Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
MTOR	2475	broad.mit.edu	37	1	11217290	11217290	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11217290T>G	uc001asd.2	-	30	4509	c.4388A>C	c.(4387-4389)TAT>TCT	p.Y1463S		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	1463	FAT.				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						TTTCTTGTCATAGGCCACAAG	0.537													21	98	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16972134	16972134	+	5'Flank	SNP	C	T	T	rs4661404	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16972134C>T	uc001azg.1	-						CROCCL1_uc001azi.1_5'Flank|uc001azj.1_5'Flank|MST1P2_uc009vow.2_RNA|MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_RNA|MST1P2_uc010oci.1_5'Flank|MST1P2_uc001azk.2_5'Flank|MST1P2_uc001azl.3_5'Flank|MST1P2_uc009vox.2_5'Flank|MST1P2_uc001azm.3_5'Flank					Homo sapiens mRNA for FLJ00313 protein.												0						GGGGTGGCTCCCACTCCTGCT	0.612													6	34	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974549	16974549	+	RNA	SNP	C	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974549C>G	uc009vow.2	+	5		c.1359C>G			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_RNA|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GGGCTGAGTGCAGCGCCTGCT	0.692													13	57	---	---	---	---	PASS
MST1P9	11223	broad.mit.edu	37	1	17085848	17085848	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17085848G>A	uc010ock.1	-	8	973	c.973C>T	c.(973-975)CCC>TCC	p.P325S	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_5'UTR	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						AAGCACCAGGGCGCCTCTGAG	0.667													5	26	---	---	---	---	PASS
ZMYM6	9204	broad.mit.edu	37	1	35470872	35470872	+	Silent	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35470872T>C	uc001byh.2	-	13	2043	c.1815A>G	c.(1813-1815)GTA>GTG	p.V605V	ZMYM6_uc001byf.1_Silent_p.V605V|ZMYM6_uc010oht.1_Silent_p.V508V|ZMYM6_uc009vup.2_Silent_p.V411V|ZMYM6_uc009vuq.1_Silent_p.V605V|ZMYM6_uc009vur.1_Silent_p.V411V	NM_007167	NP_009098	O95789	ZMYM6_HUMAN	zinc finger protein 258	605					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				TAGAAATATTTACTGATTAAA	0.378													4	113	---	---	---	---	PASS
SCMH1	22955	broad.mit.edu	37	1	41579130	41579130	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41579130G>T	uc001cgo.2	-	8	851	c.540C>A	c.(538-540)AAC>AAA	p.N180K	SCMH1_uc010ojr.1_Intron|SCMH1_uc001cgp.2_Missense_Mutation_p.N119K|SCMH1_uc001cgr.2_Missense_Mutation_p.N119K|SCMH1_uc001cgs.2_Missense_Mutation_p.N190K|SCMH1_uc001cgt.2_Missense_Mutation_p.N119K|SCMH1_uc001cgq.2_Missense_Mutation_p.N133K|SCMH1_uc010ojs.1_RNA	NM_001031694	NP_001026864	Q96GD3	SCMH1_HUMAN	sex comb on midleg 1 isoform 1	180	MBT 2.				anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				TGAAATGAGGGTTCTTCCTGT	0.512													19	73	---	---	---	---	PASS
OSBPL9	114883	broad.mit.edu	37	1	52211253	52211253	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52211253A>G	uc001cst.2	+	5	383	c.364A>G	c.(364-366)AAA>GAA	p.K122E	OSBPL9_uc001css.2_Missense_Mutation_p.K140E|OSBPL9_uc001csx.2_RNA|OSBPL9_uc009vza.2_Missense_Mutation_p.K123E|OSBPL9_uc001csu.2_Missense_Mutation_p.K145E|OSBPL9_uc001csv.2_5'UTR|OSBPL9_uc001csw.2_Missense_Mutation_p.K122E|OSBPL9_uc001csy.2_5'UTR|OSBPL9_uc001csz.2_Intron|OSBPL9_uc001cta.2_Missense_Mutation_p.K25E	NM_024586	NP_078862	Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9 isoform e	122					lipid transport		lipid binding			central_nervous_system(1)	1						TTTTGATAAGAAACTTACAGA	0.303													6	467	---	---	---	---	PASS
SLC1A7	6512	broad.mit.edu	37	1	53608095	53608095	+	Silent	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53608095C>T	uc001cuy.2	-	1	195	c.27G>A	c.(25-27)CGG>CGA	p.R9R	SLC1A7_uc001cuz.3_Silent_p.R9R	NM_006671	NP_006662	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter),	9	Cytoplasmic (Potential).					integral to membrane|plasma membrane	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|large_intestine(1)	3				Colorectal(1306;0.234)	L-Glutamic Acid(DB00142)	CGTCCCTCCCCCGTGCCAAGA	0.657													9	30	---	---	---	---	PASS
C1orf146	388649	broad.mit.edu	37	1	92711194	92711194	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92711194A>G	uc001doq.2	+	6	578	c.506A>G	c.(505-507)AAG>AGG	p.K169R	C1orf146_uc010ote.1_Missense_Mutation_p.K110R	NM_001012425	NP_001012425	Q5VVC0	CA146_HUMAN	hypothetical protein LOC388649	169										ovary(1)	1		all_lung(203;0.00528)|Lung NSC(277;0.0193)		all cancers(265;0.00846)|Epithelial(280;0.0952)		ACACTTCAGAAGATAAAACTG	0.318													5	86	---	---	---	---	PASS
CR1	1378	broad.mit.edu	37	1	207785153	207785153	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207785153T>A	uc001hfy.2	+	30	5217	c.5077T>A	c.(5077-5079)TGC>AGC	p.C1693S	CR1_uc001hfx.2_Missense_Mutation_p.C2143S	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	1693	Sushi 26.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3						GTCTCTGCACTGCACGCCCCA	0.562													11	69	---	---	---	---	PASS
HSD11B1	3290	broad.mit.edu	37	1	209880313	209880313	+	Silent	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209880313C>T	uc001hhj.2	+	5	464	c.357C>T	c.(355-357)AAC>AAT	p.N119N	HSD11B1_uc001hhk.2_Silent_p.N119N	NM_181755	NP_861420	P28845	DHI1_HUMAN	11-beta-hydroxysteroid dehydrogenase 1	119	Lumenal (Potential).|NADP.				glucocorticoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	11-beta-hydroxysteroid dehydrogenase (NADP+) activity|11-beta-hydroxysteroid dehydrogenase|binding			breast(1)	1				OV - Ovarian serous cystadenocarcinoma(81;1.04e-55)|Epithelial(68;1.57e-52)|all cancers(67;1.83e-46)|Colorectal(1306;0.115)	NADH(DB00157)	TCATTCTCAACCACATCACCA	0.433													4	91	---	---	---	---	PASS
RPS6KC1	26750	broad.mit.edu	37	1	213341274	213341274	+	Silent	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213341274C>T	uc010ptr.1	+	7	1068	c.909C>T	c.(907-909)ATC>ATT	p.I303I	RPS6KC1_uc001hkd.2_Silent_p.I291I|RPS6KC1_uc010pts.1_Silent_p.I122I|RPS6KC1_uc010ptt.1_Silent_p.I122I|RPS6KC1_uc010ptu.1_Silent_p.I122I|RPS6KC1_uc010ptv.1_5'UTR|RPS6KC1_uc001hke.2_Silent_p.I122I	NM_012424	NP_036556	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide	303	MIT.				cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		CAGAAAGTATCTCTAGTCTTT	0.423													29	279	---	---	---	---	PASS
KMO	8564	broad.mit.edu	37	1	241723981	241723981	+	Silent	SNP	C	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241723981C>G	uc009xgp.2	+	6	443	c.378C>G	c.(376-378)CCC>CCG	p.P126P	KMO_uc001hyy.2_Silent_p.P126P|KMO_uc009xgo.1_Silent_p.P126P	NM_003679	NP_003670	O15229	KMO_HUMAN	kynurenine 3-monooxygenase	126					pyridine nucleotide biosynthetic process|response to salt stress	cytosol|integral to membrane|mitochondrial outer membrane	electron carrier activity|flavin adenine dinucleotide binding|kynurenine 3-monooxygenase activity|NAD(P)H oxidase activity			ovary(2)	2	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			AGAAATACCCCAATGTGAAAA	0.383													49	198	---	---	---	---	PASS
OR2T2	401992	broad.mit.edu	37	1	248616344	248616344	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248616344G>A	uc001iek.1	+	1	246	c.246G>A	c.(244-246)ATG>ATA	p.M82I		NM_001004136	NP_001004136	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T,	82	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCCCAAGATGCTCCAGGACC	0.527													28	227	---	---	---	---	PASS
ATP6V1B1	525	broad.mit.edu	37	2	71188870	71188870	+	Intron	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71188870G>A	uc002shj.2	+						ATP6V1B1_uc002shi.1_3'UTR|ATP6V1B1_uc010fdv.2_Intron|ATP6V1B1_uc010fdw.2_Intron|ATP6V1B1_uc010fdx.2_Intron	NM_001692	NP_001683	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1						ATP hydrolysis coupled proton transport|calcium ion homeostasis|cellular iron ion homeostasis|excretion|inner ear morphogenesis|insulin receptor signaling pathway|ossification|pH reduction|sensory perception of sound|transferrin transport	apical plasma membrane|basolateral plasma membrane|cytosol|endomembrane system|lateral plasma membrane|microvillus|proton-transporting V-type ATPase, V1 domain|vacuolar proton-transporting V-type ATPase complex	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			skin(1)	1						GGCAGACCCCGTCCCCTTCCA	0.517													5	43	---	---	---	---	PASS
DNAH6	1768	broad.mit.edu	37	2	84756081	84756081	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84756081T>A	uc010fgb.2	+	4	590	c.453T>A	c.(451-453)CAT>CAA	p.H151Q	DNAH6_uc002soo.2_Intron|DNAH6_uc002sop.2_Intron	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	151	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1						AACTGCCACATACTGGTATTG	0.408													65	122	---	---	---	---	PASS
FLJ40330	645784	broad.mit.edu	37	2	89102464	89102464	+	Intron	SNP	A	G	G	rs113574892	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89102464A>G	uc010fhg.2	+						FLJ40330_uc010fhh.2_RNA|FLJ40330_uc010fhi.1_Intron	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						TACTAATTTTAGTGGATGGCT	0.269													3	13	---	---	---	---	PASS
BAZ2B	29994	broad.mit.edu	37	2	160295646	160295646	+	Silent	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160295646T>C	uc002uao.2	-	7	1126	c.774A>G	c.(772-774)GAA>GAG	p.E258E	BAZ2B_uc002uap.2_Silent_p.E256E|BAZ2B_uc002uas.1_Silent_p.E195E|BAZ2B_uc002uau.1_Silent_p.E256E|BAZ2B_uc002uaq.1_Silent_p.E186E|BAZ2B_uc002uat.3_Silent_p.E195E|BAZ2B_uc010fop.1_Silent_p.E256E	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	258	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						TACTAATGCCTTCACTTGAGG	0.353													7	609	---	---	---	---	PASS
MDH1B	130752	broad.mit.edu	37	2	207611119	207611119	+	Silent	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207611119A>G	uc002vbs.2	-	8	1303	c.1248T>C	c.(1246-1248)TTT>TTC	p.F416F	MDH1B_uc010ziw.1_RNA|MDH1B_uc010fui.2_Silent_p.F416F|MDH1B_uc010fuj.2_Silent_p.F318F|MDH1B_uc002vbt.2_RNA	NM_001039845	NP_001034934	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	416					carbohydrate metabolic process|malate metabolic process|tricarboxylic acid cycle		binding|malate dehydrogenase activity			ovary(3)|kidney(1)	4				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		CAGGCATAGAAAAGACGATCC	0.403													5	163	---	---	---	---	PASS
TRAF3IP1	26146	broad.mit.edu	37	2	239242644	239242644	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239242644C>T	uc002vye.2	+	7	1150	c.1031C>T	c.(1030-1032)ACA>ATA	p.T344I	TRAF3IP1_uc002vyf.2_Missense_Mutation_p.T344I	NM_015650	NP_056465	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting	344	DISC1-interaction domain.					cytoplasm|cytoskeleton	protein binding			ovary(1)	1		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		ACAACAAAAACATCAAAACGG	0.294													5	251	---	---	---	---	PASS
KCNH8	131096	broad.mit.edu	37	3	19554676	19554676	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19554676C>T	uc003cbk.1	+	13	2489	c.2294C>T	c.(2293-2295)TCG>TTG	p.S765L	KCNH8_uc010hex.1_Missense_Mutation_p.S226L	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	765	Cytoplasmic (Potential).					integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5						CCCTTTCACTCGCCTATCAGA	0.473													4	88	---	---	---	---	PASS
GLB1	2720	broad.mit.edu	37	3	33087643	33087643	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33087643T>G	uc003cfi.1	-	10	1154	c.1037A>C	c.(1036-1038)AAG>ACG	p.K346T	GLB1_uc003cfh.1_Missense_Mutation_p.K316T|GLB1_uc003cfj.1_Missense_Mutation_p.K215T|GLB1_uc011axk.1_Missense_Mutation_p.K394T	NM_000404	NP_000395	P16278	BGAL_HUMAN	galactosidase, beta 1 isoform a preproprotein	346			K -> N (in GM1G1).		carbohydrate metabolic process	lysosome|perinuclear region of cytoplasm	beta-galactosidase activity|cation binding|protein binding			large_intestine(1)	1		Melanoma(143;0.104)				AGCAAAATACTTCTCAGTGAG	0.522													19	56	---	---	---	---	PASS
ENTPD3	956	broad.mit.edu	37	3	40442405	40442405	+	Silent	SNP	C	T	T	rs149445548		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40442405C>T	uc003ckd.3	+	4	281	c.189C>T	c.(187-189)GCC>GCT	p.A63A	ENTPD3_uc010hhy.2_Silent_p.A63A|uc003cke.3_Intron	NM_001248	NP_001239	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase	63	Extracellular (Potential).					integral to membrane	ATP binding|hydrolase activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		TGCTGGATGCCGGGTCTTCAA	0.478													4	205	---	---	---	---	PASS
ZBTB11	27107	broad.mit.edu	37	3	101390922	101390922	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101390922C>T	uc003dve.3	-	2	676	c.446G>A	c.(445-447)AGT>AAT	p.S149N	ZBTB11_uc003dvf.2_Missense_Mutation_p.S149N	NM_014415	NP_055230	O95625	ZBT11_HUMAN	zinc finger protein ZNF-U69274	149					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						CGATTCATTACTTTCTTCTCC	0.408													4	229	---	---	---	---	PASS
POPDC2	64091	broad.mit.edu	37	3	119361244	119361244	+	3'UTR	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119361244A>G	uc003ecx.1	-	4					POPDC2_uc010hqw.1_3'UTR|POPDC2_uc003ecy.1_3'UTR	NM_022135	NP_071418	Q9HBU9	POPD2_HUMAN	popeye protein 2							integral to membrane				central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.242)		GGGTGGGAAAAGAGGCATGCC	0.507													4	50	---	---	---	---	PASS
LRRC34	151827	broad.mit.edu	37	3	169511439	169511439	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169511439A>G	uc003ffx.2	-	10	1259	c.1244T>C	c.(1243-1245)GTA>GCA	p.V415A	LRRC34_uc003ffy.2_Missense_Mutation_p.V447A|LRRC34_uc011bpn.1_3'UTR|LRRC34_uc003ffz.2_Missense_Mutation_p.V399A|LRRC34_uc003fga.3_3'UTR	NM_153353	NP_699184	Q8IZ02	LRC34_HUMAN	leucine rich repeat containing 34	415											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)			CTGTTGACCTACTGGAACAAG	0.328													4	107	---	---	---	---	PASS
LCORL	254251	broad.mit.edu	37	4	17910778	17910778	+	Silent	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17910778T>C	uc003gpq.2	-	5	632	c.621A>G	c.(619-621)GAA>GAG	p.E207E	LCORL_uc011bxk.1_Silent_p.E120E	NM_153686	NP_710153	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor	207					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0						CTTCCTGCTCTTCCTGAAGGG	0.353													6	408	---	---	---	---	PASS
SEPT11	55752	broad.mit.edu	37	4	77941776	77941776	+	Silent	SNP	T	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77941776T>G	uc003hkj.2	+	7	1068	c.906T>G	c.(904-906)CTT>CTG	p.L302L	SEPT11_uc010ijh.1_Silent_p.L294L|SEPT11_uc011cca.1_Silent_p.L312L|SEPT11_uc003hkk.1_Silent_p.L102L	NM_018243	NP_060713	Q9NVA2	SEP11_HUMAN	septin 11	302					cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0						GCTGTAAGCTTGAAGAGATGG	0.512													12	36	---	---	---	---	PASS
PTPN13	5783	broad.mit.edu	37	4	87684097	87684097	+	Silent	SNP	T	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87684097T>A	uc003hpz.2	+	24	4251	c.3771T>A	c.(3769-3771)TCT>TCA	p.S1257S	PTPN13_uc003hpy.2_Silent_p.S1257S|PTPN13_uc003hqa.2_Silent_p.S1238S|PTPN13_uc003hqb.2_Silent_p.S1066S	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	1257						cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CCAGCTTGTCTCAAAGCCAGG	0.542													9	63	---	---	---	---	PASS
CENPE	1062	broad.mit.edu	37	4	104081796	104081796	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104081796T>C	uc003hxb.1	-	21	2362	c.2272A>G	c.(2272-2274)AGG>GGG	p.R758G	CENPE_uc003hxc.1_Missense_Mutation_p.R733G	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	758	Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TTCCTCAGCCTTTCTACTTCA	0.308													5	200	---	---	---	---	PASS
ANK2	287	broad.mit.edu	37	4	114275680	114275680	+	Missense_Mutation	SNP	C	T	T	rs148760530		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114275680C>T	uc003ibe.3	+	38	6006	c.5906C>T	c.(5905-5907)ACA>ATA	p.T1969I	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_5'Flank|ANK2_uc011cgb.1_Missense_Mutation_p.T1984I	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	1936	Repeat-rich region.|Repeat A.				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)		TCTGGCAAAACAGAAAAGCAA	0.512													9	19	---	---	---	---	PASS
CAMK2D	817	broad.mit.edu	37	4	114375643	114375643	+	3'UTR	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114375643A>G	uc003ibi.2	-	19					CAMK2D_uc003ibj.2_3'UTR|CAMK2D_uc003ibk.2_3'UTR|CAMK2D_uc003ibo.3_3'UTR	NM_001221	NP_001212	Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|regulation of cell growth|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		GAGAACAGAGAATGCAGAAGT	0.418													5	199	---	---	---	---	PASS
LRBA	987	broad.mit.edu	37	4	151511868	151511868	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151511868C>G	uc010ipj.2	-	40	6697	c.6223G>C	c.(6223-6225)GCC>CCC	p.A2075P	LRBA_uc003ilt.3_Missense_Mutation_p.A723P|LRBA_uc003ilu.3_Missense_Mutation_p.A2064P	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	2075						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					AATTTACCGGCAAGATTCTCT	0.418													25	92	---	---	---	---	PASS
HMGCR	3156	broad.mit.edu	37	5	74647391	74647391	+	Silent	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74647391T>C	uc003kdp.2	+	11	1488	c.1332T>C	c.(1330-1332)CCT>CCC	p.P444P	HMGCR_uc011cst.1_Silent_p.P464P|HMGCR_uc003kdq.2_Silent_p.P444P	NM_000859	NP_000850	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	444	Linker.				cholesterol biosynthetic process|coenzyme A metabolic process|germ cell migration|gonad development|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal membrane	hydroxymethylglutaryl-CoA reductase (NADPH) activity|NADP binding			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Cerivastatin(DB00439)|Fluvastatin(DB01095)|Lovastatin(DB00227)|NADH(DB00157)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	AACCTCGGCCTAATGAAGAAT	0.423													4	128	---	---	---	---	PASS
EGR1	1958	broad.mit.edu	37	5	137802682	137802682	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137802682G>A	uc003ldb.1	+	2	814	c.544G>A	c.(544-546)GCC>ACC	p.A182T	EGR1_uc011cyu.1_Intron	NM_001964	NP_001955	P18146	EGR1_HUMAN	early growth response 1	182					cellular response to heparin|cellular response to mycophenolic acid|glomerular mesangial cell proliferation|interleukin-1-mediated signaling pathway|positive regulation of glomerular metanephric mesangial cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of protein sumoylation|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytoplasm|nucleus	histone acetyltransferase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GGCCTCCTCCGCCTCCGCCTC	0.652													8	51	---	---	---	---	PASS
CTNNA1	1495	broad.mit.edu	37	5	138269835	138269835	+	3'UTR	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138269835C>T	uc003ldh.2	+	18					CTNNA1_uc011cyx.1_3'UTR|CTNNA1_uc011cyy.1_3'UTR|CTNNA1_uc003ldi.2_3'UTR|CTNNA1_uc003ldj.2_3'UTR|CTNNA1_uc003ldl.2_3'UTR	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1						adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGTCACTGTTCGTCACTCAAA	0.517													3	19	---	---	---	---	PASS
ZMAT2	153527	broad.mit.edu	37	5	140085215	140085215	+	Silent	SNP	G	T	T	rs143727913	byFrequency	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140085215G>T	uc003lgy.1	+	6	488	c.474G>T	c.(472-474)GCG>GCT	p.A158A		NM_144723	NP_653324	Q96NC0	ZMAT2_HUMAN	zinc finger, matrin type 2	158						nucleus	DNA binding|zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			aggccaaagcgtacaagaaag	0.249													48	265	---	---	---	---	PASS
ZNF300	91975	broad.mit.edu	37	5	150275356	150275356	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150275356A>G	uc003lsy.1	-	6	1712	c.1445T>C	c.(1444-1446)ATA>ACA	p.I482T	IRGM_uc011dcl.1_Intron	NM_052860	NP_443092	Q96RE9	ZN300_HUMAN	zinc finger protein 300	482	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTCTGATGTATGATGAGCTG	0.403													4	93	---	---	---	---	PASS
BTNL8	79908	broad.mit.edu	37	5	180377360	180377360	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180377360T>A	uc003mmp.2	+	8	1553	c.1319T>A	c.(1318-1320)TTG>TAG	p.L440*	BTNL8_uc003mmq.2_3'UTR|BTNL8_uc011dhg.1_Nonsense_Mutation_p.L315*|BTNL8_uc010jll.2_3'UTR|BTNL8_uc010jlm.2_Nonsense_Mutation_p.L324*|BTNL8_uc011dhh.1_Nonsense_Mutation_p.L256*	NM_001040462	NP_001035552	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8 isoform 2 precursor	440	B30.2/SPRY.|Cytoplasmic (Potential).					integral to membrane				upper_aerodigestive_tract(1)|skin(1)	2	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAAGGCTTATTGAGGCCCTAC	0.463													92	133	---	---	---	---	PASS
ZNF184	7738	broad.mit.edu	37	6	27420477	27420477	+	Silent	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27420477G>A	uc003njj.2	-	5	1672	c.861C>T	c.(859-861)TTC>TTT	p.F287F	ZNF184_uc010jqv.2_Silent_p.F287F|ZNF184_uc003nji.2_Silent_p.F287F	NM_007149	NP_009080	Q99676	ZN184_HUMAN	zinc finger protein 184	287	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GACCCTCAATGAAGCCTTTTC	0.378													24	95	---	---	---	---	PASS
TMEM217	221468	broad.mit.edu	37	6	37186439	37186439	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37186439T>C	uc003onl.2	-	2	449	c.368A>G	c.(367-369)GAG>GGG	p.E123G	TMEM217_uc010jwr.2_Missense_Mutation_p.E123G|TMEM217_uc010jws.2_Intron|TMEM217_uc003onm.3_Missense_Mutation_p.E123G	NM_145316	NP_660359	Q8N7C4	TM217_HUMAN	transmembrane protein 217 isoform 1	123						integral to membrane					0						GATTCTGACCTCTTTAATGTC	0.413													5	174	---	---	---	---	PASS
PLA2G7	7941	broad.mit.edu	37	6	46672213	46672213	+	3'UTR	SNP	T	A	A	rs112939713		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46672213T>A	uc010jzf.2	-	12						NM_005084	NP_005075	Q13093	PAFA_HUMAN	phospholipase A2, group VII						inflammatory response|lipid catabolic process	extracellular space	1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding				0			Lung(136;0.192)			tctctctctctctcacacaca	0.159													4	30	---	---	---	---	PASS
PHF3	23469	broad.mit.edu	37	6	64421671	64421671	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64421671A>G	uc003pep.1	+	15	4213	c.4187A>G	c.(4186-4188)AAT>AGT	p.N1396S	PHF3_uc003pen.2_Missense_Mutation_p.N1308S|PHF3_uc011dxs.1_Missense_Mutation_p.N665S	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	1396					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GAGGAAGAAAATGACTTTTTT	0.368													19	90	---	---	---	---	PASS
AKD1	221264	broad.mit.edu	37	6	109940327	109940327	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109940327T>C	uc003ptn.2	-	13	1444	c.1367A>G	c.(1366-1368)AAG>AGG	p.K456R		NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1	456	Potential.				nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1						CCTGAGAAGCTTTTCTTTCAC	0.348													6	324	---	---	---	---	PASS
DDO	8528	broad.mit.edu	37	6	110714419	110714419	+	Silent	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110714419C>T	uc003puc.2	-	5	673	c.669G>A	c.(667-669)AAG>AAA	p.K223K	C6orf186_uc003pub.2_Intron|DDO_uc003pud.2_Silent_p.K164K	NM_003649	NP_003640	Q99489	OXDD_HUMAN	D-aspartate oxidase isoform a	195					aspartate catabolic process	peroxisome	binding|D-amino-acid oxidase activity|D-aspartate oxidase activity			ovary(2)|breast(1)	3		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)		CAGGGAAAATCTTTGAGTCTC	0.502													7	31	---	---	---	---	PASS
BCLAF1	9774	broad.mit.edu	37	6	136597148	136597148	+	Silent	SNP	G	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136597148G>T	uc003qgx.1	-	5	1768	c.1515C>A	c.(1513-1515)CTC>CTA	p.L505L	BCLAF1_uc003qgw.1_Intron|BCLAF1_uc003qgy.1_Silent_p.L503L|BCLAF1_uc011edc.1_Intron|BCLAF1_uc011edd.1_RNA|BCLAF1_uc011ede.1_Silent_p.L503L	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1 isoform	505					induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		AGAGGTCTTTGAGCTTTTCAG	0.393													19	467	---	---	---	---	PASS
RAET1G	353091	broad.mit.edu	37	6	150240180	150240180	+	Silent	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150240180T>C	uc010kii.1	-	3	698	c.630A>G	c.(628-630)GGA>GGG	p.G210G	uc003qni.1_Intron|RAET1G_uc003qnm.2_RNA	NM_001001788	NP_001001788	Q6H3X3	RET1G_HUMAN	retinoic acid early transcript 1G precursor	210	Extracellular (Potential).|MHC class I alpha-2 like.				antigen processing and presentation|immune response	integral to membrane|MHC class I protein complex	protein binding				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		TCCTGTTACCTCCTGCACTTG	0.463													6	219	---	---	---	---	PASS
PARK2	5071	broad.mit.edu	37	6	161781136	161781136	+	Silent	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161781136T>C	uc003qtx.3	-	11	1403	c.1269A>G	c.(1267-1269)GTA>GTG	p.V423V	PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Silent_p.V232V|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Silent_p.V395V|PARK2_uc003qtz.3_Silent_p.V274V|PARK2_uc011egf.1_Silent_p.V97V	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1	423	RING-type 2.				aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		TTTCCACTGGTACATGGCAGC	0.428													83	260	---	---	---	---	PASS
