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	11187799	11187799	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11187799T>A	uc001asd.2	-	44	6219	c.6098A>T	c.(6097-6099)GAG>GTG	p.E2033V	MTOR_uc001asc.2_Missense_Mutation_p.E238V	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	2033					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						ACGAGATGCCTCTTCCAGGCC	0.537													72	119	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974277	16974277	+	RNA	SNP	A	C	C	rs151151026	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974277A>C	uc009vow.2	+	5		c.1087A>C			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Splice_Site|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Splice_Site|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_Splice_Site|MST1P2_uc001azm.3_Splice_Site					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GGTCCATCTAAGGGTCCGAGG	0.657													6	61	---	---	---	---	PASS
CELA3B	23436	broad.mit.edu	37	1	22332319	22332319	+	3'UTR	SNP	G	A	A	rs76548941	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22332319G>A	uc009vqf.2	+	4					CELA3A_uc001bfl.2_Intron			P08861	CEL3B_HUMAN	SubName: Full=Elastase 3A, pancreatic;						cholesterol metabolic process|proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1						TGGAACCCAGGGGCTCCTCTA	0.493													6	85	---	---	---	---	PASS
CELA3B	23436	broad.mit.edu	37	1	22332332	22332332	+	3'UTR	SNP	T	C	C	rs74922245	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22332332T>C	uc009vqf.2	+	4					CELA3A_uc001bfl.2_Intron			P08861	CEL3B_HUMAN	SubName: Full=Elastase 3A, pancreatic;						cholesterol metabolic process|proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1						CTCCTCTACTTGTCCCTCCAT	0.498													6	77	---	---	---	---	PASS
CELA3B	23436	broad.mit.edu	37	1	22332333	22332333	+	3'UTR	SNP	G	A	A	rs76102053	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22332333G>A	uc009vqf.2	+	4					CELA3A_uc001bfl.2_Intron			P08861	CEL3B_HUMAN	SubName: Full=Elastase 3A, pancreatic;						cholesterol metabolic process|proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1						TCCTCTACTTGTCCCTCCATG	0.498													7	74	---	---	---	---	PASS
BCL9	607	broad.mit.edu	37	1	147096204	147096204	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147096204C>A	uc001epq.2	+	10	4465	c.3725C>A	c.(3724-3726)TCT>TAT	p.S1242Y	BCL9_uc010ozr.1_Missense_Mutation_p.S1156Y	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	1242	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					ATTATTCCATCTGAGAAGCCC	0.552			T	IGH@|IGL@	B-ALL								19	40	---	---	---	---	PASS
FLG2	388698	broad.mit.edu	37	1	152323802	152323802	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152323802T>G	uc001ezw.3	-	3	6533	c.6460A>C	c.(6460-6462)ACC>CCC	p.T2154P	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	2154	Filaggrin 10.						calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTCTAGTGGTATCTCCTGTC	0.493													16	348	---	---	---	---	PASS
CD1E	913	broad.mit.edu	37	1	158324301	158324301	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158324301C>A	uc001fse.2	+	2	432	c.193C>A	c.(193-195)CAT>AAT	p.H65N	CD1E_uc010pid.1_Missense_Mutation_p.H63N|CD1E_uc010pie.1_Intron|CD1E_uc010pif.1_Intron|CD1E_uc001fsd.2_Missense_Mutation_p.H65N|CD1E_uc001fsk.2_Missense_Mutation_p.H65N|CD1E_uc001fsj.2_Missense_Mutation_p.H65N|CD1E_uc001fsc.2_Intron|CD1E_uc010pig.1_Intron|CD1E_uc001fsa.2_Intron|CD1E_uc001fsf.2_Missense_Mutation_p.H65N|CD1E_uc001fry.2_Missense_Mutation_p.H65N|CD1E_uc001fsg.2_Intron|CD1E_uc001fsh.2_Intron|CD1E_uc001fsi.2_Missense_Mutation_p.H65N|CD1E_uc009wsv.2_Intron|CD1E_uc001frz.2_Missense_Mutation_p.H65N|CD1E_uc009wsw.2_5'Flank	NM_030893	NP_112155	P15812	CD1E_HUMAN	CD1E antigen isoform a precursor	65					antigen processing and presentation|immune response	early endosome|Golgi membrane|integral to plasma membrane|late endosome|lysosomal lumen				skin(3)	3	all_hematologic(112;0.0378)					CCTGCAGACTCATGGCTGGGA	0.557													42	69	---	---	---	---	PASS
PCP4L1	654790	broad.mit.edu	37	1	161254260	161254260	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161254260C>T	uc001gad.2	+	3	444	c.196C>T	c.(196-198)CCC>TCC	p.P66S		NM_001102566	NP_001096036	A6NKN8	PC4L1_HUMAN	Purkinje cell protein 4 like 1	66	IQ.										0	all_cancers(52;4.16e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GAAAAAGGATCCCAGCTCCTG	0.517													6	112	---	---	---	---	PASS
PPP2R5A	5525	broad.mit.edu	37	1	212506854	212506854	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212506854T>A	uc001hjb.2	+	3	968	c.394T>A	c.(394-396)TTC>ATC	p.F132I	PPP2R5A_uc010ptd.1_Missense_Mutation_p.F73I	NM_006243	NP_006234	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B	132					negative regulation of establishment of protein localization in plasma membrane|negative regulation of lipid kinase activity|positive regulation of protein dephosphorylation|signal transduction	chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex	kinase binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)		TGCTAACATCTTCCGTACACT	0.368													116	208	---	---	---	---	PASS
TP53BP2	7159	broad.mit.edu	37	1	223990159	223990159	+	Intron	SNP	G	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223990159G>C	uc010pvb.1	-						TP53BP2_uc001hod.2_Intron|TP53BP2_uc010puz.1_5'Flank|TP53BP2_uc010pva.1_5'UTR	NM_001031685	NP_001026855	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein, 2 isoform 1						apoptosis|cell cycle|induction of apoptosis|negative regulation of cell cycle|signal transduction	nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protein binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)|lung(1)	3				GBM - Glioblastoma multiforme(131;0.0958)		TCAGAATCTAGCCATAGAGTC	0.348													4	5	---	---	---	---	PASS
TP53BP2	7159	broad.mit.edu	37	1	223990160	223990160	+	Intron	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223990160C>T	uc010pvb.1	-						TP53BP2_uc001hod.2_Intron|TP53BP2_uc010puz.1_5'Flank|TP53BP2_uc010pva.1_5'UTR	NM_001031685	NP_001026855	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein, 2 isoform 1						apoptosis|cell cycle|induction of apoptosis|negative regulation of cell cycle|signal transduction	nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protein binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)|lung(1)	3				GBM - Glioblastoma multiforme(131;0.0958)		CAGAATCTAGCCATAGAGTCT	0.343													4	5	---	---	---	---	PASS
OTOF	9381	broad.mit.edu	37	2	26684967	26684967	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26684967C>A	uc002rhk.2	-	42	5402	c.5275G>T	c.(5275-5277)GAC>TAC	p.D1759Y	OTOF_uc010yla.1_Missense_Mutation_p.D489Y|OTOF_uc002rhh.2_Missense_Mutation_p.D992Y|OTOF_uc002rhi.2_Missense_Mutation_p.D1069Y|OTOF_uc002rhj.2_Missense_Mutation_p.D992Y	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	1759	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACGAAGATGTCACTGGACTTC	0.617													36	82	---	---	---	---	PASS
AAK1	22848	broad.mit.edu	37	2	69704092	69704092	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69704092A>G	uc002sfp.2	-	21	3216	c.2711T>C	c.(2710-2712)TTT>TCT	p.F904S		NM_014911	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	904						coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0						AGGGACATCAAAACCTGAGAT	0.418													123	248	---	---	---	---	PASS
AUP1	550	broad.mit.edu	37	2	74754424	74754424	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74754424T>C	uc010yrx.1	-	9	1325	c.1199A>G	c.(1198-1200)GAA>GGA	p.E400G	DQX1_uc010yrw.1_5'Flank|AUP1_uc002sme.2_Missense_Mutation_p.E76G|AUP1_uc002smf.2_Missense_Mutation_p.E343G|AUP1_uc002smg.2_RNA|AUP1_uc002smh.2_Missense_Mutation_p.E252G|HTRA2_uc002smi.1_5'Flank|HTRA2_uc002smj.1_5'Flank|HTRA2_uc002smk.1_5'Flank|HTRA2_uc002sml.1_5'Flank|HTRA2_uc002smm.1_5'Flank|HTRA2_uc002smn.1_5'Flank			Q9Y679	AUP1_HUMAN	SubName: Full=cDNA FLJ57204, highly similar to Homo sapiens ancient ubiquitous protein 1 (AUP1), transcript variant 2, mRNA;	409	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nucleus	protein binding				0						GGTGATGTCTTCAGGCATGAA	0.547													21	55	---	---	---	---	PASS
HNMT	3176	broad.mit.edu	37	2	138722057	138722057	+	5'UTR	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138722057C>T	uc002tvc.2	+	2					HNMT_uc002tvd.2_5'UTR|HNMT_uc002tve.2_5'UTR|HNMT_uc002tvf.2_5'UTR	NM_006895	NP_008826	P50135	HNMT_HUMAN	histamine N-methyltransferase isoform 1						respiratory gaseous exchange	cytoplasm	histamine N-methyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.125)	Amodiaquine(DB00613)|Histamine Phosphate(DB00667)|Quinacrine(DB01103)	CTCAGAAAACCAAATATGGCA	0.468													7	193	---	---	---	---	PASS
SCN7A	6332	broad.mit.edu	37	2	167289087	167289087	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167289087A>T	uc002udu.1	-	15	2460	c.2333T>A	c.(2332-2334)ATG>AAG	p.M778K	SCN7A_uc010fpm.1_RNA	NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	778					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1						TACATGGTCCATTGTGTCCTT	0.343													80	415	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179622487	179622487	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179622487C>A	uc010zfi.1	-	44	10546	c.10322G>T	c.(10321-10323)AGG>ATG	p.R3441M	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc002unb.2_Intron	NM_133432	NP_597676	Q8WZ42	TITIN_HUMAN	titin isoform novex-1	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCCAGAAACCCTCGCATGAAA	0.483													46	123	---	---	---	---	PASS
CLK1	1195	broad.mit.edu	37	2	201724587	201724587	+	Intron	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201724587T>C	uc002uwe.2	-						CLK1_uc002uwd.2_5'Flank|CLK1_uc010zhi.1_Intron|CLK1_uc002uwf.2_Intron|CLK1_uc002uwg.2_Translation_Start_Site|CLK1_uc010fsv.2_Intron	NM_004071	NP_004062	P49759	CLK1_HUMAN	CDC-like kinase 1 isoform 1						cell proliferation	nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			pancreas(2)	2						TATCACTAGATATTTTATTGG	0.269													14	33	---	---	---	---	PASS
ZFAND2B	130617	broad.mit.edu	37	2	220072989	220072989	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220072989T>C	uc002vka.2	+	5	618	c.446T>C	c.(445-447)ATC>ACC	p.I149T	ZFAND2B_uc010zkt.1_Missense_Mutation_p.I149T|ZFAND2B_uc010fwd.1_Missense_Mutation_p.I149T|ZFAND2B_uc002vjy.1_Missense_Mutation_p.I149T|ZFAND2B_uc002vjz.1_Missense_Mutation_p.I149T|ZFAND2B_uc002vkb.1_Missense_Mutation_p.I40T	NM_138802	NP_620157	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	149						endoplasmic reticulum	protein binding|zinc ion binding				0		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTGCTGCCATCTCCAGAGCA	0.532													30	75	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191469	10191469	+	Splice_Site	SNP	A	G	G	rs5030816		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191469A>G	uc003bvc.2	+	3	677	c.464_splice	c.e3-2	p.V155_splice	VHL_uc003bvd.2_Splice_Site_p.V114_splice	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(3)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTGCCCTTCCAGTGTATACTC	0.498		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				61	63	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47144873	47144873	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47144873A>C	uc003cqs.2	-	7	4933	c.4880T>G	c.(4879-4881)ATG>AGG	p.M1627R	SETD2_uc003cqv.2_Missense_Mutation_p.M1694R	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1627	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GCTGTGATTCATGAAACGAGA	0.333			N|F|S|Mis		clear cell renal carcinoma								23	268	---	---	---	---	PASS
HCLS1	3059	broad.mit.edu	37	3	121366274	121366274	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121366274T>G	uc003eeh.3	-	4	305	c.180A>C	c.(178-180)AAA>AAC	p.K60N	HCLS1_uc011bjj.1_Missense_Mutation_p.K60N|HCLS1_uc011bjk.1_RNA|HCLS1_uc011bjl.1_Missense_Mutation_p.K60N	NM_005335	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	60	Involved in HAX-1 binding.				erythrocyte differentiation|intracellular signal transduction|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of STAT protein|response to hormone stimulus	mitochondrion|nucleus|plasma membrane	DNA binding|sequence-specific DNA binding transcription factor activity				0				GBM - Glioblastoma multiforme(114;0.0912)		CCTCTGATACTTTGTTCCTCA	0.483													100	198	---	---	---	---	PASS
MED12L	116931	broad.mit.edu	37	3	150874118	150874118	+	Splice_Site	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150874118G>T	uc003eyp.2	+	5	764	c.726_splice	c.e5+1	p.Q242_splice	MED12L_uc011bnz.1_Splice_Site_p.Q242_splice|MED12L_uc003eym.1_Splice_Site_p.Q242_splice|MED12L_uc003eyn.2_Splice_Site_p.Q242_splice|MED12L_uc003eyo.2_Splice_Site_p.Q242_splice	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CATGTTCCAGGTAACCTTTTG	0.453													49	106	---	---	---	---	PASS
ATP13A4	84239	broad.mit.edu	37	3	193158423	193158423	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193158423A>C	uc003ftd.2	-	21	2551	c.2443T>G	c.(2443-2445)TTG>GTG	p.L815V	ATP13A4_uc003fte.1_Missense_Mutation_p.L815V|ATP13A4_uc011bsr.1_Missense_Mutation_p.L286V|ATP13A4_uc010hzi.2_RNA	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	815	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		CCATTGATCAATATCTGTAAG	0.403													52	100	---	---	---	---	PASS
SPON2	10417	broad.mit.edu	37	4	1164288	1164288	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1164288C>G	uc003gcn.3	-	4	740	c.713G>C	c.(712-714)AGG>ACG	p.R238T	SPON2_uc003gco.3_Missense_Mutation_p.R238T|SPON2_uc010ibr.2_Missense_Mutation_p.R238T|SPON2_uc003gcm.1_3'UTR	NM_012445	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	238					axon guidance|cell adhesion|innate immune response	proteinaceous extracellular matrix	metal ion binding			central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		CAGTGTCACCCTGGCGATGGG	0.642													13	161	---	---	---	---	PASS
TEC	7006	broad.mit.edu	37	4	48148400	48148400	+	Silent	SNP	A	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48148400A>T	uc003gxz.2	-	12	1114	c.1023T>A	c.(1021-1023)CTT>CTA	p.L341L		NM_003215	NP_003206	P42680	TEC_HUMAN	tec protein tyrosine kinase	341	SH2.				intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9						CTGGGTACCGAAGCCTGGTGA	0.413													105	211	---	---	---	---	PASS
TMSL3	7117	broad.mit.edu	37	4	91760207	91760207	+	5'UTR	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91760207G>A	uc003hsy.2	-	1					FAM190A_uc003hsv.3_Intron|FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsx.2_Intron	NM_183049	NP_898870			thymosin-like 3												0		all_cancers(2;6.48e-24)|all_epithelial(2;3.86e-25)|Colorectal(2;8.52e-12)|all_lung(2;3.73e-07)|Lung NSC(2;7.99e-07)|Renal(2;0.0243)|Hepatocellular(203;0.0411)		Epithelial(2;5.28e-11)|OV - Ovarian serous cystadenocarcinoma(123;8.9e-10)|all cancers(2;3.21e-09)|STAD - Stomach adenocarcinoma(1;0.0201)		AGGAAAAGCGGAGCGAGGCGC	0.473													9	21	---	---	---	---	PASS
TMSL3	7117	broad.mit.edu	37	4	91760218	91760218	+	5'UTR	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91760218G>A	uc003hsy.2	-	1					FAM190A_uc003hsv.3_Intron|FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsx.2_Intron	NM_183049	NP_898870			thymosin-like 3												0		all_cancers(2;6.48e-24)|all_epithelial(2;3.86e-25)|Colorectal(2;8.52e-12)|all_lung(2;3.73e-07)|Lung NSC(2;7.99e-07)|Renal(2;0.0243)|Hepatocellular(203;0.0411)		Epithelial(2;5.28e-11)|OV - Ovarian serous cystadenocarcinoma(123;8.9e-10)|all cancers(2;3.21e-09)|STAD - Stomach adenocarcinoma(1;0.0201)		AGCGAGGCGCGCGAGTACGAG	0.473													9	17	---	---	---	---	PASS
SEC24D	9871	broad.mit.edu	37	4	119718966	119718966	+	Splice_Site	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119718966C>T	uc003ici.3	-	8	1186	c.914_splice	c.e8-1	p.G305_splice	SEC24D_uc003icj.3_Splice_Site_p.G306_splice|SEC24D_uc003icl.2_Splice_Site|SEC24D_uc010imz.1_Splice_Site|SEC24D_uc011cgg.1_Intron	NM_014822	NP_055637	O94855	SC24D_HUMAN	Sec24-related protein D						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0						CTGGCATTTCCTGAAACATTC	0.353													43	79	---	---	---	---	PASS
GRIA2	2891	broad.mit.edu	37	4	158282180	158282180	+	Silent	SNP	A	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158282180A>C	uc003ipm.3	+	14	2769	c.2310A>C	c.(2308-2310)GCA>GCC	p.A770A	GRIA2_uc011cit.1_Intron|GRIA2_uc003ipl.3_Intron|GRIA2_uc003ipk.3_Intron|GRIA2_uc010iqh.1_RNA|GRIA2_uc011ciu.1_Silent_p.A80A|GRIA2_uc011civ.1_RNA|GRIA2_uc011ciw.1_RNA|GRIA2_uc011cix.1_Intron|GRIA2_uc011ciy.1_Intron|GRIA2_uc011ciz.1_RNA	NM_001083619	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2 isoform 2	770	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|endoplasmic reticulum membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)	TTAACCTCGCAGTACTAAAAC	0.393													61	228	---	---	---	---	PASS
MARCH1	55016	broad.mit.edu	37	4	164450028	164450028	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164450028G>T	uc003iqs.1	-	8	1719	c.742C>A	c.(742-744)CTG>ATG	p.L248M	MARCH1_uc003iqr.1_Missense_Mutation_p.L231M	NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I	248	Responsible for down-regulation of CD86 and MHC class II cell surface expression (By similarity).				antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TTCTTCTCCAGTTTTTTGGCA	0.453													32	200	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	5	33162312	33162312	+	RNA	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33162312C>A	uc003jhx.2	+	1		c.47C>A								full-length cDNA clone CS0DI021YI22 of Placenta Cot 25-normalized of Homo sapiens (human).																		CAACTGGCACCAGCGCCGCAA	0.547													3	17	---	---	---	---	PASS
ADAMTS6	11174	broad.mit.edu	37	5	64483842	64483842	+	Splice_Site	SNP	C	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64483842C>G	uc003jtp.2	-	22	3724	c.2910_splice	c.e22+1	p.E970_splice	ADAMTS6_uc003jto.2_Splice_Site|ADAMTS6_uc003jtq.2_Splice_Site	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		GATTTCCTTACCTCAGACCAG	0.433													16	92	---	---	---	---	PASS
SLC22A4	6583	broad.mit.edu	37	5	131630305	131630305	+	5'UTR	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131630305G>A	uc003kwq.2	+	1					uc003kwm.3_Intron|SLC22A4_uc010jdq.1_5'Flank	NM_003059	NP_003050	Q9H015	S22A4_HUMAN	solute carrier family 22 member 4						body fluid secretion|sodium ion transport	apical plasma membrane|integral to plasma membrane|mitochondrion	ATP binding|carnitine transporter activity|cation:cation antiporter activity|PDZ domain binding|secondary active organic cation transmembrane transporter activity|symporter activity				0		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Carnitine(DB00583)	GCGGCAGTGGGAAGCATGCGG	0.602													18	96	---	---	---	---	PASS
NME5	8382	broad.mit.edu	37	5	137474391	137474391	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137474391C>G	uc003lce.2	-	2	157	c.79G>C	c.(79-81)GAG>CAG	p.E27Q	BRD8_uc003lcc.1_Intron	NM_003551	NP_003542	P56597	NDK5_HUMAN	non-metastatic cells 5, protein expressed in	27					anti-apoptosis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatid development|UTP biosynthetic process		ATP binding|nucleoside diphosphate kinase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			ATCTCCTCCTCTTTGTCAACA	0.378													27	710	---	---	---	---	PASS
SLU7	10569	broad.mit.edu	37	5	159830295	159830295	+	Silent	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159830295C>T	uc003lyg.2	-	16	1913	c.1758G>A	c.(1756-1758)CAG>CAA	p.Q586Q		NM_006425	NP_006416	O95391	SLU7_HUMAN	step II splicing factor SLU7	586					alternative nuclear mRNA splicing, via spliceosome|nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|cytoplasm|nuclear speck|small nuclear ribonucleoprotein complex	pre-mRNA 3'-splice site binding|second spliceosomal transesterification activity|zinc ion binding			ovary(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTAGTTGCTACTGTCCAAGGA	0.403													19	378	---	---	---	---	PASS
MGAT4B	11282	broad.mit.edu	37	5	179229049	179229049	+	Intron	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179229049T>C	uc003mks.2	-						MGAT4B_uc003mkp.2_5'Flank|MGAT4B_uc003mkq.2_5'Flank|MGAT4B_uc003mkr.2_Silent_p.R21R	NM_014275	NP_055090	Q9UQ53	MGT4B_HUMAN	alpha-1,3-mannosyl-glycoprotein						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding				0	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGCGCACACATCTGGGTGTCC	0.567											OREG0017110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	34	88	---	---	---	---	PASS
DSP	1832	broad.mit.edu	37	6	7585750	7585750	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7585750G>A	uc003mxp.1	+	24	8534	c.8255G>A	c.(8254-8256)CGG>CAG	p.R2752Q	DSP_uc003mxq.1_Missense_Mutation_p.R2153Q	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	2752	Plectin 16.|Globular 2.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GAAGCCATCCGGAAGGGGTTC	0.547													6	18	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38783288	38783288	+	Silent	SNP	T	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38783288T>A	uc003ooe.1	+	24	3327	c.2727T>A	c.(2725-2727)CGT>CGA	p.R909R		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						CCATTAACCGTATGATCCAGT	0.493													8	123	---	---	---	---	PASS
TMEM151B	441151	broad.mit.edu	37	6	44274838	44274838	+	3'UTR	SNP	A	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44274838A>G	uc003oxf.2	+	3					SPATS1_uc003oxg.2_Intron|AARS2_uc010jza.1_Intron	NM_001137560	NP_001131032	Q8IW70	T151B_HUMAN	transmembrane protein 151B							integral to membrane					0						AGTGGGAAGGACGAGGTCCAG	0.592													4	16	---	---	---	---	PASS
FAM135A	57579	broad.mit.edu	37	6	71235358	71235358	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71235358A>C	uc003pfj.2	+	13	2704	c.2571A>C	c.(2569-2571)AAA>AAC	p.K857N	FAM135A_uc003pfi.2_Missense_Mutation_p.K661N|FAM135A_uc003pfh.2_Missense_Mutation_p.K644N|FAM135A_uc003pfl.2_Missense_Mutation_p.K524N|FAM135A_uc003pfn.2_Intron|FAM135A_uc003pfo.1_Missense_Mutation_p.K228N|FAM135A_uc010kan.1_5'Flank	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c	857										central_nervous_system(1)	1						ATTCTAAGAAATCTGTTGTAC	0.353													8	146	---	---	---	---	PASS
SENP6	26054	broad.mit.edu	37	6	76357474	76357474	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76357474A>C	uc003pid.3	+	7	1126	c.507A>C	c.(505-507)AAA>AAC	p.K169N	SENP6_uc003pie.3_Missense_Mutation_p.K162N|SENP6_uc003pic.2_Missense_Mutation_p.K162N|SENP6_uc003pif.1_Missense_Mutation_p.K60N	NM_015571	NP_056386	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6 isoform 1	169					proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)				ATGTCCAAAAAGTTGAAATTA	0.328													13	297	---	---	---	---	PASS
HDAC2	3066	broad.mit.edu	37	6	114262136	114262136	+	3'UTR	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114262136T>C	uc003pwd.1	-	14					HDAC2_uc003pwc.1_3'UTR|HDAC2_uc003pwe.1_3'UTR	NM_001527	NP_001518	Q92769	HDAC2_HUMAN	histone deacetylase 2						blood coagulation|dendrite development|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|maintenance of chromatin silencing|negative regulation of apoptosis|negative regulation of cell cycle|negative regulation of neuron projection development|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of proteolysis|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|ESC/E(Z) complex|NuRD complex|Sin3 complex	chromatin binding|enzyme binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|sequence-specific DNA binding|transcription factor binding			skin(2)|ovary(1)|central_nervous_system(1)	4		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Vorinostat(DB02546)	TAGTATAAAATGAAGCCAGAA	0.303													14	228	---	---	---	---	PASS
MED23	9439	broad.mit.edu	37	6	131926585	131926585	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131926585T>G	uc003qcs.1	-	14	1582	c.1408A>C	c.(1408-1410)AAT>CAT	p.N470H	MED23_uc003qcq.2_Missense_Mutation_p.N476H|MED23_uc011eca.1_Missense_Mutation_p.N111H|MED23_uc003qct.1_Missense_Mutation_p.N476H|MED23_uc011ecb.1_Intron	NM_004830	NP_004821	Q9ULK4	MED23_HUMAN	mediator complex subunit 23 isoform a	470					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		TTATAGTCATTCATCTGTAAA	0.308													15	210	---	---	---	---	PASS
NHSL1	57224	broad.mit.edu	37	6	138753025	138753025	+	Silent	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138753025C>T	uc003qhx.2	-	5	3089	c.2469G>A	c.(2467-2469)GGG>GGA	p.G823G	NHSL1_uc011edp.1_Silent_p.G819G	NM_020464	NP_065197	Q5SYE7	NHSL1_HUMAN	NHS-like 1 isoform 1	823											0						TGGCTCTGGACCCTTCTTGGA	0.582													83	161	---	---	---	---	PASS
UTRN	7402	broad.mit.edu	37	6	144803419	144803419	+	Silent	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144803419C>A	uc003qkt.2	+	26	3674	c.3582C>A	c.(3580-3582)GCC>GCA	p.A1194A		NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	1194	Spectrin 8.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TATTAGCTGCCAAGGTGCCCT	0.468													11	283	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	6	153603817	153603817	+	IGR	SNP	G	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153603817G>C								RGS17 (151428 upstream) : OPRM1 (727819 downstream)																							CGGCCGTGGCGGTGGCTCACG	0.567													6	46	---	---	---	---	PASS
OPRM1	4988	broad.mit.edu	37	6	154412543	154412543	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154412543G>T	uc003qpr.2	+	3	1337	c.1100G>T	c.(1099-1101)CGA>CTA	p.R367L	OPRM1_uc011efc.1_Missense_Mutation_p.R286L|OPRM1_uc011efd.1_Missense_Mutation_p.R267L|OPRM1_uc011efe.1_Missense_Mutation_p.R460L|OPRM1_uc003qpn.2_Missense_Mutation_p.R367L|OPRM1_uc003qpo.1_Missense_Mutation_p.R367L|OPRM1_uc011eff.1_Missense_Mutation_p.R367L|OPRM1_uc011efg.1_Missense_Mutation_p.R367L|OPRM1_uc011efh.1_Missense_Mutation_p.R367L|OPRM1_uc003qpq.1_Missense_Mutation_p.R367L|OPRM1_uc003qpt.1_Missense_Mutation_p.R367L|OPRM1_uc011efi.1_Missense_Mutation_p.R367L|OPRM1_uc003qpp.2_RNA|OPRM1_uc003qps.2_RNA|OPRM1_uc010kjg.2_Missense_Mutation_p.R267L|OPRM1_uc003qpu.2_Missense_Mutation_p.R267L	NM_000914	NP_000905	P35372	OPRM_HUMAN	opioid receptor, mu 1 isoform MOR-1	367	Cytoplasmic (Potential).				behavior|negative regulation of cell proliferation|sensory perception	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	mu-opioid receptor activity|protein binding			ovary(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tramadol(DB00193)	AACTCCACTCGAATTCGTCAG	0.443													10	19	---	---	---	---	PASS
