257458	30257458	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30257458delT								UTP6 (28729 upstream) : SUZ12 (6586 downstream)																							GCAAAACTAATTTTTTTTTTC	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33074425	33074427	+	IGR	DEL	AAG	-	-	rs71865739		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33074425_33074427delAAG								TMEM132E (108089 upstream) : CCT6B (180513 downstream)																							ctagtttcttaagaaggaatcta	0.000													1	5	---	---	---	---	
ACACA	31	broad.mit.edu	37	17	35468984	35468985	+	Intron	INS	-	CTAT	CTAT	rs138946467	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35468984_35468985insCTAT	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuy.2_Intron|ACACA_uc010wdb.1_Intron|ACACA_uc010wdc.1_Intron	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	CTTCATCAATActatctatcta	0.366													2	4	---	---	---	---	
TADA2A	6871	broad.mit.edu	37	17	35811133	35811133	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35811133delT	uc002hnt.2	+						TADA2A_uc002hnu.1_Intron|TADA2A_uc002hnv.2_Intron|TADA2A_uc010wdd.1_Intron|TADA2A_uc002hnw.2_Intron|TADA2A_uc010cvb.2_Intron	NM_001488	NP_001479	O75478	TAD2A_HUMAN	transcriptional adaptor 2A isoform a						histone H3 acetylation|transcription from RNA polymerase II promoter	chromosome|PCAF complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|zinc ion binding			breast(3)|skin(1)	4						ATTCAGAGGCtttttttttta	0.179													4	2	---	---	---	---	
DDX52	11056	broad.mit.edu	37	17	36001474	36001474	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36001474delA	uc002hoi.1	-						DDX52_uc002hoh.1_Intron|DDX52_uc002hoj.1_Intron	NM_007010	NP_008941	Q9Y2R4	DDX52_HUMAN	ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)				agtaaaatataaaattgtttc	0.000													4	2	---	---	---	---	
GPATCH8	23131	broad.mit.edu	37	17	42502062	42502062	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42502062delA	uc002igw.1	-						GPATCH8_uc002igv.1_Intron|GPATCH8_uc010wiz.1_Intron	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8							intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)|skin(1)	4		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GTCTTCAAATAAACAAATGTT	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43074017	43074017	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43074017delC								C1QL1 (28373 upstream) : DCAKD (26689 downstream)																							GGACTGTTGTCCAAGAAATCA	0.438													4	2	---	---	---	---	
HOXB13	10481	broad.mit.edu	37	17	46804808	46804809	+	Intron	INS	-	AC	AC	rs139887310	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46804808_46804809insAC	uc002ioa.2	-						hsa-mir-3185|MI0014227_5'Flank	NM_006361	NP_006352	Q92826	HXB13_HUMAN	homeobox B13						angiogenesis|epidermis development|response to wounding		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						tacatgcgcatacacacacaca	0.371													4	2	---	---	---	---	
PHOSPHO1	162466	broad.mit.edu	37	17	47306352	47306355	+	Intron	DEL	ACAA	-	-	rs72221486		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47306352_47306355delACAA	uc010wlv.1	-						PHOSPHO1_uc002ios.2_Intron	NM_178500	NP_848595	Q8TCT1	PHOP1_HUMAN	phosphatase, orphan 1 isoform 2						regulation of bone mineralization		metal ion binding|phosphoethanolamine/phosphocholine phosphatase activity				0			Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)		Choline(DB00122)	acacacacacacaAAACTCCTCAT	0.201													2	4	---	---	---	---	
ACSF2	80221	broad.mit.edu	37	17	48543624	48543625	+	Intron	INS	-	T	T	rs147047448		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48543624_48543625insT	uc002iqu.2	+						ACSF2_uc010wml.1_Intron|ACSF2_uc010wmm.1_Intron|ACSF2_uc010wmn.1_Intron|ACSF2_uc010wmo.1_Intron|CHAD_uc010dbr.2_Intron|CHAD_uc010dbs.2_Intron|ACSF2_uc010dbt.1_5'Flank	NM_025149	NP_079425	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2 precursor						fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			atttttttgtatttttttagta	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	49418506	49418507	+	Intron	INS	-	A	A	rs113719100		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49418506_49418507insA	uc002itt.1	+											Homo sapiens cDNA FLJ42842 fis, clone BRCOC2007034.																		GTGATTACTGCAAAAAAAAAAA	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53885976	53885976	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53885976delG								PCTP (31229 upstream) : ANKFN1 (344860 downstream)																							CACAGAGTTTGGATGTTCGCA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53907050	53907051	+	IGR	INS	-	AC	AC	rs139693446	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53907050_53907051insAC								PCTP (52303 upstream) : ANKFN1 (323785 downstream)																							taataatttaaacacacacaca	0.109													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	56094839	56094839	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56094839delA								SFRS1 (10132 upstream) : DYNLL2 (65941 downstream)																							actctgtctcaaaaaaaaaaa	0.134													4	3	---	---	---	---	
PRR11	55771	broad.mit.edu	37	17	57276742	57276742	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57276742delG	uc002ixf.1	+						PRR11_uc002ixg.1_Intron	NM_018304	NP_060774	Q96HE9	PRR11_HUMAN	proline rich 11											ovary(2)	2	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					aacacagagagggagcccaat	0.080													4	2	---	---	---	---	
TUBD1	51174	broad.mit.edu	37	17	57959446	57959446	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57959446delT	uc002ixw.1	-						TUBD1_uc010ddf.1_Intron|TUBD1_uc010ddg.1_Intron|TUBD1_uc010ddh.1_Intron|TUBD1_uc010wok.1_Intron|TUBD1_uc002ixx.1_Intron|TUBD1_uc010wol.1_Intron|TUBD1_uc010ddi.1_Intron	NM_016261	NP_057345	Q9UJT1	TBD_HUMAN	delta-tubulin						cell differentiation|microtubule-based movement|multicellular organismal development|protein polymerization|spermatogenesis	centriole|microtubule|nucleus	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)			tagcaacttcttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	61978838	61978839	+	IGR	INS	-	T	T	rs147941855		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61978838_61978839insT								CSH2 (4851 upstream) : CSHL1 (8126 downstream)																							ctctctctctcttttttttttt	0.203													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	62219049	62219049	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62219049delG								ERN1 (11547 upstream) : SNORD104 (4389 downstream)																							agcggggcatggtagtgcact	0.000													4	2	---	---	---	---	