RINT1	60561	broad.mit.edu	37	7	105207775	105207775	+	3'UTR	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105207775G>A	uc003vda.1	+	15					RINT1_uc010ljj.1_3'UTR|EFCAB10_uc003vdb.2_Intron|EFCAB10_uc003vdc.3_3'UTR|uc003vdd.1_5'Flank	NM_021930	NP_068749	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1						cell cycle|G2/M transition DNA damage checkpoint|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane	protein binding			ovary(3)|central_nervous_system(1)	4						TCAGAAAAAGGTTTCTTTGGT	0.303													12	60	---	---	---	---	PASS
WASL	8976	broad.mit.edu	37	7	123335918	123335918	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123335918G>A	uc003vkz.2	-	7	959	c.631C>T	c.(631-633)CAC>TAC	p.H211Y		NM_003941	NP_003932	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome gene-like protein	211	CRIB.				actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|cytosol|nucleolus|plasma membrane	actin binding|small GTPase regulator activity				0						TGTCCAATGTGCCTGAAGTAG	0.308													42	166	---	---	---	---	PASS
HEY1	23462	broad.mit.edu	37	8	80677934	80677934	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80677934G>A	uc003ybm.2	-	5	604	c.404C>T	c.(403-405)GCG>GTG	p.A135V	HEY1_uc010lzq.2_Missense_Mutation_p.A16V|HEY1_uc003ybl.2_Missense_Mutation_p.A139V	NM_012258	NP_036390	Q9Y5J3	HEY1_HUMAN	hairy/enhancer-of-split related with YRPW motif	135	Orange.				angiogenesis|negative regulation of Notch signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|Notch signaling pathway|transcription, DNA-dependent	nucleus	DNA binding|protein binding			lung(3)	3	all_lung(9;5.1e-05)		Epithelial(68;0.076)|all cancers(69;0.179)			CAGATAACGCGCAACTTCTGC	0.507											OREG0018837	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	14	---	---	---	---	PASS
DPY19L4	286148	broad.mit.edu	37	8	95773983	95773983	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95773983A>G	uc003ygx.2	+	8	915	c.791A>G	c.(790-792)GAG>GGG	p.E264G		NM_181787	NP_861452	Q7Z388	D19L4_HUMAN	dpy-19-like 4	264	Helical; (Potential).					integral to membrane				ovary(2)	2	Breast(36;3.85e-06)					ATGATGTGGGAGTATAGCCAC	0.343													6	387	---	---	---	---	PASS
TRHR	7201	broad.mit.edu	37	8	110131432	110131432	+	Silent	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110131432C>T	uc003ymz.3	+	2	961	c.945C>T	c.(943-945)ATC>ATT	p.I315I		NM_003301	NP_003292	P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	315	Helical; Name=7; (Potential).					integral to plasma membrane	thyrotropin-releasing hormone receptor activity			skin(2)|lung(1)	3			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			ACAGTGCCATCAACCCGGTGA	0.433													45	153	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110487349	110487349	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110487349A>T	uc003yne.2	+	51	8712	c.8608A>T	c.(8608-8610)ACA>TCA	p.T2870S		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	2870	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TCCTATAGGCACAAGCATTAT	0.348										HNSCC(38;0.096)			25	130	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113529436	113529436	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113529436C>G	uc003ynu.2	-	28	4742	c.4583G>C	c.(4582-4584)TGT>TCT	p.C1528S	CSMD3_uc003yns.2_Missense_Mutation_p.C800S|CSMD3_uc003ynt.2_Missense_Mutation_p.C1488S|CSMD3_uc011lhx.1_Missense_Mutation_p.C1424S	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1528	Extracellular (Potential).|Sushi 8.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TGGGTCACGACACGCAGTGGC	0.403										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	98	---	---	---	---	PASS
ENPP2	5168	broad.mit.edu	37	8	120633703	120633703	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120633703C>A	uc003yot.1	-	4	435	c.349G>T	c.(349-351)GCC>TCC	p.A117S	ENPP2_uc003yos.1_Missense_Mutation_p.A117S|ENPP2_uc010mdd.1_Missense_Mutation_p.A117S	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	autotaxin isoform 2 preproprotein	117	SMB 2.				cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CAGTGACAGGCATTTTCTTCA	0.468													29	157	---	---	---	---	PASS
LRRC6	23639	broad.mit.edu	37	8	133584514	133584514	+	3'UTR	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133584514A>G	uc003ytk.2	-	12					LRRC6_uc003ytl.2_RNA	NM_012472	NP_036604	Q86X45	LRRC6_HUMAN	leucine rich repeat containing 6							cytoplasm				ovary(1)|kidney(1)	2	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			CCAAAACTGGACCTGGTGGGT	0.448													6	230	---	---	---	---	PASS
JRK	8629	broad.mit.edu	37	8	143746492	143746492	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143746492T>A	uc003ywo.2	-	2	1500	c.986A>T	c.(985-987)CAG>CTG	p.Q329L	JRK_uc003ywp.2_Missense_Mutation_p.Q329L|JRK_uc010mew.1_Missense_Mutation_p.Q329L	NM_001077527	NP_001070995			jerky isoform b												0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ctccatgggctgcaccaatga	0.000													4	18	---	---	---	---	PASS
KLF9	687	broad.mit.edu	37	9	73027803	73027803	+	Silent	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73027803A>G	uc004aht.2	-	1	1771	c.477T>C	c.(475-477)CAT>CAC	p.H159H		NM_001206	NP_001197	Q13886	KLF9_HUMAN	Kruppel-like factor 9	159	C2H2-type 1.				regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GGGCTTTGAGATGGGAGGATT	0.577													11	41	---	---	---	---	PASS
S1PR3	1903	broad.mit.edu	37	9	91616249	91616249	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91616249T>C	uc004aqe.2	+	2	530	c.134T>C	c.(133-135)CTC>CCC	p.L45P		NM_005226	NP_005217	Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	45	Helical; Name=1; (By similarity).				anatomical structure morphogenesis|elevation of cytosolic calcium ion concentration|inflammatory response|positive regulation of cell proliferation	integral to plasma membrane	lipid binding|lysosphingolipid and lysophosphatidic acid receptor activity			ovary(2)|lung(1)|central_nervous_system(1)|skin(1)	5						ACCACCGTGCTCTTCTTGGTC	0.532											OREG0019291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	21	---	---	---	---	PASS
C9orf125	84302	broad.mit.edu	37	9	104239059	104239059	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104239059T>C	uc004bbm.2	-	2	638	c.316A>G	c.(316-318)ATC>GTC	p.I106V	uc004bbl.1_5'Flank	NM_032342	NP_115718	Q9BRR3	CI125_HUMAN	hypothetical protein LOC84302	106						integral to membrane					0		Acute lymphoblastic leukemia(62;0.0527)				ACAGTGATGATGGTGATCACC	0.622													5	16	---	---	---	---	PASS
DFNB31	25861	broad.mit.edu	37	9	117165567	117165567	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117165567G>T	uc004biz.3	-	11	3120	c.2471C>A	c.(2470-2472)GCC>GAC	p.A824D	DFNB31_uc004bix.2_Missense_Mutation_p.A473D|DFNB31_uc004biy.3_Missense_Mutation_p.A441D|DFNB31_uc004bja.3_Missense_Mutation_p.A823D	NM_015404	NP_056219	Q9P202	WHRN_HUMAN	CASK-interacting protein CIP98 isoform 1	824	PDZ 3.				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						GCCCAGGGTGGCCGCACTTTT	0.617													5	28	---	---	---	---	PASS
SEC61A2	55176	broad.mit.edu	37	10	12178106	12178106	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12178106C>G	uc001ile.2	+	3	225	c.78C>G	c.(76-78)ATC>ATG	p.I26M	SEC61A2_uc010qbq.1_Intron|SEC61A2_uc001ilf.3_RNA|SEC61A2_uc001ilh.3_RNA|SEC61A2_uc001ilg.3_Missense_Mutation_p.I26M	NM_018144	NP_060614	Q9H9S3	S61A2_HUMAN	Sec61 alpha form 2 isoform a	26	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1		Renal(717;0.228)				TTGTACAGATCCAGTTTAGAG	0.368													11	422	---	---	---	---	PASS
SYT15	83849	broad.mit.edu	37	10	46962003	46962003	+	Silent	SNP	G	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46962003G>C	uc001jea.2	-	8	1386	c.1233C>G	c.(1231-1233)CGC>CGG	p.R411R	SYT15_uc001jdz.2_Intron|SYT15_uc001jeb.2_Silent_p.R289R|SYT15_uc010qfp.1_RNA	NM_031912	NP_114118	Q9BQS2	SYT15_HUMAN	synaptotagmin XV isoform a	411	Cytoplasmic (Potential).					integral to membrane|plasma membrane					0						GCGCATGCCAGCGCTTCACCA	0.662													9	24	---	---	---	---	PASS
NCOA4	8031	broad.mit.edu	37	10	51582263	51582263	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51582263G>A	uc001jis.3	+	6	764	c.561G>A	c.(559-561)ATG>ATA	p.M187I	PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Missense_Mutation_p.M203I|NCOA4_uc010qhd.1_Missense_Mutation_p.M203I|NCOA4_uc010qhe.1_Missense_Mutation_p.M87I|NCOA4_uc010qhf.1_Missense_Mutation_p.M21I|NCOA4_uc001jit.2_Missense_Mutation_p.M187I|NCOA4_uc009xoo.2_Missense_Mutation_p.M187I	NM_001145263	NP_001138735	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4 isoform 3	187					androgen receptor signaling pathway|male gonad development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	androgen receptor binding|transcription coactivator activity			central_nervous_system(1)|kidney(1)	2						GTATCTCCATGCCAGAGCAGG	0.358			T	RET	papillary thyroid 								37	173	---	---	---	---	PASS
LRRTM3	347731	broad.mit.edu	37	10	68687373	68687373	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68687373C>A	uc001jmz.1	+	2	1249	c.699C>A	c.(697-699)AAC>AAA	p.N233K	CTNNA3_uc009xpn.1_Intron|CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|LRRTM3_uc001jmy.2_Missense_Mutation_p.N233K	NM_178011	NP_821079	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	233	Extracellular (Potential).|LRR 8.					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						GCCTTCAGAACCTTTACTTGC	0.453													16	46	---	---	---	---	PASS
HELLS	3070	broad.mit.edu	37	10	96352150	96352150	+	Splice_Site	SNP	A	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96352150A>T	uc001kjt.2	+	17	1957	c.1852_splice	c.e17-2	p.V618_splice	HELLS_uc001kjs.2_Splice_Site_p.V602_splice|HELLS_uc009xul.2_Splice_Site_p.V520_splice|HELLS_uc009xum.2_Splice_Site_p.V488_splice|HELLS_uc009xun.2_Splice_Site_p.V494_splice|HELLS_uc009xuo.2_Splice_Site_p.V664_splice|HELLS_uc001kju.2_Splice_Site_p.V257_splice|HELLS_uc009xup.2_Splice_Site|HELLS_uc009xuq.2_Splice_Site_p.V480_splice|HELLS_uc009xur.2_Splice_Site	NM_018063	NP_060533	Q9NRZ9	HELLS_HUMAN	helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		GTTTAATTTCAGGTGCTGCTT	0.328													17	110	---	---	---	---	PASS
CUZD1	50624	broad.mit.edu	37	10	124598575	124598575	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124598575T>C	uc001lgq.2	-	3	738	c.406A>G	c.(406-408)AGA>GGA	p.R136G	CUZD1_uc001lgp.2_5'Flank|CUZD1_uc009yad.2_5'Flank|CUZD1_uc009yaf.2_Intron|CUZD1_uc001lgr.2_5'UTR|CUZD1_uc010qty.1_5'UTR|CUZD1_uc009yae.2_5'UTR|CUZD1_uc001lgs.2_Missense_Mutation_p.R136G|CUZD1_uc010qtz.1_Missense_Mutation_p.R136G	NM_022034	NP_071317	Q86UP6	CUZD1_HUMAN	CUB and zona pellucida-like domains 1 precursor	136	CUB 1.|Extracellular (Potential).				cell cycle|cell division|cell proliferation|substrate-dependent cell migration, cell attachment to substrate|trypsinogen activation	integral to membrane|transport vesicle membrane|zymogen granule membrane				ovary(1)|skin(1)	2		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		AAGACAGTTCTTTGAATTCTT	0.398													6	275	---	---	---	---	PASS
OVCH2	341277	broad.mit.edu	37	11	7723751	7723751	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7723751A>G	uc010rbf.1	-	4	416	c.416T>C	c.(415-417)ATG>ACG	p.M139T		NM_198185	NP_937828			ovochymase 2 precursor												0				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)		ATCATAGTCCATTGGTTTCTT	0.423													56	253	---	---	---	---	PASS
LOC494141	494141	broad.mit.edu	37	11	18231982	18231982	+	RNA	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18231982G>A	uc009yhh.2	+	2		c.1006G>A			LOC494141_uc001mnx.3_RNA|LOC494141_uc009yhi.1_RNA	NR_026541				Homo sapiens cDNA FLJ29025 fis, clone PRS03236.												0						CTTTCCCCAAGGTTTTCCAAA	0.408													14	82	---	---	---	---	PASS
TBC1D10C	374403	broad.mit.edu	37	11	67173105	67173105	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67173105A>G	uc001ola.2	+	5	429	c.400A>G	c.(400-402)ACC>GCC	p.T134A	PPP1CA_uc001okx.1_Intron|TBC1D10C_uc001okz.2_Missense_Mutation_p.T134A|TBC1D10C_uc001olb.2_RNA	NM_198517	NP_940919	Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	134	Rab-GAP TBC.					intracellular	Rab GTPase activator activity				0			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			GTGGATGGAGACCATTGGCAG	0.647													4	62	---	---	---	---	PASS
CDK4	1019	broad.mit.edu	37	12	58144819	58144819	+	Missense_Mutation	SNP	C	T	T	rs150281463		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58144819C>T	uc001spv.2	-	4	636	c.409G>A	c.(409-411)GTT>ATT	p.V137I	CDK4_uc010ssb.1_Missense_Mutation_p.V17I|CDK4_uc001spw.2_Intron|uc010ssc.1_5'Flank	NM_000075	NP_000066	P11802	CDK4_HUMAN	cyclin-dependent kinase 4	137	Protein kinase.				cell division|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|positive regulation of fibroblast proliferation|regulation of gene expression|response to drug|S phase of mitotic cell cycle	cyclin-dependent protein kinase holoenzyme complex|cytosol|membrane	ATP binding|cyclin-dependent protein kinase activity|protein binding			lung(1)|breast(1)|central_nervous_system(1)	3	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			TCTCGGTGAACGATGCAATTG	0.498			Mis			melanoma 			Hereditary_Melanoma				3	75	---	---	---	---	PASS
MON2	23041	broad.mit.edu	37	12	62946750	62946750	+	Silent	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62946750A>G	uc001sre.2	+	24	3397	c.3006A>G	c.(3004-3006)GAA>GAG	p.E1002E	MON2_uc009zqj.2_Silent_p.E1002E|MON2_uc010ssl.1_Silent_p.E930E|MON2_uc010ssm.1_Silent_p.E979E|MON2_uc010ssn.1_Silent_p.E1002E|MON2_uc001srf.2_Silent_p.E765E	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	1003				E -> K (in Ref. 5; CAD89933).	Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		AGCAGGCAGAAGAGAAAGGAG	0.388													6	248	---	---	---	---	PASS
HMGA2	8091	broad.mit.edu	37	12	66308767	66308767	+	Intron	SNP	A	G	G	rs148485269	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66308767A>G	uc001ssx.2	+						HMGA2_uc001ssw.1_Intron|HMGA2_uc001ssu.1_3'UTR|HMGA2_uc001ssv.2_Intron	NM_003483	NP_003474	P52926	HMGA2_HUMAN	high mobility group AT-hook 2 isoform a						cell division|chromatin organization|mitosis|multicellular organismal development|regulation of growth|transcription, DNA-dependent	chromatin	AT DNA binding		HMGA2/LPP(161)|HMGA2/WIF1_ENST00000286574(14)|HMGA2/RAD51B(11)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/CCNB1IP1(2)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/COX6C(2)	soft_tissue(159)|bone(27)|salivary_gland(22)	208	all_cancers(1;5.78e-46)		GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)		AAAAATGTCTATTAGTGTTCC	0.229			T	 LHFP|RAD51L1|LPP|HEI10|COX6C|CMKOR1|NFIB|ALDH2|CCNB1IP1|EBF1|WIF1|FHIT	lipoma|leiomyoma|pleiomorphic salivary gland adenoma								38	64	---	---	---	---	PASS
HSP90B1	7184	broad.mit.edu	37	12	104341144	104341144	+	Missense_Mutation	SNP	A	G	G	rs17034989		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104341144A>G	uc001tkb.1	+	17	2423	c.2318A>G	c.(2317-2319)GAC>GGC	p.D773G	HSP90B1_uc010swg.1_Missense_Mutation_p.D438G|HSP90B1_uc009zui.1_Intron	NM_003299	NP_003290	P14625	ENPL_HUMAN	heat shock protein 90kDa beta, member 1	773					actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm	ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding			ovary(2)|skin(1)	3					Rifabutin(DB00615)	acaacagaagacacagagcaa	0.174													7	707	---	---	---	---	PASS
ZMYM5	9205	broad.mit.edu	37	13	20426164	20426164	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20426164C>A	uc010tcn.1	-	3	422	c.157G>T	c.(157-159)GAT>TAT	p.D53Y	ZMYM5_uc001umm.1_5'UTR|ZMYM5_uc001umn.2_Missense_Mutation_p.D53Y|ZMYM5_uc001umo.2_Missense_Mutation_p.D53Y	NM_001142684	NP_001136156	Q9UJ78	ZMYM5_HUMAN	zinc finger protein 237 isoform 3	53	Poly-Asp.					nucleus	zinc ion binding				0		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		tcatcatcatcTTCCACTGGT	0.363													30	118	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39264065	39264065	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39264065G>A	uc001uwv.2	+	1	2893	c.2584G>A	c.(2584-2586)GCC>ACC	p.A862T		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	862	CSPG 5.|Extracellular (Potential).				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CACTGATGTTGCCCATATCTC	0.512													13	71	---	---	---	---	PASS
C13orf23	80209	broad.mit.edu	37	13	39596482	39596482	+	Silent	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39596482A>G	uc001uwy.2	-	9	1584	c.711T>C	c.(709-711)ACT>ACC	p.T237T	C13orf23_uc001uwz.2_Silent_p.T215T	NM_025138	NP_079414	Q86XN7	CM023_HUMAN	hypothetical protein LOC80209 isoform 1	237	Pro-rich.									ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)		CAGGATTAGGAGTATATGGAG	0.373													6	236	---	---	---	---	PASS
TOX4	9878	broad.mit.edu	37	14	21966604	21966604	+	3'UTR	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21966604T>C	uc001waz.2	+	9					TOX4_uc001wba.2_RNA|TOX4_uc010tlu.1_3'UTR|TOX4_uc010tlv.1_3'UTR|METTL3_uc001wbb.2_Intron|METTL3_uc001wbc.2_Intron	NM_014828	NP_055643	O94842	TOX4_HUMAN	epidermal Langerhans cell protein LCP1							chromatin|nucleus|PTW/PP1 phosphatase complex	DNA binding|protein binding			ovary(1)	1	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		GAAGACTGCCTATCATCATAT	0.333													7	25	---	---	---	---	PASS
C14orf135	64430	broad.mit.edu	37	14	60587988	60587988	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60587988G>T	uc001xer.3	+	7	1837	c.1315G>T	c.(1315-1317)GGC>TGC	p.G439C	C14orf135_uc001xeq.2_Missense_Mutation_p.G439C|C14orf135_uc010apm.2_RNA	NM_022495	NP_071940	Q63HM2	CN135_HUMAN	hepatitis C virus F protein-binding protein 2	673						integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)		TCTGGAATGTGGCTATACTTA	0.328													75	244	---	---	---	---	PASS
KCNH5	27133	broad.mit.edu	37	14	63473094	63473094	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63473094G>T	uc001xfx.2	-	3	345	c.294C>A	c.(292-294)TAC>TAA	p.Y98*	KCNH5_uc001xfy.2_Nonsense_Mutation_p.Y98*|KCNH5_uc001xfz.1_Nonsense_Mutation_p.Y40*|KCNH5_uc001xga.2_Nonsense_Mutation_p.Y40*	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	98	PAC.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		TGTTTTTCTTGTACAGAAGAA	0.348													18	145	---	---	---	---	PASS
RBM25	58517	broad.mit.edu	37	14	73550237	73550237	+	Silent	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73550237A>G	uc001xno.2	+	5	568	c.360A>G	c.(358-360)CAA>CAG	p.Q120Q	RBM25_uc001xnn.3_Silent_p.Q120Q|RBM25_uc010ttu.1_Silent_p.Q120Q|RBM25_uc001xnp.2_Intron	NM_021239	NP_067062	P49756	RBM25_HUMAN	RNA binding motif protein 25	120	RRM.				apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		AGAGAGTACAAGGTGCTTCCG	0.318													66	209	---	---	---	---	PASS
ABCD4	5826	broad.mit.edu	37	14	74763081	74763081	+	Missense_Mutation	SNP	A	G	G	rs145669133	byFrequency	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74763081A>G	uc001xpr.2	-	5	649	c.497T>C	c.(496-498)ATC>ACC	p.I166T	ABCD4_uc001xps.2_Missense_Mutation_p.I7T|ABCD4_uc001xpt.2_Missense_Mutation_p.I7T|ABCD4_uc010tur.1_Missense_Mutation_p.I79T|ABCD4_uc001xpu.2_5'UTR|ABCD4_uc001xpv.2_RNA	NM_005050	NP_005041	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D, member 4	166	ABC transmembrane type-1.					ATP-binding cassette (ABC) transporter complex|integral to membrane|peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			upper_aerodigestive_tract(2)|large_intestine(1)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00153)		GAACGGGGAGATGATGAGCTT	0.602													11	36	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106331518	106331518	+	RNA	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106331518C>T	uc010tyt.1	-	3483		c.53177G>A			uc001yrs.2_5'Flank|uc001yrt.2_5'Flank|uc001yrw.1_5'Flank|uc001yrx.1_5'Flank|uc001yrz.1_5'Flank|uc001yse.2_5'Flank|uc001ysf.2_Intron|uc001ysj.2_5'Flank|uc001ysk.1_5'Flank|uc001ysl.1_5'Flank|uc001ysm.1_5'Flank|uc001ysn.1_5'Flank|uc001yso.1_Intron					Parts of antibodies, mostly variable regions.												0						GCCCTCCTGCCGACCTCCTTT	0.612													4	149	---	---	---	---	PASS
VPS39	23339	broad.mit.edu	37	15	42454241	42454241	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42454241C>T	uc001zpd.2	-	24	2633	c.2482G>A	c.(2482-2484)GAA>AAA	p.E828K	VPS39_uc001zpc.2_Missense_Mutation_p.E817K|VPS39_uc001zpb.2_Missense_Mutation_p.E163K	NM_015289	NP_056104	Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39	828					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)		CTCAGGAATTCTGCATGGAGA	0.448													40	177	---	---	---	---	PASS
ISL2	64843	broad.mit.edu	37	15	76634124	76634124	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76634124C>T	uc002bbw.1	+	6	1106	c.1028C>T	c.(1027-1029)TCG>TTG	p.S343L		NM_145805	NP_665804	Q96A47	ISL2_HUMAN	ISL LIM homeobox 2	343						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TCCCTGTCCTCGCAGCTCCCG	0.682													3	20	---	---	---	---	PASS
LRRK1	79705	broad.mit.edu	37	15	101606007	101606007	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101606007G>A	uc002bwr.2	+	32	5684	c.5365G>A	c.(5365-5367)GTG>ATG	p.V1789M	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA|LRRK1_uc002bws.2_RNA	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	1789					small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CATGTTTCCCGTGCGGCCCTT	0.632													6	27	---	---	---	---	PASS
OR4F15	390649	broad.mit.edu	37	15	102358740	102358740	+	Silent	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102358740C>T	uc010uts.1	+	1	351	c.351C>T	c.(349-351)GCC>GCT	p.A117A		NM_001001674	NP_001001674	Q8NGB8	O4F15_HUMAN	olfactory receptor, family 4, subfamily F,	117	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			TGCTCATAGCCATGGCCTTTG	0.453													4	132	---	---	---	---	PASS
PIGQ	9091	broad.mit.edu	37	16	629095	629095	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:629095T>C	uc002cho.2	+	7	1352	c.1250T>C	c.(1249-1251)CTG>CCG	p.L417P	PIGQ_uc010bqw.2_Missense_Mutation_p.L417P|PIGQ_uc002chn.2_Missense_Mutation_p.L417P|PIGQ_uc010uui.1_Missense_Mutation_p.L431P|PIGQ_uc002chp.2_5'Flank	NM_148920	NP_683721	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	417	Leu-rich.				C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)				ATCCATGGCCTGTCCTCACTG	0.507													16	24	---	---	---	---	PASS
NKD1	85407	broad.mit.edu	37	16	50667285	50667285	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50667285C>T	uc002egg.1	+	10	1230	c.1006C>T	c.(1006-1008)CGG>TGG	p.R336W		NM_033119	NP_149110	Q969G9	NKD1_HUMAN	naked cuticle homolog 1	336					Wnt receptor signaling pathway	cytoplasm|plasma membrane	calcium ion binding|protein binding				0		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		GCAACGGCTCCGGGGCACCCA	0.642													20	54	---	---	---	---	PASS
MT1G	4495	broad.mit.edu	37	16	56700810	56700810	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56700810T>C	uc002eju.1	-	3	239	c.167A>G	c.(166-168)AAG>AGG	p.K56R	MT1G_uc002ejv.1_RNA|MT1H_uc002ejw.2_5'Flank	NM_005950	NP_005941	P13640	MT1G_HUMAN	metallothionein 1G	57	Alpha.						metal ion binding|protein binding				0						GCAGCTGCACTTCTCCGATGC	0.547													20	67	---	---	---	---	PASS
WFDC1	58189	broad.mit.edu	37	16	84328487	84328487	+	5'UTR	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84328487C>T	uc002fhw.2	+	1					WFDC1_uc002fhv.2_5'UTR	NM_021197	NP_067020	Q9HC57	WFDC1_HUMAN	WAP four-disulfide core domain 1 precursor						negative regulation of cell growth	extracellular space	serine-type endopeptidase inhibitor activity			breast(1)	1						GTCCAGCAGACTGTGCACGCT	0.627													4	17	---	---	---	---	PASS
ZNF594	84622	broad.mit.edu	37	17	5084426	5084426	+	3'UTR	SNP	C	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5084426C>A	uc010cla.1	-	2						NM_032530	NP_115919	Q96JF6	ZN594_HUMAN	zinc finger protein 594						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(1)	3						GGCCTTCCAACATTCAGGGCA	0.428													4	51	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7669721	7669721	+	Silent	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7669721G>A	uc002giu.1	+	21	3611	c.3597G>A	c.(3595-3597)GAG>GAA	p.E1199E		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1199	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TGCGGGAAGAGGAAAATAGTC	0.552													17	59	---	---	---	---	PASS
TMEM220	388335	broad.mit.edu	37	17	10626587	10626587	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10626587T>C	uc002gmx.2	-	5	825	c.347A>G	c.(346-348)AAG>AGG	p.K116R	TMEM220_uc002gmy.2_Missense_Mutation_p.K106R	NM_001004313	NP_001004313	Q6QAJ8	TM220_HUMAN	transmembrane protein 220	116	Helical; (Potential).					integral to membrane					0						GAATACTTACTTTGAGGAACT	0.254													5	174	---	---	---	---	PASS