AHR	196	broad.mit.edu	37	7	17382640	17382640	+	Silent	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17382640G>A	uc011jxz.1	+	11	3112	c.2499G>A	c.(2497-2499)CCG>CCA	p.P833P	AHR_uc003stt.3_RNA	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor precursor	833				LNETYPAELNNINNTQTTTHLQPLHHPSEARPFPDLTSSGF L -> FK (in Ref. 1; BAA03857).	apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)					TTCATCATCCGTCAGAAGCCA	0.373													14	406	---	---	---	---	PASS
KLHL7	55975	broad.mit.edu	37	7	23183605	23183605	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23183605C>G	uc003svs.3	+	6	1047	c.754C>G	c.(754-756)CTT>GTT	p.L252V	KLHL7_uc003svr.3_Missense_Mutation_p.L230V|KLHL7_uc011jys.1_Missense_Mutation_p.L176V|KLHL7_uc011jyt.1_Missense_Mutation_p.L27V|KLHL7_uc003svt.2_Missense_Mutation_p.L204V|KLHL7_uc011jyv.1_Missense_Mutation_p.L27V	NM_001031710	NP_001026880	Q8IXQ5	KLHL7_HUMAN	kelch-like 7 isoform 1	252						Golgi apparatus|nucleolus|plasma membrane					0						AGCTGAACCACTTATTCAAGA	0.363													68	199	---	---	---	---	PASS
WASL	8976	broad.mit.edu	37	7	123332892	123332892	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123332892C>A	uc003vkz.2	-	9	1184	c.856G>T	c.(856-858)GGG>TGG	p.G286W		NM_003941	NP_003932	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome gene-like protein	286	Pro-rich.				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						ggaggtggCCCTCCCCTTGAT	0.348													4	32	---	---	---	---	PASS
ADCK2	90956	broad.mit.edu	37	7	140387007	140387007	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140387007T>A	uc003vvy.1	+	5	1701	c.1523T>A	c.(1522-1524)TTC>TAC	p.F508Y	ADCK2_uc003vvz.2_Missense_Mutation_p.F508Y	NM_052853	NP_443085	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	508	Protein kinase.					integral to membrane	ATP binding|protein serine/threonine kinase activity				0	Melanoma(164;0.00956)					CTGAGGAATTTCCGGGCAGTT	0.552													25	82	---	---	---	---	PASS
TRY6	154754	broad.mit.edu	37	7	142479940	142479940	+	Silent	SNP	C	T	T	rs58649169	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142479940C>T	uc011ksq.1	+	2	155	c.72C>T	c.(70-72)ATC>ATT	p.I24I	uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|TRY6_uc011ksn.1_RNA|uc003wan.1_Intron|TRY6_uc011kso.1_RNA|TRY6_uc011ksr.1_RNA	NR_001296				SubName: Full=Protease, serine, 3; Flags: Fragment;												0						ATGACAAGATCGTTGGGGGCT	0.557													4	94	---	---	---	---	PASS
CLTA	1211	broad.mit.edu	37	9	36209311	36209311	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36209311G>A	uc003zzc.2	+	5	695	c.533G>A	c.(532-534)GGT>GAT	p.G178D	CLTA_uc003zzd.2_Missense_Mutation_p.G178D|CLTA_uc003zze.2_Intron|CLTA_uc011lpk.1_Intron|CLTA_uc003zzf.1_Intron	NM_007096	NP_009027	P09496	CLCA_HUMAN	clathrin, light polypeptide A isoform b	178					axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol	structural molecule activity			central_nervous_system(1)	1			STAD - Stomach adenocarcinoma(86;0.228)			GACGTGATTGGTTATGTGTAT	0.398													30	510	---	---	---	---	PASS
TLE4	7091	broad.mit.edu	37	9	82340100	82340100	+	3'UTR	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82340100C>A	uc004ald.2	+	21					TLE4_uc004alc.2_3'UTR|TLE4_uc010mpr.2_3'UTR|TLE4_uc004ale.2_3'UTR|TLE4_uc011lsq.1_3'UTR|TLE4_uc010mps.2_3'UTR|TLE4_uc004alf.2_3'UTR	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4											lung(2)|ovary(1)|breast(1)|skin(1)	5						CTCCTGGTAGCACTTTGCTCT	0.413													51	110	---	---	---	---	PASS
PTCH1	5727	broad.mit.edu	37	9	98278898	98278898	+	5'UTR	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98278898C>A	uc010mrr.2	-	1					PTCH1_uc004avm.3_Intron|PTCH1_uc004avo.2_5'UTR|PTCH1_uc010mrv.1_Intron|PTCH1_uc010mrw.1_RNA	NM_001083602	NP_001077071	Q13635	PTC1_HUMAN	patched isoform M						embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1)	379		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				CCTCGTCTCCCCCTTGCCTTG	0.423									Basal_Cell_Nevus_syndrome				226	448	---	---	---	---	PASS
CEP110	11064	broad.mit.edu	37	9	123870184	123870184	+	Nonsense_Mutation	SNP	A	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123870184A>T	uc004bkx.1	+	6	944	c.913A>T	c.(913-915)AAA>TAA	p.K305*	CEP110_uc004bkw.2_Nonsense_Mutation_p.K305*	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa	305	Potential.				cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						AAATCAAGATAAATTGAATAA	0.333													68	118	---	---	---	---	PASS
MED27	9442	broad.mit.edu	37	9	134735980	134735980	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134735980G>A	uc004cbe.1	-	8	903	c.881C>T	c.(880-882)CCG>CTG	p.P294L	MED27_uc004cbf.1_Missense_Mutation_p.P258L	NM_004269	NP_004260	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	294					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleolus|transcription factor complex	protein binding|transcription coactivator activity			skin(1)	1		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		CCTCCATGTCGGGGGAAGGCC	0.597													5	70	---	---	---	---	PASS
DBH	1621	broad.mit.edu	37	9	136523584	136523584	+	3'UTR	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136523584C>A	uc004cel.2	+	12					uc010nao.1_5'Flank	NM_000787	NP_000778	P09172	DOPO_HUMAN	dopamine beta hydroxylase precursor						hormone biosynthetic process	chromaffin granule lumen|chromaffin granule membrane|extracellular region|integral to membrane|membrane fraction|soluble fraction|transport vesicle membrane	dopamine beta-monooxygenase activity|L-ascorbic acid binding			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Dopamine(DB00988)|Vitamin C(DB00126)	GGACCTACTCCTCCCCCTCCT	0.662													13	13	---	---	---	---	PASS
DIP2C	22982	broad.mit.edu	37	10	375486	375486	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:375486G>T	uc001ifp.2	-	30	3730	c.3640C>A	c.(3640-3642)CCC>ACC	p.P1214T		NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	1214						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CACAAGGCGGGGTTGGTTTCC	0.582													11	98	---	---	---	---	PASS
C10orf47	254427	broad.mit.edu	37	10	11894170	11894170	+	Silent	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11894170C>T	uc001ikx.2	+	2	248	c.94C>T	c.(94-96)CTG>TTG	p.L32L	uc001iky.1_Intron	NM_153256	NP_694988	Q86WR7	CJ047_HUMAN	hypothetical protein LOC254427	32	Ser-rich.									central_nervous_system(1)	1						AGGCGGCAGCCTGGAGAGTCG	0.552													9	24	---	---	---	---	PASS
COL17A1	1308	broad.mit.edu	37	10	105821163	105821163	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105821163C>A	uc001kxr.2	-	13	1148	c.979G>T	c.(979-981)GCC>TCC	p.A327S	COL17A1_uc010qqv.1_Missense_Mutation_p.A311S	NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	327	Cytoplasmic (Potential).|Nonhelical region (NC16).				cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CAGCACTCACCGGCGGAGGTG	0.552													3	37	---	---	---	---	PASS
NHLRC2	374354	broad.mit.edu	37	10	115664580	115664580	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115664580C>G	uc001lax.1	+	10	1921	c.1709C>G	c.(1708-1710)CCC>CGC	p.P570R	NHLRC2_uc001lay.1_Intron	NM_198514	NP_940916	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	570					cell redox homeostasis					ovary(1)	1				Epithelial(162;0.017)|all cancers(201;0.0187)		TCCTAGCTCCCCATCTTCAGA	0.338													45	98	---	---	---	---	PASS
BUB3	9184	broad.mit.edu	37	10	124917322	124917322	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124917322A>G	uc001lhe.2	+	4	585	c.343A>G	c.(343-345)AGT>GGT	p.S115G	BUB3_uc009yah.2_Missense_Mutation_p.S67G|BUB3_uc001lhf.3_Missense_Mutation_p.S115G|BUB3_uc001lhd.2_Missense_Mutation_p.S115G|BUB3_uc010qud.1_Missense_Mutation_p.S35G	NM_004725	NP_004716	O43684	BUB3_HUMAN	budding uninhibited by benzimidazoles 3 isoform	115	WD 3.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|attachment of spindle microtubules to kinetochore|cell division|meiosis|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	condensed chromosome kinetochore|cytosol|nucleus	protein binding			ovary(1)	1		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)				GGTCACTGGAAGTTGGGATCA	0.433													91	224	---	---	---	---	PASS
OR56A3	390083	broad.mit.edu	37	11	5969272	5969272	+	Silent	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5969272C>A	uc010qzt.1	+	1	696	c.696C>A	c.(694-696)CTC>CTA	p.L232L		NM_001003443	NP_001003443	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A,	232	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCTGAGACTCAAGGCAGAGG	0.517													56	145	---	---	---	---	PASS
CCKBR	887	broad.mit.edu	37	11	6292136	6292136	+	Intron	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6292136G>A	uc001mcp.2	+						CCKBR_uc001mcq.2_Intron|CCKBR_uc001mcr.2_Intron|CCKBR_uc001mcs.2_Missense_Mutation_p.R305K|CCKBR_uc001mct.1_Intron	NM_176875	NP_795344	P32239	GASR_HUMAN	cholecystokinin B receptor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	AGGGTGAGAAGGAAGCTGGAA	0.627													8	22	---	---	---	---	PASS
CLEC4C	170482	broad.mit.edu	37	12	7882078	7882078	+	3'UTR	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7882078G>A	uc001qtg.1	-	6					CLEC4C_uc001qth.1_3'UTR|CLEC4C_uc001qti.1_3'UTR	NM_130441	NP_569708	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C isoform						innate immune response	integral to membrane	sugar binding			ovary(2)|skin(1)	3				Kidney(36;0.0915)		ACAGCCTGCTGAAACATTTTA	0.239													15	27	---	---	---	---	PASS
BCAT1	586	broad.mit.edu	37	12	24970766	24970766	+	3'UTR	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24970766G>A	uc001rgd.3	-	11					BCAT1_uc001rgc.2_3'UTR|BCAT1_uc010six.1_3'UTR|BCAT1_uc010siy.1_3'UTR|BCAT1_uc001rge.3_3'UTR	NM_005504	NP_005495	P54687	BCAT1_HUMAN	branched chain aminotransferase 1, cytosolic						branched chain family amino acid biosynthetic process|branched chain family amino acid catabolic process|cell proliferation|G1/S transition of mitotic cell cycle	cytosol	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity			lung(1)|breast(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)|Pyridoxal Phosphate(DB00114)	ACCATTTGATGATTGCAATTC	0.328													11	58	---	---	---	---	PASS
ADAMTS20	80070	broad.mit.edu	37	12	43769952	43769952	+	Splice_Site	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43769952C>T	uc010skx.1	-	35	5221	c.5221_splice	c.e35-1	p.I1741_splice		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		CACAATAAATCTAAAGAAAAA	0.303													108	242	---	---	---	---	PASS
AVIL	10677	broad.mit.edu	37	12	58202005	58202005	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58202005A>G	uc001sqj.1	-	10	1195	c.1166T>C	c.(1165-1167)ATG>ACG	p.M389T	AVIL_uc009zqe.1_Missense_Mutation_p.M382T|AVIL_uc001sqk.1_5'UTR|AVIL_uc001sql.3_Missense_Mutation_p.M366T	NM_006576	NP_006567	O75366	AVIL_HUMAN	advillin	389	Core (By similarity).				actin filament capping|cilium morphogenesis|cytoskeleton organization|positive regulation of neuron projection development	actin cytoskeleton|axon|cytoplasm	actin binding			central_nervous_system(1)	1	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					ATCATCGACCATTCTTTCCTG	0.512													97	235	---	---	---	---	PASS
TMCC3	57458	broad.mit.edu	37	12	94975953	94975953	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94975953C>A	uc001tdj.2	-	2	558	c.440G>T	c.(439-441)GGA>GTA	p.G147V	TMCC3_uc001tdi.2_Missense_Mutation_p.G116V	NM_020698	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	147	Potential.					integral to membrane				ovary(1)|skin(1)	2						CCTAGAGGCTCCATTCTGCTC	0.478													35	93	---	---	---	---	PASS
RBM19	9904	broad.mit.edu	37	12	114364985	114364985	+	Silent	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114364985T>C	uc009zwi.2	-	17	2262	c.2118A>G	c.(2116-2118)GCA>GCG	p.A706A	RBM19_uc001tvn.3_Silent_p.A706A|RBM19_uc001tvm.2_Silent_p.A706A	NM_001146699	NP_001140171	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	706					multicellular organismal development|positive regulation of embryonic development	chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|RNA binding			skin(3)|ovary(1)|liver(1)|central_nervous_system(1)	6	Medulloblastoma(191;0.163)|all_neural(191;0.178)					AAGAGTTGTCTGCTCCTTCCT	0.313													53	102	---	---	---	---	PASS
MLXIP	22877	broad.mit.edu	37	12	122613773	122613773	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122613773G>T	uc001ubq.2	+	4	696	c.696G>T	c.(694-696)AGG>AGT	p.R232S	MLXIP_uc001ubr.2_5'UTR|MLXIP_uc001ubs.1_5'Flank	NM_014938	NP_055753	Q9HAP2	MLXIP_HUMAN	MLX interacting protein	232	Required for cytoplasmic localization.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial outer membrane|nucleus	DNA binding			ovary(2)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		TCAAGAAAAGGGTATCTGGCT	0.607													9	139	---	---	---	---	PASS
PCDH9	5101	broad.mit.edu	37	13	67801923	67801923	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67801923G>T	uc001vik.2	-	2	1342	c.650C>A	c.(649-651)ACC>AAC	p.T217N	PCDH9_uc001vil.2_Missense_Mutation_p.T217N|PCDH9_uc010thl.1_Missense_Mutation_p.T217N|PCDH9_uc001vin.3_Missense_Mutation_p.T217N	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	217	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		CATCACATAGGTATCTTTCTG	0.453													74	160	---	---	---	---	PASS
KCTD12	115207	broad.mit.edu	37	13	77459423	77459423	+	Silent	SNP	C	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77459423C>G	uc010aeu.1	-	1	1118	c.861G>C	c.(859-861)TCG>TCC	p.S287S	KCTD12_uc001vka.1_Silent_p.S287S	NM_138444	NP_612453	Q96CX2	KCD12_HUMAN	potassium channel tetramerisation domain	287						cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			ovary(1)	1		Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.0499)		TGTGGAAGCCCGACTCGGACA	0.632											OREG0022449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	20	29	---	---	---	---	PASS
SPTLC2	9517	broad.mit.edu	37	14	78045381	78045381	+	Silent	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78045381G>A	uc001xub.2	-	3	587	c.399C>T	c.(397-399)AAC>AAT	p.N133N		NM_004863	NP_004854	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base	133						integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	GCCGATTCCAGTTGTCTCTTA	0.418													66	88	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106311217	106311217	+	Intron	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106311217G>A	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysj.2_Missense_Mutation_p.P130L|uc001ysk.1_Missense_Mutation_p.P130L|uc001ysl.1_Missense_Mutation_p.P130L|uc001ysm.1_Missense_Mutation_p.P73L|uc001ysn.1_Missense_Mutation_p.P73L|uc001yso.1_Missense_Mutation_p.P73L					Parts of antibodies, mostly variable regions.												0						CTCTGCTTGGGGTTGTGCAGT	0.612													17	246	---	---	---	---	PASS
VPS18	57617	broad.mit.edu	37	15	41192166	41192166	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41192166C>T	uc001zne.2	+	4	1489	c.1150C>T	c.(1150-1152)CGG>TGG	p.R384W		NM_020857	NP_065908	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18	384					endosome organization|lysosome organization|protein transport	HOPS complex|late endosome membrane|lysosomal membrane	metal ion binding|protein binding			ovary(2)|large_intestine(1)	3		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CTACACTGAGCGGGCTGTCTT	0.597													11	19	---	---	---	---	PASS
PLA2G4D	283748	broad.mit.edu	37	15	42386652	42386652	+	Silent	SNP	C	T	T	rs148416017		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42386652C>T	uc001zox.2	-	1	101	c.6G>A	c.(4-6)GAG>GAA	p.E2E		NM_178034	NP_828848	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD	2					phospholipid catabolic process	cytoplasmic vesicle membrane|cytosol	metal ion binding|phospholipase A2 activity			large_intestine(1)|skin(1)	2		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GTGACAGGCTCTCCATGCTAG	0.632													10	77	---	---	---	---	PASS
CDAN1	146059	broad.mit.edu	37	15	43021465	43021465	+	Silent	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43021465G>A	uc001zql.2	-	18	2620	c.2503C>T	c.(2503-2505)CTG>TTG	p.L835L	CDAN1_uc001zqj.2_RNA|CDAN1_uc001zqk.2_Silent_p.L161L	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	835						integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		TGGGCTCCCAGGCTGGTGGTA	0.647													16	18	---	---	---	---	PASS
DMXL2	23312	broad.mit.edu	37	15	51741365	51741365	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51741365A>G	uc002abf.2	-	43	9152	c.8927T>C	c.(8926-8928)CTA>CCA	p.L2976P	DMXL2_uc002abd.2_Missense_Mutation_p.L1068P|DMXL2_uc010ufy.1_Missense_Mutation_p.L2977P|DMXL2_uc010bfa.2_Missense_Mutation_p.L2340P|DMXL2_uc002abc.2_RNA	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2976	WD 15.					cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)		TGAATGAATTAGGCCATGGCC	0.413													38	85	---	---	---	---	PASS
DMXL2	23312	broad.mit.edu	37	15	51839582	51839582	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51839582C>G	uc002abf.2	-	7	816	c.591G>C	c.(589-591)TGG>TGC	p.W197C	DMXL2_uc010ufy.1_Missense_Mutation_p.W197C|DMXL2_uc010bfa.2_Missense_Mutation_p.W197C	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	197	WD 2.					cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)		TCATAGGATACCACACTTTCA	0.313													15	124	---	---	---	---	PASS
HEXA	3073	broad.mit.edu	37	15	72642743	72642743	+	Intron	SNP	G	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72642743G>C	uc002aun.3	-						uc002aug.2_RNA|CELF6_uc002auk.3_Intron|HEXA_uc010ukn.1_Intron|HEXA_uc002auo.3_Intron|HEXA_uc010bix.2_Intron|HEXA_uc010biy.2_Intron|HEXA_uc010uko.1_Intron|HEXA_uc010biz.1_Intron	NM_000520	NP_000511	P06865	HEXA_HUMAN	hexosaminidase A preproprotein						cell death	lysosome	beta-N-acetylhexosaminidase activity|cation binding|protein heterodimerization activity			ovary(3)|upper_aerodigestive_tract(1)	4						GAAGTCGATGGAAAACATTCT	0.448													6	19	---	---	---	---	PASS
SULT1A1	6817	broad.mit.edu	37	16	28617099	28617099	+	3'UTR	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28617099T>C	uc002dqi.2	-	7					uc010vct.1_Intron|SULT1A1_uc002dqj.2_3'UTR|SULT1A1_uc002dqk.2_3'UTR|SULT1A1_uc002dql.2_3'UTR|SULT1A1_uc002dqm.2_3'UTR|SULT1A1_uc002dqn.2_3'UTR|SULT1A1_uc002dqo.2_3'UTR|SULT1A1_uc002dqp.2_3'UTR	NM_177534	NP_803878	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A,						3'-phosphoadenosine 5'-phosphosulfate metabolic process|catecholamine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity|flavonol 3-sulfotransferase activity				0						CTTGGTCAGGTTTGATTCGCA	0.373													5	86	---	---	---	---	PASS
OR3A2	4995	broad.mit.edu	37	17	3181512	3181512	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3181512C>A	uc002fvg.2	-	1	757	c.718G>T	c.(718-720)GTG>TTG	p.V240L		NM_002551	NP_002542	P47893	OR3A2_HUMAN	olfactory receptor, family 3, subfamily A,	240	Cytoplasmic (Potential).				sensory perception of smell	integral to plasma membrane	olfactory receptor activity			ovary(1)	1						CGGCCCTCCACTGAACGGATT	0.527													23	33	---	---	---	---	PASS
ACACA	31	broad.mit.edu	37	17	35640308	35640308	+	Splice_Site	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35640308T>C	uc002hnm.2	-	5	552	c.361_splice	c.e5-1	p.V121_splice	ACACA_uc002hnk.2_Splice_Site_p.V43_splice|ACACA_uc002hnl.2_Splice_Site_p.V63_splice|ACACA_uc002hnn.2_Splice_Site_p.V121_splice|ACACA_uc002hno.2_Splice_Site_p.V158_splice|ACACA_uc010cuz.2_Splice_Site_p.V121_splice|ACACA_uc002hnq.2_Splice_Site_p.V43_splice	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AATAAGAACCTGGGAGGGGGA	0.403													57	115	---	---	---	---	PASS
NAGS	162417	broad.mit.edu	37	17	42083124	42083124	+	Silent	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42083124T>C	uc002ies.2	+	2	546	c.546T>C	c.(544-546)GCT>GCC	p.A182A	PYY_uc002ieq.2_5'Flank|NAGS_uc010czn.2_Silent_p.A182A|NAGS_uc002iet.2_5'Flank	NM_153006	NP_694551	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	182					arginine biosynthetic process|urea cycle	mitochondrial matrix	acetyl-CoA:L-glutamate N-acetyltransferase activity				0		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)	L-Glutamic Acid(DB00142)	CCCCTACGGCTCCCTCGGGCT	0.662													3	15	---	---	---	---	PASS
HDAC5	10014	broad.mit.edu	37	17	42162541	42162541	+	Intron	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42162541G>T	uc002ifd.1	-						HDAC5_uc002ife.1_Intron|HDAC5_uc002iff.1_Intron|HDAC5_uc010czp.1_Intron|HDAC5_uc002ifg.1_5'UTR|HDAC5_uc002ifh.2_Intron	NM_005474	NP_005465	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 1						B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		ACAGACCTATGTGTCAGCCAG	0.602													9	19	---	---	---	---	PASS
CLTC	1213	broad.mit.edu	37	17	57754361	57754361	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57754361T>C	uc002ixq.1	+	17	3051	c.2608T>C	c.(2608-2610)TGT>CGT	p.C870R	CLTC_uc002ixp.2_Missense_Mutation_p.C870R|CLTC_uc002ixr.1_Missense_Mutation_p.C874R	NM_004859	NP_004850	Q00610	CLH1_HUMAN	clathrin heavy chain 1	870	Heavy chain arm.|Proximal segment.				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					TCATGAGGGCTGTGAGGAGCC	0.413			T	ALK|TFE3	ALCL|renal 								63	104	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	58511110	58511110	+	RNA	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58511110C>A	uc002iyr.1	-	1		c.2248G>T								Homo sapiens cDNA FLJ33664 fis, clone BRAMY2027451, moderately similar to 60S RIBOSOMAL PROTEIN L12.																		TCCACAGCACCACTGTTGATG	0.393													7	15	---	---	---	---	PASS
ACTG1	71	broad.mit.edu	37	17	79479120	79479120	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79479120C>T	uc002kaj.1	-	2	197	c.172G>A	c.(172-174)GCC>ACC	p.A58T	ACTG1_uc002kah.1_5'Flank|ACTG1_uc002kai.1_Missense_Mutation_p.A15T|ACTG1_uc002kak.1_Missense_Mutation_p.A58T|ACTG1_uc010wun.1_Missense_Mutation_p.A58T|ACTG1_uc002kal.1_Missense_Mutation_p.A58T|ACTG1_uc002kag.2_RNA	NM_001614	NP_001605	P63261	ACTG_HUMAN	actin, gamma 1 propeptide	58					adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol	ATP binding|identical protein binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			TTGCTCTGGGCCTCGTCGCCC	0.632													4	8	---	---	---	---	PASS
SERPINB11	89778	broad.mit.edu	37	18	61390295	61390295	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61390295G>C	uc002ljk.3	+	9	903	c.841G>C	c.(841-843)GAA>CAA	p.E281Q	SERPINB11_uc010xes.1_Missense_Mutation_p.E106Q|SERPINB11_uc010dqd.2_Missense_Mutation_p.E167Q|SERPINB11_uc002ljj.3_Missense_Mutation_p.E167Q|SERPINB11_uc010dqe.2_Missense_Mutation_p.E80Q|SERPINB11_uc010dqf.2_Missense_Mutation_p.E79Q	NM_080475	NP_536723	Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B, member 11	281					regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity			breast(1)	1		Esophageal squamous(42;0.129)				GATGGAAAGAGAAGTTGAAGT	0.423													14	100	---	---	---	---	PASS
ZNF709	163051	broad.mit.edu	37	19	12575498	12575498	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12575498G>A	uc002mtv.3	-	4	1399	c.1238C>T	c.(1237-1239)ACT>ATT	p.T413I	ZNF709_uc002mtw.3_Missense_Mutation_p.T381I|ZNF709_uc002mtx.3_Missense_Mutation_p.T413I	NM_152601	NP_689814	Q8N972	ZN709_HUMAN	zinc finger protein 709 isoform a	413	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TCCAGTGTGAGTTCTTTCATG	0.418													4	94	---	---	---	---	PASS
EMR3	84658	broad.mit.edu	37	19	14736333	14736333	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14736333T>C	uc002mzi.3	-	15	2039	c.1891A>G	c.(1891-1893)AAG>GAG	p.K631E	EMR3_uc010dzp.2_Missense_Mutation_p.K579E|EMR3_uc010xnv.1_Missense_Mutation_p.K505E	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	631	Cytoplasmic (Potential).				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						GGACCCATCTTGCTGGAAAGT	0.388													152	273	---	---	---	---	PASS
OR7A5	26659	broad.mit.edu	37	19	14938184	14938184	+	Silent	SNP	A	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14938184A>G	uc002mzw.2	-	1	1093	c.870T>C	c.(868-870)TAT>TAC	p.Y290Y	OR7A5_uc010xoa.1_Silent_p.Y290Y	NM_017506	NP_059976	Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A,	290	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(2)	2						TCCTCAGACTATAGATAAAGG	0.478													10	204	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	19	23329317	23329317	+	RNA	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23329317C>A	uc002nrb.1	+	4		c.1670C>A								Homo sapiens cDNA FLJ16640 fis, clone TESTI4028938, moderately similar to Zinc finger protein 85.																		AGCCTTTAGGCGGTTCTCACA	0.353													3	14	---	---	---	---	PASS
ZNF570	148268	broad.mit.edu	37	19	37975687	37975687	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37975687G>T	uc002ogk.1	+	5	1692	c.1163G>T	c.(1162-1164)TGT>TTT	p.C388F	ZNF570_uc010efl.1_Missense_Mutation_p.C444F|ZNF570_uc010xtr.1_Missense_Mutation_p.C185F	NM_144694	NP_653295	Q96NI8	ZN570_HUMAN	zinc finger protein 570	388	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCCTATGAATGTAAGGAATGT	0.408													13	72	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	38946364	38946364	+	Silent	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38946364C>A	uc002oit.2	+	16	1894	c.1764C>A	c.(1762-1764)CTC>CTA	p.L588L	RYR1_uc002oiu.2_Silent_p.L588L	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	588	Cytoplasmic.|B30.2/SPRY 1.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	TCATCTCCCTCCTGGACAAGC	0.567													12	199	---	---	---	---	PASS