RGS9	8787	broad.mit.edu	37	17	63161589	63161590	+	Intron	DEL	AA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63161589_63161590delAA	uc002jfe.2	+						RGS9_uc010dem.2_Intron|RGS9_uc002jfd.2_Intron|RGS9_uc002jff.2_Intron	NM_003835	NP_003826	O75916	RGS9_HUMAN	regulator of G-protein signaling 9 isoform 1						intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			ovary(2)|skin(2)	4						GTTGGCCCATAAAGTAGTCATT	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	63291909	63291909	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63291909delA								RGS9 (68090 upstream) : AXIN2 (232776 downstream)																							agtatgtgtgaagggctaaat	0.264													4	2	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64736272	64736273	+	Intron	DEL	GG	-	-	rs151193692		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64736272_64736273delGG	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)	ggtggtttgaggggggagattc	0.386													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	64895264	64895264	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64895264delT								CACNG5 (13908 upstream) : CACNG4 (65749 downstream)																							ACAACTTTAGTTTTTGCCTGC	0.527													4	2	---	---	---	---	
CACNG1	786	broad.mit.edu	37	17	65051153	65051153	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65051153delC	uc002jfu.2	+							NM_000727	NP_000718	Q06432	CCG1_HUMAN	voltage-dependent calcium channel gamma-1						muscle contraction	voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(12;1.04e-10)|Breast(2;1.45e-16)|all_epithelial(3;4.81e-12)				Amlodipine(DB00381)|Diltiazem(DB00343)|Ibutilide(DB00308)|Lercanidipine(DB00528)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Nitrendipine(DB01054)|Verapamil(DB00661)	ATGGTGTGGTCCCTAACGAGC	0.348													37	21	---	---	---	---	
HELZ	9931	broad.mit.edu	37	17	65173098	65173099	+	Intron	DEL	TT	-	-	rs113989752		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65173098_65173099delTT	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TCAGtttctctttttttttttt	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66046336	66046337	+	IGR	DEL	CT	-	-	rs141229293	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66046336_66046337delCT								KPNA2 (3367 upstream) : LOC651250 (51359 downstream)																							ctctctctcactctttcttttt	0.050													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66065639	66065639	+	IGR	DEL	T	-	-	rs33997644		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66065639delT								KPNA2 (22670 upstream) : LOC651250 (32057 downstream)																							aaaaaaaaaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66764552	66764553	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66764552_66764553insA								FAM20A (167457 upstream) : ABCA8 (98880 downstream)																							aagaaagaaagaaaaAaaagaa	0.099													6	3	---	---	---	---	
MAP2K6	5608	broad.mit.edu	37	17	67506943	67506943	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67506943delT	uc002jij.2	+						MAP2K6_uc002jii.2_Intron|MAP2K6_uc002jik.2_Intron	NM_002758	NP_002749	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6						activation of MAPK activity|cell cycle arrest|DNA damage induced protein phosphorylation|innate immune response|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of muscle cell differentiation|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|pancreas(1)	5	Breast(10;6.05e-10)					tgtgacatccttttttttttt	0.000													3	3	---	---	---	---	
SLC39A11	201266	broad.mit.edu	37	17	70924181	70924182	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70924181_70924182insA	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						CTGATTGCTCCAAAAAAAAAGA	0.371													4	2	---	---	---	---	
SLC39A11	201266	broad.mit.edu	37	17	70937695	70937696	+	Intron	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70937695_70937696insT	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						TCAGGACTGTGTTTTTTTTTTT	0.347													3	3	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71342547	71342547	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71342547delT	uc010dfm.2	-						SDK2_uc002jjt.3_Intron	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						AGTATATACATTTTTTTTTTT	0.378													4	2	---	---	---	---	
DNAI2	64446	broad.mit.edu	37	17	72298707	72298707	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72298707delA	uc002jkf.2	+						DNAI2_uc002jkg.2_Intron|DNAI2_uc010dfp.2_Intron|DNAI2_uc002jki.2_5'Flank	NM_023036	NP_075462	Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate polypeptide 2						cilium assembly	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	microtubule motor activity			ovary(2)|central_nervous_system(1)	3						actccatctcaaaaaaaaaac	0.159									Kartagener_syndrome				4	2	---	---	---	---	
CD300LF	146722	broad.mit.edu	37	17	72705882	72705882	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72705882delT	uc002jlg.2	-						RAB37_uc002jlc.2_Intron|RAB37_uc010dfu.2_Intron|RAB37_uc002jld.2_Intron|CD300LF_uc002jlh.2_Intron|CD300LF_uc002jli.2_Intron|CD300LF_uc010wra.1_Intron	NM_139018	NP_620587	Q8TDQ1	CLM1_HUMAN	NK inhibitory receptor precursor							integral to membrane|plasma membrane	receptor activity			upper_aerodigestive_tract(1)	1						caggctagtattttttttttt	0.000													4	2	---	---	---	---	