RDM1	201299	broad.mit.edu	37	17	34249624	34249624	+	Silent	SNP	C	T	T	rs112692396		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34249624C>T	uc002hkh.2	-	5	673	c.624G>A	c.(622-624)AAG>AAA	p.K208K	RDM1_uc010cty.2_Intron|RDM1_uc010ctz.2_Intron|RDM1_uc010cua.2_Silent_p.K185K|RDM1_uc002hkg.3_Intron|RDM1_uc010cub.2_RNA|RDM1_uc010cud.2_Intron|RDM1_uc010cuf.2_RNA|RDM1_uc010cue.2_RNA|RDM1_uc010cug.2_Intron|RDM1_uc010cuc.2_Intron|RDM1_uc010wco.1_3'UTR|RDM1_uc010wcp.1_Silent_p.K185K|RDM1_uc002hki.2_Silent_p.K208K	NM_145654	NP_663629	Q8NG50	RDM1_HUMAN	RAD52 motif 1 isoform 1	208					DNA recombination|DNA repair	Cajal body|cytoplasm|nucleolus|PML body	DNA binding|nucleotide binding|RNA binding			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CTGACAAAGCCTTCTGAATAG	0.373								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					38	127	---	---	---	---	PASS
LOC644669	644669	broad.mit.edu	37	18	15325675	15325675	+	RNA	SNP	C	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15325675C>A	uc002ktd.1	-	2		c.82G>T				NR_027417				Homo sapiens cDNA FLJ40312 fis, clone TESTI2029880.												0						ATATTTGGATCAGCACCAGAA	0.388													4	13	---	---	---	---	PASS
SERPINB5	5268	broad.mit.edu	37	18	61154179	61154179	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61154179G>C	uc002liz.3	+	3	311	c.169G>C	c.(169-171)GTT>CTT	p.V57L	SERPINB5_uc002liy.2_Missense_Mutation_p.V57L	NM_002639	NP_002630	P36952	SPB5_HUMAN	serine (or cysteine) proteinase inhibitor, clade	57					cellular component movement|regulation of proteolysis	cytoplasm|extracellular space	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1						CTCTTAACAGGTTCTTCATTT	0.383													12	92	---	---	---	---	PASS
CD209	30835	broad.mit.edu	37	19	7810629	7810629	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7810629G>A	uc002mht.2	-	4	590	c.523C>T	c.(523-525)CGG>TGG	p.R175W	CD209_uc010xju.1_Intron|CD209_uc010dvp.2_Missense_Mutation_p.R151W|CD209_uc002mhr.2_Missense_Mutation_p.R151W|CD209_uc002mhs.2_Missense_Mutation_p.R151W|CD209_uc002mhu.2_Intron|CD209_uc010dvq.2_Missense_Mutation_p.R175W|CD209_uc002mhq.2_Missense_Mutation_p.R175W|CD209_uc002mhv.2_Missense_Mutation_p.R151W|CD209_uc002mhx.2_Missense_Mutation_p.R131W|CD209_uc002mhw.2_Intron|CD209_uc010dvr.2_Intron	NM_021155	NP_066978	Q9NNX6	CD209_HUMAN	CD209 molecule isoform 1	175	4.|Extracellular (Probable).|7 X approximate tandem repeats.				cell-cell recognition|endocytosis|heterophilic cell-cell adhesion|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to membrane|plasma membrane	mannose binding|metal ion binding|peptide antigen binding|receptor activity|virion binding			skin(1)	1						GCCTTCAGCCGAGTCAGCTCC	0.557													5	14	---	---	---	---	PASS
SIGLEC12	89858	broad.mit.edu	37	19	52004612	52004612	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52004612C>T	uc002pwx.1	-	1	432	c.376G>A	c.(376-378)GGA>AGA	p.G126R	SIGLEC12_uc002pww.1_5'Flank|SIGLEC12_uc010eoy.1_5'UTR	NM_053003	NP_443729	Q96PQ1	SIG12_HUMAN	sialic acid binding immunoglobulin-like	126	Ig-like V-type 1.|Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding			ovary(3)|skin(2)	5		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		TTCATATTTCCTCTCTCTACA	0.473													30	117	---	---	---	---	PASS
KIR3DL1	3811	broad.mit.edu	37	19	55377270	55377270	+	Silent	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55377270A>G	uc002qhl.3	+	7	1074	c.1011A>G	c.(1009-1011)AGA>AGG	p.R337R	KIR3DL2_uc010esh.2_Silent_p.R320R|KIR3DL2_uc002qho.3_Silent_p.R337R			P43629	KI3L1_HUMAN	SubName: Full=KIR3DS1;	337	Extracellular (Potential).				immune response|regulation of immune response	integral to plasma membrane	HLA-B specific inhibitory MHC class I receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|skin(1)	5				GBM - Glioblastoma multiforme(193;0.0192)		GTATCTGCAGACACCTGCATG	0.353													7	715	---	---	---	---	PASS
FOXS1	2307	broad.mit.edu	37	20	30432839	30432839	+	Silent	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30432839C>T	uc002wwt.1	-	1	582	c.507G>A	c.(505-507)CTG>CTA	p.L169L		NM_004118	NP_004109	O43638	FOXS1_HUMAN	forkhead box S1	169					anti-apoptosis|artery morphogenesis|blood vessel remodeling|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|insulin receptor signaling pathway|lymphangiogenesis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|neural crest cell fate commitment|neuromuscular process controlling balance|Notch signaling pathway|ossification|paraxial mesodermal cell fate commitment|patterning of blood vessels|positive regulation of multicellular organism growth|positive regulation of transcription from RNA polymerase II promoter|regulation of blood vessel size|regulation of organ growth|somitogenesis|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(1)	1						TGGCCCCCACCAGACCCCCAA	0.647													3	16	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47246011	47246011	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47246011A>G	uc002xtw.1	-	37	4765	c.4742T>C	c.(4741-4743)GTC>GCC	p.V1581A	PREX1_uc002xtv.1_Missense_Mutation_p.V878A	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	1581					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GCCACACATGACCATCTGGCA	0.652													4	38	---	---	---	---	PASS
C21orf45	54069	broad.mit.edu	37	21	33642036	33642036	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33642036T>C	uc002ypi.2	-	4	654	c.603A>G	c.(601-603)ATA>ATG	p.I201M		NM_018944	NP_061817	Q9NYP9	MS18A_HUMAN	chromosome 21 open reading frame 45	201					cell division|CenH3-containing nucleosome assembly at centromere|mitosis	chromosome, centromeric region|nucleoplasm					0						GAGACTTTTCTATTTCAACTC	0.338													28	108	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	20976999	20976999	+	RNA	SNP	C	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20976999C>G	uc002zsv.2	-	5		c.1536G>C								Homo sapiens, clone IMAGE:5171202, mRNA.																		AACCTACCTTCCCAGGGTCGA	0.498													4	24	---	---	---	---	PASS
FLJ39582	439931	broad.mit.edu	37	22	21363175	21363175	+	Intron	SNP	T	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21363175T>A	uc002ztu.1	+						MGC16703_uc002zty.3_RNA|MGC16703_uc002ztx.3_RNA|MGC16703_uc010gss.1_RNA|FLJ39582_uc002ztv.2_RNA					Homo sapiens cDNA FLJ39582 fis, clone SKMUS2004667.												0						CTGTACAACATGCAGCAGGCC	0.567													3	9	---	---	---	---	PASS
IQSEC2	23096	broad.mit.edu	37	X	53284001	53284001	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53284001C>T	uc004dsd.2	-	4	1313	c.1112G>A	c.(1111-1113)CGC>CAC	p.R371H	IQSEC2_uc004dsc.2_Missense_Mutation_p.R166H	NM_001111125	NP_001104595	Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2 isoform1	361	IQ.				regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3						GGCTGAGCTGCGTAGCCGCTC	0.592													12	9	---	---	---	---	PASS
GPR119	139760	broad.mit.edu	37	X	129518457	129518457	+	Missense_Mutation	SNP	G	A	A	rs138209054	byFrequency	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129518457G>A	uc011muv.1	-	1	965	c.965C>T	c.(964-966)TCC>TTC	p.S322F		NM_178471	NP_848566	Q8TDV5	GP119_HUMAN	G protein-coupled receptor 119	322	Cytoplasmic (Potential).					integral to membrane|plasma membrane	lipid binding			ovary(2)	2						GATGTGACAGGAACTTTCCCT	0.542													14	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11228	11228	+	RNA	SNP	T	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11228T>C	uc004cov.3	+	1		c.651T>C			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		CCCTAGTAGGCTCCCTTCCCC	0.488													47	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	10237	10238	+	5'Flank	INS	-	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10237_10238insC	uc001aaa.3	+						uc010nxq.1_5'Flank|uc010nxr.1_5'Flank					Homo sapiens mRNA for DEAD/H box polypeptide 11 like 1 (DDX11L1 gene).																		ctaacccctaaccctaacccta	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	10433	10434	+	5'Flank	INS	-	C	C	rs56289060		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10433_10434insC	uc001aaa.3	+						uc010nxq.1_5'Flank|uc010nxr.1_5'Flank					Homo sapiens mRNA for DEAD/H box polypeptide 11 like 1 (DDX11L1 gene).																		cctaaccctaaccctaacccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	1302156	1302157	+	IGR	INS	-	AATT	AATT	rs146862390	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1302156_1302157insAATT								MXRA8 (4999 upstream) : AURKAIP1 (6953 downstream)																							acaggtgactgagtgaattggt	0.124													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	4225386	4225386	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4225386delT								LOC100133612 (391509 upstream) : LOC284661 (246725 downstream)																							TAGGATGCCCTTTGCACCCTT	0.552													4	2	---	---	---	---	
RERE	473	broad.mit.edu	37	1	8426584	8426584	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8426584delT	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc010nzx.1_Intron|RERE_uc001apd.2_Intron	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		AAACAGAAGGTGGGGAAGAAC	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	11972298	11972301	+	IGR	DEL	TCAC	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11972298_11972301delTCAC								NPPB (53306 upstream) : KIAA2013 (7823 downstream)																							ATTCATTCGTTCACTCAGGCtctc	0.167													5	4	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17257187	17257188	+	Intron	INS	-	TCCGAGGGAGCACTC	TCCGAGGGAGCACTC	rs144414935	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17257187_17257188insTCCGAGGGAGCACTC	uc001azt.2	+						CROCC_uc009voy.1_Intron|CROCC_uc009voz.1_Intron	NM_014675	NP_055490	Q5TZA2	CROCC_HUMAN	ciliary rootlet coiled-coil						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		AGGGAGCACTGTCCAAGGGAGC	0.460													4	2	---	---	---	---	
PADI6	353238	broad.mit.edu	37	1	17723476	17723477	+	Intron	INS	-	CA	CA	rs144056968	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17723476_17723477insCA	uc001bak.1	+							NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	AGGAATGCACCCAGGTGGCTGG	0.629													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18241618	18241619	+	IGR	INS	-	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18241618_18241619insG								ACTL8 (88062 upstream) : IGSF21 (192621 downstream)																							ggcactccagtggccacagcct	0.173													4	2	---	---	---	---	
HSPG2	3339	broad.mit.edu	37	1	22179402	22179403	+	Intron	INS	-	C	C	rs142340642	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22179402_22179403insC	uc001bfj.2	-						HSPG2_uc009vqd.2_Intron	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor						angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	GTCCCGGGGGGCTGCCATACCT	0.698													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	39242550	39242550	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39242550delC								POU3F1 (730100 upstream) : RRAGC (62465 downstream)																							accatggcatccctataactg	0.070													4	2	---	---	---	---	
EIF2B3	8891	broad.mit.edu	37	1	45336190	45336190	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45336190delT	uc001cmt.1	-						EIF2B3_uc001cmu.1_Intron|EIF2B3_uc001cmv.1_Intron	NM_020365	NP_065098	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B,						negative regulation of translational initiation in response to stress|oligodendrocyte development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	nucleotidyltransferase activity|protein binding|translation initiation factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					cttagattccttttcttatgt	0.015													4	2	---	---	---	---	
HSPB11	51668	broad.mit.edu	37	1	54396228	54396228	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54396228delT	uc001cwh.2	-						HSPB11_uc001cwi.1_Intron	NM_016126	NP_057210	Q9Y547	HSB11_HUMAN	heat shock protein family B (small), member 11						cell adhesion|response to stress						0						attcatgaggtttttttttta	0.174													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56222733	56222733	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56222733delA								USP24 (541971 upstream) : PPAP2B (737700 downstream)																							ATTCCAAAGGAAAGGAACTAG	0.249													4	2	---	---	---	---	
DNAJC6	9829	broad.mit.edu	37	1	65864133	65864134	+	Intron	DEL	AC	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65864133_65864134delAC	uc001dcd.1	+						DNAJC6_uc010opc.1_Intron|DNAJC6_uc001dce.1_Intron	NM_014787	NP_055602	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6						cellular membrane organization|post-Golgi vesicle-mediated transport	cytosol	heat shock protein binding|protein tyrosine phosphatase activity|SH3 domain binding			large_intestine(1)|lung(1)|ovary(1)	3						tagaggtgggacacacacacat	0.114													4	2	---	---	---	---	
NEXN	91624	broad.mit.edu	37	1	78398877	78398877	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78398877delA	uc001dic.3	+						NEXN_uc001dia.3_Intron|NEXN_uc009wcb.1_Intron|NEXN_uc001dib.3_Intron|NEXN_uc001did.1_Intron|NEXN_uc001dif.1_Intron|NEXN_uc001dig.3_5'UTR	NM_144573	NP_653174	Q0ZGT2	NEXN_HUMAN	nexilin (F actin binding protein)						regulation of cell migration|regulation of cytoskeleton organization	cytoskeleton|Z disc	actin filament binding|structural constituent of muscle			ovary(2)	2				Colorectal(170;0.114)		aaaaacaaaCAAAAAAAAGAA	0.144													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	83714187	83714188	+	IGR	INS	-	T	T	rs142488307	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83714187_83714188insT								None (None upstream) : TTLL7 (620871 downstream)																							TTAGTTTTGAACTTGAAATTTT	0.218													4	2	---	---	---	---	
RPF1	80135	broad.mit.edu	37	1	84948415	84948415	+	Intron	DEL	T	-	-	rs111427529		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84948415delT	uc001djv.3	+							NM_025065	NP_079341	Q9H9Y2	RPF1_HUMAN	RNA processing factor 1						rRNA processing|translation	nucleolus	aminoacyl-tRNA ligase activity|ATP binding|rRNA binding				0						GCCCAGATTGTTTAAAAAAAA	0.333													4	2	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	86004458	86004458	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86004458delA	uc001dlc.2	-							NM_001134445	NP_001127917	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	AGGGCAACTCAGGTGTGTAAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	86757346	86757346	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86757346delA								COL24A1 (134900 upstream) : ODF2L (57066 downstream)																							atttttggtgaatttgtgtaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	87711700	87711701	+	IGR	INS	-	GGG	GGG	rs72560756		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87711700_87711701insGGG								LOC339524 (76816 upstream) : LMO4 (82450 downstream)																							tagcctaccttactaatacaGA	0.005													4	2	---	---	---	---	
GBP2	2634	broad.mit.edu	37	1	89582474	89582474	+	Intron	DEL	A	-	-	rs57905524		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89582474delA	uc001dmz.1	-						GBP2_uc001dmy.1_Intron	NM_004120	NP_004111	P32456	GBP2_HUMAN	guanylate binding protein 2,						interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)	1		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		TTCTTTTTTTATTCTCCTTGC	0.289													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91998794	91998795	+	IGR	DEL	CA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91998794_91998795delCA								CDC7 (7474 upstream) : HSP90B3P (101773 downstream)																							GAGTGACTATcacacacacaca	0.465													4	2	---	---	---	---	
ABCA4	24	broad.mit.edu	37	1	94481004	94481005	+	Intron	INS	-	A	A	rs148696094	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94481004_94481005insA	uc001dqh.2	-						ABCA4_uc009wdp.1_Intron	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4						phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GGGAATGGCTGCCCCCAGGCTT	0.554													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	111291875	111291875	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111291875delG								KCNA3 (74220 upstream) : CD53 (121946 downstream)																							cataaaactagggcctggaga	0.000													4	2	---	---	---	---	
AMPD1	270	broad.mit.edu	37	1	115217930	115217930	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115217930delA	uc001efe.1	-						AMPD1_uc001eff.1_Intron	NM_000036	NP_000027	P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1 (isoform M)						purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|large_intestine(1)|skin(1)	4	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|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)	Adenosine monophosphate(DB00131)	TAAACTTCCCAAAAAAAAAGG	0.289													4	3	---	---	---	---	
SYCP1	6847	broad.mit.edu	37	1	115430077	115430078	+	Intron	INS	-	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115430077_115430078insA	uc001efr.2	+						SYCP1_uc010owt.1_Intron|SYCP1_uc001efq.2_Intron|SYCP1_uc009wgw.2_Intron	NM_003176	NP_003167	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1						cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)		TAATATCTTATTTTAAAATGTT	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149730038	149730038	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149730038delT								HIST2H2BF (330809 upstream) : FCGR1A (24212 downstream)																							TCTCTTTTCCTTTGGTCATTA	0.338													4	2	---	---	---	---	
FCRL1	115350	broad.mit.edu	37	1	157774046	157774047	+	Intron	INS	-	A	A	rs12133090		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157774046_157774047insA	uc001frg.2	-						FCRL1_uc001frf.2_5'Flank|FCRL1_uc001frh.2_Intron|FCRL1_uc001fri.2_Intron|FCRL1_uc001frj.2_Intron	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor							integral to membrane|plasma membrane	receptor activity			skin(4)|ovary(3)	7	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			ACCCCCCCCCCAGTGGCCCATG	0.520													3	3	---	---	---	---	
LOC400794	400794	broad.mit.edu	37	1	165539491	165539491	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165539491delG	uc001gdc.2	-						LOC400794_uc001gdd.2_Intron|LOC400794_uc009wvd.2_Intron	NR_026744				Homo sapiens cDNA FLJ35813 fis, clone TESTI2006067.												0						TCCTTTTGCCGGGTCTTTGCC	0.453													4	2	---	---	---	---	
FAM163A	148753	broad.mit.edu	37	1	179741349	179741349	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179741349delC	uc009wxj.2	+						FAM163A_uc001gnj.2_Intron|FAM163A_uc009wxk.2_Intron	NM_173509	NP_775780	Q96GL9	F163A_HUMAN	hypothetical protein LOC148753							integral to membrane				ovary(1)	1						GCCACCTCTGCCACCTTCCTT	0.537													4	2	---	---	---	---	
C1orf26	54823	broad.mit.edu	37	1	185140796	185140797	+	Intron	INS	-	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185140796_185140797insT	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988	Q5T5J6	SWT1_HUMAN	hypothetical protein LOC54823												0						GAACCTGCTTCTTTTTTTTTTG	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192562142	192562142	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192562142delT								RGS1 (12983 upstream) : RGS13 (43140 downstream)																							AAATCCTTGCTTTTAGTTGTA	0.343													4	2	---	---	---	---	
TMEM206	55248	broad.mit.edu	37	1	212556613	212556614	+	Intron	DEL	TG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212556613_212556614delTG	uc001hjc.3	-						TMEM206_uc010pte.1_Intron	NM_018252	NP_060722	Q9H813	TM206_HUMAN	transmembrane protein 206							integral to membrane				breast(1)	1				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		atgtaactattgtaacaagtgc	0.035													4	2	---	---	---	---	
SPATA17	128153	broad.mit.edu	37	1	217955876	217955876	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217955876delA	uc001hlh.1	+						SPATA17_uc001hli.2_Intron	NM_138796	NP_620151	Q96L03	SPT17_HUMAN	spermatogenesis associated 17							cytoplasm	calmodulin binding			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		CTCAAAAGACAAAAAAAAGAT	0.313													4	2	---	---	---	---	
IARS2	55699	broad.mit.edu	37	1	220273662	220273663	+	Intron	INS	-	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220273662_220273663insC	uc001hmc.2	+							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)	TTTATACGTTTCCTTTCAAATT	0.228													4	2	---	---	---	---	
DUSP10	11221	broad.mit.edu	37	1	221892814	221892814	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221892814delA	uc001hmy.1	-						DUSP10_uc001hmx.1_Intron|DUSP10_uc001hmz.1_Intron	NM_007207	NP_009138	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10 isoform a						inactivation of MAPK activity|JNK cascade|negative regulation of JNK cascade|negative regulation of JUN kinase activity|negative regulation of stress-activated MAPK cascade	Golgi apparatus|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|lung(1)	2				GBM - Glioblastoma multiforme(131;0.0103)		ACACTGGGTTAAAAAAAAAAG	0.463													4	2	---	---	---	---	
TAF1A	9015	broad.mit.edu	37	1	222736826	222736827	+	Intron	DEL	GA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222736826_222736827delGA	uc009xdz.1	-						TAF1A_uc009xdy.1_Intron|TAF1A_uc001hni.1_Intron|TAF1A_uc001hnj.2_Intron|TAF1A_uc001hnk.2_Intron	NM_139352	NP_647603	Q15573	TAF1A_HUMAN	TBP-associated factor 1A isoform 2						regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	RNA polymerase I transcription factor complex	DNA binding				0				GBM - Glioblastoma multiforme(131;0.0186)		CAATGAATCTGAAAAACTCAAT	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232426154	232426154	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232426154delT								DISC1 (249138 upstream) : SIPA1L2 (107560 downstream)																							atgtgcaatgtttagatccaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238715652	238715652	+	IGR	DEL	G	-	-	rs567090	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238715652delG								LOC339535 (66335 upstream) : CHRM3 (834213 downstream)																							GTGGGTGGAAGGAAAAGCAAA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	239527281	239527281	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239527281delT								LOC339535 (877964 upstream) : CHRM3 (22584 downstream)																							ttgggggccattctatgggat	0.000													4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246566457	246566457	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246566457delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		CTCCCTGACTAATGGAAAATT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	249240243	249240244	+	IGR	INS	-	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249240243_249240244insG								PGBD2 (26899 upstream) : None (None downstream)																							ggttagggttagggttagggtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	1596208	1596208	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1596208delA								TPO (49710 upstream) : PXDN (39452 downstream)																							AGGAGCCTAGAAAAAAAAAAT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8697383	8697383	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8697383delG								LOC339788 (580406 upstream) : ID2 (121957 downstream)																							GGAAAAAAAAGGGGGGTGGGC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19481735	19481735	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19481735delC								NT5C1B (710897 upstream) : OSR1 (69512 downstream)																							CACTGTGTTTCCCTGACCTGA	0.323													4	2	---	---	---	---	
DNMT3A	1788	broad.mit.edu	37	2	25458658	25458658	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25458658delA	uc002rgc.2	-	22	2772	c.2515delT	c.(2515-2517)TCCfs	p.S839fs	DNMT3A_uc002rgd.2_Frame_Shift_Del_p.S839fs|DNMT3A_uc010eyi.2_RNA|DNMT3A_uc002rgb.2_Frame_Shift_Del_p.S650fs	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	839					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)					TGCTTTATGGAGTTTGACCTC	0.458			Mis|F|N|S		AML								179	96	---	---	---	---	
AGBL5	60509	broad.mit.edu	37	2	27279865	27279865	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27279865delA	uc002rie.2	+						AGBL5_uc002rid.2_Intron|AGBL5_uc002rif.2_Intron	NM_021831	NP_068603	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5 isoform 1						protein branching point deglutamylation|proteolysis	cytosol|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					actccgtctcaaaaaaaaaac	0.174													6	5	---	---	---	---	
BIRC6	57448	broad.mit.edu	37	2	32836817	32836817	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32836817delT	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)					AAAAGATACATTTTTTTTTGG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37998616	37998616	+	IGR	DEL	A	-	-	rs112121172		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37998616delA								CDC42EP3 (99290 upstream) : FAM82A1 (153846 downstream)																							Ggctggggccaaagggagaca	0.169													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	40287816	40287817	+	Intron	INS	-	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40287816_40287817insG	uc002rrw.2	+											Homo sapiens cDNA clone IMAGE:5223469, partial cds.																		ttgacggagttgggggagggaa	0.193													4	2	---	---	---	---	