C19orf75	284369	broad.mit.edu	37	19	51767348	51767348	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51767348G>T	uc002pwb.1	+	2	403	c.22G>T	c.(22-24)GTA>TTA	p.V8L	C19orf75_uc010eov.1_RNA|C19orf75_uc010ycw.1_Nonsense_Mutation_p.G8*	NM_173635	NP_775906	Q8N7X8	CS075_HUMAN	hypothetical protein LOC284369	8						integral to membrane				ovary(1)|pancreas(1)	2						GCTACAGCTGGGTAAGTAAGG	0.527													35	129	---	---	---	---	PASS
LILRA2	11027	broad.mit.edu	37	19	55085805	55085805	+	Silent	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55085805C>A	uc002qgg.3	+	3	197	c.108C>A	c.(106-108)GGC>GGA	p.G36G	LILRA2_uc010ern.2_Silent_p.G36G|LILRA2_uc002qgf.2_Silent_p.G36G|LILRA2_uc010yfe.1_Silent_p.G36G|LILRA2_uc010yff.1_Silent_p.G24G|LILRA2_uc010ero.2_Silent_p.G24G|LILRA2_uc010yfg.1_Silent_p.G36G	NM_001130917	NP_001124389	Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor,	36	Extracellular (Potential).|Ig-like C2-type 1.				defense response	integral to membrane	antigen binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0963)		CTGAGCCAGGCTCTGTGATCA	0.552													36	61	---	---	---	---	PASS
SLC13A3	64849	broad.mit.edu	37	20	45192089	45192089	+	Silent	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45192089G>A	uc002xsf.1	-	12	1634	c.1596C>T	c.(1594-1596)ATC>ATT	p.I532I	SLC13A3_uc010ghn.1_Silent_p.I501I|SLC13A3_uc010zxw.1_Silent_p.I482I|SLC13A3_uc002xsg.1_Silent_p.I485I|SLC13A3_uc010gho.1_Silent_p.I450I|SLC13A3_uc010zxx.1_Silent_p.I434I|SLC13A3_uc002xse.1_Silent_p.I23I|SLC13A3_uc010ghm.1_Silent_p.I119I|SLC13A3_uc010zxv.1_Silent_p.I117I	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a	532	Cytoplasmic (Potential).					integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	AGGCGAAGGCGATGGAGTTGG	0.632													23	50	---	---	---	---	PASS
ZBTB46	140685	broad.mit.edu	37	20	62407316	62407316	+	Splice_Site	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62407316C>T	uc002ygv.1	-	3	1139	c.938_splice	c.e3-1	p.N313_splice	ZBTB46_uc002ygu.2_Splice_Site	NM_025224	NP_079500	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					AGGTCCGCATCTGGGGACAGA	0.617													16	20	---	---	---	---	PASS
LIPI	149998	broad.mit.edu	37	21	15554135	15554135	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15554135C>T	uc002yjm.2	-	4	660	c.650G>A	c.(649-651)AGC>AAC	p.S217N	LIPI_uc010gkw.1_Missense_Mutation_p.S150N	NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I	196					lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		ATCTAATCTGCTATATGGTGG	0.393													18	314	---	---	---	---	PASS
BRWD1	54014	broad.mit.edu	37	21	40572254	40572254	+	Silent	SNP	A	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40572254A>G	uc002yxk.1	-	39	4783	c.4644T>C	c.(4642-4644)TCT>TCC	p.S1548S	BRWD1_uc010goc.1_Silent_p.S191S|BRWD1_uc002yxl.2_Silent_p.S1548S	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1548	Poly-Ser.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TGCTTTCCTCAGAACTACTGG	0.428													95	253	---	---	---	---	PASS
USP18	11274	broad.mit.edu	37	22	18643020	18643020	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18643020C>A	uc002zny.2	+	3	577	c.239C>A	c.(238-240)ACC>AAC	p.T80N		NM_017414	NP_059110	Q9UMW8	UBP18_HUMAN	ubiquitin specific protease 18	80					regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway|ubiquitin-dependent protein catabolic process	cytosol|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			breast(1)	1						GTGGACTTCACCAGGATATTG	0.318													101	241	---	---	---	---	PASS
MAPK1	5594	broad.mit.edu	37	22	22142621	22142621	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22142621T>C	uc002zvn.2	-	6	1021	c.781A>G	c.(781-783)AGG>GGG	p.R261G	MAPK1_uc002zvo.2_Missense_Mutation_p.R261G|MAPK1_uc010gtk.1_Intron	NM_002745	NP_002736	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	261	|Protein kinase.				activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|epidermal growth factor receptor signaling pathway|ERK1 and ERK2 cascade|induction of apoptosis|innate immune response|insulin receptor signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|synaptic transmission|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|transcription, DNA-dependent	cytosol|nucleoplasm	ATP binding|DNA binding|MAP kinase activity|phosphatase binding|RNA polymerase II carboxy-terminal domain kinase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)	AAATAGTTCCTAGCTTTTAAA	0.348													13	283	---	---	---	---	PASS
FBLN1	2192	broad.mit.edu	37	22	45928965	45928965	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45928965G>T	uc003bgj.1	+	6	714	c.567G>T	c.(565-567)CAG>CAT	p.Q189H	FBLN1_uc003bgg.1_Missense_Mutation_p.Q189H|FBLN1_uc003bgh.2_Missense_Mutation_p.Q189H|FBLN1_uc010gzz.2_Missense_Mutation_p.Q227H|FBLN1_uc003bgi.1_Missense_Mutation_p.Q189H	NM_006486	NP_006477	P23142	FBLN1_HUMAN	fibulin 1 isoform D	189	EGF-like 1.				interspecies interaction between organisms	extracellular space|soluble fraction	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		GCAAGCAGCAGTGCCGAGACA	0.627													28	64	---	---	---	---	PASS
MSL3	10943	broad.mit.edu	37	X	11783803	11783803	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11783803G>A	uc004cuw.2	+	9	1231	c.1126G>A	c.(1126-1128)GAC>AAC	p.D376N	MSL3_uc004cuv.1_Missense_Mutation_p.D376N|MSL3_uc004cux.2_Missense_Mutation_p.D317N|MSL3_uc011mig.1_Missense_Mutation_p.D227N|MSL3_uc011mih.1_Missense_Mutation_p.D364N|MSL3_uc004cuy.2_Missense_Mutation_p.D210N	NM_078629	NP_523353	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3-like 1 isoform a	376					histone H4-K16 acetylation|multicellular organismal development|transcription from RNA polymerase II promoter	MSL complex	DNA binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						CCGGCAGCAGGACACATCCGC	0.602													6	81	---	---	---	---	PASS
GLRA2	2742	broad.mit.edu	37	X	14748581	14748581	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14748581C>T	uc010nep.2	+	10	1665	c.1333C>T	c.(1333-1335)CGG>TGG	p.R445W	GLRA2_uc010neq.2_Missense_Mutation_p.R445W|GLRA2_uc004cwe.3_Missense_Mutation_p.R445W|GLRA2_uc011mio.1_Missense_Mutation_p.R356W|GLRA2_uc011mip.1_Missense_Mutation_p.R423W	NM_001118885	NP_001112357	P23416	GLRA2_HUMAN	glycine receptor, alpha 2 isoform A	445					neuropeptide signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(1)|lung(1)	2	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)	CAAGATCATTCGGCATGAAGA	0.438													13	210	---	---	---	---	PASS
KLHL15	80311	broad.mit.edu	37	X	24007140	24007140	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24007140G>T	uc004dba.3	-	4	969	c.713C>A	c.(712-714)ACA>AAA	p.T238K		NM_030624	NP_085127	Q96M94	KLH15_HUMAN	kelch-like 15	238										ovary(1)|breast(1)	2						AAATTCTGATGTCTTAACCTA	0.373													4	34	---	---	---	---	PASS
UBA1	7317	broad.mit.edu	37	X	47062342	47062342	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47062342G>A	uc004dhj.3	+	12	1385	c.1234G>A	c.(1234-1236)GCC>ACC	p.A412T	UBA1_uc004dhk.3_Missense_Mutation_p.A412T|INE1_uc004dhl.2_5'Flank	NM_153280	NP_695012	P22314	UBA1_HUMAN	ubiquitin-activating enzyme E1	412	2 approximate repeats.				cell death|protein modification process		ATP binding|ligase activity|protein binding|small protein activating enzyme activity			ovary(1)	1						CCCTCTCCAGGCCTGCTCCGG	0.577													35	79	---	---	---	---	PASS
FLJ44635	392490	broad.mit.edu	37	X	71380205	71380205	+	3'UTR	SNP	T	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71380205T>G	uc004eal.1	+	2						NM_207422	NP_997305	Q56UQ5	TPT1L_HUMAN	hypothetical protein LOC392490											lung(1)	1	Renal(35;0.156)					GTTAACAAATTTGGCAATTAC	0.398													4	44	---	---	---	---	PASS
FLJ44635	392490	broad.mit.edu	37	X	71380215	71380215	+	3'UTR	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71380215C>T	uc004eal.1	+	2						NM_207422	NP_997305	Q56UQ5	TPT1L_HUMAN	hypothetical protein LOC392490											lung(1)	1	Renal(35;0.156)					TTGGCAATTACTTTGGATCTA	0.383													4	46	---	---	---	---	PASS
PCDH11X	27328	broad.mit.edu	37	X	91137907	91137907	+	Intron	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91137907C>A	uc004efk.1	+						PCDH11X_uc004efl.1_Intron|PCDH11X_uc004efo.1_Intron|PCDH11X_uc010nmv.1_Intron|PCDH11X_uc004efm.1_Intron|PCDH11X_uc004efn.1_Intron|PCDH11X_uc004efh.1_Missense_Mutation_p.T1012N	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						TTGTCCTAGACTGATTCCAGG	0.338													95	681	---	---	---	---	PASS
COL4A5	1287	broad.mit.edu	37	X	107929324	107929324	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107929324G>T	uc004enz.1	+	47	4482	c.4280G>T	c.(4279-4281)GGG>GTG	p.G1427V	COL4A5_uc011mso.1_Missense_Mutation_p.G1424V|COL4A5_uc011msp.1_Missense_Mutation_p.G103V	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor	1421	Triple-helical region.		G -> W (in APSX; adult type).		axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4						GGTGCAGGAGGGCGCAAAGGA	0.517									Alport_syndrome_with_Diffuse_Leiomyomatosis				46	95	---	---	---	---	PASS
OCRL	4952	broad.mit.edu	37	X	128720994	128720994	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128720994C>T	uc004euq.2	+	20	2320	c.2155C>T	c.(2155-2157)CAA>TAA	p.Q719*	OCRL_uc004eur.2_Nonsense_Mutation_p.Q711*|OCRL_uc010nrb.2_5'Flank	NM_000276	NP_000267	Q01968	OCRL_HUMAN	phosphatidylinositol polyphosphate 5-phosphatase	719					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	clathrin-coated vesicle|cytosol|early endosome|Golgi stack|Golgi-associated vesicle	GTPase activator activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			lung(2)|ovary(1)|kidney(1)	4						ATCCCTTCTGCAAATGGTTCC	0.423													91	187	---	---	---	---	PASS
PRRG3	79057	broad.mit.edu	37	X	150869198	150869198	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150869198C>A	uc004few.1	+	4	779	c.389C>A	c.(388-390)CCC>CAC	p.P130H		NM_024082	NP_076987	Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3	130	Cytoplasmic (Potential).					extracellular region|integral to membrane	calcium ion binding			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					CACACCCTCCCCCGGGTCATG	0.652													21	23	---	---	---	---	PASS
F8	2157	broad.mit.edu	37	X	154129670	154129670	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154129670G>A	uc004fmt.2	-	20	6334	c.6163C>T	c.(6163-6165)CAG>TAG	p.Q2055*	F8_uc010nvi.1_Intron	NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	2055	F5/8 type C 1.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	GCTGTAATCTGAAAATCTCTA	0.388													91	176	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2617	2617	+	5'Flank	SNP	A	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2617A>T	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		cttgttccttaaatagggacc	0.209													12	408	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2635	2635	+	5'Flank	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2635G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		acctgtatgaatggctccacg	0.174													250	140	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3010	3010	+	5'Flank	SNP	G	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:3010G>A	uc004coq.3	-						uc004cos.3_RNA|uc011mfh.1_5'Flank					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		TCAGGACATCCCGATGGTGCA	0.453													37	293	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	4216	4216	+	RNA	SNP	T	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:4216T>C	uc004cos.3	+	2		c.2509T>C			uc011mfh.1_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP47.																		TACTTATATGATATGTCTCCA	0.388													7	201	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11251	11251	+	RNA	SNP	A	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11251A>G	uc004cov.3	+	1		c.674A>G			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		CTCATCGCACTAATTTACACT	0.473													20	413	---	---	---	---	PASS
CROCC	9696	broad.mit.edu	37	1	17204339	17204340	+	Intron	INS	-	C	C	rs137984380	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17204339_17204340insC	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		gaaaaccaaaacctcaagagtc	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25018774	25018774	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25018774delA								SRRM1 (19003 upstream) : CLIC4 (52986 downstream)																							tcttgaaaacaaaaaaaaaca	0.000													3	5	---	---	---	---	
CSMD2	114784	broad.mit.edu	37	1	34592792	34592792	+	Intron	DEL	C	-	-	rs74928487	byFrequency	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34592792delC	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CGGCATCCGACCCCCCAGGTC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	36979319	36979319	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36979319delC								CSF3R (30810 upstream) : GRIK3 (281809 downstream)																							TGGATGACCACCCCTTTTTGC	0.572													4	2	---	---	---	---	
PTPRF	5792	broad.mit.edu	37	1	44025845	44025846	+	Intron	INS	-	TG	TG	rs142071261	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44025845_44025846insTG	uc001cjr.2	+						PTPRF_uc001cjq.3_Intron|PTPRF_uc001cjs.2_Intron|PTPRF_uc001cjt.3_Intron	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ATGCAGCAGGCTGTGGTGTGTA	0.490													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	45998201	45998201	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45998201delG								PRDX1 (10592 upstream) : AKR1A1 (18297 downstream)																							aaaaaaaaaagaaaaaaaTTG	0.129													4	2	---	---	---	---	
SGIP1	84251	broad.mit.edu	37	1	67005579	67005579	+	Intron	DEL	T	-	-	rs79523553		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67005579delT	uc001dcr.2	+							NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3						ttgctttcagtgcatgggctg	0.000													3	3	---	---	---	---	
RPE65	6121	broad.mit.edu	37	1	68915826	68915826	+	5'Flank	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68915826delC	uc001dei.1	-							NM_000329	NP_000320	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein						visual perception	cytoplasm|plasma membrane	all-trans-retinyl-palmitate hydrolase activity|metal ion binding|retinol isomerase activity			ovary(1)	1						TGGCTGTTTTCCAGAGACCTC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	74364316	74364316	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74364316delA								None (None upstream) : LRRIQ3 (127388 downstream)																							tagggaagcgaatggaatgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	80289972	80289973	+	IGR	DEL	AC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80289972_80289973delAC								ELTD1 (817477 upstream) : None (None downstream)																							TCCTCAGAGAACACACACACAC	0.391													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	97364190	97364191	+	IGR	DEL	AC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97364190_97364191delAC								PTBP2 (83591 upstream) : DPYD (179111 downstream)																							AGCCTCCGAAACACACACACAC	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143181181	143181181	+	Intron	DEL	C	-	-	rs71237956		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143181181delC	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		atgacccaagctgtacctgtg	0.000													4	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144815036	144815036	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144815036delG	uc009wig.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF9_uc009wii.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						AGGACTTCTTGGGTAAGAACG	0.473													4	3	---	---	---	---	
SEC22B	9554	broad.mit.edu	37	1	145116147	145116148	+	3'UTR	INS	-	A	A	rs138980379		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145116147_145116148insA	uc001eml.1	+	7					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron	NM_004892	NP_004883	O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|melanosome	protein binding				0						AGTAGATTGTTATTTCGTTTTT	0.416													6	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145215207	145215208	+	Intron	DEL	CT	-	-	rs111871027		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145215207_145215208delCT	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_Intron|NOTCH2NL_uc001emm.3_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ACTTGCTGGCCTCACTTAGTAC	0.386													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	146767816	146767816	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146767816delA	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																		GGGAATTGTGAAAAGGGCGCA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149358395	149358396	+	IGR	DEL	AA	-	-	rs140522593		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149358395_149358396delAA								LOC388692 (66653 upstream) : FCGR1C (10898 downstream)																							AATTTTCCCCAAAGAGGACCTG	0.327													3	3	---	---	---	---	
UBAP2L	9898	broad.mit.edu	37	1	154227047	154227049	+	Intron	DEL	TTG	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154227047_154227049delTTG	uc001fep.3	+						UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc010pen.1_Intron|UBAP2L_uc001feq.2_5'Flank|UBAP2L_uc001fer.2_5'Flank	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGTTTTAGGTTTGGGGTGTCTTC	0.419													4	3	---	---	---	---	
ARHGEF2	9181	broad.mit.edu	37	1	155924927	155924927	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155924927delT	uc001fmt.2	-						ARHGEF2_uc001fmr.2_Intron|ARHGEF2_uc001fms.2_Intron|ARHGEF2_uc001fmu.2_Intron	NM_001162383	NP_001155855	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor 2						actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					Cttttctttcttttttttttg	0.219													5	3	---	---	---	---	
FMO9P	116123	broad.mit.edu	37	1	166578761	166578761	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166578761delT	uc010pld.1	+							NR_002925				Homo sapiens flavin containing monooxygenase 9 pseudogene, mRNA (cDNA clone IMAGE:3997249).												0						cgtcagagcattttctaaagg	0.000													4	2	---	---	---	---	
C1orf112	55732	broad.mit.edu	37	1	169795996	169796000	+	Intron	DEL	GTTTA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169795996_169796000delGTTTA	uc001ggp.2	+						C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggq.2_Intron|C1orf112_uc009wvt.2_Intron|C1orf112_uc010plu.1_Intron|C1orf112_uc009wvu.1_Intron|C1orf112_uc001ggr.2_Intron|C1orf112_uc010plv.1_Intron	NM_018186	NP_060656	Q9NSG2	CA112_HUMAN	hypothetical protein LOC55732												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TTATGGCTATGTTTAGTTTAGAGAT	0.234													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	175730005	175730005	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175730005delA								TNR (17253 upstream) : RFWD2 (183962 downstream)																							ccctcaccctaaggcccagca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	182609219	182609220	+	IGR	DEL	TC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182609219_182609220delTC								RGS16 (35671 upstream) : RGS8 (6572 downstream)																							ATCTCTTCTGTCTCTCTCTCTC	0.371													4	2	---	---	---	---	
IGFN1	91156	broad.mit.edu	37	1	201169062	201169062	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201169062delT	uc001gwb.2	+											Homo sapiens eEF1A2 binding protein mRNA, complete cds.											ovary(2)|pancreas(1)	3						AATGATGTACTTTTTTTTTTT	0.229													4	2	---	---	---	---	
PPP1R12B	4660	broad.mit.edu	37	1	202436349	202436349	+	Intron	DEL	T	-	-	rs76794254		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202436349delT	uc001gya.1	+						PPP1R12B_uc001gxz.1_Intron|PPP1R12B_uc001gyb.1_Intron|PPP1R12B_uc001gyc.1_Intron	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			TGTCTCTCTCTTTtttttttt	0.214													3	3	---	---	---	---	
KLHL12	59349	broad.mit.edu	37	1	202861464	202861466	+	3'UTR	DEL	CTG	-	-	rs35443455		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202861464_202861466delCTG	uc001gyo.1	-	12					KLHL12_uc001gym.1_3'UTR|KLHL12_uc001gyn.1_3'UTR|KLHL12_uc010pqc.1_3'UTR	NM_021633	NP_067646	Q53G59	KLH12_HUMAN	kelch-like 12						Wnt receptor signaling pathway		protein binding				0			BRCA - Breast invasive adenocarcinoma(75;0.166)			CCTGGAATATCTGTTACCCACCC	0.473													4	2	---	---	---	---	
CNTN2	6900	broad.mit.edu	37	1	205043281	205043281	+	3'UTR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205043281delG	uc001hbr.2	+	23					CNTN2_uc001hbs.2_3'UTR	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor						axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TCCTAGGCCCGGCAGGAACAC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209552776	209552777	+	IGR	INS	-	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209552776_209552777insT								None (None upstream) : LOC642587 (49391 downstream)																							taacaggaatgttcatcctctg	0.158													4	2	---	---	---	---	
SLC30A10	55532	broad.mit.edu	37	1	219883480	219883481	+	Intron	DEL	AC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219883480_219883481delAC	uc001hlu.1	-									Q6XR72	ZNT10_HUMAN	Synthetic construct DNA, clone: pF1KB7405, Homo sapiens SLC30A10 gene for solute carrier family 30, member 10, without stop codon, in Flexi system.						zinc ion transport	integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)		aggattgacaacaagagaaatg	0.025													4	2	---	---	---	---	
PARP1	142	broad.mit.edu	37	1	226561658	226561658	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226561658delA	uc001hqd.3	-							NM_001618	NP_001609	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase family, member 1						cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nuclear envelope|nucleolus|transcription factor complex	DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding			lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1)	10	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		tctgtctcagaaaaaaagtac	0.214								Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					4	2	---	---	---	---	
NUP133	55746	broad.mit.edu	37	1	229602743	229602744	+	Intron	INS	-	TTTA	TTTA	rs145850949	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229602743_229602744insTTTA	uc001htn.2	-							NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TTACTGAGATTTTTAAGCGATG	0.317													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	233020093	233020093	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233020093delA								KIAA1383 (74001 upstream) : C1orf57 (66277 downstream)																							gggtgggaggaagctctatag	0.114													4	2	---	---	---	---	
SNTG2	54221	broad.mit.edu	37	2	1243959	1243960	+	Intron	DEL	TC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1243959_1243960delTC	uc002qwq.2	+						SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		AAAGCTTCATTCTCAGGAGGGC	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	13635414	13635415	+	IGR	INS	-	CTT	CTT	rs112268419		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13635414_13635415insCTT								TRIB2 (752558 upstream) : None (None downstream)																							AACACACACACCTCCTTATAGC	0.386													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	17601183	17601183	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17601183delT								FAM49A (754087 upstream) : RAD51AP2 (90803 downstream)																							atggtggttatttttttaccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	24650926	24650926	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24650926delT								ITSN2 (67529 upstream) : NCOA1 (136253 downstream)																							tgtcacatccttagagaagct	0.000													4	2	---	---	---	---	
PPM1G	5496	broad.mit.edu	37	2	27608334	27608334	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27608334delA	uc002rkl.2	-						PPM1G_uc002rkm.2_5'UTR	NM_002707	NP_002698	O15355	PPM1G_HUMAN	protein phosphatase 1G						cell cycle arrest|protein dephosphorylation	cytoplasm|nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					TCTTGAGGGGAAAAAAAAGCA	0.423													4	2	---	---	---	---	
LTBP1	4052	broad.mit.edu	37	2	33482145	33482145	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33482145delA	uc002ros.2	+						LTBP1_uc002rot.2_Intron|LTBP1_uc002rou.2_Intron|LTBP1_uc002rov.2_Intron|LTBP1_uc010ymz.1_Intron|LTBP1_uc010yna.1_Intron	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AATGTTTAGTAAAAAAAAAGT	0.234													4	3	---	---	---	---	
STRN	6801	broad.mit.edu	37	2	37120836	37120837	+	Intron	INS	-	T	T	rs10597051		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37120836_37120837insT	uc002rpn.2	-						STRN_uc010ezx.2_Intron	NM_003162	NP_003153	O43815	STRN_HUMAN	striatin, calmodulin binding protein						dendrite development|locomotory behavior|negative regulation of cell proliferation|tight junction assembly|Wnt receptor signaling pathway	cytoplasm|dendritic spine|neuronal cell body|postsynaptic density|postsynaptic membrane|tight junction	armadillo repeat domain binding|calmodulin binding|estrogen receptor binding|protein complex binding|protein phosphatase 2A binding			skin(1)	1		Ovarian(717;0.0129)|all_hematologic(82;0.21)				TATTGTTGTTGTTTTTTTTTCT	0.297													4	2	---	---	---	---	
CCDC75	253635	broad.mit.edu	37	2	37323065	37323065	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37323065delT	uc010ezz.2	+						CCDC75_uc002rpr.3_Intron	NM_174931	NP_777591	Q8N954	CCD75_HUMAN	coiled-coil domain containing 75							intracellular	nucleic acid binding				0		all_hematologic(82;0.21)				AATCCATTCCTTTTTTTTTCC	0.318													3	3	---	---	---	---	
C2orf56	55471	broad.mit.edu	37	2	37462402	37462403	+	Intron	INS	-	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37462402_37462403insA	uc002rqa.3	+						C2orf56_uc010ynj.1_Intron|C2orf56_uc002rqc.3_Intron|C2orf56_uc010ynk.1_Intron|C2orf56_uc010ynl.1_Intron	NM_144736	NP_653337	Q7L592	MIDA_HUMAN	hypothetical protein LOC55471 isoform 1						mitochondrial respiratory chain complex I assembly	mitochondrion	enzyme binding|methyltransferase activity			central_nervous_system(1)	1		all_hematologic(82;0.21)				AGGCTAATAAGAAAAAAAAAAA	0.119													3	5	---	---	---	---	