KIAA0195	9772	broad.mit.edu	37	17	73478434	73478434	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73478434delA	uc002jnz.3	+						KIAA0195_uc010wsa.1_Intron	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772						ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			ctcaaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SEC14L1	6397	broad.mit.edu	37	17	75169988	75169988	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75169988delT	uc002jto.2	+						SEC14L1_uc010dhc.2_Intron|SEC14L1_uc010wth.1_Intron|SEC14L1_uc002jtm.2_Intron	NM_003003	NP_002994	Q92503	S14L1_HUMAN	SEC14 (S. cerevisiae)-like 1 isoform a						transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2						tctttttttcttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75708000	75708001	+	IGR	INS	-	T	T	rs138157815	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75708000_75708001insT								SEPT9 (211324 upstream) : FLJ45079 (167108 downstream)																							ctgtatctatctttttttacct	0.000													4	3	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77240840	77240842	+	Intron	DEL	CTT	-	-	rs60766552		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77240840_77240842delCTT	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)			tccttccttccttttcttccttc	0.108													1	8	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77305188	77305189	+	Intron	INS	-	AA	AA	rs34845518		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77305188_77305189insAA	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)			gactctgtctcaaaaaaaaaaa	0.054													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	78978830	78978831	+	3'UTR	DEL	TG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78978830_78978831delTG	uc002jyx.1	+	1										Homo sapiens clone PP552 unknown mRNA.																		gttTGTTGATtgtgtgtgtgtg	0.010													4	2	---	---	---	---	
COLEC12	81035	broad.mit.edu	37	18	410120	410120	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:410120delG	uc002kkm.2	-							NM_130386	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12						carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				ccaagcacaTGGTAGACACTT	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	2240234	2240235	+	IGR	DEL	AC	-	-	rs146032316		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2240234_2240235delAC								C18orf2 (833053 upstream) : METTL4 (297290 downstream)																							ATTATTTAAAacacacacacac	0.322													4	4	---	---	---	---	
L3MBTL4	91133	broad.mit.edu	37	18	6238531	6238532	+	Intron	INS	-	A	A	rs75625739		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6238531_6238532insA	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron|L3MBTL4_uc002kmy.3_Intron	NM_173464	NP_775735	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)				gattccatctcaaaaaaaaaaa	0.173													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	9638334	9638334	+	IGR	DEL	A	-	-	rs36029103		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9638334delA								PPP4R1 (23734 upstream) : RAB31 (69894 downstream)																							gctctgacagaaggaagcaga	0.095													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10512954	10512962	+	IGR	DEL	GTGTGTGTA	-	-	rs147841280	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10512954_10512962delGTGTGTGTA								APCDD1 (24257 upstream) : NAPG (12911 downstream)																							gtgtgtgtgtgtgtgtgtagtgtgtgtct	0.211													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	12924073	12924074	+	IGR	DEL	AC	-	-	rs35717634		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12924073_12924074delAC								PTPN2 (39739 upstream) : SEH1L (23909 downstream)																							AATcacaaatacacacacacac	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15098676	15098676	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15098676delT								ANKRD30B (245939 upstream) : LOC644669 (214879 downstream)																							ATCACAATGATTATAAGAGGG	0.184													4	2	---	---	---	---	
ROCK1	6093	broad.mit.edu	37	18	18548273	18548273	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18548273delT	uc002kte.2	-							NM_005406	NP_005397	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein						actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)					ATCCTAtttcttttttttttt	0.164													3	3	---	---	---	---	
TTC39C	125488	broad.mit.edu	37	18	21602725	21602726	+	Intron	DEL	TG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21602725_21602726delTG	uc002kuw.2	+						TTC39C_uc002kuu.2_Intron	NM_001135993	NP_001129465	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C isoform 1								binding			ovary(1)	1						TCCGATGTCCTGTGATGTGGCC	0.540													4	2	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34300698	34300699	+	Intron	INS	-	CTCCTC	CTCCTC	rs138482898	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34300698_34300699insCTCCTC	uc002kzt.1	+						FHOD3_uc002kzs.1_Intron|FHOD3_uc010dmz.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				tccttcttcttctcctcctcct	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	42155562	42155563	+	IGR	INS	-	AATG	AATG	rs138763238	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42155562_42155563insAATG								None (None upstream) : SETBP1 (104575 downstream)																							ttcataatttaaatgaatgaat	0.010													4	2	---	---	---	---	
MYO5B	4645	broad.mit.edu	37	18	47588536	47588536	+	Intron	DEL	A	-	-	rs79311754		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47588536delA	uc002leb.2	-						MYO5B_uc002lec.1_Intron	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		ATTACACATGAAAAAAAAAAA	0.348													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	52221528	52221528	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52221528delT								C18orf54 (313125 upstream) : C18orf26 (33460 downstream)																							cttatctagattttttttttc	0.030													4	2	---	---	---	---	
ZNF532	55205	broad.mit.edu	37	18	56589341	56589341	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56589341delA	uc002lho.2	+						ZNF532_uc002lhp.2_Intron|ZNF532_uc010xeg.1_Intron|ZNF532_uc002lhr.2_Intron|ZNF532_uc002lhs.2_Intron	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN	zinc finger protein 532						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2						ccctgtctccaaaaaaaaaaa	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76776695	76776696	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76776695_76776696insA								SALL3 (18504 upstream) : ATP9B (52701 downstream)																							GATCAGTCCCCTCCTTACTACT	0.475													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	481338	481338	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:481338delG								ODF3L2 (6355 upstream) : MADCAM1 (15152 downstream)																							ggatgatggagaaggatgatg	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	5154358	5154358	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5154358delG								KDM4B (752 upstream) : PTPRS (4148 downstream)																							tgattgctgtggggaggagac	0.000													4	2	---	---	---	---	