PPM1B	5495	broad.mit.edu	37	2	44428223	44428223	+	Intron	DEL	A	-	-	rs72277187		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44428223delA	uc002rtt.2	+						PPM1B_uc002rts.2_Intron|PPM1B_uc002rtu.2_Intron|PPM1B_uc002rtv.2_Intron|PPM1B_uc002rtw.2_Intron|PPM1B_uc002rtx.2_Intron	NM_002706	NP_002697	O75688	PPM1B_HUMAN	protein phosphatase 1B isoform 1						protein dephosphorylation	protein serine/threonine phosphatase complex	magnesium ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			kidney(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GGATAATACTAAAAAAAATAC	0.348													4	2	---	---	---	---	
FBXO11	80204	broad.mit.edu	37	2	48067087	48067087	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48067087delT	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)			ATGTGGAAGAttttttttttt	0.164													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57716185	57716185	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57716185delA								None (None upstream) : VRK2 (418601 downstream)																							CTTTTCAGACAAAAAAATTGG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64576204	64576205	+	IGR	INS	-	GG	GG			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64576204_64576205insGG								PELI1 (204599 upstream) : HSPC159 (105122 downstream)																							GGAAATGGAAAGGAGCCACTCT	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67697375	67697375	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67697375delT								ETAA1 (59842 upstream) : C1D (571958 downstream)																							Atttcttttctttttttggag	0.219													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	79860603	79860603	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79860603delC	uc010yse.1	+						CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						tgattctcctccttagcctgg	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	104385817	104385817	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104385817delT								TMEM182 (951681 upstream) : LOC150568 (664988 downstream)																							acccaatgccttttttttcaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105607006	105607016	+	IGR	DEL	AAGAGCAGAAG	-	-	rs142005627		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105607006_105607016delAAGAGCAGAAG								POU3F3 (133536 upstream) : MRPS9 (47467 downstream)																							ctaagacagcaagagcagaagaagagcagtc	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107652540	107652543	+	IGR	DEL	TGAG	-	-	rs78710449		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107652540_107652543delTGAG								ST6GAL2 (148977 upstream) : LOC729121 (786977 downstream)																							agtgagtgaatgagtgagtgaccc	0.000													2	4	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	115940588	115940589	+	Intron	DEL	CA	-	-	rs72465489		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115940588_115940589delCA	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						TATTTacacgcacacacacaca	0.322													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	127609718	127609718	+	IGR	DEL	T	-	-	rs11677887	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127609718delT								GYPC (155473 upstream) : BIN1 (195889 downstream)																							TCCATATTTGTTTTTTTCCCC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133107688	133107688	+	IGR	DEL	G	-	-	rs59503674		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133107688delG								NCRNA00164 (92146 upstream) : GPR39 (66459 downstream)																							cttcatttctgtttacttctg	0.000													4	2	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	133460931	133460931	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133460931delT	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						TTGGAAATTCTTTTTTGGAAA	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	138797444	138797444	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138797444delT								HNMT (23511 upstream) : SPOPL (461906 downstream)																							TTTCAACTTGTTTTTTTTTTA	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146205921	146205921	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146205921delA								ZEB2 (927990 upstream) : None (None downstream)																							tgttatgaagaaaaaaaaagt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177504618	177504619	+	5'Flank	INS	-	CA	CA			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177504618_177504619insCA	uc002ukz.1	-						uc002ula.1_Intron					Homo sapiens hypothetical gene supported by BC013438, mRNA (cDNA clone IMAGE:3899073), partial cds.																		ATTGCCTCCATCACACGTGTGT	0.416													4	2	---	---	---	---	
PDE11A	50940	broad.mit.edu	37	2	178600139	178600140	+	Intron	DEL	AC	-	-	rs142899778	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178600139_178600140delAC	uc002ulq.2	-						PDE11A_uc002ulp.2_Intron|PDE11A_uc002ulr.2_Intron|PDE11A_uc002uls.1_Intron|PDE11A_uc002ult.1_Intron|PDE11A_uc002ulu.1_Intron	NM_016953	NP_058649	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A isoform 4						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)			GAAAAAAAAAACCCCAAAAAAC	0.411									Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	183540349	183540349	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183540349delT								PDE1A (152842 upstream) : DNAJC10 (40650 downstream)																							gcatctgttattttttgactt	0.000													4	2	---	---	---	---	
NUP35	129401	broad.mit.edu	37	2	184024575	184024575	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184024575delA	uc002upf.2	+						NUP35_uc010zfs.1_Intron|NUP35_uc010zft.1_Intron|NUP35_uc002upg.2_Intron	NM_138285	NP_612142	Q8NFH5	NUP53_HUMAN	nucleoporin 35kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	intermediate filament cytoskeleton|nuclear membrane|nuclear pore|plasma membrane					0						ATCATGaattaaaaaaaaaaa	0.289													4	2	---	---	---	---	
FAM126B	285172	broad.mit.edu	37	2	201876532	201876532	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201876532delT	uc002uws.3	-						FAM126B_uc002uwu.2_Intron|FAM126B_uc002uwv.2_Intron|FAM126B_uc002uww.1_Intron	NM_173822	NP_776183	Q8IXS8	F126B_HUMAN	hypothetical protein LOC285172							intracellular				ovary(1)	1						TTACAAGTGATTAGCTCCTTT	0.303													4	2	---	---	---	---	
CASP10	843	broad.mit.edu	37	2	202070366	202070366	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202070366delG	uc002uxl.1	+						CASP10_uc010zhn.1_Intron|CASP10_uc002uxj.1_Intron|CASP10_uc002uxk.1_Intron|CASP10_uc010fta.1_Intron|CASP10_uc002uxm.1_Intron|CASP10_uc010ftb.1_Intron	NM_032974	NP_116756	Q92851	CASPA_HUMAN	caspase 10 isoform b preproprotein						apoptosis|induction of apoptosis by extracellular signals|proteolysis	cytosol|plasma membrane	cysteine-type endopeptidase activity|identical protein binding|protein binding			skin(3)|ovary(1)|pancreas(1)|breast(1)	6						GCTGATCCATGGGATCTTAAT	0.463													4	2	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	205889984	205889985	+	Intron	DEL	TG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205889984_205889985delTG	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		ATTGCATGCTTGTGACTCATAA	0.485													4	2	---	---	---	---	
NDUFS1	4719	broad.mit.edu	37	2	207014339	207014340	+	Intron	INS	-	AC	AC	rs141671378	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207014339_207014340insAC	uc002vbe.2	-						NDUFS1_uc010ziq.1_Intron|NDUFS1_uc010zir.1_Intron|NDUFS1_uc010zis.1_Intron|NDUFS1_uc010zit.1_Intron|NDUFS1_uc010ziu.1_Intron	NM_005006	NP_004997	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)	ACAATTATATGACATGTGTTTG	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	224231701	224231702	+	IGR	DEL	TT	-	-	rs76060077		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224231701_224231702delTT								KCNE4 (311348 upstream) : SCG2 (229958 downstream)																							caacagtctattttttttttca	0.074													4	2	---	---	---	---	
MFF	56947	broad.mit.edu	37	2	228222186	228222186	+	3'UTR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228222186delA	uc002vos.2	+	11					MFF_uc002vot.2_3'UTR|MFF_uc002vou.2_3'UTR|MFF_uc002vov.2_3'UTR|MFF_uc002vow.2_3'UTR|MFF_uc002vox.2_3'UTR|MFF_uc002voy.2_3'UTR|MFF_uc002voz.2_3'UTR|MFF_uc002vpa.2_3'UTR	NM_020194	NP_064579	Q9GZY8	MFF_HUMAN	mitochondrial fission factor							integral to membrane|mitochondrial outer membrane				large_intestine(1)	1						ATTGATTCAGAAAAGTGTCTG	0.333													4	2	---	---	---	---	
LRRFIP1	9208	broad.mit.edu	37	2	238660202	238660202	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238660202delT	uc002vxe.2	+						LRRFIP1_uc002vxc.2_Intron|LRRFIP1_uc010znm.1_Intron|LRRFIP1_uc002vxd.2_Intron|LRRFIP1_uc002vxf.2_Intron	NM_001137552	NP_001131024	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|cytoskeleton|nucleus	DNA binding|double-stranded RNA binding|protein binding			breast(3)	3		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		TTAAAACCAGTTTCTCATTTC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	241248083	241248083	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241248083delC								OTOS (168010 upstream) : GPC1 (127032 downstream)																							GCCTTCTCCTCCAtgtgtctc	0.080													4	2	---	---	---	---	
AGXT	189	broad.mit.edu	37	2	241811807	241811809	+	Intron	DEL	GGT	-	-	rs62189565	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241811807_241811809delGGT	uc002waa.3	+						AGXT_uc010zoi.1_Intron	NM_000030	NP_000021	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase						glyoxylate metabolic process|protein targeting to peroxisome	mitochondrial matrix|peroxisomal matrix	alanine-glyoxylate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|serine-pyruvate transaminase activity				0		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)	Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	TGAACATGCAGGTGGAGGAGGGT	0.581													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	1643462	1643462	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1643462delA								CNTN6 (198185 upstream) : CNTN4 (497088 downstream)																							taAAAGgcttatggtgttgtg	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	3665935	3665935	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3665935delC								CRBN (444545 upstream) : SUMF1 (157101 downstream)																							gccactttgacctacatctct	0.000													4	2	---	---	---	---	
ITPR1	3708	broad.mit.edu	37	3	4686171	4686171	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4686171delT	uc003bqa.2	+						ITPR1_uc010hbz.2_Intron|ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc010hcb.1_Intron	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		TGAGGGGTTGTTTTTTCATTG	0.448													4	2	---	---	---	---	
GRM7	2917	broad.mit.edu	37	3	7005728	7005728	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7005728delC	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)	TCACCACCATCCACCACCCCT	0.383													4	2	---	---	---	---	
RASSF1	11186	broad.mit.edu	37	3	50375606	50375607	+	Intron	INS	-	C	C	rs146696636	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50375606_50375607insC	uc003dad.1	-						RASSF1_uc003dab.1_5'Flank|RASSF1_uc003dac.2_5'UTR|RASSF1_uc003dae.1_Intron|RASSF1_uc010hlk.1_Intron|RASSF1_uc003daf.1_Intron|RASSF1_uc011bdq.1_Intron	NM_170714	NP_733832	Q9NS23	RASF1_HUMAN	Ras association domain family 1 isoform D						cell cycle arrest|negative regulation of cell cycle arrest|positive regulation of protein ubiquitination|protein stabilization|Ras protein signal transduction|response to DNA damage stimulus	microtubule|microtubule cytoskeleton|microtubule organizing center|nucleus|spindle pole	identical protein binding|protein binding|protein N-terminus binding|zinc ion binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000278)|OV - Ovarian serous cystadenocarcinoma(275;0.0015)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		AATGTTGGCCACCTGGGCGTCT	0.619													4	3	---	---	---	---	
MAGI1	9223	broad.mit.edu	37	3	65605351	65605351	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65605351delG	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hny.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		TCAGTCACATGGGCCATAGAA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	78483399	78483399	+	IGR	DEL	A	-	-	rs112578448		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78483399delA								ROBO2 (786738 upstream) : ROBO1 (162989 downstream)																							TAACAACAACAAAAAAAAAAT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90472105	90472105	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90472105delG								EPHA3 (940823 upstream) : None (None downstream)																							gcctcaaagcgctccaaatat	0.000													4	2	---	---	---	---	
DZIP3	9666	broad.mit.edu	37	3	108353508	108353508	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108353508delT	uc003dxd.2	+						DZIP3_uc003dxf.1_Intron|DZIP3_uc011bhm.1_Intron|DZIP3_uc003dxe.1_Intron|DZIP3_uc003dxg.1_5'Flank	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger						protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						ATTATTGACCTTTTTTTTACT	0.299													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	133947480	133947481	+	IGR	INS	-	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133947480_133947481insA								RYK (-22106 upstream) : RYK (-71503 downstream)																							gtggaatctttaaaaaaaagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	141550279	141550279	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141550279delT								GRK7 (14389 upstream) : ATP1B3 (45191 downstream)																							tttccttttctttttttTCAT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147325262	147325263	+	IGR	INS	-	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147325262_147325263insA								ZIC1 (190758 upstream) : None (None downstream)																							agtataaacagaaaaaaaaaat	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147479622	147479622	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147479622delC								ZIC1 (345118 upstream) : AGTR1 (936036 downstream)																							CAAGAAACTGCCCCACAACTC	0.328													4	2	---	---	---	---	
HPS3	84343	broad.mit.edu	37	3	148873458	148873458	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148873458delT	uc003ewu.1	+						HPS3_uc011bnq.1_Intron	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)			GGGAGCATCCTTACTGATCTA	0.368									Hermansky-Pudlak_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149766187	149766188	+	IGR	DEL	TG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149766187_149766188delTG								PFN2 (77446 upstream) : TSC22D2 (360600 downstream)																							TTGCTGCCTCTGTGTGTGAACA	0.569													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	155807217	155807218	+	IGR	INS	-	A	A	rs145633922	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155807217_155807218insA								GMPS (151699 upstream) : KCNAB1 (31119 downstream)																							atttGGAAGTTAAAAAAAAAGA	0.124													4	2	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	168864961	168864961	+	5'Flank	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168864961delC	uc003ffi.3	-						MECOM_uc003ffj.3_5'Flank|MECOM_uc011bpi.1_5'Flank|MECOM_uc003ffn.3_5'Flank|MECOM_uc003ffk.2_5'UTR|MECOM_uc003ffl.2_Intron|MECOM_uc011bpj.1_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc003ffm.1_5'Flank|MECOM_uc003ffo.1_5'Flank	NM_005241	NP_005232	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform b						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						TTATCTGAAACCCACTAAAAC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	169441092	169441092	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169441092delA								MECOM (59529 upstream) : TERC (41306 downstream)																							tcctgtctctaaaaaaatttt	0.000													4	2	---	---	---	---	
EIF4G1	1981	broad.mit.edu	37	3	184043926	184043927	+	Intron	DEL	AC	-	-	rs112208190		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184043926_184043927delAC	uc003fnp.2	+						EIF4G1_uc003fnt.2_Intron|EIF4G1_uc003fnq.2_Intron|EIF4G1_uc003fnr.2_Intron|EIF4G1_uc010hxx.2_Intron|EIF4G1_uc003fns.2_Intron|EIF4G1_uc010hxy.2_Intron|EIF4G1_uc003fnv.3_Intron|EIF4G1_uc003fnu.3_Intron|EIF4G1_uc003fnw.2_Intron|EIF4G1_uc003fnx.2_Intron|EIF4G1_uc003fny.3_Intron|EIF4G1_uc003foa.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4						insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGTTTGGCAAacacacacacac	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184208688	184208688	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184208688delT								CHRD (101069 upstream) : EPHB3 (70899 downstream)																							CTTTTGCCACTTGCTGTGCCT	0.378													4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	187983659	187983660	+	Intron	DEL	GT	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187983659_187983660delGT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		GATTACTCTGgtgtgtgtgtgt	0.307			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193923439	193923440	+	IGR	DEL	CA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193923439_193923440delCA								HES1 (67043 upstream) : LOC100131551 (93984 downstream)																							cacacatatgcacacacacaca	0.381													4	2	---	---	---	---	
LETM1	3954	broad.mit.edu	37	4	1834801	1834801	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1834801delT	uc003gdv.2	-							NM_012318	NP_036450	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane						cristae formation	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			central_nervous_system(1)	1			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)			CTACttcttcttttttttttt	0.299													4	2	---	---	---	---	
STK32B	55351	broad.mit.edu	37	4	5271059	5271059	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5271059delG	uc003gih.1	+						STK32B_uc010ida.1_Intron	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B								ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						tctcaggaatggggggtacta	0.000													4	2	---	---	---	---	
AFAP1	60312	broad.mit.edu	37	4	7766120	7766120	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7766120delA	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron|LOC84740_uc003gkd.3_Intron	NM_198595	NP_940997	Q8N556	AFAP1_HUMAN	actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0						caaaaaatataaaaaAAAAag	0.000													4	2	---	---	---	---	
CPEB2	132864	broad.mit.edu	37	4	15018610	15018610	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15018610delA	uc003gni.1	+						CPEB2_uc003gnj.1_Intron|CPEB2_uc003gnk.1_Intron|CPEB2_uc003gnl.1_Intron|CPEB2_uc003gnm.1_Intron|CPEB2_uc003gnn.1_Intron	NM_182485	NP_872291	Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding						regulation of translation	cytoplasm	nucleotide binding|RNA binding			skin(1)	1						TTTAAGAGATAAATATACTGA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	15457267	15457267	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15457267delT								C1QTNF7 (9477 upstream) : CC2D2A (14222 downstream)																							TTTTGTTTTGTTTTTTTTCCA	0.109													4	2	---	---	---	---	
TAPT1	202018	broad.mit.edu	37	4	16168614	16168614	+	Intron	DEL	C	-	-	rs5856341		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16168614delC	uc010ied.1	-						TAPT1_uc011bxd.1_Intron|TAPT1_uc011bxe.1_Intron	NM_153365	NP_699196	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation							integral to membrane	growth hormone-releasing hormone receptor activity				0						CCTTAGttctctttttttttt	0.199													4	2	---	---	---	---	
TBC1D19	55296	broad.mit.edu	37	4	26744434	26744434	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26744434delT	uc003gsf.3	+						TBC1D19_uc010iew.2_Intron|TBC1D19_uc011bxu.1_Intron	NM_018317	NP_060787	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19							intracellular	Rab GTPase activator activity			breast(1)	1		Breast(46;0.0503)				TCTTATTTACTAGGATTTTTG	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	43264870	43264870	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43264870delT								GRXCR1 (232197 upstream) : KCTD8 (911052 downstream)																							acattagttctttaaatttaa	0.000													4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	55120794	55120794	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55120794delA	uc003han.3	+						PDGFRA_uc003haa.2_Intron|PDGFRA_uc003hal.2_Intron|PDGFRA_uc010igq.1_Intron|PDGFRA_uc003ham.2_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	TAAATGTGATAAAAGCCACGA	0.438			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	56978693	56978693	+	IGR	DEL	T	-	-	rs35371345		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56978693delT								CEP135 (79167 upstream) : KIAA1211 (57668 downstream)																							ctctggctagttggggggacc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	57815206	57815206	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57815206delT								REST (16867 upstream) : C4orf14 (14311 downstream)																							TGCTATTAACTTTTTTTTTTT	0.020													3	3	---	---	---	---	
EPHA5	2044	broad.mit.edu	37	4	66315197	66315197	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66315197delG	uc003hcy.2	-						EPHA5_uc003hcx.2_Intron|EPHA5_uc003hcz.2_Intron|EPHA5_uc011cah.1_Intron|EPHA5_uc011cai.1_Intron|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						gaagcagaaagggatatgtac	0.000										TSP Lung(17;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	66880145	66880145	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66880145delG								EPHA5 (344492 upstream) : MIR1269 (262397 downstream)																							cagggagtttggtgtattagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	68172590	68172591	+	IGR	INS	-	AC	AC	rs147272530	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68172590_68172591insAC								None (None upstream) : CENPC1 (165398 downstream)																							caccatctgtgactcccactgt	0.000													3	5	---	---	---	---	
TET2	54790	broad.mit.edu	37	4	106088365	106088365	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106088365delC	uc003hxk.2	+						TET2_uc011cez.1_Intron|TET2_uc010ilp.1_Intron|TET2_uc003hxi.1_Intron	NM_001127208	NP_001120680	Q6N021	TET2_HUMAN	tet oncogene family member 2 isoform a						cell cycle|myeloid cell differentiation		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			haematopoietic_and_lymphoid_tissue(732)|pancreas(1)	733		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		agtccattttctattctctga	0.085			Mis N|F		MDS								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	109302652	109302652	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109302652delT								LEF1 (213074 upstream) : LOC285456 (156694 downstream)																							CTAATAATTCTTTTTTTTTTT	0.368													4	3	---	---	---	---	
RNF150	57484	broad.mit.edu	37	4	141811457	141811457	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141811457delA	uc003iio.1	-						RNF150_uc010iok.1_Intron	NM_020724	NP_065775	Q9ULK6	RN150_HUMAN	ring finger protein 150 precursor							integral to membrane	zinc ion binding			ovary(1)	1	all_hematologic(180;0.162)					taactgctacaaaaaaaacta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	147168552	147168552	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147168552delA								LSM6 (57340 upstream) : SLC10A7 (6585 downstream)																							ACACTGCAGGAAAAAAGAATA	0.289													4	2	---	---	---	---	
KIAA0922	23240	broad.mit.edu	37	4	154463551	154463552	+	Intron	INS	-	GTT	GTT	rs141082901	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154463551_154463552insGTT	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				GCAAGGGCCACGTTGCAGAGAG	0.480													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	156103131	156103131	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156103131delA								RBM46 (353167 upstream) : NPY2R (26650 downstream)																							gaaggaatccaaaaaaataca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	181199012	181199012	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181199012delA								None (None upstream) : None (None downstream)																							actccatcgcaaaaaaaaaga	0.000													3	3	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183686757	183686757	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183686757delT	uc003ivd.1	+							NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		CATCTTAGGCTTTTTTTCCTT	0.348													4	2	---	---	---	---	