KCNG3	170850	broad.mit.edu	37	2	42717724	42717724	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42717724delC	uc002rsn.2	-						KCNG3_uc002rsm.2_Intron	NM_133329	NP_579875	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G,							endoplasmic reticulum|voltage-gated potassium channel complex	protein binding			central_nervous_system(1)	1						GATTCCTACACCACCAACTTG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43147662	43147662	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43147662delC								HAAO (127911 upstream) : ZFP36L2 (301880 downstream)																							GATGGCAGAGCCCACCGGACC	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45369594	45369594	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45369594delC								SIX2 (133051 upstream) : SRBD1 (246226 downstream)																							TACATGAACTCCAGAACCTTC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	48488499	48488500	+	IGR	INS	-	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48488499_48488500insT								FBXO11 (355685 upstream) : FOXN2 (53295 downstream)																							cctgtgtgtaatcccctgttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49519036	49519039	+	IGR	DEL	TTCG	-	-	rs3034026		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49519036_49519039delTTCG								FSHR (137406 upstream) : NRXN1 (626605 downstream)																							actaactagattcgttcgtcagtg	0.000													4	4	---	---	---	---	
SERTAD2	9792	broad.mit.edu	37	2	64868782	64868783	+	Intron	DEL	GT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64868782_64868783delGT	uc002sde.1	-							NM_014755	NP_055570	Q14140	SRTD2_HUMAN	SERTA domain containing 2						negative regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleus					0						ACAGAGCCAGGTGTGTGTGTGT	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	66961251	66961252	+	IGR	DEL	TG	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66961251_66961252delTG								MEIS1 (161361 upstream) : ETAA1 (663190 downstream)																							ACAGTAGTTTTGTGTGTGTGTG	0.401													4	2	---	---	---	---	
ANTXR1	84168	broad.mit.edu	37	2	69354796	69354796	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69354796delG	uc002sfg.2	+						ANTXR1_uc002sfe.2_Intron|ANTXR1_uc002sff.2_Intron	NM_032208	NP_115584	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1 isoform 1 precursor						actin cytoskeleton reorganization|substrate adhesion-dependent cell spreading	filopodium membrane|integral to membrane|lamellipodium membrane	actin filament binding|collagen binding|metal ion binding|protein binding|transmembrane receptor activity			ovary(2)|skin(2)	4						ggttgaatcaggggagggcaa	0.000									Familial_Infantile_Hemangioma				4	2	---	---	---	---	
SLC4A5	57835	broad.mit.edu	37	2	74487059	74487059	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74487059delG	uc002sko.1	-						SLC4A5_uc002skl.2_Intron|SLC4A5_uc002skn.2_Intron|SLC4A5_uc010ffc.1_Intron|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a							apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	9						tcaccaGGCTGTCTACTCTGG	0.284													4	3	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	80224853	80224854	+	Intron	INS	-	CT	CT			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80224853_80224854insCT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						AGTTTGCTGGACTCTCCTCTTC	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	84502007	84502007	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84502007delA								None (None upstream) : FUNDC2P2 (15799 downstream)																							AGAGAAAGAGAAAGGGAAGGA	0.428													4	2	---	---	---	---	
EIF2AK3	9451	broad.mit.edu	37	2	88861515	88861515	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88861515delC	uc002stc.3	-							NM_004836	NP_004827	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha						activation of caspase activity|bone mineralization|calcium-mediated signaling|chondrocyte development|endocrine pancreas development|endoplasmic reticulum organization|endoplasmic reticulum unfolded protein response|ER overload response|insulin secretion|insulin-like growth factor receptor signaling pathway|negative regulation of myelination|negative regulation of translational initiation in response to stress|protein autophosphorylation|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|identical protein binding			ovary(3)	3						CCTTGTGGTTCCCCTAGATTT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92187157	92187157	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92187157delA								FKSG73 (56663 upstream) : None (None downstream)																							TCTAGTAATGAAAAAAaaaac	0.164													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96526347	96526348	+	Intron	INS	-	AA	AA	rs146912162	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96526347_96526348insAA	uc002sva.1	-						uc002suz.1_Intron|uc002svb.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		atacattaaactgattttcaac	0.035													6	4	---	---	---	---	
ACTR1B	10120	broad.mit.edu	37	2	98280699	98280699	+	5'Flank	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98280699delA	uc002syb.2	-							NM_005735	NP_005726	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B,							centrosome|dynactin complex	ATP binding|protein binding			skin(1)	1						GCTCCGTCTTAAAGGGGACGC	0.627													4	2	---	---	---	---	
RFX8	731220	broad.mit.edu	37	2	102026853	102026854	+	Intron	INS	-	CACA	CACA	rs5832964		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102026853_102026854insCACA	uc010yvx.1	-						RFX8_uc002tbb.1_Intron	NM_001145664	NP_001139136	Q6ZV50	RFX8_HUMAN	regulatory factor X, 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0						atgcccacactcacacacacac	0.213													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	104016001	104016001	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104016001delA								TMEM182 (581865 upstream) : None (None downstream)																							CTCTTTCTCTAAAAAAAAGAC	0.299													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133054043	133054043	+	IGR	DEL	A	-	-	rs112881670		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133054043delA								NCRNA00164 (38501 upstream) : GPR39 (120104 downstream)																							tcaacttaggaacttggttaa	0.000													4	3	---	---	---	---	
LYPD6	130574	broad.mit.edu	37	2	150255613	150255613	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150255613delA	uc002twy.2	+						LYPD6_uc010fnt.2_Intron|LYPD6_uc002twz.2_Intron|LYPD6_uc002txa.2_Intron	NM_194317	NP_919298	Q86Y78	LYPD6_HUMAN	LY6/PLAUR domain containing 6 precursor							extracellular region					0				BRCA - Breast invasive adenocarcinoma(221;0.0667)		GGAAGGTGTTAAAAAAAAAAT	0.303													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	157587601	157587601	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157587601delA								GPD2 (117354 upstream) : GALNT5 (526739 downstream)																							caggtggaggaaaaaaggcac	0.000													4	2	---	---	---	---	
LY75	4065	broad.mit.edu	37	2	160691876	160691878	+	Intron	DEL	GAC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160691876_160691878delGAC	uc002ubc.3	-						LY75_uc002ubb.3_Intron|LY75_uc010fos.2_Intron	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		AAAAAGACATGACTATAATTTCT	0.251													12	10	---	---	---	---	
LY75	4065	broad.mit.edu	37	2	160691880	160691880	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160691880delA	uc002ubc.3	-						LY75_uc002ubb.3_Intron|LY75_uc010fos.2_Intron	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		AGACATGACTATAATTTCTTC	0.254													16	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181710094	181710095	+	IGR	DEL	AA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181710094_181710095delAA								CWC22 (838254 upstream) : UBE2E3 (135017 downstream)																							aagacagaagaaagagggggtg	0.000													4	2	---	---	---	---	
ALS2	57679	broad.mit.edu	37	2	202625340	202625340	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202625340delA	uc002uyo.2	-						ALS2_uc002uyp.3_Intron|ALS2_uc002uyq.2_Intron|ALS2_uc002uyr.2_3'UTR	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1						cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						TACTAGCAAGAAAAAAAAATG	0.313													6	3	---	---	---	---	
CD28	940	broad.mit.edu	37	2	204571164	204571164	+	5'Flank	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204571164delA	uc002vah.3	+						CD28_uc002vag.1_5'Flank|CD28_uc010zio.1_5'Flank|CD28_uc010ftx.2_5'Flank|CD28_uc002vaj.3_5'Flank	NM_006139	NP_006130	P10747	CD28_HUMAN	CD28 antigen precursor						cell surface receptor linked signaling pathway|cytokine biosynthetic process|humoral immune response|positive regulation of anti-apoptosis|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation of translation|positive regulation of viral genome replication|regulation of defense response to virus by virus|regulatory T cell differentiation|T cell costimulation|viral reproduction	cytosol|external side of plasma membrane|integral to plasma membrane	coreceptor activity|protease binding|SH3/SH2 adaptor activity				0						TTTCAGTGACAAAAAAAAAGT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221753581	221753582	+	IGR	DEL	TC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221753581_221753582delTC								None (None upstream) : EPHA4 (529167 downstream)																							acttgaaacttctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	222895636	222895637	+	IGR	DEL	GA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222895636_222895637delGA								EPHA4 (456714 upstream) : PAX3 (168970 downstream)																							ctgctcctctgagagtctgttc	0.000													4	2	---	---	---	---	
FARSB	10056	broad.mit.edu	37	2	223505808	223505808	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223505808delA	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	aaaaaaaaacaaaaaaaaaaa	0.045													9	7	---	---	---	---	
IQCA1	79781	broad.mit.edu	37	2	237349397	237349397	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237349397delG	uc002vvz.1	-						IQCA1_uc002vwb.2_Intron|IQCA1_uc002vwa.1_Intron|IQCA1_uc010zni.1_Intron	NM_024726	NP_079002	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1								ATP binding			ovary(1)	1						GAGGGAAGCTGGGACCAGAAC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	237726572	237726572	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237726572delG								CXCR7 (235580 upstream) : COPS8 (267512 downstream)																							TGAGTGGGATGGGAGGATTCC	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239484977	239484978	+	IGR	INS	-	C	C	rs146984030	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239484977_239484978insC								ASB1 (124087 upstream) : TWIST2 (271695 downstream)																							cttcaaggacaccccccaccgc	0.000													2	5	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	239974955	239974955	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239974955delG	uc002vyk.3	-						HDAC4_uc010fyy.2_Intron	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		TGGCCTGGCAGCCCCGGGTCC	0.617													15	7	---	---	---	---	
ZNF385D	79750	broad.mit.edu	37	3	21575894	21575895	+	Intron	DEL	CA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21575894_21575895delCA	uc003cce.2	-						ZNF385D_uc010hfb.1_Intron	NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5						TAATCGCCACCACACACACACA	0.386													8	5	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41795894	41795895	+	Frame_Shift_Ins	INS	-	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41795894_41795895insA	uc003ckv.3	-	22	2480_2481	c.2279_2280insT	c.(2278-2280)TTGfs	p.L760fs		NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4	760							ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		GGTTATAAATCAAAATATATAG	0.381													136	160	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52623124	52623124	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52623124delT	uc003des.2	-	18	2939	c.2927delA	c.(2926-2928)CATfs	p.H976fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.H976fs|PBRM1_uc003der.2_Frame_Shift_Del_p.H944fs|PBRM1_uc003det.2_Frame_Shift_Del_p.H991fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.H991fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.H976fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.H976fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.H976fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.H975fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.H888fs|PBRM1_uc003dfa.1_Frame_Shift_Del_p.H322fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	976	BAH 1.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		ACAGACGATATGTGGTTGTAG	0.418			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								85	93	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75995347	75995347	+	IGR	DEL	G	-	-	rs113471147		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75995347delG								ZNF717 (160677 upstream) : None (None downstream)																							AAATGCTGAAGACACAAAATG	0.328													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	99525674	99525674	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99525674delC								COL8A1 (10516 upstream) : C3orf26 (11007 downstream)																							GACAAAAGTTCTTAGCTATCT	0.289													4	2	---	---	---	---	
PDIA5	10954	broad.mit.edu	37	3	122829997	122829997	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122829997delT	uc003egc.1	+						PDIA5_uc003egd.1_Intron	NM_006810	NP_006801	Q14554	PDIA5_HUMAN	protein disulfide isomerase A5 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding|response to stress	endoplasmic reticulum lumen	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0427)		TCTGCGCCTCTTTTCCTTCAT	0.557													40	21	---	---	---	---	
PTPLB	201562	broad.mit.edu	37	3	123262268	123262268	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123262268delA	uc003egj.2	-							NM_198402	NP_940684	Q6Y1H2	HACD2_HUMAN	protein tyrosine phosphatase-like (proline						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	lyase activity|protein binding			kidney(1)	1				GBM - Glioblastoma multiforme(114;0.1)		ggaaagaatcaaAGTAAAAAA	0.264													2	4	---	---	---	---	
SLC12A8	84561	broad.mit.edu	37	3	124894600	124894601	+	Intron	INS	-	A	A	rs138567022		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124894600_124894601insA	uc003ehv.3	-						SLC12A8_uc003ehw.3_Intron|SLC12A8_uc010hrz.1_Intron	NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8						potassium ion transport	integral to membrane	symporter activity				0						ACATGGCCAGGAAAAAAAAAAA	0.347													6	3	---	---	---	---	
RAB7A	7879	broad.mit.edu	37	3	128532447	128532448	+	3'UTR	DEL	CA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128532447_128532448delCA	uc003eks.1	+	6					RAB7A_uc010hsv.1_3'UTR|RAB7A_uc003ekt.2_Frame_Shift_Del_p.H194fs	NM_004637	NP_004628	P51149	RAB7A_HUMAN	RAB7, member RAS oncogene family						endocytosis|endosome to lysosome transport|epidermal growth factor catabolic process|protein transport|small GTPase mediated signal transduction	Golgi apparatus|late endosome|lysosome|melanosome|phagocytic vesicle	GDP binding|GTP binding|GTPase activity|protein binding				0				GBM - Glioblastoma multiforme(114;0.231)		cacacacacgcacacacacaca	0.426													6	3	---	---	---	---	
CLRN1OS	116933	broad.mit.edu	37	3	150599639	150599639	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150599639delT	uc011bny.1	+											Homo sapiens usher critical region protein (UCRP) pseudogene mRNA, complete sequence.												0						TCAGACACTATTTTTTTGATG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152495269	152495271	+	IGR	DEL	TTC	-	-	rs10576161		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152495269_152495271delTTC								MBNL1 (311701 upstream) : P2RY1 (57465 downstream)																							GCTGCTGCTTTTCTTGTTTCTCC	0.345													6	3	---	---	---	---	
VEPH1	79674	broad.mit.edu	37	3	157211868	157211868	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157211868delA	uc003fbj.1	-						VEPH1_uc003fbk.1_Intron|VEPH1_uc010hvu.1_Intron|VEPH1_uc003fbm.2_Intron|VEPH1_uc003fbn.2_Intron	NM_024621	NP_078897	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain homolog 1							plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			AATTGCCATCAAAGACATTAC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157356732	157356732	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157356732delA								C3orf55 (37713 upstream) : SHOX2 (457069 downstream)																							TCTATTGCAGAAAAAaaaaat	0.179													4	2	---	---	---	---	
PLD1	5337	broad.mit.edu	37	3	171456105	171456105	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171456105delA	uc003fhs.2	-						PLD1_uc003fht.2_Intron	NM_002662	NP_002653	Q13393	PLD1_HUMAN	phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	aaaaaaaaagaaaaaaaaaaG	0.274													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	171740471	171740471	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171740471delT								TMEM212 (163363 upstream) : FNDC3B (16947 downstream)																							TGCCTCACTGTTGTGTAGTGG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181222925	181222925	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181222925delC								DNAJC19 (515395 upstream) : SOX2OT (58584 downstream)																							AGATATGGGACCCAGGACAAT	0.438													4	2	---	---	---	---	
ST6GAL1	6480	broad.mit.edu	37	3	186759808	186759809	+	Intron	INS	-	TA	TA	rs56119830	byFrequency	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186759808_186759809insTA	uc003frb.2	+						ST6GAL1_uc003frc.2_Intron|ST6GAL1_uc003frd.2_Intron	NM_173216	NP_775323	P15907	SIAT1_HUMAN	ST6 beta-galactosamide						humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		CTGCACAAAACTGTGGTGGAGA	0.480													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3621168	3621168	+	IGR	DEL	G	-	-	rs11339032		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3621168delG								LRPAP1 (86944 upstream) : ADRA2C (146907 downstream)																							catttacactgaagattttac	0.159													4	4	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7719044	7719044	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7719044delC	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						cccagggatgccccagccagc	0.000													4	2	---	---	---	---	
SH3TC1	54436	broad.mit.edu	37	4	8242813	8242814	+	3'UTR	INS	-	T	T	rs148038345	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8242813_8242814insT	uc003gkv.3	+	18					SH3TC1_uc003gkw.3_3'UTR|SH3TC1_uc003gkx.3_RNA|SH3TC1_uc003gky.2_RNA	NM_018986	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1								binding			large_intestine(2)|pancreas(1)	3						AATGGGTTTTGTTTTTTTTTTG	0.550													4	2	---	---	---	---	
ANAPC4	29945	broad.mit.edu	37	4	25418397	25418397	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25418397delT	uc003gro.2	+						ANAPC4_uc003grp.2_Intron|ANAPC4_uc003grq.2_Intron	NM_013367	NP_037499	Q9UJX5	APC4_HUMAN	anaphase-promoting complex subunit 4						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5		Breast(46;0.0503)				CCTTAATAGCTTTTTTTGTCC	0.363													4	2	---	---	---	---	
SLC34A2	10568	broad.mit.edu	37	4	25664605	25664605	+	Intron	DEL	T	-	-	rs34583336		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25664605delT	uc003grr.2	+						SLC34A2_uc003grs.2_Intron|SLC34A2_uc010iev.2_Intron	NM_006424	NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (sodium phosphate),						cellular phosphate ion homeostasis	apical plasma membrane|brush border membrane|integral to plasma membrane	phosphate binding|sodium ion binding|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			skin(3)|ovary(1)|kidney(1)	5		Breast(46;0.0503)				CCCTCTCATCttttttttttt	0.269													5	3	---	---	---	---	
LIAS	11019	broad.mit.edu	37	4	39472556	39472557	+	Intron	INS	-	CAAA	CAAA	rs139815066	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39472556_39472557insCAAA	uc003guf.2	+						LIAS_uc003gug.2_Intron|LIAS_uc003guh.2_Intron	NM_006859	NP_006850	O43766	LIAS_HUMAN	lipoic acid synthetase isoform 1 precursor						inflammatory response|response to lipopolysaccharide|response to oxidative stress	mitochondrion	4 iron, 4 sulfur cluster binding|lipoate synthase activity|metal ion binding				0					Lipoic Acid(DB00166)	ACCTTTTCTACCAGACTCCTAC	0.351													4	3	---	---	---	---	
APBB2	323	broad.mit.edu	37	4	40895623	40895623	+	Intron	DEL	A	-	-	rs10714456		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40895623delA	uc003gvl.2	-						APBB2_uc010ifu.2_Intron|APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron|APBB2_uc011byt.1_Intron	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						tttgctatttaaaaaaatgta	0.060													3	4	---	---	---	---	
SCFD2	152579	broad.mit.edu	37	4	53750600	53750600	+	Intron	DEL	C	-	-	rs11322100		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53750600delC	uc003gzu.2	-						SCFD2_uc010igm.2_Intron	NM_152540	NP_689753	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2						protein transport|vesicle docking involved in exocytosis					ovary(2)|pancreas(1)	3			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			gggaagacatccccaggctct	0.065													4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54867492	54867492	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54867492delT	uc003haa.2	+							NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	AATACTTGGGTTTTTTTGGTA	0.388			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
MRPL1	65008	broad.mit.edu	37	4	78815092	78815092	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78815092delG	uc003hku.2	+						MRPL1_uc010iji.1_Intron	NM_020236	NP_064621	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1 precursor								RNA binding				0						TTAAGGATGTGGCTGTTTTTA	0.318													4	2	---	---	---	---	
WDFY3	23001	broad.mit.edu	37	4	85869975	85869975	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85869975delC	uc003hpd.2	-							NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AATTCCCAATCCCAAGGACTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	104420515	104420515	+	IGR	DEL	C	-	-	rs67789270		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104420515delC								CENPE (300949 upstream) : TACR3 (90110 downstream)																							ctccagtcctccagtccaacc	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	104420518	104420520	+	IGR	DEL	GTC	-	-	rs34116296		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104420518_104420520delGTC								CENPE (300952 upstream) : TACR3 (90105 downstream)																							cagtcctccagtccaaccaacat	0.099													4	2	---	---	---	---	
NPNT	255743	broad.mit.edu	37	4	106819448	106819449	+	Intron	DEL	TC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106819448_106819449delTC	uc003hya.2	+						NPNT_uc011cfc.1_Intron|NPNT_uc011cfd.1_Intron|NPNT_uc011cfe.1_Intron|NPNT_uc010ilt.1_Intron|NPNT_uc011cff.1_Intron|NPNT_uc010ilu.1_Intron	NM_001033047	NP_001028219	Q6UXI9	NPNT_HUMAN	nephronectin precursor						cell differentiation	membrane	calcium ion binding			skin(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		CAGGTTTATTtctctctctctc	0.243													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	122645680	122645680	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122645680delA								ANXA5 (27533 upstream) : TMEM155 (34405 downstream)																							TAATTGACCCACCAACAAATA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	124399130	124399131	+	IGR	DEL	GA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124399130_124399131delGA								SPRY1 (74223 upstream) : LOC285419 (172291 downstream)																							CCTGTGACGTGAAGAAGTGGTG	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	148521452	148521452	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148521452delC								EDNRA (55346 upstream) : TMEM184C (17087 downstream)																							TCTCTTCATGCCCAGTCCAAT	0.517													4	2	---	---	---	---	
C4orf45	152940	broad.mit.edu	37	4	159943014	159943014	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159943014delG	uc003iqf.1	-						C4orf45_uc010iqt.1_Intron	NM_152543	NP_689756	Q96LM5	CD045_HUMAN	hypothetical protein LOC152940												0						ATCCTGGTGAGGGGTGGTGAT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190200905	190200906	+	IGR	INS	-	A	A	rs113873531		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190200905_190200906insA								None (None upstream) : FRG1 (661068 downstream)																							agcatgaacttagagtaatcaa	0.139													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190565126	190565126	+	IGR	DEL	A	-	-	rs71876512		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190565126delA								None (None upstream) : FRG1 (296848 downstream)																							ATATCAGTAGAAAAAAAAAAC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190567803	190567805	+	IGR	DEL	ACA	-	-	rs66528226		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190567803_190567805delACA								None (None upstream) : FRG1 (294169 downstream)																							CCGTCCAAACACAACAGTTGCTA	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2129071	2129071	+	IGR	DEL	T	-	-	rs33913124		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2129071delT								IRX4 (246191 upstream) : IRX2 (617210 downstream)																							TTTTTTCCAATTTTTTTTTTC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5758842	5758843	+	IGR	INS	-	TG	TG	rs582010	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5758842_5758843insTG								KIAA0947 (268505 upstream) : FLJ33360 (551711 downstream)																							ATAGTGgtgtctgtgtgtgtgt	0.099													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8936128	8936129	+	IGR	INS	-	A	A	rs139717069	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8936128_8936129insA								None (None upstream) : SEMA5A (99009 downstream)																							gctgccctatcaaatacttacc	0.000													1	5	---	---	---	---	