PTPRS	5802	broad.mit.edu	37	19	5279197	5279197	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5279197delA	uc002mbv.2	-						PTPRS_uc002mbu.1_Intron|PTPRS_uc010xin.1_Intron|PTPRS_uc002mbw.2_Intron|PTPRS_uc002mbx.2_Intron|PTPRS_uc002mby.2_Intron|PTPRS_uc002mbz.1_Intron	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,						cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)		actctgtctcaaaaaaaaaag	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	5859983	5859984	+	IGR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5859983_5859984insA								FUT3 (8498 upstream) : FUT5 (5854 downstream)																							ctcacaaaaacaaaacaaaaca	0.218													4	2	---	---	---	---	
RFX2	5990	broad.mit.edu	37	19	6001479	6001479	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6001479delG	uc002meb.2	-						RFX2_uc002mec.2_Intron	NM_000635	NP_000626	P48378	RFX2_HUMAN	regulatory factor X2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(4)|ovary(1)|skin(1)	6						attttccccagggtcgtctca	0.025													4	2	---	---	---	---	
VAV1	7409	broad.mit.edu	37	19	6776171	6776178	+	Intron	DEL	CCATCCAT	-	-	rs71862172		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6776171_6776178delCCATCCAT	uc002mfu.1	+						VAV1_uc010xjh.1_Intron|VAV1_uc010dva.1_Intron	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16						atctatccacccatccatccatccatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	9140607	9140607	+	IGR	DEL	A	-	-	rs112759960		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9140607delA								MUC16 (48589 upstream) : OR1M1 (63314 downstream)																							accctgtctcaaaaaaaaaaa	0.000													1	6	---	---	---	---	
DOCK6	57572	broad.mit.edu	37	19	11338688	11338688	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11338688delT	uc002mqs.3	-						DOCK6_uc010xlq.1_Intron	NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3						GCtttccctcttttttttttt	0.229													4	3	---	---	---	---	
NFIX	4784	broad.mit.edu	37	19	13105126	13105127	+	5'Flank	INS	-	GT	GT	rs139318180	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13105126_13105127insGT	uc002mwd.2	+							NM_002501	NP_002492	Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			TGGGCAACCCAgtgtgtgtgtg	0.436													4	2	---	---	---	---	
MPV17L2	84769	broad.mit.edu	37	19	18304953	18304953	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18304953delG	uc002nid.2	+						MPV17L2_uc010ebj.2_Intron	NM_032683	NP_116072	Q567V2	M17L2_HUMAN	MPV17 mitochondrial membrane protein-like 2							integral to membrane					0						CCCCCTGTTTGGGTCGCCCTG	0.587													4	3	---	---	---	---	
ZNF626	199777	broad.mit.edu	37	19	20829833	20829834	+	Intron	INS	-	TAC	TAC	rs146795407	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20829833_20829834insTAC	uc002npb.1	-						ZNF626_uc002npc.1_Intron|ZNF626_uc002npd.1_Intron	NM_001076675	NP_001070143	Q68DY1	ZN626_HUMAN	zinc finger protein 626 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						ttttcgtagttttagtagagat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27852050	27852051	+	IGR	INS	-	A	A	rs139076706		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27852050_27852051insA								None (None upstream) : LOC148189 (429351 downstream)																							ctgcagttactacaaaaagact	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27865507	27865508	+	IGR	INS	-	T	T	rs71224979		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27865507_27865508insT								None (None upstream) : LOC148189 (415894 downstream)																							ttgaacgtatcttttTTTTTtt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30559749	30559752	+	IGR	DEL	TCCA	-	-	rs112405644		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30559749_30559752delTCCA								C19orf2 (53138 upstream) : ZNF536 (303576 downstream)																							cttccatctgtccatccatccatc	0.029													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31443095	31443098	+	IGR	DEL	CTTT	-	-	rs12459562	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31443095_31443098delCTTT								ZNF536 (394130 upstream) : DKFZp566F0947 (197685 downstream)																							tccttccttcctttcttctttcct	0.005													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31495750	31495756	+	IGR	DEL	TCTCTTA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31495750_31495756delTCTCTTA								ZNF536 (446785 upstream) : DKFZp566F0947 (145027 downstream)																							TTAGCCTCCCTCTCTTATCTCTTATtc	0.063													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31557664	31557664	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31557664delA								ZNF536 (508699 upstream) : DKFZp566F0947 (83119 downstream)																							TGTGGTGGTTAAACCCCTCGC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	35873167	35873167	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35873167delG								FFAR3 (21780 upstream) : FFAR2 (66036 downstream)																							CTACAAATGTGGTGGCATCAA	0.443													16	10	---	---	---	---	
FBXO27	126433	broad.mit.edu	37	19	39521999	39521999	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39521999delC	uc002okh.2	-							NM_178820	NP_849142	Q8NI29	FBX27_HUMAN	F-box protein 27						protein catabolic process	SCF ubiquitin ligase complex	glycoprotein binding			ovary(1)	1	all_cancers(60;3.79e-07)|all_lung(34;1.26e-07)|Lung NSC(34;1.46e-07)|all_epithelial(25;4.69e-07)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			GTTCCAGTCGCCCGCCTGTTG	0.617													7	8	---	---	---	---	
TMEM91	641649	broad.mit.edu	37	19	41888897	41888898	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41888897_41888898insA	uc002oqk.3	+						CYP2F1_uc010xvw.1_Intron|TMEM91_uc002oqi.2_3'UTR|TMEM91_uc010ehq.2_Intron|TMEM91_uc002oql.2_3'UTR|TMEM91_uc010ehr.2_Intron|TMEM91_uc010ehs.2_Intron|TMEM91_uc010eht.2_Intron|BCKDHA_uc002oqm.3_Intron|TMEM91_uc002oqn.2_Intron	NM_001098821	NP_001092291	Q6ZNR0	TMM91_HUMAN	transmembrane protein 91 isoform a						response to biotic stimulus	integral to membrane					0						AACAAAGAGCCATATACCTGAG	0.332													36	21	---	---	---	---	