TRIP13	9319	broad.mit.edu	37	5	896445	896445	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:896445delA	uc003jbr.2	+						TRIP13_uc010ite.1_Intron	NM_004237	NP_004228	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13						double-strand break repair|reciprocal meiotic recombination|synaptonemal complex assembly|transcription from RNA polymerase II promoter		ATP binding|identical protein binding|nucleoside-triphosphatase activity|transcription cofactor activity				0			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			taagttaattaaaaaaaaaca	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3544963	3544963	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3544963delG								C5orf38 (789451 upstream) : IRX1 (51205 downstream)																							TCATCTCAGTGGAATGATTTG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7182134	7182134	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7182134delT								PAPD7 (424973 upstream) : ADCY2 (214209 downstream)																							ACTGTCACCCTTTTCAAAGTT	0.443													4	2	---	---	---	---	
SEMA5A	9037	broad.mit.edu	37	5	9237029	9237029	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9237029delT	uc003jek.2	-							NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						TGAAATTGGGTAAAAAAAAGG	0.428													4	2	---	---	---	---	
MARCH6	10299	broad.mit.edu	37	5	10367775	10367775	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10367775delA	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						AACTTTGATGAAATGGGCTGA	0.363													4	2	---	---	---	---	
FAM105B	90268	broad.mit.edu	37	5	14678605	14678606	+	Intron	INS	-	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14678605_14678606insC	uc003jfk.2	+							NM_138348	NP_612357	Q96BN8	F105B_HUMAN	hypothetical protein LOC90268											ovary(2)	2	Lung NSC(4;0.00696)					ccattgggagacccccatggtt	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17080411	17080411	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17080411delC								MYO10 (144026 upstream) : LOC285696 (49726 downstream)																							TGAAGTCTTTCCATATTTTAA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	32926808	32926809	+	IGR	DEL	TT	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32926808_32926809delTT								C5orf23 (134989 upstream) : TARS (513993 downstream)																							ATTAACCCTGTTTAGCCAGAGC	0.267													4	2	---	---	---	---	
C5orf33	133686	broad.mit.edu	37	5	36241678	36241680	+	In_Frame_Del	DEL	CCA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36241678_36241680delCCA	uc003jkf.3	-	1	221_223	c.221_223delTGG	c.(220-225)GTGGCC>GCC	p.V74del	C5orf33_uc003jkg.3_Intron|C5orf33_uc011cov.1_Intron	NM_001085411	NP_001078880	Q4G0N4	NAKD1_HUMAN	hypothetical protein LOC133686 isoform 1	74							NAD+ kinase activity				0	all_lung(31;5.63e-05)		Epithelial(62;0.0254)|all cancers(62;0.0805)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GTGGTTTTGGCCACCACCACCAC	0.429													4	2	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38464857	38464857	+	3'UTR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38464857delT	uc003jlc.1	+	23					EGFLAM_uc003jle.1_3'UTR|EGFLAM_uc003jlf.1_3'UTR|EGFLAM_uc003jlg.1_3'UTR|EGFLAM_uc003jlh.1_3'UTR	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					CTTGCACACCTTTCCTAAAAA	0.423													4	2	---	---	---	---	
SV2C	22987	broad.mit.edu	37	5	75387522	75387522	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75387522delT	uc003kei.1	+							NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		TCTATGAGACTTTTTTTTTTT	0.204													4	2	---	---	---	---	
MSH3	4437	broad.mit.edu	37	5	79975047	79975047	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79975047delA	uc003kgz.2	+							NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		GTGGAAATTTAAAAAAAAAAG	0.139								MMR					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	97763504	97763504	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97763504delT								None (None upstream) : RGMB (341495 downstream)																							CCATTTTTGGTTTTTTTTTTA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	99135839	99135839	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99135839delG								CHD1 (873601 upstream) : LOC100133050 (579370 downstream)																							ccaaaaccaaggggttacagg	0.000													4	2	---	---	---	---	
MAN2A1	4124	broad.mit.edu	37	5	109138450	109138450	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109138450delT	uc003kou.1	+							NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		AGGTGTTGACTTTTTTTTTCT	0.343													4	2	---	---	---	---	
MAN2A1	4124	broad.mit.edu	37	5	109149740	109149740	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109149740delG	uc003kou.1	+							NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		CCTGAATTATGGGGGCCCAAT	0.418													4	2	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111638688	111638688	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111638688delA	uc003kpv.1	-						EPB41L4A_uc003kpw.1_Intron	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		TCATAAAGTCAAAGGGTTACC	0.428													4	2	---	---	---	---	
HINT1	3094	broad.mit.edu	37	5	130498538	130498538	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130498538delT	uc003kve.3	-						HINT1_uc011cxd.1_Intron|HINT1_uc003kvf.3_Intron	NM_005340	NP_005331	P49773	HINT1_HUMAN	histidine triad nucleotide binding protein 1						signal transduction	cytoplasm|cytoskeleton|nucleus	hydrolase activity|protein kinase C binding				0		all_cancers(142;0.0452)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Adenosine monophosphate(DB00131)	catggaagtcttttttttttt	0.000													5	3	---	---	---	---	
RAPGEF6	51735	broad.mit.edu	37	5	131008744	131008744	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131008744delG	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron|FNIP1_uc010jdm.1_Intron	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TCGtttttttgtttttttttt	0.149													4	2	---	---	---	---	
CDKL3	51265	broad.mit.edu	37	5	133609707	133609707	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133609707delG	uc011cxm.1	-						CDKL3_uc011cxn.1_Intron	NM_001113575	NP_001107047	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3 isoform 1							cytoplasm	ATP binding|cyclin-dependent protein kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ctttcttcctggggggaaact	0.000													4	2	---	---	---	---	
NRG2	9542	broad.mit.edu	37	5	139341843	139341844	+	Intron	DEL	GG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139341843_139341844delGG	uc003lex.1	-						NRG2_uc003lev.1_Intron|NRG2_uc003lew.1_Intron|NRG2_uc003ley.1_Intron	NM_004883	NP_004874	O14511	NRG2_HUMAN	neuregulin 2 isoform 1						embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGCCAGAACGGGGGATAGCTA	0.535													4	2	---	---	---	---	
HBEGF	1839	broad.mit.edu	37	5	139716192	139716192	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139716192delC	uc003lfi.2	-						HBEGF_uc010jfj.2_Intron	NM_001945	NP_001936	Q99075	HBEGF_HUMAN	heparin-binding EGF-like growth factor						epidermal growth factor receptor signaling pathway|muscle organ development|positive regulation of protein kinase B signaling cascade|positive regulation of wound healing	cell surface|extracellular space|integral to plasma membrane	epidermal growth factor receptor binding|eukaryotic cell surface binding|growth factor activity|heparin binding|receptor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACTCCAGCTCCCCCTGGGTG	0.547													4	2	---	---	---	---	
HBEGF	1839	broad.mit.edu	37	5	139725313	139725314	+	Intron	INS	-	AG	AG			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139725313_139725314insAG	uc003lfi.2	-						HBEGF_uc010jfj.2_Intron	NM_001945	NP_001936	Q99075	HBEGF_HUMAN	heparin-binding EGF-like growth factor						epidermal growth factor receptor signaling pathway|muscle organ development|positive regulation of protein kinase B signaling cascade|positive regulation of wound healing	cell surface|extracellular space|integral to plasma membrane	epidermal growth factor receptor binding|eukaryotic cell surface binding|growth factor activity|heparin binding|receptor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGCAATGACAAGAGAGAGAGA	0.525											OREG0016844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
PCDHA1	56147	broad.mit.edu	37	5	140223632	140223632	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140223632delC	uc003lhb.2	+						PCDHA1_uc003lha.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor						homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAAAGTATTCCCCCAAAGCG	0.353													4	2	---	---	---	---	
PCDHA1	56147	broad.mit.edu	37	5	140305549	140305550	+	Intron	INS	-	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140305549_140305550insA	uc003lhb.2	+						PCDHA1_uc003lha.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_5'Flank|PCDHAC1_uc003lig.1_5'Flank	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor						homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTATCACGCAAAAAAAAAGC	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8495018	8495018	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8495018delT	uc003mye.2	+											Homo sapiens, clone IMAGE:5539086, mRNA.																		ctaatttttcttttttttttc	0.015													4	2	---	---	---	---	
FLJ22536	401237	broad.mit.edu	37	6	22104327	22104327	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22104327delT	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0						cacagggagatttgcactcct	0.000													4	2	---	---	---	---	
LRRC16A	55604	broad.mit.edu	37	6	25535524	25535524	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25535524delG	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron|LRRC16A_uc003nfa.1_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						GCGTAGGCATGGGAaaaggag	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28989831	28989831	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28989831delT								ZNF311 (16738 upstream) : OR2W1 (22159 downstream)																							cagcatctacttttttttcgc	0.000													2	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57360174	57360175	+	Intron	DEL	TG	-	-	rs145904207		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57360174_57360175delTG	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)		ATAAATAAACTGTGAGTGAGAT	0.317													5	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57397644	57397645	+	Intron	DEL	TT	-	-	rs113340682		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57397644_57397645delTT	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)		tgtgacaaaattgtataaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57534556	57534556	+	IGR	DEL	T	-	-	rs67039622		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57534556delT								PRIM2 (21181 upstream) : GUSBL2 (711603 downstream)																							cttattctgatgtagttacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	61903302	61903303	+	IGR	DEL	GT	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:61903302_61903303delGT								None (None upstream) : KHDRBS2 (486562 downstream)																							tacaaaaagagtgtttcaaaac	0.000													4	2	---	---	---	---	
UBE2CBP	90025	broad.mit.edu	37	6	83775094	83775094	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83775094delA	uc003pjp.2	-						UBE2CBP_uc011dyx.1_Intron|UBE2CBP_uc003pjr.2_Intron|DOPEY1_uc003pjs.1_5'Flank	NM_198920	NP_944602	Q7Z6J8	UB2CB_HUMAN	ubiquitin-conjugating enzyme E2C binding							cytoplasm	ligase activity			ovary(1)	1		all_cancers(76;0.000374)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0548)		BRCA - Breast invasive adenocarcinoma(397;0.0944)		aaatcttgttaaaatataagt	0.204													4	2	---	---	---	---	
SNAP91	9892	broad.mit.edu	37	6	84361288	84361288	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84361288delT	uc011dze.1	-						SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Intron|SNAP91_uc011dzf.1_Intron	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog						clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		tttgttattatttttagttta	0.000													4	2	---	---	---	---	
UBE2J1	51465	broad.mit.edu	37	6	90060309	90060309	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90060309delT	uc010kcb.2	-						UBE2J1_uc003pnc.2_Intron	NM_016021	NP_057105	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1							endoplasmic reticulum membrane|integral to membrane	ATP binding|ubiquitin-protein ligase activity				0		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)		AAGCATTGTGTTTTTTTTTTT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	95001698	95001698	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95001698delA								TSG1 (515499 upstream) : None (None downstream)																							AACAAACAATAAAAAACCCGG	0.194													4	2	---	---	---	---	
MCHR2	84539	broad.mit.edu	37	6	100402771	100402771	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100402771delA	uc003pqh.1	-						MCHR2_uc003pqi.1_Intron	NM_001040179	NP_001035269	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2							integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	8		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		ctatgagtataaggtataagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112647042	112647042	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112647042delT								LAMA4 (71214 upstream) : RFPL4B (21490 downstream)																							GCTTTGCAGCTTTTTTTTTTC	0.453													4	2	---	---	---	---	
HBS1L	10767	broad.mit.edu	37	6	135311319	135311319	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135311319delA	uc003qez.2	-						HBS1L_uc003qey.2_Intron|HBS1L_uc011ecy.1_Intron|HBS1L_uc011ecz.1_Intron|HBS1L_uc011eda.1_Intron	NM_006620	NP_006611	Q9Y450	HBS1L_HUMAN	Hsp70 subfamily B suppressor 1-like protein						signal transduction		GTP binding|GTPase activity|translation elongation factor activity			skin(2)	2	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		TACTATCTCCAAAAAATTACT	0.239													4	2	---	---	---	---	
ECT2L	345930	broad.mit.edu	37	6	139213173	139213174	+	Intron	DEL	TC	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139213173_139213174delTC	uc003qif.1	+						ECT2L_uc011edq.1_Intron	NM_001077706	NP_001071174	Q008S8	ECT2L_HUMAN	epithelial cell transforming sequence 2						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0						atttcttctgtctctcttcatc	0.000													4	2	---	---	---	---	
ESR1	2099	broad.mit.edu	37	6	152393488	152393488	+	Intron	DEL	T	-	-	rs80276775		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152393488delT	uc003qom.3	+						ESR1_uc010kin.2_Intron|ESR1_uc010kio.2_Intron|ESR1_uc010kip.2_Intron|ESR1_uc003qon.3_Intron|ESR1_uc003qoo.3_Intron|ESR1_uc010kiq.2_Intron|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_Intron|ESR1_uc011eeu.1_Intron|ESR1_uc011eev.1_Intron|ESR1_uc011eew.1_Intron|ESR1_uc010kis.2_Intron|ESR1_uc011eex.1_Intron|ESR1_uc011eey.1_Intron	NM_001122742	NP_001116214	P03372	ESR1_HUMAN	estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)	TTGCCACTGATTTTTTTTTAA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4505468	4505468	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4505468delG								SDK1 (196839 upstream) : FOXK1 (177920 downstream)																							TAAATCTCTAGGGAAAGCGTA	0.408													4	2	---	---	---	---	
FBXL18	80028	broad.mit.edu	37	7	5553835	5553835	+	5'Flank	DEL	T	-	-	rs71808371		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5553835delT	uc003son.3	-						FBXL18_uc003soo.2_5'Flank|uc003sop.1_Intron	NM_024963	NP_079239	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18											central_nervous_system(2)|ovary(1)	3		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		cgacggtatcttttttttttt	0.000													5	3	---	---	---	---	
ISPD	729920	broad.mit.edu	37	7	16414444	16414444	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16414444delA	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						catccacctgaaaaaaaaatc	0.000										Multiple Myeloma(15;0.18)			4	2	---	---	---	---	
DPY19L1	23333	broad.mit.edu	37	7	35036524	35036524	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35036524delG	uc003tem.3	-							NM_015283	NP_056098	Q2PZI1	D19L1_HUMAN	dpy-19-like 1							integral to membrane					0						caagactggtggggagcagag	0.030													4	2	---	---	---	---	
DPY19L2P1	554236	broad.mit.edu	37	7	35163808	35163808	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35163808delT	uc003teq.1	-						DPY19L2P1_uc003tep.1_Intron|DPY19L2P1_uc010kwz.1_Intron					RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						AATGGTGAAGTTTTTTTAAAA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57059466	57059466	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57059466delT								DKFZp434L192 (494489 upstream) : ZNF479 (127862 downstream)																							AGAAGGGGCGTTTTGTTCCTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67884356	67884356	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67884356delC								None (None upstream) : None (None downstream)																							TCACCATCCTCCCCCTTCCCC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	72976441	72976441	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72976441delT								BCL7B (4417 upstream) : TBL2 (6838 downstream)																							actggcctccttgctcgtctg	0.000													4	2	---	---	---	---	
ELN	2006	broad.mit.edu	37	7	73451145	73451145	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73451145delT	uc003tzw.2	+						RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_Intron|ELN_uc011kfe.1_Intron|ELN_uc003tzn.2_Intron|ELN_uc003tzz.2_Intron|ELN_uc003tzo.2_Intron|ELN_uc003tzp.2_Intron|ELN_uc003tzq.2_Intron|ELN_uc003tzr.2_Intron|ELN_uc003tzs.2_Intron|ELN_uc003tzt.2_Intron|ELN_uc003tzu.2_Intron|ELN_uc003tzv.2_Intron|ELN_uc003tzx.2_Intron|ELN_uc011kff.1_Intron|ELN_uc003tzy.2_Intron	NM_000501	NP_001075224	P15502	ELN_HUMAN	elastin isoform a precursor						blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)	CTATTTCTTCTTTTTTTTGGT	0.338			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	80602756	80602756	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80602756delA								SEMA3C (51081 upstream) : HGF (728689 downstream)																							AATACGTGGTAAAAAAGAAAA	0.294													4	2	---	---	---	---	
SEMA3D	223117	broad.mit.edu	37	7	84657701	84657701	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84657701delA	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						CAGTTTAGACAAAAAAAAAAA	0.393													4	2	---	---	---	---	
ZNF804B	219578	broad.mit.edu	37	7	88892290	88892291	+	Intron	INS	-	G	G	rs11386388		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88892290_88892291insG	uc011khi.1	+							NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ACTTTGTAGCTTAGTTGTCCTG	0.421										HNSCC(36;0.09)			4	2	---	---	---	---	
ZNF804B	219578	broad.mit.edu	37	7	88892292	88892293	+	Intron	INS	-	C	C	rs11386387		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88892292_88892293insC	uc011khi.1	+							NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TTTGTAGCTTAGTTGTCCTGTA	0.426										HNSCC(36;0.09)			4	2	---	---	---	---	
ORC5L	5001	broad.mit.edu	37	7	103816207	103816207	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103816207delA	uc003vcb.2	-						ORC5L_uc011klp.1_Intron|ORC5L_uc003vcc.2_Intron	NM_002553	NP_002544	O43913	ORC5_HUMAN	origin recognition complex subunit 5 isoform 1						cell cycle checkpoint|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	cytoplasm|nuclear origin of replication recognition complex|nucleoplasm	ATP binding|DNA replication origin binding|identical protein binding				0						ccaccctgctaaaacgcttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	112711587	112711587	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112711587delT								C7orf60 (131655 upstream) : GPR85 (8881 downstream)																							ATTCATTTTCTTTTTACCAAA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	113035427	113035427	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113035427delA								LOC401397 (276790 upstream) : PPP1R3A (481455 downstream)																							GAAGTATTTCAAAAAAAGATT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	116874849	116874849	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116874849delA								ST7 (4776 upstream) : WNT2 (41839 downstream)																							ccgtgagttcaattgttttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	119381339	119381340	+	IGR	INS	-	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119381339_119381340insT								None (None upstream) : KCND2 (532382 downstream)																							atttcctcttcttttttttttc	0.000													4	2	---	---	---	---	
C7orf58	79974	broad.mit.edu	37	7	120656051	120656051	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120656051delT	uc003vjq.3	+						C7orf58_uc003vjr.1_Intron|C7orf58_uc003vjs.3_Intron	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1							endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)					AACTTATCTCTTTTTTTTAAC	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	121453084	121453084	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121453084delC								FAM3C (416662 upstream) : PTPRZ1 (60075 downstream)																							acactgacatcaggcaacaac	0.124													4	2	---	---	---	---	
C7orf45	136263	broad.mit.edu	37	7	129855536	129855536	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129855536delA	uc003vpp.2	+							NM_145268	NP_660311	Q8WWF3	CG045_HUMAN	hypothetical protein LOC136263							integral to membrane					0	Melanoma(18;0.0435)					GGAAAAGTTTAGAGATCTTTT	0.378													4	2	---	---	---	---	
ATP6V0A4	50617	broad.mit.edu	37	7	138405024	138405024	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138405024delG	uc003vuf.2	-						ATP6V0A4_uc003vug.2_Intron|ATP6V0A4_uc003vuh.2_Intron	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit						cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1						AAGAGAAACAGGGGGAGGCAC	0.363													4	2	---	---	---	---	
SGCZ	137868	broad.mit.edu	37	8	14205783	14205783	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14205783delT	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		acaccaaaaatttgagatggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23521283	23521284	+	IGR	DEL	GA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23521283_23521284delGA								SLC25A37 (91222 upstream) : NKX3-1 (14923 downstream)																							GTTAGAATCTGAGAGGTGCAGC	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49118033	49118033	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49118033delA								UBE2V2 (143581 upstream) : EFCAB1 (505318 downstream)																							gagaaaacctaaataagtgtt	0.000													4	2	---	---	---	---	
SNTG1	54212	broad.mit.edu	37	8	51386375	51386375	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51386375delA	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				agccagtcacaaaacaataca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	60150698	60150698	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60150698delC								TOX (118931 upstream) : CA8 (950725 downstream)																							AGAAGAAGTACCAGAGTAGTC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	80673929	80673929	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80673929delC								STMN2 (95535 upstream) : HEY1 (2317 downstream)																							ATGACGTCCTCCCTGGGTCAT	0.378													4	2	---	---	---	---	