FAM105B	90268	broad.mit.edu	37	5	14691277	14691277	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14691277delT	uc003jfk.2	+							NM_138348	NP_612357	Q96BN8	F105B_HUMAN	hypothetical protein LOC90268											ovary(2)	2	Lung NSC(4;0.00696)					CTTAATGAGGTTTTTTTTATT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	15155708	15155708	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15155708delG								ANKH (283821 upstream) : FBXL7 (344597 downstream)																							tggggcatccgctcagcacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	15488643	15488643	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15488643delC								ANKH (616756 upstream) : FBXL7 (11662 downstream)																							aggaagttctcttagcagcaa	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	15488646	15488648	+	IGR	DEL	AGC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15488646_15488648delAGC								ANKH (616759 upstream) : FBXL7 (11657 downstream)																							aagttctcttagcagcaattact	0.133													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23966114	23966114	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23966114delC	uc003jgq.1	+											Homo sapiens cDNA FLJ34836 fis, clone NT2NE2010400.																		cgtgagaacaccatctgccca	0.000													4	2	---	---	---	---	
GOLPH3	64083	broad.mit.edu	37	5	32135385	32135386	+	Intron	DEL	AC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32135385_32135386delAC	uc003jhp.1	-							NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3						cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1						ggggtttgttaccaccacagct	0.119													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	52449190	52449190	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52449190delC								MOCS2 (43592 upstream) : FST (327405 downstream)																							AGGCTCCAGACCCATACATCT	0.333													4	2	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59284181	59284181	+	3'UTR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59284181delT	uc003jse.1	-	5					PDE4D_uc003jsb.2_Intron|PDE4D_uc010iwj.1_3'UTR			Q08499	PDE4D_HUMAN	Homo sapiens cAMP-specific phosphodiesterase PDE4D7 (PDE4D) mRNA, complete cds; alternatively spliced.						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	AAATTCATCCTTTTTTTTTTG	0.348													11	7	---	---	---	---	
IPO11	51194	broad.mit.edu	37	5	61779326	61779326	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61779326delG	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtb.1_Intron	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2							cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		GCCATTTTTTGTAGCACAAAT	0.313													4	2	---	---	---	---	
IPO11	51194	broad.mit.edu	37	5	61779329	61779329	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61779329delG	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtb.1_Intron	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2							cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		ATTTTTTGTAGCACAAATTGG	0.313													4	2	---	---	---	---	
ADAMTS6	11174	broad.mit.edu	37	5	64520557	64520558	+	Intron	DEL	AG	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64520557_64520558delAG	uc003jtp.2	-						ADAMTS6_uc003jto.2_Intron|ADAMTS6_uc003jtq.2_Intron|ADAMTS6_uc003jtr.1_Intron	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		GAAGTTAAGTAGAGAGAGAGAA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	71949013	71949014	+	IGR	DEL	TG	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71949013_71949014delTG								ZNF366 (145764 upstream) : TNPO1 (163404 downstream)																							GTCAGTCCTCTGTGTGTGTGTG	0.351													4	2	---	---	---	---	
SV2C	22987	broad.mit.edu	37	5	75396932	75396932	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75396932delG	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)		TCTTGTGAATGGGGGTGCAGA	0.498													4	2	---	---	---	---	
JMY	133746	broad.mit.edu	37	5	78608021	78608021	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78608021delT	uc003kfx.3	+						JMY_uc003kfw.1_Intron	NM_152405	NP_689618	Q8N9B5	JMY_HUMAN	junction-mediating and regulatory protein						'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		ACTAAAACTGTGTATTAAAAA	0.164													6	3	---	---	---	---	
ZFYVE16	9765	broad.mit.edu	37	5	79746634	79746634	+	Intron	DEL	T	-	-	rs72398531		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79746634delT	uc003kgr.3	+						ZFYVE16_uc003kgp.2_Intron|ZFYVE16_uc003kgq.3_Intron|ZFYVE16_uc003kgs.3_Intron|ZFYVE16_uc003kgt.3_Intron	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16						BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		CTTATATCCAttttttttttt	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	84986441	84986442	+	IGR	INS	-	C	C	rs141469447	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84986441_84986442insC								None (None upstream) : NBPF22P (591820 downstream)																							AGTCAGTGTCACCACCTTCTGT	0.218													3	4	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	90164781	90164781	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90164781delC	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TCCAGCAGTTCGACCACTTCC	0.378													4	2	---	---	---	---	
FLJ42709	441094	broad.mit.edu	37	5	92879248	92879248	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92879248delA	uc003kkc.2	-						FLJ42709_uc003kkd.2_Intron|FLJ42709_uc011cud.1_Intron|FLJ42709_uc003kke.2_Intron|FLJ42709_uc011cue.1_Intron|FLJ42709_uc010jbb.1_Intron|FLJ42709_uc003kkf.2_Intron|FLJ42709_uc003kkg.2_Intron|FLJ42709_uc010jbc.2_RNA|FLJ42709_uc003kki.2_RNA|FLJ42709_uc003kkh.2_RNA					Homo sapiens cDNA FLJ38400 fis, clone FEBRA2008159.												0						ggcagataagaaaaaaaaaat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	98340057	98340057	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98340057delA								CHD1 (77819 upstream) : None (None downstream)																							tgattaagacaaaaaaaaatt	0.040													11	5	---	---	---	---	
TMEM232	642987	broad.mit.edu	37	5	109953890	109953890	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109953890delA	uc011cvh.1	-						TMEM232_uc003kow.1_Intron|TMEM232_uc003kox.2_Intron|TMEM232_uc010jbs.2_Intron|TMEM232_uc003koy.3_Intron			C9JQI7	TM232_HUMAN	SubName: Full=cDNA FLJ54480;							integral to membrane					0						TGCATTTAATAAAAAAAAAAC	0.294													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	110402145	110402146	+	IGR	DEL	TG	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110402145_110402146delTG								SLC25A46 (303663 upstream) : TSLP (3632 downstream)																							GATGGCTGCATGTGATGACATC	0.292													4	2	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112371511	112371511	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112371511delA	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ACTTTATTGGAAAAAAAATCT	0.378													4	2	---	---	---	---	
COMMD10	51397	broad.mit.edu	37	5	115627846	115627847	+	Intron	INS	-	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115627846_115627847insA	uc003krt.1	+							NM_016144	NP_057228	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)		catgtctcattAAAAAAAAAAT	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	115717850	115717850	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115717850delT								COMMD10 (88872 upstream) : SEMA6A (61402 downstream)																							CAAAGCACACTTTTATAGAGC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	125572736	125572736	+	IGR	DEL	T	-	-	rs113144340		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125572736delT								None (None upstream) : GRAMD3 (123052 downstream)																							TTTCCCCCCCTCTCATTCTTG	0.373													4	3	---	---	---	---	
C5orf48	389320	broad.mit.edu	37	5	125971527	125971528	+	Intron	DEL	TA	-	-	rs142814403	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125971527_125971528delTA	uc003kub.1	+							NM_207408	NP_997291	Q6ZNM6	CE048_HUMAN	hypothetical protein LOC389320											ovary(1)	1						cctaattttttattttttgtat	0.000													3	3	---	---	---	---	
LMNB1	4001	broad.mit.edu	37	5	126114828	126114828	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126114828delT	uc003kud.1	+						LMNB1_uc003kuc.2_Intron|LMNB1_uc010jdb.1_Intron|LMNB1_uc011cxb.1_Intron	NM_005573	NP_005564	P20700	LMNB1_HUMAN	lamin B1						cellular component disassembly involved in apoptosis	lamin filament|nuclear inner membrane	protein binding|structural molecule activity			kidney(1)|central_nervous_system(1)	2		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		TGAATGTCCCTGTCCGAAGTC	0.408													4	2	---	---	---	---	
ADAMTS19	171019	broad.mit.edu	37	5	129022479	129022479	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129022479delA	uc003kvb.1	+						ADAMTS19_uc010jdh.1_Intron	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GTGAAGTTATAAGGAATTCAC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129191050	129191051	+	IGR	DEL	AT	-	-	rs138686810		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129191050_129191051delAT								ADAMTS19 (116674 upstream) : CHSY3 (49472 downstream)																							GTGGGCTCACATGTCTCCCTCA	0.322													2	4	---	---	---	---	
CCNI2	645121	broad.mit.edu	37	5	132083979	132083979	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132083979delG	uc003kxq.1	+						CCNI2_uc011cxg.1_Intron|CCNI2_uc011cxh.1_Intron	NM_001039780	NP_001034869	Q6ZMN8	CCNI2_HUMAN	cyclin I family, member 2						regulation of cyclin-dependent protein kinase activity		protein kinase binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCCTGCTGCTGGGGGACCAGG	0.657													40	42	---	---	---	---	
C5orf32	84418	broad.mit.edu	37	5	139586192	139586193	+	Intron	INS	-	TTGT	TTGT	rs139063778	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139586192_139586193insTTGT	uc003lfd.2	+						C5orf32_uc010jfi.2_Intron	NM_032412	NP_115788	Q9H1C7	CE032_HUMAN	hypothetical protein LOC84418												0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGAGCACTGttgtttgtttg	0.257													5	4	---	---	---	---	
STK32A	202374	broad.mit.edu	37	5	146652198	146652199	+	Intron	INS	-	TAA	TAA	rs146607699	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146652198_146652199insTAA	uc010jgn.1	+						STK32A_uc003lol.3_Intron|STK32A_uc003lom.2_Intron|STK32A_uc011dbw.1_Intron	NM_001112724	NP_001106195	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A isoform 1								ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAAGGATTTGTTAATGGTTGCT	0.327													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148040962	148040962	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148040962delC	uc003lpp.1	-						HTR4_uc003lpq.1_Intron	NM_024577		Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAAAGAGGGACAAGGTGAGTG	0.478													4	2	---	---	---	---	
ADAM19	8728	broad.mit.edu	37	5	156940149	156940151	+	Intron	DEL	CCA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156940149_156940151delCCA	uc003lwz.2	-						ADAM19_uc003lww.1_Intron|ADAM19_uc011ddr.1_Intron	NM_033274	NP_150377	Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19 preproprotein						proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			tTTTAAAATTCCACCAGGAAAAT	0.148													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162685109	162685109	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162685109delC								None (None upstream) : CCNG1 (179468 downstream)																							ATAAAATCTTCCCAGGTGCTA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	177625681	177625681	+	IGR	DEL	A	-	-	rs67220211		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177625681delA								GMCL1L (11248 upstream) : HNRNPAB (5827 downstream)																							actctgtctcaaaaaaaaaaa	0.234													5	3	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5564652	5564652	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5564652delT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	tacccatcccttttttttgtt	0.000													6	3	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5709776	5709776	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5709776delA	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	TCCTGGATTTAAAAAAAAAAT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	20394177	20394177	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20394177delA								MBOAT1 (181507 upstream) : E2F3 (7960 downstream)																							TCTCTCTGAGAAAAAAAAAAA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26006236	26006237	+	IGR	INS	-	T	T	rs140025187	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26006236_26006237insT								TRIM38 (20886 upstream) : HIST1H1A (11024 downstream)																							tgatacgtttgtccacttttcc	0.020													3	3	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32521545	32521546	+	Intron	INS	-	AAGG	AAGG	rs70993877		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32521545_32521546insAAGG	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obm.1_Intron|HLA-DRB6_uc003obn.1_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						TTGGGGAAAGACTTTATCCAGG	0.436													3	3	---	---	---	---	
HLA-DQA1	3117	broad.mit.edu	37	6	32605027	32605028	+	5'Flank	INS	-	ACA	ACA	rs144342006	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32605027_32605028insACA	uc003obr.2	+						HLA-DQA1_uc003obs.2_5'Flank|HLA-DQA1_uc003obt.1_5'Flank	NM_002122	NP_002113	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to plasma membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0						GAGGCTGCATCACAAGGGGATT	0.450													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	37069762	37069763	+	IGR	INS	-	G	G	rs142493476	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37069762_37069763insG								FGD2 (72917 upstream) : PIM1 (68159 downstream)																							TTAAATGATGAGCAGCTCTCTG	0.441													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	39942542	39942542	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39942542delA								MOCS1 (40288 upstream) : TDRG1 (403621 downstream)																							GTCAGCTCAGAAAAGGCAGGC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	47126067	47126068	+	IGR	INS	-	CACA	CACA	rs138582041	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47126067_47126068insCACA								GPR110 (115985 upstream) : TNFRSF21 (73201 downstream)																							acacgcgcgtgcacacacacac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50227614	50227614	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50227614delG								DEFB112 (211250 upstream) : TFAP2D (453643 downstream)																							gggtggtagtgggggacccag	0.000													4	2	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51606194	51606194	+	Intron	DEL	T	-	-	rs71894206		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51606194delT	uc003pah.1	-						PKHD1_uc010jzn.1_Intron|PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					TGTTTTTCtcttttttttttc	0.169													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57454042	57454042	+	Intron	DEL	G	-	-	rs67619850		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57454042delG	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)		ataaaagacaggatagtgtta	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57516345	57516346	+	IGR	INS	-	T	T	rs151188373		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57516345_57516346insT								PRIM2 (2970 upstream) : GUSBL2 (729813 downstream)																							TGGAAGCTGCGTTTTGGATAGG	0.406													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57567372	57567374	+	IGR	DEL	GAA	-	-	rs142174260		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57567372_57567374delGAA								PRIM2 (53997 upstream) : GUSBL2 (678785 downstream)																							ttagagattggaagagaagcaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	62007101	62007101	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62007101delA								None (None upstream) : KHDRBS2 (382764 downstream)																							tatatgttggaatttatcaaa	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85557206	85557206	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85557206delT								TBX18 (83307 upstream) : NT5E (602096 downstream)																							CTTGGAAATGTTTTTTTATTC	0.423													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	95898441	95898442	+	IGR	INS	-	G	G	rs139999796	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95898441_95898442insG								None (None upstream) : MANEA (126971 downstream)																							TGCATTCTGCTGGCCCATTCCA	0.465													4	6	---	---	---	---	
FBXL4	26235	broad.mit.edu	37	6	99357257	99357257	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99357257delC	uc003ppf.1	-						FBXL4_uc003ppg.1_Intron|FBXL4_uc003pph.1_Intron	NM_012160	NP_036292	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4						ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex				skin(2)	2		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		aattccatctcctgcagcctc	0.219											OREG0031914	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112613412	112613412	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112613412delG								LAMA4 (37584 upstream) : RFPL4B (55120 downstream)																							aaataagtgtggaactgcttt	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	116760262	116760264	+	IGR	DEL	CCT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116760262_116760264delCCT								DSE (822 upstream) : FAM26F (22292 downstream)																							ATTTACTTAACCTCACTCAACAT	0.315													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	118640203	118640203	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118640203delT								SLC35F1 (1366 upstream) : C6orf204 (146036 downstream)																							TCTCGAGTACTTTTTTTTTTC	0.299													3	4	---	---	---	---	
EYA4	2070	broad.mit.edu	37	6	133827608	133827608	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133827608delC	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron|uc003qef.1_Intron|uc003qeg.1_Intron	NM_004100	NP_004091	O95677	EYA4_HUMAN	eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		ACTCTTGGTTCTTTTAGTGTT	0.383													4	2	---	---	---	---	
AHI1	54806	broad.mit.edu	37	6	135607700	135607700	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135607700delG	uc003qgi.2	-						AHI1_uc003qgf.2_Intron|AHI1_uc003qgg.2_Intron|AHI1_uc003qgh.2_Intron|AHI1_uc003qgj.2_Intron	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a							adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		TGGCAAGAAAGGGCAATGGCT	0.512													4	2	---	---	---	---	
PEX7	5191	broad.mit.edu	37	6	137193134	137193135	+	Intron	INS	-	AC	AC	rs59254619		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137193134_137193135insAC	uc003qhd.2	+						PEX7_uc010kgx.2_Intron	NM_000288	NP_000279	O00628	PEX7_HUMAN	peroxisomal biogenesis factor 7						ether lipid biosynthetic process|protein import into peroxisome matrix	peroxisome	peroxisome matrix targeting signal-2 binding				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)		TGTAAAAATATTTTTCCTGAAG	0.282													4	2	---	---	---	---	
TNFAIP3	7128	broad.mit.edu	37	6	138196578	138196579	+	Intron	INS	-	T	T	rs140188597	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138196578_138196579insT	uc003qhr.2	+						TNFAIP3_uc003qhs.2_Intron	NM_006290	NP_006281	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3						anti-apoptosis|apoptosis|B-1 B cell homeostasis|negative regulation of B cell activation|negative regulation of bone resorption|negative regulation of CD40 signaling pathway|negative regulation of endothelial cell apoptosis|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of interleukin-2 production|negative regulation of interleukin-6 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of osteoclast proliferation|negative regulation of protein ubiquitination|negative regulation of smooth muscle cell proliferation|negative regulation of toll-like receptor 2 signaling pathway|negative regulation of toll-like receptor 3 signaling pathway|negative regulation of tumor necrosis factor production|negative regulation of type I interferon production|positive regulation of protein catabolic process|protein K48-linked ubiquitination|protein K63-linked deubiquitination|protein oligomerization|regulation of defense response to virus by host|regulation of germinal center formation|regulation of vascular wound healing|tolerance induction to lipopolysaccharide	centrosome|cytosol|nucleus	caspase inhibitor activity|DNA binding|protease binding|protein self-association|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-protein ligase activity|ubiquitin-specific protease activity|zinc ion binding	p.0?(22)		haematopoietic_and_lymphoid_tissue(133)|lung(3)|ovary(1)	137	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		CTCATCAGGGATTTTTTTTTAA	0.426			D|N|F		marginal zone B-cell lymphomas|Hodgkin's lymphoma|primary mediastinal B cell lymphoma								4	2	---	---	---	---	
NHSL1	57224	broad.mit.edu	37	6	138817193	138817193	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138817193delA	uc003qhx.2	-						NHSL1_uc011edp.1_Intron|NHSL1_uc003qhy.2_Intron	NM_020464	NP_065197	Q5SYE7	NHSL1_HUMAN	NHS-like 1 isoform 1												0						ggacacagccaaaccatatca	0.124													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	153916832	153916832	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153916832delG								RGS17 (464443 upstream) : OPRM1 (414804 downstream)																							agtcttagctgggggtgaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	158222929	158222929	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158222929delT								ZDHHC14 (127953 upstream) : SNX9 (21365 downstream)																							GATGGGACACTTTTTAAAAGA	0.478													4	2	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162551264	162551265	+	Intron	INS	-	T	T	rs146587579	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162551264_162551265insT	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						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)		CTCAGAAATCCTTTTTTGTCTT	0.416													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166146054	166146054	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166146054delC								PDE10A (70470 upstream) : C6orf176 (191482 downstream)																							CTCATCACATCCACCCTATTG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168516116	168516117	+	IGR	INS	-	CATC	CATC	rs148062873	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168516116_168516117insCATC								FRMD1 (36277 upstream) : DACT2 (191469 downstream)																							atccacctattcatccatccat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	481548	481549	+	IGR	INS	-	AGG	AGG			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:481548_481549insAGG								FAM20C (180837 upstream) : PDGFA (55350 downstream)																							AGGGGGAAGGAAGGAGGAAGAA	0.609													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1664817	1664817	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1664817delC								TFAMP1 (8490 upstream) : ELFN1 (83981 downstream)																							CCAGACCCAGCACTGCAAGGA	0.587													4	2	---	---	---	---	
EIF3B	8662	broad.mit.edu	37	7	2403011	2403024	+	Intron	DEL	TTGAGCCTGGGAGG	-	-	rs66483346		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2403011_2403024delTTGAGCCTGGGAGG	uc003slx.2	+						EIF3B_uc003sly.2_Intron|EIF3B_uc003slz.1_Intron|EIF3B_uc003sma.2_Intron	NM_003751	NP_003742	P55884	EIF3B_HUMAN	eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	nucleotide binding|protein complex scaffold|translation initiation factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		ggaggatcacttgagcctgggaggttgagcctgg	0.009													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	8002853	8002853	+	IGR	DEL	A	-	-	rs35129884		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8002853delA								RPA3 (244615 upstream) : GLCCI1 (5570 downstream)																							tctctaattcaatgctttaag	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	12839526	12839526	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12839526delA								ARL4A (108970 upstream) : None (None downstream)																							AATCTGACACAAAAACTAAAA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	19643169	19643169	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19643169delT								FERD3L (458125 upstream) : TWISTNB (91916 downstream)																							gacatcagcattttttatgtc	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25947917	25947917	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25947917delA								NPVF (679812 upstream) : MIR148A (41622 downstream)																							GTTGTTCTATAAAAACATTTC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	26651447	26651447	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26651447delA								KIAA0087 (73003 upstream) : C7orf71 (26043 downstream)																							GCCTTAAAGGAAAAAAAACCC	0.443													4	2	---	---	---	---	
DPY19L2P1	554236	broad.mit.edu	37	7	35165175	35165175	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35165175delA	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						catcatgcacaaaaaaagaaa	0.000													4	2	---	---	---	---	
SEPT7	989	broad.mit.edu	37	7	35904275	35904276	+	Intron	INS	-	TAA	TAA	rs147180013		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35904275_35904276insTAA	uc010kxc.2	+						SEPT7_uc011kat.1_Intron|SEPT7_uc011kau.1_Intron|SEPT7_uc011kav.1_Intron|SEPT7_uc003tey.2_Intron	NM_001788	NP_001779	Q16181	SEPT7_HUMAN	cell division cycle 10 isoform 1						cilium morphogenesis|cytokinesis|mitosis|protein heterooligomerization|regulation of embryonic cell shape	cilium axoneme|cleavage furrow|condensed chromosome kinetochore|midbody|nucleus|septin complex|spindle|stress fiber	GTP binding|protein binding|structural molecule activity				0						ttaaaagtggctaagaaaatta	0.079													4	2	---	---	---	---	