PHLDB3	653583	broad.mit.edu	37	19	43994163	43994164	+	Intron	INS	-	A	A	rs77696385		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43994163_43994164insA	uc002own.3	-						PHLDB3_uc010eit.2_Intron	NM_198850	NP_942147	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B,												0		Prostate(69;0.0153)				tgccaaaaaggaaaaaaaaaaa	0.035													4	2	---	---	---	---	
ZNF180	7733	broad.mit.edu	37	19	45001591	45001592	+	Intron	INS	-	AG	AG			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45001591_45001592insAG	uc002ozf.3	-						ZNF180_uc002ozh.3_Intron|ZNF180_uc002ozi.3_Intron|ZNF180_uc002ozg.3_Intron|ZNF180_uc010ejm.2_Intron	NM_013256	NP_037388	Q9UJW8	ZN180_HUMAN	zinc finger protein 180						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)				TGTGTATGTACTGAGAGTCCCT	0.564													4	2	---	---	---	---	
FKRP	79147	broad.mit.edu	37	19	47252666	47252667	+	Intron	DEL	TT	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47252666_47252667delTT	uc002pfn.2	+						STRN4_uc002pfm.2_5'Flank|STRN4_uc002pfl.2_5'Flank|STRN4_uc010xyf.1_5'Flank|STRN4_uc010xyg.1_5'Flank|FKRP_uc002pfp.2_Intron	NM_024301	NP_077277	Q9H9S5	FKRP_HUMAN	fukutin-related protein							extracellular space|Golgi apparatus|rough endoplasmic reticulum|sarcolemma	transferase activity			pancreas(1)	1		all_epithelial(76;5.08e-05)|Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000541)|all cancers(93;0.00128)|Epithelial(262;0.0207)|GBM - Glioblastoma multiforme(486;0.0336)		ctttgtttcctttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	49213854	49213854	+	IGR	DEL	T	-	-	rs35728097		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49213854delT								FUT2 (4664 upstream) : MAMSTR (2401 downstream)																							CTGAAACCTAttttttttttt	0.025													6	3	---	---	---	---	
TEAD2	8463	broad.mit.edu	37	19	49856358	49856358	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49856358delT	uc002pnj.2	-						TEAD2_uc002png.2_Intron|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		actcccattcttttttttttt	0.010													4	2	---	---	---	---	
ALDH16A1	126133	broad.mit.edu	37	19	49964763	49964763	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49964763delA	uc002pnt.2	+						ALDH16A1_uc010yar.1_Intron|ALDH16A1_uc010yas.1_Intron|ALDH16A1_uc010yat.1_Intron	NM_153329	NP_699160	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1								oxidoreductase activity|protein binding			skin(1)	1		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		gaggggctggagtctggactc	0.030													2	4	---	---	---	---	
SNAR-B2	100170217	broad.mit.edu	37	19	50640097	50640098	+	5'Flank	DEL	AA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50640097_50640098delAA	uc010yby.1	-							NR_024231				Homo sapiens small ILF3/NF90-associated RNA B2 (SNAR-B2), non-coding RNA.												0						gctgcgtctcaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	8964143	8964144	+	IGR	INS	-	A	A	rs144414180	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8964143_8964144insA								PLCB1 (98598 upstream) : PLCB4 (85557 downstream)																							TGCTATCACAGAAAAAAAAAAG	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	9471822	9471825	+	IGR	DEL	CACA	-	-	rs113207500		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9471822_9471825delCACA								PLCB4 (10362 upstream) : C20orf103 (23446 downstream)																							cacatgcacgcacacacacacaca	0.108													4	2	---	---	---	---	
KIF16B	55614	broad.mit.edu	37	20	16256404	16256405	+	Intron	DEL	TA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16256404_16256405delTA	uc002wpg.1	-						KIF16B_uc002wpe.1_Intron|KIF16B_uc002wpf.1_Intron|KIF16B_uc010gch.1_Intron	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23						cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						TAATTATTTTTATCAGAGGGGC	0.386													4	2	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17322815	17322816	+	Intron	DEL	AC	-	-	rs73617204		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17322815_17322816delAC	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AATTACACATACACACACACAT	0.376													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	18834496	18834497	+	IGR	INS	-	T	T	rs141087384		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18834496_18834497insT								C20orf79 (39463 upstream) : SLC24A3 (358793 downstream)																							gtttctgttgattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22790773	22790773	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22790773delC								FOXA2 (224672 upstream) : SSTR4 (225284 downstream)																							TGCAAGCTGTCCGGGAGAGGA	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25079440	25079440	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25079440delA								VSX1 (16673 upstream) : LOC284798 (41994 downstream)																							caggtggatcaagaggtcagg	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25741448	25741449	+	IGR	INS	-	TT	TT	rs150930071		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25741448_25741449insTT								ZNF337 (63979 upstream) : FAM182B (2653 downstream)																							caggtttgcagtgagaaaatta	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25741473	25741473	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25741473delT								ZNF337 (64004 upstream) : FAM182B (2629 downstream)																							ggctgatatctggaaagagga	0.045													5	3	---	---	---	---	
FAM182B	728882	broad.mit.edu	37	20	25747973	25747973	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25747973delA	uc010zth.1	-						FAM182B_uc002wvd.1_Intron	NR_027061				Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						atagaaaaagaaatatatatc	0.000													2	7	---	---	---	---	