TPD52	7163	broad.mit.edu	37	8	80960441	80960442	+	Intron	DEL	CT	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80960441_80960442delCT	uc003ybr.1	-						TPD52_uc010lzr.2_Intron|TPD52_uc010lzs.1_Intron|TPD52_uc003ybs.1_Intron|TPD52_uc003ybt.1_Intron|TPD52_uc003ybq.1_Intron|TPD52_uc003ybu.1_Intron	NM_001025252	NP_001020423	P55327	TPD52_HUMAN	tumor protein D52 isoform 1						anatomical structure morphogenesis|B cell differentiation|secretion	endoplasmic reticulum|perinuclear region of cytoplasm	calcium ion binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)			TCAAGAGCAGCTCTCTCTCTCT	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	83489575	83489575	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83489575delC								SNX16 (735054 upstream) : None (None downstream)																							ttccaaaaagccccacctcct	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	95114171	95114172	+	IGR	INS	-	A	A	rs141553164	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95114171_95114172insA								PDP1 (175877 upstream) : CDH17 (25222 downstream)																							ACTGATTCAGCGCTCAGTGATG	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	108190387	108190387	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108190387delA								ABRA (407915 upstream) : ANGPT1 (71324 downstream)																							aaaggtgattaaaaaaacaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139953327	139953328	+	IGR	INS	-	TG	TG			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139953327_139953328insTG								COL22A1 (27091 upstream) : KCNK9 (659754 downstream)																							gtgtgtgtccatgtgtgtgtat	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	11022468	11022468	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11022468delA								PTPRD (409745 upstream) : None (None downstream)																							AATACATCTGAAAATTTCACA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	14021794	14021794	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14021794delT								MPDZ (742231 upstream) : NFIB (60054 downstream)																							ACCTTCACTGTTTTTAGTTTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	21617405	21617406	+	IGR	INS	-	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21617405_21617406insG								LOC554202 (57573 upstream) : MTAP (185229 downstream)																							ATGAGAATGATGGGGGCGGAAT	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	26259337	26259338	+	IGR	INS	-	G	G	rs150800545	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26259337_26259338insG								TUSC1 (580481 upstream) : C9orf82 (581346 downstream)																							cgggttagccagatggtcttga	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	28943721	28943721	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28943721delA								MIR873 (54768 upstream) : None (None downstream)																							TAATGGATGGAAAAAAAGGAT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	32803821	32803821	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32803821delA								TMEM215 (14624 upstream) : APTX (168788 downstream)																							aagaaagaataaaaaagaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66466327	66466327	+	RNA	DEL	G	-	-	rs141830071		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66466327delG	uc004aec.2	+	3		c.960delG								Homo sapiens, clone IMAGE:5213378, mRNA.																		agcaggtccaggaatgcactt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66477358	66477358	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66477358delT								FAM74A4 (982972 upstream) : LOC442421 (19112 downstream)																							agaagaaaaatttaaaaattt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68421770	68421770	+	IGR	DEL	C	-	-	rs112360481		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68421770delC								FAM27B (627581 upstream) : MIR1299 (580469 downstream)																							CTGtttttttcagttattttt	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	71146117	71146118	+	IGR	DEL	AA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71146117_71146118delAA								PGM5 (141 upstream) : C9orf71 (5382 downstream)																							GACATGTATTAAATGGAACAGA	0.396													4	2	---	---	---	---	
PIP5K1B	8395	broad.mit.edu	37	9	71459865	71459865	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71459865delA	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron|PIP5K1B_uc004agv.2_Intron	NM_003558	NP_003549	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)		AGTGGGAGGGAAAAAAAAACA	0.348													4	2	---	---	---	---	
MAMDC2	256691	broad.mit.edu	37	9	72823312	72823313	+	Intron	DEL	TG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72823312_72823313delTG	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron|uc004ahq.1_Intron	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						ttgaagcaattgtgaatgggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	78902375	78902375	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78902375delT								PCSK5 (94037 upstream) : RFK (98058 downstream)																							GCATGTCATCttttttttgtt	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	85225531	85225531	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85225531delA								FLJ46321 (615361 upstream) : RASEF (371786 downstream)																							GACATGGTATAATAGTCATTT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92748429	92748429	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92748429delA								LOC100129066 (413755 upstream) : DIRAS2 (623685 downstream)																							GGTGGAAGGCAATGAGCAGAC	0.577													4	2	---	---	---	---	
FANCC	2176	broad.mit.edu	37	9	98009495	98009496	+	Intron	DEL	GT	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98009495_98009496delGT	uc004avh.2	-						FANCC_uc004avi.3_Intron|FANCC_uc010mrm.1_Intron|FANCC_uc011lul.1_Intron	NM_000136	NP_000127	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C						protein complex assembly	cytosol|nucleoplasm	protein binding			kidney(1)	1		Acute lymphoblastic leukemia(62;0.138)				gcgtgcacgcgtgtgtgtgtgt	0.287			D|Mis|N|F|S			AML|leukemia		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	2	---	---	---	---	
TNC	3371	broad.mit.edu	37	9	117793629	117793629	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117793629delC	uc004bjj.3	-						TNC_uc010mvf.2_Intron	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor						cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7						gggactgaatccagatgggct	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	124560907	124560907	+	IGR	DEL	G	-	-	rs77802316	byFrequency	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124560907delG								DAB2IP (13100 upstream) : TTLL11 (23298 downstream)																							TGCAGAGGGTGGGGGTGGGCT	0.512													4	2	---	---	---	---	
FBXW5	54461	broad.mit.edu	37	9	139837701	139837701	+	Intron	DEL	C	-	-	rs11339872		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139837701delC	uc004cjx.2	-						FBXW5_uc010nbx.2_5'Flank|FBXW5_uc004cjy.2_Intron|FBXW5_uc004cjz.2_Intron|C8G_uc004cka.2_5'Flank	NM_018998	NP_061871	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5								catalytic activity|protein binding				0	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		GCCTGACCCACCCCCCCCCCC	0.692													5	4	---	---	---	---	
WDR85	92715	broad.mit.edu	37	9	140468517	140468517	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140468517delA	uc004cnk.1	-						WDR85_uc004cnl.1_Intron|WDR85_uc004cnm.1_Intron|WDR85_uc004cnn.1_Intron	NM_138778	NP_620133	Q9BTV6	WDR85_HUMAN	WD repeat domain 85						peptidyl-diphthamide biosynthetic process from peptidyl-histidine						0	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.00029)|Epithelial(140;0.000509)		actcagtttcaaaaaaaaaaG	0.239													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4483440	4483440	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4483440delT								KLF6 (655967 upstream) : LOC100216001 (138004 downstream)																							ctttcttttctttttactctc	0.000													4	2	---	---	---	---	
ANKRD16	54522	broad.mit.edu	37	10	5925286	5925286	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5925286delT	uc010qat.1	-						ANKRD16_uc009xie.2_Intron|ANKRD16_uc009xif.2_Intron|ANKRD16_uc001iiq.2_Intron	NM_019046	NP_061919	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16 isoform a												0						CAAAGGAttctttttttttga	0.224													4	2	---	---	---	---	
ITIH5	80760	broad.mit.edu	37	10	7711112	7711112	+	5'Flank	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7711112delT	uc001ijq.2	-						ITIH5_uc001ijr.1_5'Flank	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4						ATCTGATCTCTTTTTTTTTCC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8753966	8753966	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8753966delT								GATA3 (636804 upstream) : None (None downstream)																							ttgtttatcatttttttttga	0.085													4	2	---	---	---	---	
CUBN	8029	broad.mit.edu	37	10	17169011	17169012	+	Intron	INS	-	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17169011_17169012insT	uc001ioo.2	-							NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTTTTTTTAAGTTTTTTTTTAA	0.391													4	2	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	34879487	34879487	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34879487delA	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				AAATTCAGCTAAAGAACAGCA	0.393													4	2	---	---	---	---	
CREM	1390	broad.mit.edu	37	10	35480866	35480867	+	Intron	INS	-	CCACCTGGTG	CCACCTGGTG	rs148904125	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35480866_35480867insCCACCTGGTG	uc001iyb.2	+						CREM_uc001ixy.2_Intron|CREM_uc001ixz.2_Intron|CREM_uc001iya.2_Intron|CREM_uc001iyc.2_Intron|CREM_uc001iyd.2_Intron|CREM_uc001iye.2_Intron|CREM_uc001iyf.2_Intron|CREM_uc001iyg.2_Intron|CREM_uc001iyh.2_Intron|CREM_uc001iyi.2_Intron|CREM_uc001iyj.2_Intron|CREM_uc001iyk.2_Intron	NM_181571	NP_853549	Q03060	CREM_HUMAN	cAMP responsive element modulator isoform a						cell differentiation|multicellular organismal development|signal transduction|spermatogenesis	nucleus	cAMP response element binding protein binding|protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CCACTACTATCCTTGATGCCAG	0.465													6	3	---	---	---	---	
GPRIN2	9721	broad.mit.edu	37	10	47005612	47005614	+	3'UTR	DEL	AGA	-	-	rs150293212		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47005612_47005614delAGA	uc010qfq.1	+	1						NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth												0						ATAATAAAGCAGAAGAACACCTG	0.488													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47065654	47065655	+	Intron	INS	-	T	T	rs151210596	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47065654_47065655insT	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						aagaaaactagtaccttgagaa	0.000													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47106937	47106938	+	Intron	INS	-	A	A	rs140415031		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47106937_47106938insA	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						TACTCAGAAGGAAAGGCATGTG	0.455													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	50478130	50478130	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50478130delC								C10orf128 (81723 upstream) : C10orf71 (29057 downstream)																							atctgtccctccatcccctca	0.000													4	2	---	---	---	---	
FAM13C	220965	broad.mit.edu	37	10	61044502	61044503	+	Intron	DEL	CA	-	-	rs35225282		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61044502_61044503delCA	uc001jkn.2	-						FAM13C_uc001jko.2_Intron|FAM13C_uc010qid.1_Intron|FAM13C_uc010qie.1_Intron|FAM13C_uc010qif.1_Intron|FAM13C_uc001jkp.2_Intron	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1											ovary(2)	2						CCCCACCTTCCACACACACACA	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65732810	65732810	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65732810delG								REEP3 (350839 upstream) : ANXA2P3 (852475 downstream)																							GTGGAGGTGTGGGGATAAACT	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	82895509	82895510	+	IGR	DEL	GA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82895509_82895510delGA								SH2D4B (489193 upstream) : NRG3 (739560 downstream)																							TTCTCTTCTTGAGATTTGAATG	0.441													4	2	---	---	---	---	
LIPA	3988	broad.mit.edu	37	10	91061670	91061670	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91061670delA	uc001kgc.3	-						LIPA_uc001kgb.3_Intron|uc001kgd.2_Intron|IFIT2_uc009xts.2_5'Flank	NM_001127605	NP_001121077	P38571	LICH_HUMAN	lipase A precursor						lipid catabolic process	lysosome	lipase activity|sterol esterase activity				0		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		TAATAAAAAGAAAAAAAGAAA	0.418													4	2	---	---	---	---	
BTAF1	9044	broad.mit.edu	37	10	93717316	93717316	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93717316delA	uc001khr.2	+						BTAF1_uc009xua.1_Intron|BTAF1_uc001khs.1_Intron	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)				CCCAGGCAGTAAAAAAAATAC	0.338													4	2	---	---	---	---	
GPR120	338557	broad.mit.edu	37	10	95343817	95343817	+	Intron	DEL	G	-	-	rs67687051		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95343817delG	uc010qnt.1	+						GPR120_uc010qnu.1_Intron	NM_181745	NP_859529	Q5NUL3	O3FA1_HUMAN	G protein-coupled receptor 120						negative regulation of cytokine secretion|negative regulation of inflammatory response|regulation of glucose transport	integral to membrane|plasma membrane	fatty acid binding				0		Colorectal(252;0.122)				TTCCTCTGCAGCCCACCCACC	0.527													4	2	---	---	---	---	
SLIT1	6585	broad.mit.edu	37	10	98830008	98830008	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98830008delG	uc001kmw.2	-						SLIT1_uc009xvh.1_Intron	NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		gcagtgttttgaagtcattgg	0.184													4	2	---	---	---	---	
GOT1	2805	broad.mit.edu	37	10	101163850	101163850	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101163850delT	uc001kpr.2	-						GOT1_uc009xwh.2_Intron|GOT1_uc001kpq.1_Intron	NM_002079	NP_002070	P17174	AATC_HUMAN	aspartate aminotransferase 1						aspartate catabolic process|cellular response to insulin stimulus|gluconeogenesis|response to glucocorticoid stimulus	cytosol	L-aspartate:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding				0		Ovarian(717;0.028)|Colorectal(252;0.234)		Epithelial(162;4.76e-10)|all cancers(201;3.84e-08)	L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	AAGTAAATTGTCCTAGAGTGT	0.388													4	2	---	---	---	---	
NFKB2	4791	broad.mit.edu	37	10	104158973	104158973	+	Intron	DEL	A	-	-	rs146186127		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104158973delA	uc001kvb.2	+						NFKB2_uc001kva.2_Intron|NFKB2_uc001kvd.2_Intron|NFKB2_uc009xxc.2_Intron	NM_001077494	NP_001070962	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|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	Bcl3/NF-kappaB2 complex|cytosol|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			lung(3)	3		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)		actccgtctcaaaaaaaaaaa	0.264			T	IGH@	B-NHL								6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	112070805	112070805	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112070805delT								SMNDC1 (6098 upstream) : DUSP5 (186820 downstream)																							GTGATAGGAATTTTTTTTTCA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113809097	113809097	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113809097delA								ADRA2A (968437 upstream) : GPAM (100525 downstream)																							attggtccacaaaaaaaagga	0.000													4	2	---	---	---	---	
FAM53B	9679	broad.mit.edu	37	10	126396651	126396651	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126396651delC	uc001lhv.1	-						FAM53B_uc001lhu.1_Intron|FAM53B_uc001lhw.2_Intron|uc001lhx.2_Intron	NM_014661	NP_055476	Q14153	FA53B_HUMAN	hypothetical protein LOC9679											ovary(1)|pancreas(1)	2		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		ATACAAGGAACCTGAAGATCA	0.353													4	2	---	---	---	---	
COPB1	1315	broad.mit.edu	37	11	14490716	14490716	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14490716delT	uc001mli.2	-						COPB1_uc001mlg.2_Intron|COPB1_uc001mlh.2_Intron	NM_016451	NP_057535	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1						COPI coating of Golgi vesicle|interspecies interaction between organisms|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|ER-Golgi intermediate compartment|plasma membrane	protein binding|structural molecule activity			ovary(1)|central_nervous_system(1)	2						aattttctcattttttttgtt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	28657590	28657590	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28657590delT								METT5D1 (302536 upstream) : None (None downstream)																							ATCATTTTCCTTTTTTCTGTT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	29573059	29573060	+	IGR	INS	-	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29573059_29573060insA								None (None upstream) : KCNA4 (458706 downstream)																							ccggaccattcaaattcatcat	0.104													4	2	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	40647704	40647704	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40647704delA	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)				attgtgcttcaaacacagtag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	47902673	47902673	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47902673delA								NUP160 (32616 upstream) : PTPRJ (99437 downstream)																							agaaggaaagaaaaaaaaaag	0.323													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	61781020	61781020	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61781020delC								FTH1 (45888 upstream) : INCENP (110425 downstream)																							GCCAAATACTCCCCCAAGTCC	0.592													4	2	---	---	---	---	
ZBTB3	79842	broad.mit.edu	37	11	62519423	62519423	+	3'UTR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62519423delA	uc001nuz.2	-	2						NM_024784	NP_079060	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3						ataaaagattaaaaaaaaaaa	0.239													5	3	---	---	---	---	
PITPNM1	9600	broad.mit.edu	37	11	67262282	67262283	+	Intron	INS	-	GA	GA	rs67466581		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67262282_67262283insGA	uc001olx.2	-						PITPNM1_uc001olw.2_Intron|PITPNM1_uc001oly.2_Intron|PITPNM1_uc001olz.2_Intron	NM_004910	NP_004901	O00562	PITM1_HUMAN	phosphatidylinositol transfer protein,						brain development|lipid metabolic process|phototransduction|protein transport	cleavage furrow|endoplasmic reticulum membrane|Golgi cisterna membrane|lipid particle|membrane fraction|midbody	metal ion binding|phosphatidylinositol transporter activity			lung(2)|central_nervous_system(1)	3						CGAGAGTGGGCGAGTGGGCGAG	0.703													10	7	---	---	---	---	
CTTN	2017	broad.mit.edu	37	11	70266152	70266152	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70266152delT	uc001opv.3	+						CTTN_uc001opu.2_Intron|CTTN_uc001opw.3_Intron|CTTN_uc010rqm.1_5'Flank|CTTN_uc001opx.2_5'Flank	NM_005231	NP_005222	Q14247	SRC8_HUMAN	cortactin isoform a							cell cortex|cytoskeleton|lamellipodium|ruffle|soluble fraction	protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		AGCTTGAGTGTTATGGCGCTC	0.542													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83326248	83326248	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83326248delT	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc010rsw.1_Intron|DLG2_uc010rsx.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				TGCAGCATTATTACAGGTGAA	0.358													4	2	---	---	---	---	
EED	8726	broad.mit.edu	37	11	85975481	85975482	+	Intron	INS	-	TATT	TATT	rs138959322	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85975481_85975482insTATT	uc001pbp.2	+						EED_uc010rtm.1_Intron|EED_uc001pbq.2_Intron|EED_uc001pbr.2_Intron|EED_uc001pbs.2_Intron|EED_uc010rtn.1_Intron	NM_003797	NP_003788	O75530	EED_HUMAN	embryonic ectoderm development isoform a						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|identical protein binding			skin(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				AGTAAAGACtatatttatttat	0.312													4	3	---	---	---	---	
PDGFD	80310	broad.mit.edu	37	11	103870622	103870626	+	Intron	DEL	TCTTG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103870622_103870626delTCTTG	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484	Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		GTCTACGCTATCTTGTCTGTTAGGG	0.434													4	2	---	---	---	---	
GUCY1A2	2977	broad.mit.edu	37	11	106816239	106816240	+	Intron	DEL	AC	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106816239_106816240delAC	uc001pjg.1	-						GUCY1A2_uc010rvo.1_Intron|GUCY1A2_uc009yxn.1_Intron	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2						intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)		GAACCCTACAacacacacatag	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109070783	109070783	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109070783delT								DDX10 (259137 upstream) : C11orf87 (222092 downstream)																							ccctcaattattagagcgatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119859594	119859594	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119859594delA								PVRL1 (260159 upstream) : TRIM29 (122401 downstream)																							cctcacctataagggggacaa	0.104													4	2	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126329269	126329269	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126329269delT	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		TCTCCTGCACTTTCCCTTCCT	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133532528	133532528	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133532528delG								OPCML (130125 upstream) : SPATA19 (177989 downstream)																							gcactgtgctgggtgctgtgg	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4041207	4041208	+	IGR	INS	-	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4041207_4041208insT								PARP11 (58599 upstream) : CCND2 (341694 downstream)																							TCCCCCCAAGATTTTTTTTTTA	0.455													4	2	---	---	---	---	
A2ML1	144568	broad.mit.edu	37	12	9026207	9026207	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9026207delT	uc001quz.3	+						A2ML1_uc001qva.1_Intron|A2ML1_uc010sgm.1_Intron|A2ML1_uc001qvb.1_Intron	NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor							extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3						tacacacacattttttttcag	0.000													4	2	---	---	---	---	
OVCH1	341350	broad.mit.edu	37	12	29596214	29596214	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29596214delA	uc001rix.1	-							NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					CATGTAAGCCACATACTGAAT	0.284													63	36	---	---	---	---	
FGD4	121512	broad.mit.edu	37	12	32776128	32776128	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32776128delA	uc001rkz.2	+						FGD4_uc001rlc.2_Intron|FGD4_uc001rky.2_Intron|FGD4_uc001rla.2_Intron|FGD4_uc010ske.1_Intron|FGD4_uc001rlb.1_Intron	NM_139241	NP_640334	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					TATAAAGGGGAAAAAAATCTA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	42183499	42183499	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42183499delG								PDZRN4 (215115 upstream) : GXYLT1 (292151 downstream)																							TGCTGCTTGTGGAAGATAACA	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	42274884	42274884	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42274884delA								PDZRN4 (306500 upstream) : GXYLT1 (200766 downstream)																							GCCATTAGGTAAAAGGTACAT	0.323													4	2	---	---	---	---	
SPATS2	65244	broad.mit.edu	37	12	49854539	49854540	+	Intron	INS	-	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49854539_49854540insT	uc001rud.2	+						SPATS2_uc001ruc.2_Intron|SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron|SPATS2_uc001rug.2_5'Flank	NM_023071	NP_075559	Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1						GTGTGTTTGTGTTTTTCCCTCC	0.337													4	2	---	---	---	---	
GALNT6	11226	broad.mit.edu	37	12	51762523	51762527	+	Intron	DEL	AGGTG	-	-	rs141272423		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51762523_51762527delAGGTG	uc001ryk.2	-						GALNT6_uc009zma.1_Intron|GALNT6_uc001ryl.1_Intron	NM_007210	NP_009141	Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6						protein O-linked glycosylation	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2						CTGGACAGACAGGTGAGGTGATTAT	0.302													3	3	---	---	---	---	
TPH2	121278	broad.mit.edu	37	12	72374550	72374551	+	Intron	DEL	AG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72374550_72374551delAG	uc009zrw.1	+						TPH2_uc001swy.2_Intron	NM_173353	NP_775489	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2						aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity			ovary(2)|central_nervous_system(1)|skin(1)	4					L-Tryptophan(DB00150)	ATAGGTATGCAGAGAGAGAGAG	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80122409	80122410	+	IGR	INS	-	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80122409_80122410insA								PAWR (37619 upstream) : PPP1R12A (44934 downstream)																							aaagcaatgagaaaaaaaatga	0.000													4	2	---	---	---	---	
RASSF9	9182	broad.mit.edu	37	12	86216590	86216591	+	Intron	INS	-	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86216590_86216591insC	uc001taf.1	-							NM_005447	NP_005438	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family						endosome transport|protein targeting|signal transduction	cytosol|endosome|trans-Golgi network transport vesicle membrane	protein binding|transporter activity			ovary(1)	1						GACCACATATTCCCCTCCACTA	0.391													4	2	---	---	---	---	
APAF1	317	broad.mit.edu	37	12	99116684	99116684	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99116684delT	uc001tfz.2	+						APAF1_uc001tfy.2_Intron|APAF1_uc001tga.2_Intron|APAF1_uc001tgb.2_Intron|APAF1_uc001tgc.2_Intron|APAF1_uc009zto.2_Intron	NM_181861	NP_863651	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1 isoform						activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)	ATATTGTGTGTTTTTTTTTTT	0.328													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	105706168	105706168	+	IGR	DEL	C	-	-	rs35219638		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105706168delC								APPL2 (76160 upstream) : C12orf75 (18246 downstream)																							ccgttgctctccctcagtatc	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106381178	106381179	+	IGR	DEL	CA	-	-	rs144372432		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106381178_106381179delCA								C12orf75 (615883 upstream) : NUAK1 (75946 downstream)																							gggaggagaccacacacaaggg	0.064													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	107548047	107548047	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107548047delT								CRY1 (60449 upstream) : BTBD11 (164150 downstream)																							ctcctgactattttcccttgc	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108982821	108982821	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108982821delA								ISCU (19663 upstream) : TMEM119 (803 downstream)																							GAACAAGAAGAAAGCACAGCC	0.483													4	2	---	---	---	---	