AOAH	313	broad.mit.edu	37	7	36654055	36654058	+	Intron	DEL	TGTT	-	-	rs5883565		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36654055_36654058delTGTT	uc003tfh.3	-						AOAH_uc010kxf.2_Intron|AOAH_uc011kba.1_Intron	NM_001637	NP_001628	P28039	AOAH_HUMAN	acyloxyacyl hydrolase precursor						inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity			skin(1)	1						tttgaatttgtgtttgttatgtga	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	45225638	45225639	+	IGR	INS	-	GCG	GCG	rs59976629		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45225638_45225639insGCG								RAMP3 (1791 upstream) : ADCY1 (388100 downstream)																							gtatgtgtgtatgtgtgtgagc	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	45977542	45977543	+	IGR	DEL	GT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45977542_45977543delGT								IGFBP3 (16671 upstream) : None (None downstream)																							GAGGAAGGTGgtgtgtgtgttt	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	51627818	51627818	+	IGR	DEL	A	-	-	rs141844643		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51627818delA								COBL (243303 upstream) : None (None downstream)																							gggaggggccaggggcagaat	0.000													6	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52933231	52933231	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52933231delC								None (None upstream) : POM121L12 (170118 downstream)																							cctgctactaccaccaaagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56676762	56676762	+	IGR	DEL	T	-	-	rs35549662		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56676762delT								DKFZp434L192 (111785 upstream) : ZNF479 (510566 downstream)																							TTTTCCCTGATTTTTTTTTAA	0.279													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	63284014	63284015	+	IGR	DEL	AG	-	-	rs66629179		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63284014_63284015delAG								LOC100287704 (471863 upstream) : ZNF727 (221806 downstream)																							GGCCAGAAACAGAGGTGTGGGC	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68418805	68418805	+	IGR	DEL	C	-	-	rs144474228		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68418805delC								None (None upstream) : AUTS2 (645100 downstream)																							CCGACCCTTGCTTTTTTTTTT	0.318													4	3	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69114501	69114501	+	Intron	DEL	T	-	-	rs74531286		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69114501delT	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CACTGTATGCTTTTTTTTTTG	0.458													7	6	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71831814	71831815	+	Intron	INS	-	A	A	rs142707953	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71831814_71831815insA	uc003twb.3	-						CALN1_uc003twc.3_Intron	NM_031468	NP_113656	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 1							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				atataaccaacaaaaaaaaagg	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	73089317	73089317	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73089317delA								VPS37D (2878 upstream) : DNAJC30 (5931 downstream)																							CCTTTTGCCTAAAACCTTCTT	0.478													4	2	---	---	---	---	
STAG3L1	54441	broad.mit.edu	37	7	74991056	74991056	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74991056delT	uc003ucu.1	+						PMS2L2_uc011kfp.1_5'Flank|PMS2L2_uc011kfq.1_5'Flank|PMS2L2_uc003ucq.2_5'Flank|PMS2L2_uc003uct.1_5'Flank|PMS2L2_uc010lcy.1_5'Flank|STAG3L1_uc010lcz.1_Intron|STAG3L1_uc003ucv.1_Intron|STAG3L1_uc011kfw.1_Intron|STAG3L1_uc011kfx.1_Intron	NM_018991	NP_061864	P0CL83	ST3L1_HUMAN	stromal antigen 3-like 1 isoform 1							nucleus	binding				0						ACTCAAGGAATTTTTTTTTTA	0.328													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	76691454	76691455	+	IGR	INS	-	A	A	rs142177237		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76691454_76691455insA								LOC100132832 (9099 upstream) : CCDC146 (60479 downstream)																							tcaaaaaaaaTAACCTGCGAGT	0.218													4	3	---	---	---	---	
PION	54103	broad.mit.edu	37	7	76961876	76961876	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76961876delT	uc003ugf.2	-						PION_uc003ugg.1_Intron	NM_017439	NP_059135	A4D1B5	GSAP_HUMAN	pigeon homolog						beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1						tgtgtttgtatgagcgctctt	0.109													4	2	---	---	---	---	
CD36	948	broad.mit.edu	37	7	80120545	80120545	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80120545delT	uc003uhc.2	+						GNAT3_uc011kgu.1_Intron	NM_001127444	NP_001120916	P16671	CD36_HUMAN	CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1						GGGTGAAGGCTTAGCATAACT	0.338													4	2	---	---	---	---	
HGF	3082	broad.mit.edu	37	7	81351562	81351562	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81351562delT	uc003uhl.2	-						HGF_uc003uhm.2_Intron	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1						epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4						TCTATTTCTCTTTTTTTAATT	0.055													4	2	---	---	---	---	
KIAA1324L	222223	broad.mit.edu	37	7	86538865	86538865	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86538865delT	uc011kha.1	-						KIAA1324L_uc003uif.1_Intron|KIAA1324L_uc011kgz.1_Intron|KIAA1324L_uc003uie.2_Intron	NM_001142749	NP_001136221	A8MWY0	K132L_HUMAN	hypothetical protein LOC222223 isoform 1							integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)					CCTCTTAAAGTTCTAGAAAGT	0.299													4	2	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90742169	90742170	+	Intron	DEL	GA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90742169_90742170delGA	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						tgtatgtgtggagagagagaga	0.292													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	90927606	90927607	+	IGR	INS	-	G	G	rs11349884		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90927606_90927607insG								FZD1 (29475 upstream) : MTERF (503853 downstream)																							AGAGTCAAGGAGGGGGGGGGTC	0.381													4	2	---	---	---	---	
LMTK2	22853	broad.mit.edu	37	7	97831431	97831431	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97831431delT	uc003upd.1	+							NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor						early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					ttcctccaggttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100614843	100614843	+	IGR	DEL	C	-	-	rs67310012		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100614843delC								ACHE (120304 upstream) : MUC12 (33232 downstream)																							ACCTCCTTTACCCCCACCCGG	0.592													9	6	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122359447	122359447	+	Intron	DEL	T	-	-	rs11359712		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122359447delT	uc010lkp.2	-						CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						ACTATCCCCCTATCCTTCTGT	0.502													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	123432895	123432896	+	IGR	INS	-	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123432895_123432896insA								WASL (43779 upstream) : HYALP1 (21297 downstream)																							AGGGGGAAGGGAGTAATATCAG	0.495													4	2	---	---	---	---	
SND1	27044	broad.mit.edu	37	7	127512615	127512615	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127512615delT	uc003vmi.2	+						SND1_uc010lle.2_Intron	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						TAGATGAGGATTTTTTTTTCC	0.239													4	2	---	---	---	---	
FAM180A	389558	broad.mit.edu	37	7	135423347	135423347	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135423347delT	uc003vtd.2	-						FAM180A_uc010lmt.2_Intron|FAM180A_uc010lmu.2_Intron	NM_205855	NP_995327	Q6UWF9	F180A_HUMAN	hypothetical protein LOC389558 precursor							extracellular region				ovary(2)	2						TGAATTGCTATTAGAGGTACA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	140739426	140739426	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140739426delT								MRPS33 (24645 upstream) : AGK (511652 downstream)																							tctttggccatttctctttgg	0.005													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147994757	147994757	+	Intron	DEL	T	-	-	rs71527891		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147994757delT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			aatatcttaatttttttttat	0.000										HNSCC(39;0.1)			4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148347109	148347109	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148347109delA								C7orf33 (34158 upstream) : CUL1 (47897 downstream)																							accctgtctcaaaaaaaaaaa	0.204													4	5	---	---	---	---	
ZNF767	79970	broad.mit.edu	37	7	149281954	149281954	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149281954delA	uc003wfy.3	-						ZNF767_uc003wfx.2_Intron|ZNF767_uc011kuq.1_Intron	NR_027789				Homo sapiens cDNA FLJ12700 fis, clone NT2RP1000721.											central_nervous_system(1)	1	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00434)			TCCACCCTGCAAAAAAAATGA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152775206	152775207	+	IGR	INS	-	GA	GA	rs138877604	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152775206_152775207insGA								ACTR3B (222743 upstream) : DPP6 (809212 downstream)																							GTGCTTCAGTGGGTAGACATCC	0.485													1	6	---	---	---	---	
RBM33	155435	broad.mit.edu	37	7	155493869	155493870	+	Intron	INS	-	A	A	rs143521704	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155493869_155493870insA	uc010lqk.1	+						RBM33_uc003wme.2_3'UTR|RBM33_uc011kvv.1_Intron	NM_053043	NP_444271	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33								nucleotide binding|RNA binding			ovary(1)	1	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		ttaagataattaaaaaaaattt	0.356													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155814680	155814680	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155814680delG								SHH (209713 upstream) : C7orf4 (518505 downstream)																							ACCTGCTAGAGGACTGGAAGA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	158778697	158778698	+	IGR	INS	-	A	A	rs143866567	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158778697_158778698insA								WDR60 (39815 upstream) : LOC154822 (22347 downstream)																							ATGATATTGGCAAAAAAAAAGG	0.441													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	8038564	8038564	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8038564delC								MIR548I3 (91953 upstream) : FLJ10661 (47528 downstream)																							ccccacatttccttcttccct	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	12455601	12455601	+	Intron	DEL	C	-	-	rs71234540		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12455601delC	uc003wvy.3	-						uc003wwc.3_Intron					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		CTAGGAGAGACTTTTCTCTCT	0.532													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21538476	21538476	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21538476delT								None (None upstream) : GFRA2 (11054 downstream)																							TGGAACATCATTTTTTTTTAA	0.463													3	3	---	---	---	---	
PHYHIP	9796	broad.mit.edu	37	8	22088977	22088978	+	Intron	DEL	CA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22088977_22088978delCA	uc003xbk.3	-						PHYHIP_uc003xbj.3_Intron	NM_001099335	NP_001092805	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein												0				Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)		CGCGAGCGCGCACACACACACG	0.614													4	2	---	---	---	---	
PBK	55872	broad.mit.edu	37	8	27697882	27697882	+	5'Flank	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27697882delA	uc003xgi.2	-						PBK_uc011lap.1_5'Flank	NM_018492	NP_060962	Q96KB5	TOPK_HUMAN	PDZ binding kinase						mitosis		ATP binding|protein binding|protein serine/threonine kinase activity				0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		CTGCCAATGGAAAAAAAAACa	0.284													4	3	---	---	---	---	
EIF4EBP1	1978	broad.mit.edu	37	8	37904202	37904204	+	Intron	DEL	CAT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37904202_37904204delCAT	uc003xks.2	+							NM_004095	NP_004086	Q13541	4EBP1_HUMAN	eukaryotic translation initiation factor 4E						G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|positive regulation of mitotic cell cycle|TOR signaling cascade|translation	cytosol					0	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)				ttggcactaccatcatcatcatc	0.054													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	62700828	62700831	+	IGR	DEL	TTTT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62700828_62700831delTTTT								ASPH (73629 upstream) : NKAIN3 (460670 downstream)																							TTAATTTTTCTTTTTTTTTCAGGA	0.284													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	64595925	64595926	+	IGR	INS	-	GACT	GACT			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64595925_64595926insGACT								YTHDF3 (470580 upstream) : MIR124-2 (695780 downstream)																							TAGACCAAGAAGACTGAGTGAT	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	72108599	72108599	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72108599delA								XKR9 (460423 upstream) : EYA1 (1071 downstream)																							CATGGTAGGGAAAAAAAAGTC	0.279													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	110096106	110096106	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110096106delA								TMEM74 (296336 upstream) : TRHR (3633 downstream)																							attatgtgttaaaAAAAACAG	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	135918133	135918134	+	IGR	INS	-	C	C	rs148914710	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135918133_135918134insC								MIR30D (100945 upstream) : LOC286094 (328240 downstream)																							GAACGCCACCACTTGCCTATGC	0.485											OREG0019010	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139536118	139536119	+	IGR	INS	-	A	A	rs151304933	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139536118_139536119insA								FAM135B (27053 upstream) : COL22A1 (64360 downstream)																							AACAAGTACTGAAAAGCTCCAT	0.510													4	6	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141468248	141468257	+	5'Flank	DEL	GGAGGGAGAT	-	-	rs66770170		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141468248_141468257delGGAGGGAGAT	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						gaggagggaaggagggagatggagggagat	0.205													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143939533	143939534	+	IGR	DEL	AG	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143939533_143939534delAG								GML (11272 upstream) : CYP11B1 (14240 downstream)																							tggtggcagcagagagagagag	0.124													4	2	---	---	---	---	
C9orf93	203238	broad.mit.edu	37	9	15900507	15900521	+	Intron	DEL	GACACCCGAGCAGAG	-	-	rs139479264		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15900507_15900521delGACACCCGAGCAGAG	uc003zmd.2	+						C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron	NM_173550	NP_775821	Q6TFL3	CI093_HUMAN	hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)		agcctgctgagacacccgagcagaggaccccacta	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	24312761	24312761	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24312761delA								ELAVL2 (486698 upstream) : None (None downstream)																							ACCTCTGATTAAAAAAAATAA	0.338													4	2	---	---	---	---	
ACO1	48	broad.mit.edu	37	9	32407652	32407652	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32407652delT	uc003zqw.3	+						ACO1_uc010mjh.1_Intron|ACO1_uc003zqx.3_Intron|ACO1_uc003zqy.3_Intron	NM_002197	NP_002188	P21399	ACOC_HUMAN	aconitase 1						citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		aacaCGCCACTTTTTCTAATA	0.219													4	2	---	---	---	---	
UBAP2	55833	broad.mit.edu	37	9	33943266	33943267	+	Intron	INS	-	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33943266_33943267insC	uc003ztq.1	-						UBAP2_uc011loc.1_Intron|UBAP2_uc011lod.1_Intron|UBAP2_uc011loe.1_Intron|UBAP2_uc011lof.1_Intron|UBAP2_uc011log.1_Intron|UBAP2_uc003ztr.2_Intron|UBAP2_uc003zts.2_Intron	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2											ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		agaaactgagactgtctgctac	0.064													276	135	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68398095	68398095	+	IGR	DEL	C	-	-	rs74487823		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68398095delC								FAM27B (603906 upstream) : MIR1299 (604144 downstream)																							CCATGCTTAGCTTGGGTTTCT	0.353													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68418203	68418204	+	IGR	INS	-	TG	TG	rs145604244		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68418203_68418204insTG								FAM27B (624014 upstream) : MIR1299 (584035 downstream)																							AGAAAATTAGATGTGTGTGTTT	0.262													4	2	---	---	---	---	
FXN	2395	broad.mit.edu	37	9	71668426	71668427	+	Intron	INS	-	GG	GG	rs58150402	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668426_71668427insGG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135	Q16595	FRDA_HUMAN	frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0						gatggatggatagatagataga	0.059													7	5	---	---	---	---	
FXN	2395	broad.mit.edu	37	9	71668427	71668428	+	Intron	INS	-	TG	TG	rs75408130	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668427_71668428insTG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135	Q16595	FRDA_HUMAN	frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0						atggatggatagatagatagat	0.059													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	74078714	74078716	+	IGR	DEL	AAG	-	-	rs138466631	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74078714_74078716delAAG								TRPM3 (16894 upstream) : TMEM2 (219566 downstream)																							Aaaaaaaaaaaagaaagaaagaa	0.153													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	83615621	83615621	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83615621delA								None (None upstream) : TLE1 (582979 downstream)																							ggtctgagtcaccaccttgta	0.000													3	5	---	---	---	---	
GKAP1	80318	broad.mit.edu	37	9	86384117	86384117	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86384117delT	uc004amy.2	-						GKAP1_uc004amz.2_Intron|GKAP1_uc011lsu.1_Intron	NM_025211	NP_079487	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1 isoform a						signal transduction	Golgi apparatus					0						ATACTTCATATTTTTTGGACT	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	87082278	87082279	+	IGR	INS	-	TG	TG			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87082278_87082279insTG								SLC28A3 (98865 upstream) : NTRK2 (201187 downstream)																							ggtgtgtgtgctgtgcgtgtgg	0.000													4	2	---	---	---	---	
CTSL1	1514	broad.mit.edu	37	9	90343025	90343026	+	Frame_Shift_Del	DEL	AC	-	-	rs141209993	byFrequency	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90343025_90343026delAC	uc004aph.2	+	3	560_561	c.210_211delAC	c.(208-213)AAACACfs	p.K70fs	CTSL1_uc004api.2_Frame_Shift_Del_p.K70fs|CTSL1_uc004apj.2_Frame_Shift_Del_p.K15fs|CTSL1_uc010mqh.2_Intron|CTSL1_uc004apk.2_Frame_Shift_Del_p.K70fs|CTSL1_uc004apl.2_Frame_Shift_Del_p.K70fs	NM_001912	NP_001903	P07711	CATL1_HUMAN	cathepsin L1 preproprotein	70_71					macrophage apoptosis|proteolysis	extracellular region|lysosome|nucleus	cysteine-type endopeptidase activity|histone binding			ovary(3)	3					Glucagon recombinant(DB00040)	GGGAAGGGAAACACAGCTTCAC	0.465													316	144	---	---	---	---	
FKBP15	23307	broad.mit.edu	37	9	115968524	115968524	+	Intron	DEL	A	-	-	rs5900042		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115968524delA	uc004bgs.2	-						FKBP15_uc010muu.1_Intron|FKBP15_uc011lxd.1_Intron|FKBP15_uc010mut.1_Intron|FKBP15_uc004bgt.2_Intron	NM_015258	NP_056073	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa						endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3						AACAACAAACAAACAAAAAAA	0.229													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	120063241	120063241	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120063241delT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						GAACTGCATCTTTTACATGAA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	126061654	126061654	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126061654delT								STRBP (30811 upstream) : CRB2 (56794 downstream)																							atacaggagatttttttttca	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	128792672	128792672	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128792672delG								PBX3 (63019 upstream) : FAM125B (296456 downstream)																							aaagcataaaggaaaaaaaaa	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	128921367	128921367	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128921367delC								PBX3 (191714 upstream) : FAM125B (167761 downstream)																							agacagtcctccacaaacatt	0.020													4	2	---	---	---	---	
FUBP3	8939	broad.mit.edu	37	9	133491210	133491211	+	Intron	DEL	AT	-	-	rs139142592		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133491210_133491211delAT	uc004bzr.1	+						FUBP3_uc010mzd.1_Intron|FUBP3_uc004bzs.1_Intron	NM_003934	NP_003925	Q96I24	FUBP3_HUMAN	far upstream element (FUSE) binding protein 3						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|RNA binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000279)		CTTAAAAGTCATAGAGCAGTGT	0.480													3	3	---	---	---	---	
LARP4B	23185	broad.mit.edu	37	10	910364	910364	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:910364delA	uc001ifs.1	-							NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B								nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3						GTTCaaaattaaaaaaaaaaa	0.388													5	3	---	---	---	---	
GTPBP4	23560	broad.mit.edu	37	10	1061586	1061592	+	Intron	DEL	CTGAGCA	-	-	rs72135483		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1061586_1061592delCTGAGCA	uc001ift.2	+						GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		gtcctgagcgctgagcactgagcctgg	0.101													10	5	---	---	---	---	
PFKP	5214	broad.mit.edu	37	10	3157269	3157269	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3157269delC	uc001igp.2	+						PFKP_uc001igq.2_Intron|PFKP_uc009xhr.2_Intron|PFKP_uc009xhs.1_Intron|PFKP_uc009xht.2_Intron|PFKP_uc009xhu.2_Intron	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet						glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		tacacgcaggcataaacagag	0.045													4	2	---	---	---	---	
UPF2	26019	broad.mit.edu	37	10	12076804	12076805	+	Intron	INS	-	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12076804_12076805insT	uc001ila.2	-						UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron|UPF2_uc009xiz.1_Intron	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				attccgtctcaaaataaataaa	0.134													6	3	---	---	---	---	
NMT2	9397	broad.mit.edu	37	10	15191331	15191333	+	Intron	DEL	CAT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15191331_15191333delCAT	uc001inz.1	-						NMT2_uc001ioa.1_Intron|NMT2_uc009xjo.1_Intron|NMT2_uc010qbz.1_Intron	NM_004808	NP_004799	O60551	NMT2_HUMAN	N-myristoyltransferase 2						N-terminal protein myristoylation|protein lipoylation	Golgi apparatus|plasma membrane	glycylpeptide N-tetradecanoyltransferase activity			ovary(1)	1						accaccatcacatcatcatcacc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	32283082	32283083	+	IGR	INS	-	T	T	rs141570486	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32283082_32283083insT								ARHGAP12 (65312 upstream) : KIF5B (14857 downstream)																							GGTCTAGGAGGTGGTGGTGCTA	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37598246	37598246	+	IGR	DEL	A	-	-	rs12261580	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37598246delA								ANKRD30A (76751 upstream) : ZNF248 (492201 downstream)																							ATTATTTTTTAAAAAAAAAAG	0.279													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42627717	42627717	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42627717delT								None (None upstream) : LOC441666 (199598 downstream)																							ACAAATAACATTTAAACTTTA	0.294													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45579314	45579314	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45579314delG								ZNF22 (78538 upstream) : LOC100133308 (15619 downstream)																							AGAGCAGCTTGGGGTTTTTGT	0.289													4	2	---	---	---	---	
GPRIN2	9721	broad.mit.edu	37	10	46992445	46992445	+	5'Flank	DEL	A	-	-	rs5784699		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46992445delA	uc001jec.2	+							NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth												0						GCCCTATAGGAAACGGGGTCT	0.627													5	3	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47014164	47014165	+	Intron	INS	-	GAGA	GAGA	rs147034575		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47014164_47014165insGAGA	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						TGTGGGGCAGGgagagagagag	0.272													3	4	---	---	---	---	
ANTXRL	195977	broad.mit.edu	37	10	47681754	47681754	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47681754delC	uc001jel.2	+							NR_003601				Homo sapiens cDNA FLJ32754 fis, clone TESTI2001671.												0						CAGTTCTGGTCCCGATATTGT	0.522													4	2	---	---	---	---	