FAM182B	728882	broad.mit.edu	37	20	25752737	25752738	+	Intron	INS	-	C	C	rs146971641		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25752737_25752738insC	uc010zth.1	-						FAM182B_uc002wvd.1_Intron|FAM182B_uc010zti.1_RNA	NR_027061				Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						CAGGCCAAAAGAGAAATCAGAA	0.520													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25903695	25903695	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25903695delA								FAM182B (54909 upstream) : LOC100134868 (86740 downstream)																							TTAAGATGACAAAAAAACACC	0.428													9	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26207651	26207653	+	IGR	DEL	TTC	-	-	rs77404334		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26207651_26207653delTTC								MIR663 (18737 upstream) : None (None downstream)																							ATTCATTCCATTCTTCTTATAAT	0.300													1	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29590215	29590216	+	IGR	INS	-	T	T	rs142088020		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29590215_29590216insT								None (None upstream) : FRG1B (21663 downstream)																							tgtcttcttagtttggttattt	0.015													8	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29600261	29600261	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29600261delA								None (None upstream) : FRG1B (11618 downstream)																							aaataaagacaaaaaatacaa	0.000													7	4	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29609373	29609373	+	5'Flank	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29609373delT	uc002wvm.1	+						FRG1B_uc010ztj.1_5'Flank|FRG1B_uc010gdr.1_5'Flank	NR_003579				Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						CATCTTTAACTGTAAATATGA	0.313													3	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29617331	29617332	+	Intron	INS	-	A	A	rs145046210		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29617331_29617332insA	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0						aaaaaaaaaggaaaaaaatctc	0.000													3	3	---	---	---	---	
RBL1	5933	broad.mit.edu	37	20	35639164	35639165	+	Intron	DEL	TG	-	-	rs36003402		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35639164_35639165delTG	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron	NM_002895	NP_002886	P28749	RBL1_HUMAN	retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)				cacatgactAtgtgtgtgtgtg	0.005													5	3	---	---	---	---	
RPN2	6185	broad.mit.edu	37	20	35852038	35852039	+	Intron	INS	-	T	T	rs149522077		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35852038_35852039insT	uc002xgp.2	+						RPN2_uc002xgo.3_Intron|RPN2_uc010gfw.2_Intron|RPN2_uc002xgq.2_Intron	NM_002951	NP_002942	P04844	RPN2_HUMAN	ribophorin II isoform 1 precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|nucleus|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				ttttcttcttcttttttttttt	0.312													2	4	---	---	---	---	
SLC13A3	64849	broad.mit.edu	37	20	45308547	45308547	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45308547delA	uc002xsg.1	-						SLC13A3_uc010gho.1_Intron	NM_001011554	NP_001011554	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform b							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	actctgtctcaaaaaaaaaaa	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46962567	46962567	+	IGR	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46962567delC								SULF2 (547207 upstream) : LOC284749 (26087 downstream)																							ccaTGCATCACCTTTGCAAGG	0.124													4	2	---	---	---	---	
TMEM189	387521	broad.mit.edu	37	20	48741399	48741400	+	3'UTR	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48741399_48741400insA	uc002xvg.2	-	6					TMEM189-UBE2V1_uc002xvf.2_Intron|TMEM189_uc010zyq.1_RNA|TMEM189_uc010gif.2_3'UTR|TMEM189_uc010zyp.1_3'UTR	NM_199129	NP_954580	A5PLL7	TM189_HUMAN	transmembrane protein 189 isoform 1							endoplasmic reticulum membrane|integral to membrane					0			BRCA - Breast invasive adenocarcinoma(9;3.02e-07)			AGGGGCCGAGGAAAAAAAAAAA	0.550													4	3	---	---	---	---	
TAF4	6874	broad.mit.edu	37	20	60568561	60568562	+	Intron	DEL	AC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60568561_60568562delAC	uc002ybs.2	-							NM_003185	NP_003176	O00268	TAF4_HUMAN	TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			ggagggccctacagattTTTAA	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	60680813	60680816	+	IGR	DEL	GATG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60680813_60680816delGATG								TAF4 (39947 upstream) : LSM14B (16701 downstream)																							tagatgggcagatggatggatgga	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9655453	9655456	+	IGR	DEL	ATAG	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9655453_9655456delATAG								None (None upstream) : None (None downstream)																							ttaaatagttatagataaagacaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10756953	10756954	+	IGR	INS	-	AAAG	AAAG			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10756953_10756954insAAAG								None (None upstream) : TPTE (149789 downstream)																							ctgctgtatcaaaagattcaac	0.015													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10782276	10782276	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10782276delA								None (None upstream) : TPTE (124467 downstream)																							aatggagtggaatggaatgga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10827362	10827366	+	IGR	DEL	CACCC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10827362_10827366delCACCC								None (None upstream) : TPTE (79377 downstream)																							gaatggaatgcacccgaatggaatg	0.000													8	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11031726	11031726	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11031726delA	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aacctgctacaagagtctact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14356250	14356251	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14356250_14356251insT								None (None upstream) : C21orf99 (54236 downstream)																							cttctttctagtttttatgtga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14362029	14362030	+	IGR	INS	-	A	A	rs151036820		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14362029_14362030insA								None (None upstream) : C21orf99 (48457 downstream)																							actggtcaatcaaaagaaaggt	0.000													4	2	---	---	---	---	
IFNGR2	3460	broad.mit.edu	37	21	34792155	34792156	+	Intron	INS	-	G	G			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34792155_34792156insG	uc002yrp.3	+						IFNGR2_uc002yrq.3_Intron|IFNGR2_uc010gma.2_Intron|IFNGR2_uc002yrr.3_Intron	NM_005534	NP_005525	P38484	INGR2_HUMAN	interferon gamma receptor 2 precursor						regulation of interferon-gamma-mediated signaling pathway|response to virus	endoplasmic reticulum|integral to plasma membrane	interferon-gamma receptor activity				0					Interferon gamma-1b(DB00033)	CGGCAGTGGCAGGGGTTTGGGG	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	34858017	34858017	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34858017delT								TMEM50B (5736 upstream) : DNAJC28 (2222 downstream)																							TAATTCCCACttttttttttt	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	43058192	43058193	+	IGR	DEL	AA	-	-	rs138873128		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43058192_43058193delAA								TMPRSS2 (155149 upstream) : NCRNA00111 (41269 downstream)																							cattctcgacaaggggagacag	0.000													4	3	---	---	---	---	