TAOK3	51347	broad.mit.edu	37	12	118684808	118684808	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118684808delA	uc001twx.2	-						TAOK3_uc001twy.3_Intron	NM_016281	NP_057365	Q9H2K8	TAOK3_HUMAN	TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ATTAAGCGTGAAAAAAAAATT	0.289													4	2	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124953385	124953386	+	Intron	INS	-	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124953385_124953386insT	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		cctcatcaccccatcatcctca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128360106	128360108	+	IGR	DEL	TGC	-	-	rs111882175		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128360106_128360108delTGC								None (None upstream) : TMEM132C (539183 downstream)																							CTCAATCCTTTGCTTTCTTGTTC	0.404													4	3	---	---	---	---	
IFT88	8100	broad.mit.edu	37	13	21156193	21156194	+	Intron	INS	-	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21156193_21156194insT	uc001unh.2	+						IFT88_uc001uni.2_Intron|IFT88_uc001unj.2_Intron|IFT88_uc010tcq.1_Intron	NM_175605	NP_783195	Q13099	IFT88_HUMAN	intraflagellar transport 88 homolog isoform 1						cilium morphogenesis	centriole|intraflagellar transport particle B|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		ACAAGTGTGTATTTTTGTGGGA	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21892698	21892698	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21892698delA	uc001unz.1	+											Homo sapiens cDNA FLJ33446 fis, clone BRAMY1000095.																		actattatggaaaaaaaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	39151569	39151569	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39151569delA								UFM1 (214427 upstream) : FREM2 (109604 downstream)																							ATTCTCTATCAGACCCTTTTC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	43114677	43114677	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43114677delC								AKAP11 (217275 upstream) : TNFSF11 (22195 downstream)																							TTCTGTGACTCAGTTACTCCT	0.383													4	2	---	---	---	---	
SETDB2	83852	broad.mit.edu	37	13	50034541	50034542	+	Intron	INS	-	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50034541_50034542insT	uc001vcz.2	+						SETDB2_uc010adg.2_Intron|SETDB2_uc001vcy.3_Intron|SETDB2_uc010adh.2_Intron|SETDB2_uc001vda.2_Intron	NM_031915	NP_114121	Q96T68	SETB2_HUMAN	SET domain, bifurcated 2 isoform a						cell division|chromosome segregation|heart looping|left/right axis specification|mitosis|negative regulation of transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone methyltransferase activity (H3-K9 specific)|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)		CCTCATTTATCTTTTTTTTTAG	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	76789811	76789812	+	IGR	INS	-	T	T			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76789811_76789812insT								LMO7 (355807 upstream) : KCTD12 (664492 downstream)																							ggagtgttgaaggagatgaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	80144792	80144792	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80144792delT								NDFIP2 (14587 upstream) : SPRY2 (765322 downstream)																							AAAAGAGCCCTCATGATGAGA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	88850149	88850150	+	IGR	INS	-	A	A	rs144108295	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88850149_88850150insA								SLITRK5 (518281 upstream) : None (None downstream)																							aatcaggcaagaaaaaaaaaat	0.000													4	2	---	---	---	---	
TGDS	23483	broad.mit.edu	37	13	95228830	95228830	+	Intron	DEL	A	-	-	rs116036564	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95228830delA	uc001vlw.2	-						TGDS_uc001vlx.2_Intron	NM_014305	NP_055120	O95455	TGDS_HUMAN	TDP-glucose 4,6-dehydratase						cellular metabolic process		coenzyme binding|dTDP-glucose 4,6-dehydratase activity|protein binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					GTATATATTTAAAAAAAAAAA	0.348													5	3	---	---	---	---	
SLC15A1	6564	broad.mit.edu	37	13	99357792	99357794	+	Intron	DEL	CAG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99357792_99357794delCAG	uc001vno.2	-							NM_005073	NP_005064	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide						digestion|protein transport	integral to plasma membrane|membrane fraction	peptide:hydrogen symporter activity			ovary(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Cefadroxil(DB01140)|Ceftibuten(DB01415)|Cyclacillin(DB01000)	ttccaggctccagcagcagcagc	0.015													4	2	---	---	---	---	
KDELC1	79070	broad.mit.edu	37	13	103438935	103438935	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103438935delT	uc001vpq.3	-						KDELC1_uc001vpr.3_Intron	NM_024089	NP_076994	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1 precursor							endoplasmic reticulum lumen				ovary(1)	1	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TTTCCATGACTTTTTTTTTTA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	104105845	104105845	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104105845delT								SLC10A2 (386649 upstream) : None (None downstream)																							AAAGTCACAGTAGATATCATG	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107764076	107764076	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107764076delT								ARGLU1 (543562 upstream) : FAM155A (56804 downstream)																							ttcttcctcatttgtgaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111763361	111763362	+	IGR	INS	-	TT	TT	rs60148903		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111763361_111763362insTT								ANKRD10 (195945 upstream) : ARHGEF7 (4262 downstream)																							TCTGAGTGATGATAGTAAGTTC	0.406													4	2	---	---	---	---	
TUBGCP3	10426	broad.mit.edu	37	13	113153644	113153644	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113153644delT	uc001vse.1	-						TUBGCP3_uc010tjq.1_Intron|TUBGCP3_uc001vsf.2_Intron	NM_006322	NP_006313	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3						G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					attcattccctcaccacacat	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35190106	35190107	+	IGR	DEL	TG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35190106_35190107delTG								CFL2 (6077 upstream) : BAZ1A (31832 downstream)																							ttttgtaatatgtgatctttgt	0.000													4	2	---	---	---	---	
SRP54	6729	broad.mit.edu	37	14	35456082	35456082	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35456082delA	uc001wso.2	+						SRP54_uc010tpp.1_Intron|SRP54_uc010tpq.1_Intron	NM_003136	NP_003127	P61011	SRP54_HUMAN	signal recognition particle 54kDa isoform 1						GTP catabolic process|response to drug|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition|SRP-dependent cotranslational protein targeting to membrane, translocation	cytosol|nuclear speck|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|drug binding|endoplasmic reticulum signal peptide binding|GDP binding|GTP binding|nucleoside-triphosphatase activity|ribonucleoprotein binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		actctgtctcaaaaaaaaaaa	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	61044565	61044565	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61044565delG								SIX6 (66042 upstream) : SIX1 (66853 downstream)																							TGGGAGCTATGGGGGAAGAAT	0.418													4	2	---	---	---	---	
GPHN	10243	broad.mit.edu	37	14	67632166	67632187	+	Intron	DEL	TATCAAAGCACATTCCAAATCC	-	-	rs3830996		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67632166_67632187delTATCAAAGCACATTCCAAATCC	uc001xiy.2	+						GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		agataatatatatcaaagcacattccaaatcctatcaaagca	0.153			T	MLL	AL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20556467	20556467	+	IGR	DEL	A	-	-	rs113687016		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20556467delA								None (None upstream) : GOLGA6L6 (180627 downstream)																							ATGTGGGGGGAAACCCACACC	0.607													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20850795	20850795	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20850795delC								GOLGA8C (69769 upstream) : BCL8 (19261 downstream)																							tctcatggtacccagaaaata	0.095													4	2	---	---	---	---	
OR4N4	283694	broad.mit.edu	37	15	22358679	22358679	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22358679delT	uc001yuc.1	+						LOC727924_uc001yua.2_Intron|LOC727924_uc001yub.1_Intron	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		AAGAGACAGCTTCATCATTTT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22492548	22492551	+	IGR	DEL	GCCA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22492548_22492551delGCCA								OR4N3P (78163 upstream) : MIR1268 (20678 downstream)																							CAAGCCTCATGCCAGCCACCTTCT	0.539													4	2	---	---	---	---	
GOLGA8DP	100132979	broad.mit.edu	37	15	22714032	22714032	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22714032delA	uc010axw.2	-						GOLGA8DP_uc010axx.2_Intron	NM_001012423	NP_001012423			golgi autoantigen, golgin subfamily a, 8E												0						TCATGGCTAGAAAAAAAAAGA	0.378													5	3	---	---	---	---	
SNRPN	6638	broad.mit.edu	37	15	25098427	25098427	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25098427delC	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		ggaatcccatccaggatgaca	0.000									Prader-Willi_syndrome				4	2	---	---	---	---	
OCA2	4948	broad.mit.edu	37	15	28011663	28011663	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28011663delG	uc001zbh.3	-						OCA2_uc010ayv.2_Intron	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II						eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		TGCTTAGTGAGGACACTAGGC	0.408									Oculocutaneous_Albinism				4	2	---	---	---	---	
SORD	6652	broad.mit.edu	37	15	45361942	45361942	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45361942delT	uc001zul.3	+						SORD_uc010uel.1_Intron|SORD_uc001zum.3_Intron|SORD_uc010bdz.2_Intron	NM_003104	NP_003095	Q00796	DHSO_HUMAN	sorbitol dehydrogenase						fructose biosynthetic process|glucose metabolic process|L-xylitol catabolic process|sorbitol catabolic process|sperm motility	cilium|extracellular space|flagellum|membrane fraction|mitochondrial membrane|soluble fraction	L-iditol 2-dehydrogenase activity|NAD binding|sugar binding|zinc ion binding				0		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)	NADH(DB00157)	TCTTATTTTATTGAGGAAAAC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	48256021	48256021	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48256021delA								SEMA6D (189602 upstream) : SLC24A5 (157148 downstream)																							CCTGTTGTGTAAGAATGCAAC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	55033226	55033227	+	IGR	INS	-	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55033226_55033227insA								UNC13C (112421 upstream) : RSL24D1 (440294 downstream)																							gcaggagttgcaaaaataaaaa	0.000													4	2	---	---	---	---	
IGDCC4	57722	broad.mit.edu	37	15	65686158	65686159	+	Intron	DEL	AC	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65686158_65686159delAC	uc002aou.1	-						IGDCC4_uc002aot.1_Intron	NM_020962	NP_066013	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member							integral to membrane|plasma membrane				ovary(1)|pancreas(1)|skin(1)	3						TCCCCTGCCAACACACACACAC	0.569													4	2	---	---	---	---	
MEGF11	84465	broad.mit.edu	37	15	66216446	66216448	+	Intron	DEL	CAG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66216446_66216448delCAG	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821	A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1						CCAGCCCTACCAGCAGCAGGAGA	0.532													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	74392546	74392546	+	IGR	DEL	A	-	-	rs3214584		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74392546delA								GOLGA6A (17655 upstream) : LOC283731 (26168 downstream)																							GGTGCCTCATACATCGCGCGA	0.647													16	19	---	---	---	---	
GOLGA6C	653641	broad.mit.edu	37	15	75552532	75552532	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75552532delT	uc002azs.1	+							NM_001145224	NP_001138696	A6NDK9	GOG6C_HUMAN	golgi autoantigen, golgin subfamily a, 6D											ovary(1)	1						CCCCCCACACTTTTTTTTTTA	0.443													4	2	---	---	---	---	
C15orf27	123591	broad.mit.edu	37	15	76407656	76407656	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76407656delC	uc002bbq.2	+						C15orf27_uc010bkp.2_Intron	NM_152335	NP_689548	Q2M3C6	CO027_HUMAN	hypothetical protein LOC123591							integral to membrane					0						CCTTCACTTTCCCATCACCTG	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	80524453	80524453	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80524453delG								FAH (45771 upstream) : ARNT2 (172239 downstream)																							TAGGAGTGGTGGGTATCTGAC	0.552													4	2	---	---	---	---	
ARNT2	9915	broad.mit.edu	37	15	80755720	80755721	+	Intron	INS	-	A	A	rs141377248	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80755720_80755721insA	uc002bfr.2	+						ARNT2_uc002bfq.2_Intron|ARNT2_uc010unm.1_Intron|ARNT2_uc002bfs.2_Intron	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator						central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)			CCTGCCTCTACAGTCTCAGTTC	0.460													3	3	---	---	---	---	
FAM108C1	58489	broad.mit.edu	37	15	81005137	81005137	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81005137delT	uc002bfu.2	+						FAM108C1_uc002bft.2_Intron	NM_021214	NP_067037	Q6PCB6	F108C_HUMAN	hypothetical protein LOC58489								hydrolase activity				0						ATTCAAACAATTTTTTTCTAA	0.348													4	2	---	---	---	---	
MESP2	145873	broad.mit.edu	37	15	90311773	90311773	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90311773delC	uc010uqa.1	+									Q0VG99	MESP2_HUMAN	Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 231282.						Notch signaling pathway	nucleus	DNA binding				0	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			CGTGCCtctgcagacaaccgt	0.114													4	2	---	---	---	---	
SLCO3A1	28232	broad.mit.edu	37	15	92705292	92705294	+	Intron	DEL	GAT	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92705292_92705294delGAT	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)			CTCAGCAGAGGATGATGATGATA	0.369													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	97515591	97515591	+	IGR	DEL	T	-	-	rs11322975		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97515591delT								SPATA8 (186747 upstream) : LOC91948 (770255 downstream)																							GAGGTCAGGGTGTCAGAACCA	0.448													6	3	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6203538	6203538	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6203538delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		ccattgtacgttttttttttc	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9575492	9575493	+	IGR	DEL	AG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9575492_9575493delAG								C16orf72 (361947 upstream) : GRIN2A (271774 downstream)																							gtgtttcattagagtgcttatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	10937283	10937283	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10937283delT								FAM18A (24662 upstream) : CIITA (33772 downstream)																							CATTTTCGAAttttttttttt	0.249													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12664640	12664641	+	3'UTR	INS	-	AG	AG	rs3842349		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12664640_12664641insAG	uc002dby.3	+	14						NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						AATAATGCAACAGTCCCCCATT	0.465													2	4	---	---	---	---	
PDXDC1	23042	broad.mit.edu	37	16	15076412	15076412	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15076412delA	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	actccatctcaaaaaaaaaag	0.174													4	2	---	---	---	---	
CRYM	1428	broad.mit.edu	37	16	21270411	21270411	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21270411delT	uc002dik.2	-						CRYM_uc010bwq.1_Intron|CRYM_uc002dil.2_Intron|CRYM_uc002dim.2_Intron	NM_001888	NP_001879	Q14894	CRYM_HUMAN	crystallin, mu isoform 1						negative regulation of transcription from RNA polymerase II promoter|sensory perception of sound|thyroid hormone transport	cytoplasm|nucleus|plasma membrane	NADP binding|protein homodimerization activity|thyroid hormone binding|transcription corepressor activity				0				GBM - Glioblastoma multiforme(48;0.0573)	Levothyroxine(DB00451)	GCTGAGCAAAttttttttttt	0.209													4	2	---	---	---	---	
CRYM	1428	broad.mit.edu	37	16	21304834	21304835	+	Intron	INS	-	G	G			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21304834_21304835insG	uc002dim.2	-						CRYM_uc002dil.2_Intron	NM_001014444	NP_001014444	Q14894	CRYM_HUMAN	crystallin, mu isoform 2						negative regulation of transcription from RNA polymerase II promoter|sensory perception of sound|thyroid hormone transport	cytoplasm|nucleus|plasma membrane	NADP binding|protein homodimerization activity|thyroid hormone binding|transcription corepressor activity				0				GBM - Glioblastoma multiforme(48;0.0573)	Levothyroxine(DB00451)	TCCTGGTTATAGGGGGAAATAA	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22955554	22955554	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22955554delC								HS3ST2 (27897 upstream) : USP31 (117175 downstream)																							gagcatgcgaccaaggccatc	0.000													4	2	---	---	---	---	
USP31	57478	broad.mit.edu	37	16	23161923	23161923	+	5'Flank	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23161923delA	uc002dll.2	-							NM_020718	NP_065769	Q70CQ4	UBP31_HUMAN	ubiquitin specific peptidase 31						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(3)|lung(3)|breast(2)|pancreas(1)|skin(1)	10				GBM - Glioblastoma multiforme(48;0.0187)		TGGTTCCATTAAAAAAAAAAT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25391759	25391763	+	IGR	DEL	AAAAC	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25391759_25391763delAAAAC								ZKSCAN2 (122904 upstream) : HS3ST4 (311584 downstream)																							TCTGTCAGAAaaaacaaaacaaaac	0.195													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33946421	33946422	+	IGR	INS	-	A	A	rs112464617		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33946421_33946422insA								None (None upstream) : MIR1826 (19086 downstream)																							caaacagcatcacatgctacag	0.000													4	2	---	---	---	---	
N4BP1	9683	broad.mit.edu	37	16	48592725	48592726	+	Intron	INS	-	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48592725_48592726insC	uc002efp.2	-							NM_153029	NP_694574	O75113	N4BP1_HUMAN	Nedd4 binding protein 1						negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination	nucleolus|PML body					0		all_cancers(37;0.179)|all_lung(18;0.11)				TTGCTGGGTTTCCCCTAACAGG	0.411													4	2	---	---	---	---	
PAPD5	64282	broad.mit.edu	37	16	50258316	50258316	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50258316delT	uc010vgo.1	+						PAPD5_uc010cbi.2_Intron|PAPD5_uc002efz.2_Intron|PAPD5_uc002ega.2_Intron	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a						cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		TGCATAACTGTTTATGTATGG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51341454	51341454	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51341454delG								SALL1 (156271 upstream) : None (None downstream)																							acatgtgctaggaaatgatat	0.119													4	2	---	---	---	---	
RPGRIP1L	23322	broad.mit.edu	37	16	53669572	53669573	+	Intron	DEL	TG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53669572_53669573delTG	uc002ehp.2	-						RPGRIP1L_uc002eho.3_Intron|RPGRIP1L_uc010vgy.1_Intron|RPGRIP1L_uc010cbx.2_Intron|RPGRIP1L_uc010vgz.1_Intron	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a						negative regulation of G-protein coupled receptor protein signaling pathway	cell-cell junction|centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)				AAACTAAGAATGTGTGAAGGAA	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	60935785	60935785	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60935785delT								None (None upstream) : CDH8 (751450 downstream)																							CTTTCAGAACTTTTTTTTGAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66016614	66016614	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66016614delT								LOC283867 (406411 upstream) : CDH5 (383911 downstream)																							ccaaggatggttttgataggt	0.085													4	2	---	---	---	---	
CES8	283848	broad.mit.edu	37	16	67042602	67042603	+	Intron	DEL	CA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67042602_67042603delCA	uc002eqv.2	+						CES8_uc010vix.1_Intron|CES8_uc002eqw.2_Intron|CES8_uc002eqy.2_Intron|CES8_uc002eqx.2_Intron|CES8_uc010viy.1_Intron|CES8_uc010viz.1_Intron|CES8_uc002eqz.2_Intron	NM_173815	NP_776176	Q5XG92	EST4A_HUMAN	carboxylesterase 8 (putative)							extracellular region	carboxylesterase activity				0						caggcctggccacacacacact	0.000													4	2	---	---	---	---	
SMPD3	55512	broad.mit.edu	37	16	68471560	68471561	+	Intron	DEL	CT	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68471560_68471561delCT	uc002ewa.2	-							NM_018667	NP_061137	Q9NY59	NSMA2_HUMAN	neutral sphingomyelin phosphodiesterase 3						cell cycle|multicellular organismal development|sphingomyelin catabolic process	Golgi membrane|integral to membrane|plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity			skin(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	CATCAAGAGACTCTCTCATAGC	0.450													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	71352357	71352357	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71352357delC								FTSJD1 (28844 upstream) : CALB2 (40269 downstream)																							CTGTTGCTTTCCAGATTGGCC	0.333													4	2	---	---	---	---	
PKD1L3	342372	broad.mit.edu	37	16	72003577	72003578	+	Intron	INS	-	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72003577_72003578insA	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0						GGAACCAAAGGAAAAAAAAATA	0.322													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	76828590	76828590	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76828590delA								CNTNAP4 (235455 upstream) : MON1B (396246 downstream)																							GGACAACACTAACGCTTTTAC	0.264													4	2	---	---	---	---	
PLCG2	5336	broad.mit.edu	37	16	81975169	81975170	+	Intron	DEL	TT	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81975169_81975170delTT	uc002fgt.2	+							NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8						AAGTTTCTGATTTTTTTTTTTT	0.307													4	2	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	83659995	83659996	+	Intron	DEL	TG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83659995_83659996delTG	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)		GCAGGAGAGATGTGAAAGTGCT	0.332													4	2	---	---	---	---	
ATP2C2	9914	broad.mit.edu	37	16	84479755	84479755	+	Intron	DEL	T	-	-	rs112030939		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84479755delT	uc002fhx.2	+						ATP2C2_uc010chj.2_Intron|ATP2C2_uc002fhy.2_Intron|ATP2C2_uc002fhz.2_Intron	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2						ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						GAGAAGAGACTTTTTTTTTTT	0.418													3	4	---	---	---	---	
USP10	9100	broad.mit.edu	37	16	84756179	84756179	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84756179delT	uc002fii.2	+						USP10_uc010voe.1_Intron|USP10_uc010vof.1_Intron|USP10_uc002fij.2_Intron	NM_005153	NP_005144	Q14694	UBP10_HUMAN	ubiquitin specific protease 10						DNA damage response, signal transduction by p53 class mediator|DNA repair|protein deubiquitination|ubiquitin-dependent protein catabolic process	early endosome|intermediate filament cytoskeleton|nucleus	cystic fibrosis transmembrane conductance regulator binding|p53 binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0						gtcagtcttctttttttgaga	0.000													4	2	---	---	---	---	