DKK1	22943	broad.mit.edu	37	10	54074083	54074084	+	5'UTR	INS	-	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54074083_54074084insC	uc001jjr.2	+	1					uc001jjq.1_5'Flank|uc009xox.1_5'Flank	NM_012242	NP_036374	O94907	DKK1_HUMAN	dickkopf homolog 1 precursor						negative regulation of peptidyl-serine phosphorylation|negative regulation of protein complex assembly|negative regulation of transcription from RNA polymerase II promoter|positive regulation of heart induction by negative regulation of canonical Wnt receptor signaling pathway|regulation of receptor internalization	extracellular space|plasma membrane	growth factor activity|low-density lipoprotein particle receptor binding|receptor antagonist activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3						TGGGACCGCAGGGGGCTCCCGG	0.649											OREG0020191	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65527085	65527085	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65527085delA								REEP3 (145114 upstream) : None (None downstream)																							GATTCAAGAGAAAAAAAAAAT	0.398													4	2	---	---	---	---	
CAMK2G	818	broad.mit.edu	37	10	75611423	75611424	+	Intron	INS	-	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75611423_75611424insA	uc001jvv.1	-						CAMK2G_uc001jvm.1_Intron|CAMK2G_uc001jvo.1_Intron|CAMK2G_uc001jvq.1_Intron|CAMK2G_uc001jvr.1_Intron|CAMK2G_uc001jvp.1_Intron|CAMK2G_uc001jvs.1_Intron|CAMK2G_uc001jvt.1_Intron|CAMK2G_uc001jvu.1_Intron|CAMK2G_uc010qkv.1_Intron	NM_172171	NP_751911	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II						insulin secretion|interferon-gamma-mediated signaling pathway|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding|calmodulin-dependent protein kinase activity			lung(1)|stomach(1)	2	Prostate(51;0.0112)					CATGGTAGTGCAAAAAAAAAGT	0.342													4	2	---	---	---	---	
VCL	7414	broad.mit.edu	37	10	75842373	75842374	+	Intron	DEL	AT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75842373_75842374delAT	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706	P18206	VINC_HUMAN	vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)					AAAGAAAGAAATTTTCCCATAA	0.421													23	13	---	---	---	---	
DUSP13	51207	broad.mit.edu	37	10	76864484	76864485	+	Intron	DEL	CA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76864484_76864485delCA	uc001jws.2	-						DUSP13_uc001jwu.2_Intron|DUSP13_uc001jww.2_Intron|DUSP13_uc009xrs.2_Intron|DUSP13_uc001jwt.2_Intron|DUSP13_uc001jwv.2_Intron	NM_001007271	NP_001007272	Q6B8I1	MDSP_HUMAN	muscle-restricted dual specificity phosphatase							cytoplasm	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					AGTTTCTTATCACAGTCACCCC	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	79908545	79908545	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79908545delT								RPS24 (91975 upstream) : LOC283050 (794539 downstream)																							GCTCACTCTATTTTTTTTTGT	0.433													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	94485543	94485543	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94485543delC								HHEX (30137 upstream) : EXOC6 (105392 downstream)																							gctttctttacataaaatcac	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	98531021	98531021	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98531021delA								PIK3AP1 (50742 upstream) : MIR607 (57405 downstream)																							TATGCAAATTAAAAAAAAAAA	0.179													4	2	---	---	---	---	
VTI1A	143187	broad.mit.edu	37	10	114208800	114208800	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114208800delG	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron|ZDHHC6_uc001kzv.2_5'Flank|ZDHHC6_uc001kzw.2_5'Flank|ZDHHC6_uc009xya.1_5'Flank|VTI1A_uc001kzx.2_RNA	NM_145206	NP_660207	Q96AJ9	VTI1A_HUMAN	SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		ACCAAGCTCTGCTGCCTCAGA	0.313													4	2	---	---	---	---	
TACC2	10579	broad.mit.edu	37	10	123837828	123837828	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123837828delA	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing							microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CCGACTCCTGAAAACCTGGTC	0.323													4	2	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	129240376	129240376	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129240376delC	uc001ljt.2	+						DOCK1_uc010qun.1_Intron|DOCK1_uc009yaq.2_Intron	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GCGCTTGGCTCCCCCGACAGC	0.572													4	3	---	---	---	---	
PWWP2B	170394	broad.mit.edu	37	10	134208802	134208802	+	5'Flank	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134208802delC	uc001lll.3	+						PWWP2B_uc009ybe.2_5'Flank	NM_138499	NP_612508	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2 isoform 1												0		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)		CCCACCCCCACCCCCACCTCG	0.637													4	2	---	---	---	---	
RRP8	23378	broad.mit.edu	37	11	6621799	6621800	+	Frame_Shift_Ins	INS	-	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6621799_6621800insT	uc001med.2	-	6	1246_1247	c.1167_1168insA	c.(1165-1170)AAAGTGfs	p.K389fs		NM_015324	NP_056139	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase,	389_390					chromatin modification|chromatin silencing at rDNA|rRNA processing|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	methylated histone residue binding|S-adenosylmethionine-dependent methyltransferase activity				0						ACCTCAGCCACTTTCAGGAGAC	0.525													65	29	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	11753633	11753633	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11753633delT								GALNTL4 (110072 upstream) : USP47 (109337 downstream)																							GGCTAGACCATTTTCCACAAG	0.393													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	20950220	20950220	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20950220delT	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						acatgggctattttttttttt	0.070													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	26840119	26840119	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26840119delG								SLC5A12 (95145 upstream) : FIBIN (175509 downstream)																							tgtgatttttgggggtgtgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	29542108	29542108	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29542108delT								None (None upstream) : KCNA4 (489658 downstream)																							caaaccttcatttatcagcct	0.000													4	2	---	---	---	---	
CCDC73	493860	broad.mit.edu	37	11	32740543	32740545	+	Intron	DEL	CCA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32740543_32740545delCCA	uc001mtv.2	-						CCDC73_uc001mtw.1_Intron|CCDC73_uc009yjt.2_Intron	NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79											ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)					cccctatcttccaccaccaccac	0.000													4	2	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	40584497	40584497	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40584497delT	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)				tttttttttcttttttttttg	0.000													3	5	---	---	---	---	
NUP160	23279	broad.mit.edu	37	11	47869201	47869201	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47869201delG	uc001ngm.2	-						NUP160_uc009ylw.2_Intron|NUP160_uc001ngn.1_Intron	NM_015231	NP_056046	Q12769	NU160_HUMAN	nucleoporin 160kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7						GTGTGGGGGTGGGGGGGGGGA	0.458													0	8	---	---	---	---	
ALDH3B2	222	broad.mit.edu	37	11	67435468	67435469	+	Intron	INS	-	AC	AC			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67435468_67435469insAC	uc001omr.2	-						ALDH3B2_uc001oms.2_Intron|ALDH3B2_uc009ysa.1_Intron	NM_000695	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3B2						alcohol metabolic process|cellular aldehyde metabolic process|lipid metabolic process		3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase			lung(1)|kidney(1)	2					NADH(DB00157)	TCCTTGCGCAGACACACACCCA	0.653													4	2	---	---	---	---	
NUMA1	4926	broad.mit.edu	37	11	71734462	71734462	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71734462delC	uc001orl.1	-						NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc009ysx.1_Intron|NUMA1_uc001oro.1_Intron|NUMA1_uc009ysy.1_Intron|NUMA1_uc001orp.2_Intron|NUMA1_uc001orq.2_Intron	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1						G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8						GTTGCACTCTCCCACCCACTC	0.498			T	RARA	APL								4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83532462	83532462	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83532462delT	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.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)				TTATTATGGATTTTTTTTAGA	0.353													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	86503587	86503587	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86503587delA								ME3 (119909 upstream) : PRSS23 (7904 downstream)																							acaCCCAGCCAAAAAAGGTGC	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	92665010	92665010	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92665010delT								FAT3 (35377 upstream) : MTNR1B (37779 downstream)																							CTGGGGGTCCTTCTTAGAGCT	0.483													4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99283414	99283414	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99283414delC	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		atataaaattcccgaggtcgc	0.169													4	2	---	---	---	---	
CASP5	838	broad.mit.edu	37	11	104871386	104871386	+	Intron	DEL	T	-	-	rs45440097		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104871386delT	uc010rva.1	-						CASP5_uc010ruz.1_Intron|CASP5_uc010rvb.1_Intron|CASP5_uc010rvc.1_Intron|CASP5_uc009yxh.2_Intron|CASP5_uc010rvd.1_Intron	NM_004347	NP_004338	P51878	CASP5_HUMAN	caspase 5 isoform a precursor						apoptosis|cellular response to mechanical stimulus|proteolysis|regulation of apoptosis	intracellular	cysteine-type endopeptidase activity|protein binding			ovary(2)|lung(1)	3		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		TTTTGTTTTGTTTTTTTTTTC	0.363													4	2	---	---	---	---	
DDX10	1662	broad.mit.edu	37	11	108548785	108548785	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108548785delT	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		CATTTGATTATTTTTTTTTCT	0.353			T	NUP98	AML*								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	110823669	110823669	+	IGR	DEL	G	-	-	rs35282135		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110823669delG								ARHGAP20 (239757 upstream) : C11orf53 (303038 downstream)																							GAGGCTGAGAGGGTCAGAGCA	0.512													3	3	---	---	---	---	
BACE1	23621	broad.mit.edu	37	11	117164935	117164935	+	Intron	DEL	C	-	-	rs113659541		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117164935delC	uc001pqz.2	-						BACE1_uc001pqw.2_Intron|BACE1_uc001pqx.2_Intron|BACE1_uc001pqy.2_Intron|BACE1_uc001pra.1_Intron|BACE1_uc010rxg.1_Intron|BACE1_uc010rxh.1_Intron|BACE1_uc009yzo.1_5'Flank	NM_012104	NP_036236	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1 isoform A						beta-amyloid metabolic process|membrane protein ectodomain proteolysis	cell surface|cytoplasmic vesicle membrane|endoplasmic reticulum|endosome|integral to plasma membrane|trans-Golgi network	aspartic-type endopeptidase activity|beta-aspartyl-peptidase activity|protein binding			ovary(1)	1	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		ATTCATAGATCtttttttttt	0.229													3	3	---	---	---	---	
DSCAML1	57453	broad.mit.edu	37	11	117353908	117353908	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117353908delC	uc001prh.1	-							NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CCTTTCTCCTCCGCCCAACTC	0.612													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	118746668	118746670	+	IGR	DEL	TGC	-	-	rs139637756	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118746668_118746670delTGC								DDX6 (84696 upstream) : CXCR5 (7871 downstream)																							gctgtgttgttgctgtgggttgt	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119776423	119776423	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119776423delA								PVRL1 (176988 upstream) : TRIM29 (205572 downstream)																							agcttgaatcaaaaaaaaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	123352163	123352164	+	IGR	INS	-	AAC	AAC	rs151157792	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123352163_123352164insAAC								ASAM (286156 upstream) : GRAMD1B (44364 downstream)																							cttcgtctAAAaacaacaacaa	0.183													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133532913	133532913	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133532913delT								OPCML (130510 upstream) : SPATA19 (177604 downstream)																							ACAGTGGAGATTTAGATACAG	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133647939	133647939	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133647939delG								OPCML (245536 upstream) : SPATA19 (62578 downstream)																							GAAAAGGGCTGGAGGAAAGCC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	5616702	5616702	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5616702delC								NTF3 (12239 upstream) : ANO2 (55115 downstream)																							ATGGGCTGTTCCCCATCCTCC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8969490	8969490	+	IGR	DEL	T	-	-	rs150142957		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8969490delT								RIMKLB (33805 upstream) : A2ML1 (5660 downstream)																							tctgttgtccttttttttttt	0.080													5	3	---	---	---	---	
RPL13AP20	387841	broad.mit.edu	37	12	13026142	13026142	+	5'Flank	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13026142delT	uc010sho.1	+							NR_003932				SubName: Full=Ribosomal protein L13a variant; Flags: Fragment;												0						CTCTGAGGGCttttttttttc	0.249													5	4	---	---	---	---	
GUCY2C	2984	broad.mit.edu	37	12	14841194	14841195	+	Intron	INS	-	TCTC	TCTC	rs140246622	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14841194_14841195insTCTC	uc001rcd.2	-						GUCY2C_uc009zhz.2_Intron	NM_004963	NP_004954	P25092	GUC2C_HUMAN	guanylate cyclase 2C precursor						intracellular signal transduction|receptor guanylyl cyclase signaling pathway	integral to membrane	ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity			ovary(4)|skin(2)	6						tcatctctgtttctctctctct	0.144													6	3	---	---	---	---	
TMTC1	83857	broad.mit.edu	37	12	29720136	29720136	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29720136delT	uc001rjb.2	-						TMTC1_uc001riz.2_Intron|TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					ccgagggtgctccttaataaa	0.045													4	2	---	---	---	---	
VDR	7421	broad.mit.edu	37	12	48287248	48287248	+	Intron	DEL	A	-	-	rs36108348		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48287248delA	uc001rqm.2	-						VDR_uc001rql.2_Intron|VDR_uc001rqn.2_Intron|VDR_uc010slq.1_Intron	NM_001017535	NP_001017535	P11473	VDR_HUMAN	vitamin D (1,25-dihydroxyvitamin D3) receptor						decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	AGCTGAATAGAAAAAAAAAAG	0.413													5	3	---	---	---	---	
MBD6	114785	broad.mit.edu	37	12	57917736	57917737	+	Intron	DEL	GA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57917736_57917737delGA	uc001soj.1	+						MBD6_uc001sok.1_5'Flank|MBD6_uc001sol.1_5'Flank	NM_052897	NP_443129	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6							chromosome|nucleus	chromatin binding|DNA binding			central_nervous_system(3)|ovary(1)	4						TCTTTCTTTTGAGAGGGTGCTG	0.540													4	2	---	---	---	---	
SRGAP1	57522	broad.mit.edu	37	12	64328431	64328432	+	Intron	INS	-	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64328431_64328432insC	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		CACAACCACCACCCCCCCCAAC	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68247719	68247719	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68247719delT								DYRK2 (191276 upstream) : IFNG (300831 downstream)																							CTTCGCTTCATTTTCCTCTTC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	69489552	69489553	+	IGR	INS	-	T	T	rs143826620	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69489552_69489553insT								CPM (132532 upstream) : CPSF6 (143764 downstream)																							CCAAAGGTGGAGCCCTTTAAGT	0.485													1	5	---	---	---	---	
TSPAN8	7103	broad.mit.edu	37	12	71534382	71534382	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71534382delA	uc009zrt.1	-						TSPAN8_uc001swk.1_Intron|TSPAN8_uc001swj.1_Intron	NM_004616	NP_004607	P19075	TSN8_HUMAN	transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)			ATATGAAGGGAAAAAAAATCC	0.378													4	2	---	---	---	---	
PTPRQ	374462	broad.mit.edu	37	12	80935152	80935152	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80935152delT	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0						TTTTGAATGatttttaaaata	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92130966	92130966	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92130966delA								DCN (554160 upstream) : BTG1 (247900 downstream)																							aatattcagtaaaaaaaatga	0.164													4	2	---	---	---	---	
MYBPC1	4604	broad.mit.edu	37	12	102030746	102030746	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102030746delT	uc001tii.2	+						MYBPC1_uc001tif.1_Intron|MYBPC1_uc001tig.2_Intron|MYBPC1_uc010svq.1_Intron|MYBPC1_uc001tih.2_Intron|MYBPC1_uc001tij.2_Intron|MYBPC1_uc010svr.1_Intron|MYBPC1_uc010svs.1_Intron|MYBPC1_uc010svt.1_Intron|MYBPC1_uc010svu.1_Intron|MYBPC1_uc001tik.2_Intron	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3						cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4						TCTTCACCTATTTTTTTTTAA	0.323													4	2	---	---	---	---	
POLR3B	55703	broad.mit.edu	37	12	106894292	106894292	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106894292delA	uc001tlp.2	+						POLR3B_uc001tlq.2_Intron	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2						ccacggtatcaaaaggggcaa	0.000													4	2	---	---	---	---	
KDM2B	84678	broad.mit.edu	37	12	122012939	122012939	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122012939delA	uc001uat.2	-						KDM2B_uc001uas.2_Intron|KDM2B_uc001uau.2_Intron|KDM2B_uc001uav.3_Intron	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2						GTTCAGAGGGAAAAAAAGACA	0.423													4	2	---	---	---	---	
CCDC62	84660	broad.mit.edu	37	12	123275559	123275559	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123275559delG	uc001udc.2	+						CCDC62_uc010tah.1_Intron|CCDC62_uc001udf.2_Intron|CCDC62_uc001ude.2_Intron	NM_201435	NP_958843	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62 isoform b							cytoplasm|nucleus				ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		gaacggcggtggggagatggg	0.015													4	2	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124824410	124824411	+	Intron	DEL	AT	-	-	rs112752180		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124824410_124824411delAT	uc010tay.1	-						NCOR2_uc010taz.1_Intron|NCOR2_uc010tax.1_Intron	NM_006312	NP_006303	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 1						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)		CTACTCACACATAGTCTATTCT	0.064													5	4	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	130041012	130041012	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130041012delT	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GGGGTGGAGCTTTTTTTTTTC	0.458													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130689873	130689873	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130689873delT								FZD10 (39589 upstream) : PIWIL1 (132741 downstream)																							GCCTGAAGCCTCCCGcccagc	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132926774	132926774	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132926774delT								GALNT9 (20869 upstream) : FBRSL1 (140383 downstream)																							GGGAGCTCTCTCAATACATCC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	133410850	133410850	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133410850delA								GOLGA3 (5400 upstream) : CHFR (6088 downstream)																							agtgtctgCCACAGAGACCTA	0.313													4	2	---	---	---	---	
SPATA13	221178	broad.mit.edu	37	13	24647559	24647559	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24647559delA	uc001upd.1	+						C1QTNF9_uc001upe.2_Intron	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		atatctgtctatacctatctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27390384	27390385	+	IGR	INS	-	TCTG	TCTG	rs146845699	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27390384_27390385insTCTG								GPR12 (55462 upstream) : USP12 (252053 downstream)																							TCTGTTATATTTCTATGTCAGT	0.520													4	2	---	---	---	---	
POMP	51371	broad.mit.edu	37	13	29242951	29242952	+	Intron	INS	-	T	T	rs142194436	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29242951_29242952insT	uc001usf.2	+							NM_015932	NP_057016	Q9Y244	POMP_HUMAN	proteasome maturation protein						proteasome assembly	cytosol|endoplasmic reticulum|membrane|microsome|nucleus|proteasome complex					0		Lung SC(185;0.0367)		all cancers(112;0.141)|OV - Ovarian serous cystadenocarcinoma(117;0.216)		GTTTTTCTGGGTTTTTTTTTTA	0.074													4	2	---	---	---	---	
EEF1DP3	196549	broad.mit.edu	37	13	32498930	32498930	+	Intron	DEL	C	-	-	rs77563122		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32498930delC	uc001utu.2	+						EEF1DP3_uc010tdv.1_Intron					Homo sapiens similar to hypothetical protein FLJ20897, mRNA (cDNA clone IMAGE:5267252).												0						CTTTCTGTTTCTGTGTCTCAC	0.199													3	5	---	---	---	---	
EEF1DP3	196549	broad.mit.edu	37	13	32498932	32498932	+	Intron	DEL	G	-	-	rs5802623		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32498932delG	uc001utu.2	+						EEF1DP3_uc010tdv.1_Intron					Homo sapiens similar to hypothetical protein FLJ20897, mRNA (cDNA clone IMAGE:5267252).												0						TTCTGTTTCTGTGTCTCACAC	0.199													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	57037072	57037073	+	IGR	INS	-	CT	CT	rs149271908	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57037072_57037073insCT								None (None upstream) : PRR20C (677979 downstream)																							gtggaaaagtagagtcaaggca	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	66189979	66189980	+	IGR	DEL	CT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66189979_66189980delCT								None (None upstream) : PCDH9 (686987 downstream)																							ctctctatgcctctctctctct	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	90726855	90726855	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90726855delA								None (None upstream) : MIR622 (156581 downstream)																							ATTGATTAGTAAACCTAGGCC	0.403													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102543276	102543276	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102543276delT	uc001vpe.2	-						FGF14_uc001vpf.2_Intron	NM_004115	NP_004106	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1A						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TTCAAGAGCCTTTTTTTTTTC	0.458													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111170792	111170792	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111170792delC								COL4A2 (5421 upstream) : RAB20 (4622 downstream)																							GCATTCCAGGCCCCCATGCCT	0.572													4	2	---	---	---	---	
ATP11A	23250	broad.mit.edu	37	13	113365278	113365279	+	Intron	INS	-	CCAC	CCAC	rs142877275	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113365278_113365279insCCAC	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	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)	all_lung(25;0.134)|all_epithelial(44;0.141)				ACCACCCGGAGccacccaccca	0.589													4	3	---	---	---	---	
CUL4A	8451	broad.mit.edu	37	13	113885542	113885543	+	Intron	DEL	GT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113885542_113885543delGT	uc010tjy.1	+						CUL4A_uc010tjx.1_Intron|CUL4A_uc010agu.2_Intron|CUL4A_uc001vtl.1_5'Flank	NM_001008895	NP_001008895	Q13619	CUL4A_HUMAN	cullin 4A isoform 1						cell cycle arrest|DNA repair|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	ubiquitin protein ligase binding			central_nervous_system(2)|skin(1)	3	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			CCTGGTTGAGGTGTGTGTGGGC	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20303168	20303168	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20303168delA								OR4N2 (6638 upstream) : OR4K2 (41259 downstream)																							ctgaccccccaagttatgctg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	40138246	40138246	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40138246delA								FBXO33 (236542 upstream) : None (None downstream)																							aagcaggaagaaagcaaacat	0.020													4	2	---	---	---	---	
MDGA2	161357	broad.mit.edu	37	14	47860348	47860348	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47860348delC	uc001wwj.3	-						MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						ggtatgatatcctctgtgaag	0.090													4	2	---	---	---	---	
C14orf101	54916	broad.mit.edu	37	14	57113905	57113905	+	Intron	DEL	A	-	-	rs34295946		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57113905delA	uc001xcm.2	+						C14orf101_uc001xcj.2_Intron|C14orf101_uc001xcn.2_Intron|C14orf101_uc010trf.1_Intron|C14orf101_uc001xco.2_Intron	NM_017799	NP_060269	Q9NX78	CN101_HUMAN	hypothetical protein LOC54916							integral to membrane				breast(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(311;0.226)		TTTGTTTTTGAAAAAAAAAAA	0.318													11	5	---	---	---	---	
HEATR4	399671	broad.mit.edu	37	14	73986075	73986075	+	Intron	DEL	A	-	-	rs68181245		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73986075delA	uc010tub.1	-						HEATR4_uc010tua.1_Intron	NM_203309	NP_976054			HEAT repeat containing 4											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		TCTGTGGGGGAAAAAAAAAAG	0.428													8	4	---	---	---	---	