NCRNA00111	54090	broad.mit.edu	37	21	43114019	43114020	+	Intron	INS	-	AAAT	AAAT			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43114019_43114020insAAAT	uc011aes.1	+							NR_024367				Homo sapiens non-protein coding RNA 111 (NCRNA00111), non-coding RNA.												0						tccatccatccacccatccatc	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	47502506	47502507	+	IGR	INS	-	C	C	rs145989549	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47502506_47502507insC								COL6A1 (77543 upstream) : COL6A2 (15526 downstream)																							TGATCTCTCTTCCCATCTGACC	0.644													3	4	---	---	---	---	
GNB1L	54584	broad.mit.edu	37	22	19828333	19828334	+	Intron	DEL	AA	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19828333_19828334delAA	uc002zqe.1	-						GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqf.1_Intron	NM_053004	NP_443730	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	internal side of plasma membrane|intracellular				breast(1)	1	Colorectal(54;0.0993)					actccgtctcaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
HIC2	23119	broad.mit.edu	37	22	21803269	21803269	+	3'UTR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21803269delT	uc002zur.3	+	3					HIC2_uc002zus.3_3'UTR	NM_015094	NP_055909	Q96JB3	HIC2_HUMAN	hypermethylated in cancer 2						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	focal adhesion|nucleus	DNA binding|protein C-terminus binding|zinc ion binding			skin(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00438)|Colorectal(54;0.0968)	Lung SC(17;0.0262)|all_lung(157;0.205)				CCTCCCGGGCTGTGGGCAGCC	0.592													5	4	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22779673	22779673	+	Intron	DEL	T	-	-	rs112301757		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22779673delT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						CTCCTTCTCCTTTTTTTTTTT	0.448													4	2	---	---	---	---	
GGT1	2678	broad.mit.edu	37	22	24997928	24997928	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24997928delG	uc003aan.1	+						GGT1_uc003aas.1_5'Flank|GGT1_uc003aat.1_5'Flank|GGT1_uc003aau.1_5'Flank|GGT1_uc003aav.1_5'Flank|GGT1_uc003aaw.1_5'Flank	NM_013430	NP_038347	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1 precursor						glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)	AGGAGCTAATGGACACCCACC	0.587													4	2	---	---	---	---	
CHEK2	11200	broad.mit.edu	37	22	29104352	29104353	+	Intron	DEL	TG	-	-	rs10694007		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29104352_29104353delTG	uc003adu.1	-						CHEK2_uc003ads.1_Intron|CHEK2_uc010gvh.1_Intron|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_Intron|CHEK2_uc010gvk.1_Intron|CHEK2_uc003adt.1_Intron|CHEK2_uc003adv.1_Intron|CHEK2_uc003adw.1_Intron|CHEK2_uc003adx.1_Intron|CHEK2_uc003ady.1_Intron|CHEK2_uc003adz.1_Intron	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a						cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20						tctaaaaaTAtgtgtgtgtgtg	0.119			F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				4	2	---	---	---	---	
CHEK2	11200	broad.mit.edu	37	22	29110064	29110066	+	Intron	DEL	TTG	-	-	rs17883042		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29110064_29110066delTTG	uc003adu.1	-						CHEK2_uc003ads.1_Intron|CHEK2_uc010gvh.1_Intron|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_Intron|CHEK2_uc010gvk.1_Intron|CHEK2_uc003adt.1_Intron|CHEK2_uc003adv.1_Intron|CHEK2_uc003adw.1_Intron|CHEK2_uc003adx.1_Intron|CHEK2_uc003ady.1_Intron|CHEK2_uc003adz.1_Intron	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a						cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20						ctgttgttgtttgttgttgttgt	0.000			F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	30181072	30181072	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30181072delT								UQCR10 (14670 upstream) : ASCC2 (3531 downstream)																							ACATAGTCGATTTTTGGCGAA	0.463													4	2	---	---	---	---	
TBC1D10A	83874	broad.mit.edu	37	22	30707590	30707590	+	Intron	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30707590delG	uc011akt.1	-						TBC1D10A_uc010gvu.2_Intron|TBC1D10A_uc003ahk.3_Intron	NM_031937	NP_114143	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A							intracellular|microvillus	guanyl-nucleotide exchange factor activity|PDZ domain binding|Rab GTPase activator activity			ovary(1)	1						ACCCTTCACTGGCCTTGGTGC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	36502009	36502010	+	IGR	INS	-	TC	TC	rs145777070	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36502009_36502010insTC								RBM9 (77424 upstream) : APOL3 (34362 downstream)																							AAAGAAATCAATCTCTCATTTC	0.416													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	36619474	36619475	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36619474_36619475insT								APOL4 (18595 upstream) : APOL2 (2781 downstream)																							TTTCTCTTTCCTTTGGTGAGAA	0.347													4	2	---	---	---	---	
BAIAP2L2	80115	broad.mit.edu	37	22	38483805	38483805	+	Intron	DEL	A	-	-	rs145400280	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38483805delA	uc003auw.2	-						BAIAP2L2_uc003auv.2_5'Flank	NM_025045	NP_079321	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2						filopodium assembly|signal transduction		cytoskeletal adaptor activity|SH3 domain binding			pancreas(1)	1	Melanoma(58;0.045)					TCCATCCAGCACCCCCTCACC	0.572													4	2	---	---	---	---	