KLHDC4	54758	broad.mit.edu	37	16	87772873	87772876	+	Intron	DEL	CATC	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87772873_87772876delCATC	uc002fki.2	-						KLHDC4_uc010cht.1_Intron|KLHDC4_uc002fkj.2_Intron|KLHDC4_uc002fkk.2_Intron|KLHDC4_uc002fkl.2_Intron|KLHDC4_uc010chu.1_Intron	NM_017566	NP_060036	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4											pancreas(2)	2				BRCA - Breast invasive adenocarcinoma(80;0.0283)		ACCAGCATCTCATCCATCCACACA	0.338													4	3	---	---	---	---	
SLC7A5	8140	broad.mit.edu	37	16	87871681	87871682	+	Intron	INS	-	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87871681_87871682insC	uc002fkm.2	-							NM_003486	NP_003477	Q01650	LAT1_HUMAN	solute carrier family 7 (cationic amino acid						blood coagulation|cell differentiation|cellular amino acid metabolic process|ion transport|leukocyte migration|nervous system development	apical plasma membrane|cytosol|integral to membrane	neutral amino acid transmembrane transporter activity|peptide antigen binding				0				BRCA - Breast invasive adenocarcinoma(80;0.049)		TGGGAACCAGGCCCCTCCAGCC	0.678													3	3	---	---	---	---	
CA5A	763	broad.mit.edu	37	16	87936357	87936357	+	Intron	DEL	A	-	-	rs71391363		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87936357delA	uc002fkn.1	-							NM_001739	NP_001730	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial precursor						one-carbon metabolic process	mitochondrial matrix	carbonate dehydratase activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0513)		ctaaaaatacaaaaaaaaaaa	0.000													2	4	---	---	---	---	
USP6	9098	broad.mit.edu	37	17	5038288	5038289	+	Intron	INS	-	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5038288_5038289insA	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron|uc002gay.1_5'Flank|uc002gba.2_5'Flank|uc002gbb.2_5'Flank	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5						gtgtgcaaaagaaaaaaaaaat	0.168			T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								4	2	---	---	---	---	
XAF1	54739	broad.mit.edu	37	17	6655918	6655918	+	5'Flank	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6655918delC	uc010clr.1	+							NM_017523	NP_059993	Q6GPH4	XAF1_HUMAN	XIAP associated factor 1 isoform 1						apoptosis|type I interferon-mediated signaling pathway	mitochondrion|nucleus	zinc ion binding				0						CACAGATATTCCCAGGCTTGA	0.517													4	2	---	---	---	---	
ZBTB4	57659	broad.mit.edu	37	17	7363126	7363126	+	3'UTR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7363126delA	uc002ghc.3	-	5					ZBTB4_uc002ghd.3_3'UTR	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		CAATTCTCCCAAAAAAAAATG	0.393													3	3	---	---	---	---	
SHISA6	388336	broad.mit.edu	37	17	11285391	11285392	+	Intron	DEL	AG	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11285391_11285392delAG	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269	Q6ZSJ9	SHSA6_HUMAN	shisa homolog 6							integral to membrane				breast(1)	1						TCCGTTTTTTAGAGAGAGAGAG	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21527552	21527559	+	IGR	DEL	GTGTGTTC	-	-	rs144113905	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21527552_21527559delGTGTGTTC								C17orf51 (49821 upstream) : FAM27L (297811 downstream)																							gtgtgtgtgtgtgtgttcgtgtgtAAGG	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25758643	25758644	+	RNA	DEL	GA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25758643_25758644delGA	uc002gzg.2	+	13		c.3077_3078delGA								Homo sapiens similar to ubiquitin specific protease 6, mRNA (cDNA clone IMAGE:5168266), with apparent retained intron.																		GTTTACTGTTGAAATGATTTTA	0.208											OREG0024258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
RNF135	84282	broad.mit.edu	37	17	29302175	29302175	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29302175delA	uc002hfz.2	+						RNF135_uc002hga.2_Intron|RNF135_uc010csm.2_Intron|RNF135_uc002hgb.2_Intron|DPRXP4_uc002hgc.2_5'Flank	NM_032322	NP_115698	Q8IUD6	RN135_HUMAN	ring finger protein 135 isoform 1						innate immune response|negative regulation of type I interferon production|positive regulation of interferon-beta production|regulation of innate immune response	cytosol	protein binding|ribonucleoprotein binding|ubiquitin-protein ligase activity|zinc ion binding	p.?(1)		skin(2)	2		all_cancers(10;8.65e-08)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Myeloproliferative disorder(56;0.0255)				agacccaatgaaaaaaaaaag	0.000													4	2	---	---	---	---	
RHBDL3	162494	broad.mit.edu	37	17	30620814	30620815	+	Intron	DEL	AC	-	-	rs150022121		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30620814_30620815delAC	uc002hhe.1	+						RHBDL3_uc010csw.1_Intron|RHBDL3_uc010csx.1_Intron|RHBDL3_uc010csy.1_Intron|RHBDL3_uc002hhf.1_Intron	NM_138328	NP_612201	P58872	RHBL3_HUMAN	rhomboid protease 3						proteolysis	integral to membrane	calcium ion binding|serine-type endopeptidase activity			ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)				CGGCCATTTGACACAAAATAAG	0.342													4	3	---	---	---	---	
TBC1D3	729873	broad.mit.edu	37	17	36364836	36364837	+	Intron	INS	-	TG	TG			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36364836_36364837insTG	uc010wdn.1	-						uc002hpx.2_RNA			Q8IZP1	TBC3A_HUMAN	Homo sapiens TBC1D3 mRNA for TBC1 domain family, member 3, complete cds.							intracellular	Rab GTPase activator activity				0	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GTTTGAATGTCTGTGTGTATAA	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	62117156	62117157	+	RNA	DEL	AC	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62117156_62117157delAC	uc002jdy.1	-	1		c.2047_2048delGT								Homo sapiens cDNA FLJ42435 fis, clone BLADE2006849.																		TATCCACCAAACACACACACAG	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66830119	66830119	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66830119delC								FAM20A (233024 upstream) : ABCA8 (33314 downstream)																							GCTCTATGTGCCCAGCTGAGG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	67703569	67703569	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67703569delA								MAP2K6 (165107 upstream) : KCNJ16 (367857 downstream)																							GGGCTTCCAGAAAAAAAAAAA	0.428													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68434654	68434655	+	IGR	INS	-	A	A	rs139367724	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68434654_68434655insA								KCNJ2 (258473 upstream) : None (None downstream)																							AGTATCCCACCCTTTTGCTTAA	0.302													4	2	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71541553	71541554	+	Intron	DEL	CA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71541553_71541554delCA	uc010dfm.2	-							NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						TAAATGAATGCACACACACACG	0.540													4	2	---	---	---	---	
SLC9A3R1	9368	broad.mit.edu	37	17	72762892	72762892	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72762892delA	uc002jlo.2	+						SLC9A3R1_uc002jlp.2_Intron	NM_004252	NP_004243	O14745	NHRF1_HUMAN	sodium/hydrogen exchanger regulatory factor 1						apoptosis|bile acid secretion|glutathione transport|microvillus assembly|negative regulation of cell proliferation|negative regulation of ERK1 and ERK2 cascade|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|protein complex assembly|regulation of protein kinase activity|regulation of sodium:hydrogen antiporter activity|renal absorption|Wnt receptor signaling pathway	actin cytoskeleton|apical plasma membrane|centrosome|endomembrane system|filopodium|intracellular membrane-bounded organelle|microvillus membrane|ruffle	beta-2 adrenergic receptor binding|beta-catenin binding|chloride channel regulator activity|growth factor receptor binding|PDZ domain binding|phosphatase binding|protein self-association				0						ccatctctataaaaaaaaaaT	0.144													5	3	---	---	---	---	
SMCHD1	23347	broad.mit.edu	37	18	2658537	2658537	+	Intron	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2658537delC	uc002klm.3	+							NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0						CCTCCTTCCTCCCACTTTATC	0.338													4	2	---	---	---	---	
EPB41L3	23136	broad.mit.edu	37	18	5529928	5529929	+	Intron	DEL	TG	-	-	rs72089625		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5529928_5529929delTG	uc002kmt.1	-						EPB41L3_uc010wzh.1_Intron|EPB41L3_uc002kmu.1_Intron|EPB41L3_uc010dkq.1_Intron|EPB41L3_uc010dks.1_Intron|EPB41L3_uc002kmv.1_Intron	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						AACTCATATAtgtgtgtgtgtg	0.302													3	3	---	---	---	---	
EPB41L3	23136	broad.mit.edu	37	18	5572450	5572450	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5572450delT	uc010dkq.1	-						EPB41L3_uc010dks.1_Intron|EPB41L3_uc002kmv.1_Intron	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						AGTGCCTTTGTTTTAGAATAA	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	20276665	20276665	+	IGR	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20276665delG								CTAGE1 (278787 upstream) : RBBP8 (236630 downstream)																							GCTGGCAGCTGGGGAGTGGTC	0.468													4	2	---	---	---	---	
ZNF521	25925	broad.mit.edu	37	18	22642387	22642387	+	3'UTR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22642387delT	uc002kvk.2	-	8					ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_3'UTR|ZNF521_uc002kvl.2_3'UTR	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					GGTCATAGTCTTTTTTTTTTT	0.308			T	PAX5	ALL								4	3	---	---	---	---	
DTNA	1837	broad.mit.edu	37	18	32444213	32444213	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32444213delT	uc010dmn.1	+						DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dml.2_Intron|DTNA_uc002kyb.3_Intron|DTNA_uc010dmm.2_Intron|DTNA_uc010xby.1_Intron|DTNA_uc010dmo.2_Intron|DTNA_uc002kyd.3_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						GAACACAttcttttttttttt	0.179													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	61409685	61409685	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61409685delT								SERPINB11 (16021 upstream) : SERPINB7 (10592 downstream)																							GTGGCTAAGCTTTTTCCTGGC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	72796990	72796990	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72796990delT								ZNF407 (19362 upstream) : ZADH2 (112289 downstream)																							AAAAAGTCTCTTTAATTTTGA	0.368													4	2	---	---	---	---	
LMNB2	84823	broad.mit.edu	37	19	2442212	2442212	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2442212delG	uc002lvy.2	-						LMNB2_uc002lwa.1_Intron	NM_032737	NP_116126	Q03252	LMNB2_HUMAN	lamin B2							nuclear inner membrane	structural molecule activity			large_intestine(1)|ovary(1)	2		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)		ccagtgctttgggaggctgag	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	4812185	4812186	+	IGR	INS	-	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4812185_4812186insC								FEM1A (16616 upstream) : TICAM1 (3753 downstream)																							ctccttttcttccccccaggtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	5504501	5504501	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5504501delT								ZNRF4 (47635 upstream) : PLAC2 (53679 downstream)																							CCTTCAGGACTTTACCCACAC	0.502													4	2	---	---	---	---	
C19orf62	29086	broad.mit.edu	37	19	17387980	17387983	+	Intron	DEL	CTTG	-	-	rs71334697		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17387980_17387983delCTTG	uc002nfu.2	+						C19orf62_uc010xpl.1_3'UTR|C19orf62_uc002nfv.2_Intron|C19orf62_uc010ean.2_Intron|C19orf62_uc002nfw.2_Intron	NM_014173	NP_054892	Q9NWV8	BABA1_HUMAN	mediator of Rap80 interactions and targeting 40						chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of DNA repair|protein K63-linked deubiquitination|response to ionizing radiation	BRCA1-A complex|BRISC complex|cytoplasm	protein binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2						tcctttctttcttgcttgcttgct	0.235													4	2	---	---	---	---	
CRLF1	9244	broad.mit.edu	37	19	18707343	18707343	+	Intron	DEL	A	-	-	rs78616489		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18707343delA	uc010ebt.1	-							NM_004750	NP_004741	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1 precursor						negative regulation of neuron apoptosis|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	cytokine binding|protein heterodimerization activity|receptor activity			central_nervous_system(1)	1						gtctcaaaagaaaaaaaaaag	0.249													3	3	---	---	---	---	
HOMER3	9454	broad.mit.edu	37	19	19039998	19039999	+	Intron	DEL	CA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19039998_19039999delCA	uc002nko.1	-						HOMER3_uc002nkp.1_Intron			Q9NSC5	HOME3_HUMAN	Homo sapiens epsilon-COP mRNA, complete cds.						metabotropic glutamate receptor signaling pathway|protein targeting	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	protein binding				0			Epithelial(12;0.0107)			ACCCACATACCACACACACACA	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	20055928	20055928	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20055928delT								ZNF93 (10163 upstream) : ZNF682 (59301 downstream)																							ctgatttgcctcctaccaccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31364301	31364302	+	IGR	DEL	TC	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31364301_31364302delTC								ZNF536 (315336 upstream) : DKFZp566F0947 (276481 downstream)																							GAGCATGCATTCTCAAGAGTAA	0.554													4	2	---	---	---	---	
SIPA1L3	23094	broad.mit.edu	37	19	38495507	38495508	+	Intron	INS	-	T	T	rs141877478	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38495507_38495508insT	uc002ohk.2	+							NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TATTCATTCTCTTATATTCAGT	0.490													4	4	---	---	---	---	
CYP2F1	1572	broad.mit.edu	37	19	41767896	41767897	+	Intron	DEL	AC	-	-	rs72262253		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41767896_41767897delAC	uc010xvw.1	+						HNRNPUL1_uc002opz.3_5'Flank|HNRNPUL1_uc002oqa.3_5'Flank|HNRNPUL1_uc002oqb.3_5'Flank|HNRNPUL1_uc010ehm.2_5'Flank|HNRNPUL1_uc002oqc.3_5'Flank|HNRNPUL1_uc002oqe.3_5'Flank|HNRNPUL1_uc002oqd.3_5'Flank|HNRNPUL1_uc010ehn.2_5'Flank|HNRNPUL1_uc010ehl.1_5'Flank			P24903	CP2F1_HUMAN	SubName: Full=cDNA FLJ51986, highly similar to Homo sapiens cytochrome P450, family 2, subfamily F, polypeptide 1 (CYP2F1), mRNA;						naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0						AGGATcacagacacacacacac	0.391													4	2	---	---	---	---	
PSG6	5675	broad.mit.edu	37	19	43431131	43431131	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43431131delG	uc002ovh.1	-						PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_5'Flank|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG7_uc002ovl.3_Intron|PSG7_uc010xwl.1_Intron			Q00889	PSG6_HUMAN	SubName: Full=Putative uncharacterized protein PSG6;						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)				ACATGTCAGTGGGAGTCACAG	0.547													4	2	---	---	---	---	
TRPM4	54795	broad.mit.edu	37	19	49685612	49685615	+	Intron	DEL	TCCA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49685612_49685615delTCCA	uc002pmw.2	+						TRPM4_uc010emu.2_Intron|TRPM4_uc010yak.1_Intron|TRPM4_uc002pmx.2_Intron|TRPM4_uc010emv.2_Intron|TRPM4_uc010yal.1_Intron|TRPM4_uc002pmy.2_5'Flank	NM_017636	NP_060106	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel,						dendritic cell chemotaxis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|protein sumoylation|regulation of T cell cytokine production	endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	ATP binding|calcium activated cation channel activity|calmodulin binding			ovary(1)|central_nervous_system(1)	2		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		catccctctgtccatccatccatc	0.000													3	3	---	---	---	---	
PEG3	5178	broad.mit.edu	37	19	57339676	57339676	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57339676delT	uc002qnv.2	-						ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnw.2_Intron|PEG3_uc002qnx.2_Intron|PEG3_uc010etr.2_Intron	NM_006210	NP_006201	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1						apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		caataaataCTTATGATATTG	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57422127	57422128	+	IGR	INS	-	A	A	rs144777762	by1000genomes	TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57422127_57422128insA								MIMT1 (62205 upstream) : USP29 (209381 downstream)																							GAGAATGACAGAAGCACCGATC	0.460													0	6	---	---	---	---	
SNPH	9751	broad.mit.edu	37	20	1281055	1281055	+	Intron	DEL	G	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1281055delG	uc002wes.2	+						SNPH_uc002wet.2_Intron	NM_014723	NP_055538	O15079	SNPH_HUMAN	syntaphilin						synaptic vesicle docking involved in exocytosis	cell junction|integral to membrane|synapse|synaptosome	syntaxin-1 binding			ovary(2)	2						CCAGAAGGCTGGGGGTTCTCC	0.587													5	3	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9324812	9324813	+	Intron	DEL	TT	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9324812_9324813delTT	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						aatctctctctttcctcctacg	0.000													4	2	---	---	---	---	
RBBP9	10741	broad.mit.edu	37	20	18468690	18468690	+	3'UTR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18468690delT	uc002wqy.2	-	5						NM_006606	NP_006597	O75884	RBBP9_HUMAN	retinoblastoma binding protein 9							cytoplasm|nucleus	hydrolase activity			haematopoietic_and_lymphoid_tissue(1)	1						CCTTTCCTGATTTTTTTTGTC	0.358													4	2	---	---	---	---	
RIN2	54453	broad.mit.edu	37	20	19951830	19951830	+	Intron	DEL	T	-	-	rs33916413		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19951830delT	uc002wro.1	+						RIN2_uc010gcu.1_Intron|RIN2_uc010gcv.1_Intron	NM_018993	NP_061866	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2						endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5						GCGTGCATGATTTTTTTTTTT	0.478													4	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29648450	29648450	+	Intron	DEL	T	-	-	rs143554592		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29648450delT	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						cagaactccctctcctgtttt	0.000													4	2	---	---	---	---	
DNMT3B	1789	broad.mit.edu	37	20	31387738	31387741	+	Intron	DEL	TAGT	-	-	rs145092112		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31387738_31387741delTAGT	uc002wyc.2	+						DNMT3B_uc010zty.1_Intron|DNMT3B_uc002wyd.2_Intron|DNMT3B_uc002wye.2_Intron|DNMT3B_uc010gee.2_Intron|DNMT3B_uc010gef.2_Intron|DNMT3B_uc010ztz.1_Intron|DNMT3B_uc010zua.1_Intron|DNMT3B_uc002wyf.2_Intron|DNMT3B_uc002wyg.2_Intron|DNMT3B_uc010geg.2_5'Flank|DNMT3B_uc010geh.2_5'Flank	NM_006892	NP_008823	Q9UBC3	DNM3B_HUMAN	DNA cytosine-5 methyltransferase 3 beta isoform						negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5						GGAGATAAACTAGTTAACAACTAC	0.363													4	5	---	---	---	---	
EDEM2	55741	broad.mit.edu	37	20	33734435	33734435	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33734435delT	uc002xbo.2	-						EDEM2_uc010zuv.1_Intron|EDEM2_uc010zus.1_5'Flank|EDEM2_uc002xbq.2_Intron|EDEM2_uc010zut.1_Intron|EDEM2_uc002xbp.2_Intron|EDEM2_uc002xbn.2_Intron|EDEM2_uc002xbr.2_Intron|EDEM2_uc010zuu.1_Intron	NM_018217	NP_060687	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00936)			AATCCAGGACTTTTTTTTTCA	0.552													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41107374	41107374	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41107374delT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				ctcgatgacattttttttcct	0.000													4	2	---	---	---	---	
PHACTR3	116154	broad.mit.edu	37	20	58364536	58364537	+	Intron	INS	-	TG	TG	rs11472957		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58364536_58364537insTG	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron|PHACTR3_uc002yaw.2_Intron|PHACTR3_uc002yax.2_Intron	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			ATGCAACAGACTTGAAATCCCA	0.396													4	3	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	59951068	59951069	+	Intron	INS	-	TGA	TGA			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59951068_59951069insTGA	uc002ybn.1	+							NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			cttggtggtggtgatactgtgg	0.010													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10414497	10414497	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10414497delT								None (None upstream) : TPTE (492246 downstream)																							AATTCAGAACTTTAAAAATAA	0.229													4	2	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10918246	10918246	+	Intron	DEL	G	-	-	rs113499448		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10918246delG	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						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)		TCCATAGGCTGGGAAAGAGCA	0.478													4	2	---	---	---	---	
ADAMTS5	11096	broad.mit.edu	37	21	28302499	28302500	+	Intron	INS	-	A	A	rs71331597		TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28302499_28302500insA	uc002ymg.2	-							NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						ACAGTCCATTGAAAAAAAAAAA	0.347													4	3	---	---	---	---	
PLAC4	191585	broad.mit.edu	37	21	42551676	42551677	+	Translation_Start_Site	INS	-	A	A			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42551676_42551677insA	uc002yyz.2	-	1	5490_5491	c.-121_-120insT	c.(-123--118)CCAGGC>CCATGGC		BACE2_uc002yyw.2_Intron|BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_182832	NP_878252	Q8WY50	PLAC4_HUMAN	placenta-specific 4												0		Prostate(19;2.29e-06)				CTGAGGGTGCCTGGTGTGGGGT	0.381													8	4	---	---	---	---	
C21orf29	54084	broad.mit.edu	37	21	45936669	45936669	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45936669delA	uc002zfe.1	-						C21orf29_uc010gpv.1_Intron|C21orf90_uc002zff.3_5'Flank|C21orf90_uc002zfg.3_5'Flank	NM_144991	NP_659428	Q8WU66	TSEAR_HUMAN	chromosome 21 open reading frame 29 precursor						cell adhesion	extracellular region	structural molecule activity				0						GGACGGGTTCACCTGCTTCGT	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17216701	17216701	+	IGR	DEL	C	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17216701delC								psiTPTE22 (37180 upstream) : XKR3 (47612 downstream)																							TGCTGAAATGCCCAGCAGCAA	0.413													4	2	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26184052	26184052	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26184052delT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						AGTGGTTTGCTTTTTTTCCTC	0.428													4	2	---	---	---	---	
KREMEN1	83999	broad.mit.edu	37	22	29521778	29521778	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29521778delT	uc011akm.1	+						KREMEN1_uc003ael.2_Intron|KREMEN1_uc011akn.1_Intron	NM_032045	NP_114434	Q96MU8	KREM1_HUMAN	kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5						CTTTTGACTGTTTTTTTTTTA	0.333													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45486601	45486602	+	IGR	INS	-	C	C			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45486601_45486602insC								PHF21B (80792 upstream) : NUP50 (73124 downstream)																							AGAAGCCACGGCTGCCGATGAC	0.480													4	2	---	---	---	---	
EIF1AX	1964	broad.mit.edu	37	X	20150405	20150407	+	Intron	DEL	AAA	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20150405_20150407delAAA	uc004czt.2	-							NM_001412	NP_001403	P47813	IF1AX_HUMAN	X-linked eukaryotic translation initiation							cytosol	translation initiation factor activity			ovary(1)	1						AAATAACTTTAAAAAACTGATCA	0.286													29	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	40767276	40767276	+	IGR	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40767276delA								LOC100132831 (74827 upstream) : USP9X (177612 downstream)																							CAAGATTGTCAAAAAGAGAAC	0.473													4	2	---	---	---	---	
AMMECR1	9949	broad.mit.edu	37	X	109442257	109442257	+	Intron	DEL	A	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109442257delA	uc004eoo.2	-						AMMECR1_uc004eop.2_Intron|AMMECR1_uc004eoq.2_Intron	NM_015365	NP_056180	Q9Y4X0	AMER1_HUMAN	AMMECR1 protein isoform 1												0						ACCATTAAGTAACAACAACAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9972631	9972631	+	IGR	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9972631delT								TTTY22 (321777 upstream) : None (None downstream)																							aaagcaggcatccttgttttt	0.000													4	2	---	---	---	---	
USP9Y	8287	broad.mit.edu	37	Y	14889873	14889873	+	Intron	DEL	T	-	-			TCGA-B0-5697-01A-11D-1534-10	TCGA-B0-5697-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:14889873delT	uc004fst.1	+						USP9Y_uc010nwu.1_Intron	NM_004654	NP_004645	O00507	USP9Y_HUMAN	ubiquitin specific protease 9, Y-linked						BMP signaling pathway|protein deubiquitination|spermatogenesis|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0						attttCAGGGTTTTTTTTAGC	0.254													4	2	---	---	---	---	