PHF5A	84844	broad.mit.edu	37	22	41859899	41859899	+	Intron	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41859899delA	uc003bab.2	-							NM_032758	NP_116147	Q7RTV0	PHF5A_HUMAN	PHD-finger 5A						nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent	nuclear speck|U12-type spliceosomal complex|U2 snRNP	DNA binding|sequence-specific DNA binding transcription factor activity				0						actgcgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ARFGAP3	26286	broad.mit.edu	37	22	43226278	43226279	+	Intron	INS	-	A	A	rs149813710	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43226278_43226279insA	uc003bdd.2	-						ARFGAP3_uc010gzf.2_Intron|ARFGAP3_uc011apu.1_Intron	NM_014570	NP_055385	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating						intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding			breast(1)	1						cgtgcacaacctgcctggcTAT	0.203													4	3	---	---	---	---	
PHF21B	112885	broad.mit.edu	37	22	45380039	45380040	+	Intron	INS	-	ACCATCACA	ACCATCACA	rs111775801		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45380039_45380040insACCATCACA	uc003bfn.2	-						PHF21B_uc003bfm.2_Intron|PHF21B_uc011aqk.1_Intron|PHF21B_uc011aql.1_Intron|PHF21B_uc011aqm.1_Intron	NM_138415	NP_612424	Q96EK2	PF21B_HUMAN	PHD finger protein 21B isoform 1								zinc ion binding			ovary(2)|skin(1)	3		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		tcaccaccatcaccaccatcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45836963	45836963	+	IGR	DEL	A	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45836963delA								RIBC2 (8670 upstream) : FBLN1 (61756 downstream)																							agaacaggacagggatttttg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47953044	47953047	+	IGR	DEL	TGTA	-	-	rs142069996	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47953044_47953047delTGTA								TBC1D22A (383322 upstream) : FAM19A5 (932241 downstream)																							taggtgtatgtgtatgtatgtatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48056075	48056075	+	Intron	DEL	C	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48056075delC	uc003bik.1	+											Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																		ttcatctcttcctcatctata	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48309658	48309673	+	IGR	DEL	TTTTTTTTTTTTTTTT	-	-	rs72356591		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48309658_48309673delTTTTTTTTTTTTTTTT								TBC1D22A (739936 upstream) : FAM19A5 (575615 downstream)																							TAATTCCCTCtttttttttttttttttttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49153222	49153231	+	IGR	DEL	AGGAAGGAGA	-	-	rs61243974	by1000genomes	TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49153222_49153231delAGGAAGGAGA								FAM19A5 (5480 upstream) : C22orf34 (654945 downstream)																							gaggaggaggaggaAGGAGAAGGGATAgag	0.152													5	3	---	---	---	---	
BRD1	23774	broad.mit.edu	37	22	50204634	50204635	+	Intron	INS	-	A	A			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50204634_50204635insA	uc003biv.2	-						BRD1_uc011arf.1_Intron|BRD1_uc011arg.1_Intron|BRD1_uc011arh.1_Intron|BRD1_uc003biu.3_Intron	NM_014577	NP_055392	O95696	BRD1_HUMAN	bromodomain containing protein 1						histone H3 acetylation	MOZ/MORF histone acetyltransferase complex	zinc ion binding			pancreas(1)	1		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		tccaaagtaggaaaaaaacaaa	0.000													4	2	---	---	---	---	
SHANK3	85358	broad.mit.edu	37	22	51130712	51130712	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51130712delT	uc003bne.1	+							NM_001080420	NP_001073889	F2Z3L0	F2Z3L0_HUMAN	SH3 and multiple ankyrin repeat domains 3											central_nervous_system(1)	1		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		cttctctctcttttttttttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	2426999	2427000	+	IGR	DEL	TC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2426999_2427000delTC								DHRSX (7984 upstream) : CD99 (182228 downstream)																							ttctttctcttctctctctctc	0.000													4	2	---	---	---	---	
SMS	6611	broad.mit.edu	37	X	21989957	21989957	+	Intron	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21989957delT	uc004dag.2	+						SMS_uc011mjq.1_Intron|SMS_uc004daf.1_Intron	NM_004595	NP_004586	P52788	SPSY_HUMAN	spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)	TCTCTCTCTCTTTTTTTTTTA	0.363													4	2	---	---	---	---	
EFHC2	80258	broad.mit.edu	37	X	44084157	44084159	+	Intron	DEL	TGC	-	-	rs66878536		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44084157_44084159delTGC	uc004dgb.3	-							NM_025184	NP_079460	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2								calcium ion binding			breast(3)|ovary(2)|central_nervous_system(1)	6						GGGCTCTCAGtgctgctgctgct	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61773240	61773240	+	IGR	DEL	G	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61773240delG								None (None upstream) : SPIN4 (793868 downstream)																							tcgtctcacagagttaaactt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	109086456	109086456	+	IGR	DEL	T	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109086456delT								ACSL4 (109835 upstream) : TMEM164 (159407 downstream)																							tttctttttcttttttttttt	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9933061	9933062	+	IGR	INS	-	T	T			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9933061_9933062insT								TTTY22 (282207 upstream) : None (None downstream)																							tgtatttgttgtttttggtgtc	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9941802	9941802	+	IGR	DEL	G	-	-	rs113135217		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9941802delG								TTTY22 (290948 upstream) : None (None downstream)																							AAAACTTTTTGGTTAGTGATT	0.338													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10019375	10019376	+	IGR	INS	-	CT	CT	rs33969087		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10019375_10019376insCT								TTTY22 (368521 upstream) : None (None downstream)																							tgaacacccccgtcagaagttt	0.015													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13137964	13137968	+	IGR	DEL	TTACC	-	-			TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13137964_13137968delTTACC								None (None upstream) : None (None downstream)																							ttccactccattacccgccactcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59013019	59013019	+	IGR	DEL	A	-	-	rs148494923		TCGA-18-3416-01A-01D-0983-08	TCGA-18-3416-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59013019delA								None (None upstream) : None (None downstream)																							gtctcaaaagaaaaaaaaaaT	0.189													10	5	---	---	---	---	