ITPK1	3705	broad.mit.edu	37	14	93565698	93565698	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93565698delA	uc001ybg.2	-						ITPK1_uc001ybe.2_Intron|ITPK1_uc001ybf.2_Intron|ITPK1_uc001ybh.2_Intron	NM_014216	NP_055031	Q13572	ITPK1_HUMAN	inositol 1,3,4-triphosphate 5/6 kinase isoform						blood coagulation|inositol trisphosphate metabolic process|signal transduction	cytosol	ATP binding|hydrolase activity|inositol tetrakisphosphate 1-kinase activity|inositol-1,3,4-trisphosphate 5/6-kinase activity|isomerase activity|ligase activity|magnesium ion binding				0		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		GGACAGGGTCAAACAGCAACA	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95512697	95512700	+	IGR	DEL	TGAG	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95512697_95512700delTGAG								GSC (276198 upstream) : DICER1 (39865 downstream)																							tcccacaGACTGAGTGAGTGAGTG	0.328													4	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106106813	106106813	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106106813delA	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron					Parts of antibodies, mostly variable regions.												0						GGCTGGGAGGAAGGCCGTCTG	0.592													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20128001	20128002	+	IGR	DEL	AA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20128001_20128002delAA								None (None upstream) : GOLGA6L6 (609092 downstream)																							AGAAAAATACAAGTTTAAAATA	0.287													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24765469	24765469	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24765469delT								PWRN2 (350374 upstream) : PWRN1 (13370 downstream)																							GTTTGTTTGCTTTTTGCTTTT	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24871166	24871166	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24871166delA								PWRN1 (38242 upstream) : C15orf2 (49375 downstream)																							aaagagagagaaaaatgcatg	0.000													4	2	---	---	---	---	
CHRFAM7A	89832	broad.mit.edu	37	15	30664654	30664655	+	Intron	INS	-	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30664654_30664655insA	uc001zdt.1	-						DKFZP434L187_uc001zds.2_Intron|CHRFAM7A_uc001zdu.1_Intron|CHRFAM7A_uc010azn.2_Intron	NM_139320	NP_647536	Q494W8	CRFM7_HUMAN	CHRNA7-FAM7A fusion isoform 1							integral to membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity			skin(1)	1		all_lung(180;3.42e-11)|Breast(32;0.000153)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		tgcaaagtgctaaaaaaaaaaa	0.104													4	5	---	---	---	---	
SLC12A6	9990	broad.mit.edu	37	15	34543442	34543443	+	Intron	INS	-	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34543442_34543443insT	uc001zhw.2	-						SLC12A6_uc001zhv.2_Intron|SLC12A6_uc001zhx.2_Intron|SLC12A6_uc001zhy.2_Intron|SLC12A6_uc001zhz.2_Intron|SLC12A6_uc001zia.2_Intron|SLC12A6_uc001zib.2_Intron|SLC12A6_uc001zic.2_Intron|SLC12A6_uc010bau.2_Intron|SLC12A6_uc001zid.2_Intron|SLC12A6_uc001zht.2_5'Flank|SLC12A6_uc001zhu.2_Intron	NM_133647	NP_598408	Q9UHW9	S12A6_HUMAN	solute carrier family 12, member 6 isoform a						angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity			central_nervous_system(5)|ovary(1)|skin(1)	7		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	TAAAAACATAGttttttttttg	0.168													4	2	---	---	---	---	
C15orf41	84529	broad.mit.edu	37	15	36902808	36902808	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36902808delT	uc001zje.3	+						C15orf41_uc001zjd.2_Intron|C15orf41_uc010bbb.1_Intron|C15orf41_uc001zjf.2_Intron	NM_001130010	NP_001123482	Q9Y2V0	CO041_HUMAN	hypothetical protein LOC84529 isoform 1								protein binding			pancreas(1)	1		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		TTTTGTTTGCTTTATGTGTAA	0.373													4	2	---	---	---	---	
NUSAP1	51203	broad.mit.edu	37	15	41630658	41630658	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41630658delG	uc001zns.3	+						NUSAP1_uc001znq.3_Intron|NUSAP1_uc001znr.3_Intron|NUSAP1_uc010bce.2_Intron|NUSAP1_uc001znt.3_Intron|NUSAP1_uc001znv.3_Intron|NUSAP1_uc001znu.3_Intron|NUSAP1_uc010ucw.1_Intron	NM_016359	NP_057443	Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1						cytokinesis after mitosis|establishment of mitotic spindle localization|mitotic chromosome condensation|positive regulation of mitosis	chromosome|cytoplasm|nucleolus	DNA binding				0		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		atccattcttgtcagcacctc	0.000													4	2	---	---	---	---	
ZFP106	64397	broad.mit.edu	37	15	42736773	42736774	+	Intron	INS	-	CCCCTTTCTTGCTGT	CCCCTTTCTTGCTGT	rs139713226	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42736773_42736774insCCCCTTTCTTGCTGT	uc001zpw.2	-						ZFP106_uc001zpu.2_Intron|ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron	NM_022473	NP_071918	Q9H2Y7	ZF106_HUMAN	zinc finger protein 106 homolog							nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)		tagggagaacacccttgtgggg	0.000													4	2	---	---	---	---	
SLC28A2	9153	broad.mit.edu	37	15	45562049	45562049	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45562049delA	uc001zva.2	+							NM_004212	NP_004203	O43868	S28A2_HUMAN	solute carrier family 28 (sodium-coupled						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity			ovary(4)	4		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)		TTGATGGTCTAAGGTCCCCTT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46734690	46734690	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46734690delT								SQRDL (751212 upstream) : SEMA6D (741713 downstream)																							TCTGATGGCATTTTTGGCTGG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	48193918	48193918	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48193918delC								SEMA6D (127499 upstream) : SLC24A5 (219251 downstream)																							tccaggaactccccacaccaa	0.129													4	2	---	---	---	---	
TMOD2	29767	broad.mit.edu	37	15	52091347	52091347	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52091347delG	uc002abk.2	+						TMOD2_uc002abl.3_Intron|TMOD2_uc010bfb.2_Intron	NM_014548	NP_055363	Q9NZR1	TMOD2_HUMAN	neuronal tropomodulin isoform a						nervous system development	cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(2)	2				all cancers(107;0.00435)		CTCTGGCCATGGGGAAGGGTC	0.537													4	2	---	---	---	---	
TMOD3	29766	broad.mit.edu	37	15	52213781	52213781	+	RNA	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52213781delC	uc010bfc.1	+	11		c.1420delC				NM_014547		Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)							cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1				all cancers(107;0.00194)		acttcctcctccatgcagcct	0.005													4	2	---	---	---	---	
PRTG	283659	broad.mit.edu	37	15	55918980	55918981	+	Intron	INS	-	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55918980_55918981insA	uc002adg.2	-							NM_173814	NP_776175	Q2VWP7	PRTG_HUMAN	protogenin precursor						multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		aaagaaaaaagaaaaaAAAAGA	0.153													4	2	---	---	---	---	
ZNF609	23060	broad.mit.edu	37	15	64950070	64950070	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64950070delT	uc002ann.2	+							NM_015042	NP_055857	O15014	ZN609_HUMAN	zinc finger protein 609							nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						TATTTACTTCTTTTTTTTTTA	0.333													6	4	---	---	---	---	
DIS3L	115752	broad.mit.edu	37	15	66621933	66621933	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66621933delT	uc010ujm.1	+						DIS3L_uc002app.2_Intron|DIS3L_uc010bho.2_Intron	NM_001143688	NP_001137160	Q8TF46	DI3L1_HUMAN	DIS3 mitotic control homolog (S.						rRNA catabolic process	cytoplasm|exosome (RNase complex)	exonuclease activity|protein binding|ribonuclease activity|RNA binding			ovary(2)	2						GATTATCAGATTTTTTTTTTT	0.338													5	3	---	---	---	---	
TLE3	7090	broad.mit.edu	37	15	70382679	70382679	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70382679delA	uc002asm.2	-						TLE3_uc002ask.2_Intron|TLE3_uc002asl.2_Intron|TLE3_uc010ukd.1_Intron|TLE3_uc010bik.1_Intron|TLE3_uc010bil.1_Intron|TLE3_uc002asn.2_Intron|TLE3_uc002asp.2_Intron|TLE3_uc002aso.2_Intron	NM_005078	NP_005069	Q04726	TLE3_HUMAN	transducin-like enhancer protein 3 isoform a						organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding			lung(2)	2						GGCAAAAAAGAAAAAAAAAAT	0.468													4	4	---	---	---	---	
LRRC49	54839	broad.mit.edu	37	15	71186231	71186231	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71186231delT	uc002asw.2	+						LRRC49_uc002asu.2_Intron|LRRC49_uc002asx.2_Intron|LRRC49_uc010ukf.1_Intron|LRRC49_uc002asy.2_5'Flank|LRRC49_uc002asz.2_5'Flank|THAP10_uc002asv.2_5'Flank	NM_017691	NP_060161	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49							cytoplasm|microtubule				ovary(1)	1						acatttacacttttttttttc	0.104													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	78150178	78150178	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78150178delA								LINGO1 (161703 upstream) : LOC645752 (56381 downstream)																							GATTTCAACGAAAAAAAAAAG	0.478													4	3	---	---	---	---	
RASGRF1	5923	broad.mit.edu	37	15	79252704	79252706	+	3'UTR	DEL	GGC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79252704_79252706delGGC	uc002beq.2	-	28					RASGRF1_uc002bep.2_3'UTR|RASGRF1_uc002beo.2_3'UTR	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine						activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6						GACACATCTGGGCAGGATGGCAT	0.369													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79928500	79928500	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79928500delC								KIAA1024 (163858 upstream) : MTHFS (208820 downstream)																							GAGCTTCAGACCAGCAGACAT	0.333													4	2	---	---	---	---	
SH3GL3	6457	broad.mit.edu	37	15	84266783	84266783	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84266783delT	uc002bjw.2	+						SH3GL3_uc002bjx.2_Intron|SH3GL3_uc002bju.2_Intron|SH3GL3_uc002bjv.2_Intron	NM_003027	NP_003018	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3						central nervous system development|endocytosis|signal transduction	early endosome membrane	identical protein binding|lipid binding			pancreas(1)|central_nervous_system(1)|skin(1)	3						TGTGCACAACTTTTTATTTGA	0.398													2	5	---	---	---	---	
NTRK3	4916	broad.mit.edu	37	15	88788929	88788930	+	Intron	DEL	AC	-	-	rs72427727		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88788929_88788930delAC	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010bnh.1_Intron|NTRK3_uc002bmg.2_Intron	NM_001012338	NP_001012338	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	281			BRCA - Breast invasive adenocarcinoma(143;0.211)			AAATAGTtttacacacacacac	0.198			T	ETV6	congenital fibrosarcoma|Secretory breast 					TSP Lung(13;0.10)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	90692960	90692963	+	IGR	DEL	TGTG	-	-	rs66487395		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90692960_90692963delTGTG								IDH2 (47252 upstream) : SEMA4B (35189 downstream)																							TCCAAATCTAtgtgtgtgtgtgtg	0.152													1	5	---	---	---	---	
BLM	641	broad.mit.edu	37	15	91295312	91295312	+	Intron	DEL	A	-	-	rs66739913		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91295312delA	uc002bpr.2	+						BLM_uc010uqh.1_Intron|BLM_uc010uqi.1_Intron|BLM_uc010bnx.2_Intron	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein						double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TGAAAGCCTCAAAAAAAAACC	0.249			Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	97642991	97642991	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97642991delC								SPATA8 (314147 upstream) : LOC91948 (642855 downstream)																							gacctcctctcccccagaaag	0.000													4	2	---	---	---	---	
ADAMTS17	170691	broad.mit.edu	37	15	100815990	100815992	+	Intron	DEL	GCT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100815990_100815992delGCT	uc002bvv.1	-						ADAMTS17_uc002bvx.1_Intron	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		GGGGCCAGTGGCTGACGCTAATC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	4356578	4356578	+	IGR	DEL	C	-	-	rs112476875		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4356578delC								TFAP4 (33577 upstream) : GLIS2 (25647 downstream)																							AGACTGGCAACCCCCAGGCCT	0.612													4	2	---	---	---	---	
PPL	5493	broad.mit.edu	37	16	4953313	4953313	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4953313delC	uc002cyd.1	-							NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin						keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6						CGGAAGAGCTCGCTCAAAAGC	0.348													4	2	---	---	---	---	
ARL6IP1	23204	broad.mit.edu	37	16	18810349	18810349	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18810349delT	uc002dfl.1	-						ARL6IP1_uc010van.1_Intron|ARL6IP1_uc010bvz.1_Intron	NM_015161	NP_055976	Q15041	AR6P1_HUMAN	ADP-ribosylation factor-like 6 interacting							integral to membrane	protein binding				0						gttttttgtgttttttttttt	0.119													6	3	---	---	---	---	
IL4R	3566	broad.mit.edu	37	16	27367405	27367405	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27367405delC	uc002don.2	+						IL4R_uc002dop.3_Intron|IL4R_uc010bxy.2_Intron|IL4R_uc002doo.2_Intron	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a						immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2						CCACttttttctttttttttt	0.219													4	3	---	---	---	---	
MAZ	4150	broad.mit.edu	37	16	29820816	29820817	+	Intron	INS	-	C	C			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29820816_29820817insC	uc002dty.2	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MAZ_uc002dtv.1_Intron|MAZ_uc010vdx.1_Intron|MAZ_uc002dtw.2_Intron|MAZ_uc002dtx.2_Intron|MAZ_uc010bzg.2_Intron|MAZ_uc002dtz.1_3'UTR|MAZ_uc002dua.2_Intron|MAZ_uc010vdy.1_Intron|uc002duc.1_Intron|PRRT2_uc002dud.2_5'Flank|PRRT2_uc002due.3_5'Flank|PRRT2_uc002duf.1_5'Flank	NM_002383	NP_002374	P56270	MAZ_HUMAN	MYC-associated zinc finger protein isoform 1						regulation of transcription, DNA-dependent|termination of RNA polymerase II transcription|transcription initiation from RNA polymerase II promoter	nucleus	DNA binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1						CTCTGGGGTCTCCGCCTGGCTG	0.668													20	15	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32443299	32443300	+	IGR	DEL	CA	-	-	rs111926096		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32443299_32443300delCA								HERC2P4 (279425 upstream) : TP53TG3B (241541 downstream)																							TAACCAGtcccagctactcagg	0.124													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49496435	49496436	+	IGR	DEL	AG	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49496435_49496436delAG								C16orf78 (63118 upstream) : ZNF423 (28086 downstream)																							gagcagagacagagagagagag	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59792271	59792272	+	IGR	DEL	CT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59792271_59792272delCT								None (None upstream) : None (None downstream)																							atcctcccccctctctctctgt	0.000													4	2	---	---	---	---	
RANBP10	57610	broad.mit.edu	37	16	67836763	67836763	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67836763delA	uc002eud.2	-						RANBP10_uc010ceo.2_Intron|RANBP10_uc010vju.1_Intron|RANBP10_uc010vjv.1_Intron|RANBP10_uc010vjx.1_Intron|RANBP10_uc010vjy.1_Intron	NM_020850	NP_065901	Q6VN20	RBP10_HUMAN	RAN binding protein 10											ovary(1)	1		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		CTCATCTCTCAAAAAATACAA	0.378													4	2	---	---	---	---	
TSNAXIP1	55815	broad.mit.edu	37	16	67854645	67854645	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67854645delA	uc002euj.2	+						TSNAXIP1_uc010cep.2_Intron|TSNAXIP1_uc010vjz.1_Intron|TSNAXIP1_uc002euf.3_Intron|TSNAXIP1_uc010vka.1_Intron|TSNAXIP1_uc010vkb.1_Intron|TSNAXIP1_uc002eug.3_Intron|TSNAXIP1_uc002euh.3_Intron|TSNAXIP1_uc002eui.3_Intron|TSNAXIP1_uc002euk.2_5'Flank	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN	translin-associated factor X interacting protein						cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm					0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)		agactgtctcaaaaaaaaaaa	0.254													5	6	---	---	---	---	
SLC12A4	6560	broad.mit.edu	37	16	68003353	68003355	+	5'Flank	DEL	CTC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68003353_68003355delCTC	uc002euz.2	-						SLC12A4_uc010vkh.1_5'Flank|SLC12A4_uc010vki.1_5'Flank|SLC12A4_uc010vkj.1_5'Flank|SLC12A4_uc002eva.2_5'Flank|SLC12A4_uc010cew.1_5'Flank	NM_005072	NP_005063	Q9UP95	S12A4_HUMAN	solute carrier family 12, member 4 isoform a						cell volume homeostasis|potassium ion transport|sodium ion transport	integral to plasma membrane|membrane fraction	potassium:chloride symporter activity			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CTATTTTTTTCTCTATCAGAAAA	0.458													4	2	---	---	---	---	
CIRH1A	84916	broad.mit.edu	37	16	69202534	69202534	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69202534delA	uc002ews.3	+						CIRH1A_uc002ewt.3_Intron|CIRH1A_uc010cfi.2_Intron	NM_032830	NP_116219	Q969X6	CIR1A_HUMAN	cirhin							nucleolus	protein binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.125)		tctaaaaaataaaaaaaaaaG	0.169													6	3	---	---	---	---	
WDR59	79726	broad.mit.edu	37	16	74943867	74943868	+	Intron	INS	-	T	T	rs113238843		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74943867_74943868insT	uc002fdh.1	-						WDR59_uc002fdi.2_Intron|WDR59_uc002fdg.1_Intron	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59											ovary(1)|breast(1)	2						TCTCTGATAGGttttttttttt	0.252													11	9	---	---	---	---	
CDYL2	124359	broad.mit.edu	37	16	80722486	80722487	+	Intron	INS	-	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80722486_80722487insT	uc002ffs.2	-							NM_152342	NP_689555	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2							nucleus	catalytic activity|protein binding			central_nervous_system(1)	1						AGAAAACACTGTTTTTCCTGAA	0.391													4	2	---	---	---	---	
BCMO1	53630	broad.mit.edu	37	16	81302906	81302906	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81302906delC	uc002fgn.1	+						BCMO1_uc010vnp.1_Intron	NM_017429	NP_059125	Q9HAY6	BCDO1_HUMAN	beta-carotene 15,15'-monooxygenase						retinoid metabolic process|steroid metabolic process	cytosol	beta-carotene 15,15'-monooxygenase activity|metal ion binding|monooxygenase activity				0						tttagtttttctttttttttt	0.264													4	2	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	83508011	83508011	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83508011delC	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)		tccaaggattccactctcaag	0.055													4	2	---	---	---	---	
RPA1	6117	broad.mit.edu	37	17	1792382	1792383	+	Intron	INS	-	TGA	TGA	rs150154237	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1792382_1792383insTGA	uc002fto.2	+							NM_002945	NP_002936	P27694	RFA1_HUMAN	replication protein A1						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	actin cytoskeleton|cytoplasm|DNA replication factor A complex|PML body	metal ion binding|protein binding|single-stranded DNA binding				0						CACTTGCCTGCTAACTGCTATG	0.416								NER					3	3	---	---	---	---	
KIAA0664	23277	broad.mit.edu	37	17	2613682	2613683	+	Intron	DEL	TA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2613682_2613683delTA	uc002fuy.1	-							NM_015229	NP_056044	O75153	K0664_HUMAN	hypothetical protein LOC23277								binding			breast(2)	2						GCAACTCCGCTATGATGGGAAC	0.579													4	2	---	---	---	---	
MYH13	8735	broad.mit.edu	37	17	10209537	10209538	+	Intron	INS	-	TG	TG	rs66516471		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10209537_10209538insTG	uc002gmk.1	-							NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle						muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						ACCAAAATAGAtgtgtgtgtgt	0.287													4	2	---	---	---	---	
MYH8	4626	broad.mit.edu	37	17	10308044	10308045	+	Intron	DEL	AC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10308044_10308045delAC	uc002gmm.2	-						uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						TGCAGGCTTTacacacacacac	0.307									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				6	3	---	---	---	---	
RICH2	9912	broad.mit.edu	37	17	12753926	12753926	+	Intron	DEL	G	-	-	rs11319940		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12753926delG	uc002gnr.3	+						RICH2_uc010vvk.1_Intron|RICH2_uc010vvl.1_Intron|RICH2_uc002gns.3_Intron|RICH2_uc010vvm.1_Intron|RICH2_uc010vvn.1_Intron	NM_014859	NP_055674	Q17R89	RHG44_HUMAN	Rho GTPase-activating protein RICH2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0						gctccagaaagagagtctcac	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21250069	21250069	+	IGR	DEL	C	-	-	rs66672846		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21250069delC								MAP2K3 (31520 upstream) : KCNJ12 (29630 downstream)																							GTTCTTTGTGCTGTAGCTGCA	0.343													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21518703	21518704	+	IGR	INS	-	A	A	rs150372573	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21518703_21518704insA								C17orf51 (40972 upstream) : FAM27L (306666 downstream)																							TTCAAGGAATCAAAAAATGAAA	0.218													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	26549427	26549427	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26549427delC								NLK (26025 upstream) : PYY2 (4162 downstream)																							ACTAGAAACTCCCTATCCCCC	0.552													4	2	---	---	---	---	
SGK494	124923	broad.mit.edu	37	17	26926101	26926102	+	Intron	INS	-	G	G	rs138449345	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26926101_26926102insG	uc010waq.1	-						SPAG5_uc002hbq.2_5'Flank					Homo sapiens coiled-coil related protein DEEPEST (DEEPEST) mRNA, complete cds.												0						GGGTAGAgcccggggggcgggg	0.589													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35240141	35240141	+	IGR	DEL	G	-	-	rs34331874		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35240141delG								MRM1 (274735 upstream) : LHX1 (54358 downstream)																							ttcccctgatggggggacaga	0.139													1	5	---	---	---	---	
TBX2	6909	broad.mit.edu	37	17	59480290	59480291	+	Intron	DEL	AT	-	-	rs61046721		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59480290_59480291delAT	uc010wox.1	+						TBX2_uc002ize.2_Intron|TBX2_uc002izg.2_Intron	NM_005994	NP_005985	Q13207	TBX2_HUMAN	T-box 2						cell aging|positive regulation of cell proliferation		sequence-specific DNA binding				0						ggaagaaCCGATagagagagag	0.139													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	71651060	71651060	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71651060delA								SDK2 (10833 upstream) : C17orf54 (94349 downstream)																							tccctgctctaaaaaaacttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76476483	76476483	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76476483delT								DNAH17 (7627 upstream) : CYTH1 (193648 downstream)																							atattgtatgtaacatactta	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	6634900	6634900	+	IGR	DEL	T	-	-	rs111803053		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6634900delT								L3MBTL4 (219990 upstream) : ARHGAP28 (153593 downstream)																							ttcagagtgattttttttttt	0.000													4	3	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13418133	13418133	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13418133delC	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		CTGAGGCCCTCCCAGGCTGGC	0.602													4	2	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13594051	13594052	+	Intron	DEL	AC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13594051_13594052delAC	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		ATATATTCATACACACACACAC	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	13880481	13880482	+	IGR	DEL	AG	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13880481_13880482delAG								MC5R (53741 upstream) : MC2R (1561 downstream)																							ctcagtaggtagagagagagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	19924109	19924109	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19924109delT								GATA6 (141882 upstream) : CTAGE1 (69455 downstream)																							gtttttgttcttttttttttt	0.179													4	3	---	---	---	---	
HRH4	59340	broad.mit.edu	37	18	22052627	22052628	+	Intron	INS	-	G	G			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22052627_22052628insG	uc002kvi.2	+						HRH4_uc010xbd.1_Intron|HRH4_uc010dlx.2_Intron	NM_021624	NP_067637	Q9H3N8	HRH4_HUMAN	histamine H4 receptor isoform 1							integral to membrane|plasma membrane	histamine receptor activity			ovary(2)	2	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Clozapine(DB00363)	ACAGTGTGATAGGGGAAAGGGA	0.475													4	2	---	---	---	---	
CELF4	56853	broad.mit.edu	37	18	34921995	34921996	+	Intron	DEL	GT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34921995_34921996delGT	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						gtgtgtgtgcgtgtgtgtgtgt	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38352103	38352103	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38352103delT								LOC647946 (971821 upstream) : KC6 (708135 downstream)																							gtatcactgatttttttttct	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39003993	39003993	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39003993delG								None (None upstream) : KC6 (56245 downstream)																							taacagtggagggaggctcag	0.035													4	2	---	---	---	---	
SLC14A1	6563	broad.mit.edu	37	18	43322319	43322319	+	Intron	DEL	T	-	-	rs72235948		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43322319delT	uc010xcn.1	+						SLC14A1_uc010dnk.2_Intron|SLC14A1_uc002lbf.3_Intron|SLC14A1_uc002lbg.3_Intron|SLC14A1_uc010xco.1_Intron|SLC14A1_uc002lbh.3_Intron|SLC14A1_uc002lbi.3_Intron|SLC14A1_uc002lbj.3_Intron|SLC14A1_uc002lbk.3_Intron	NM_001146036	NP_001139508	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter),							integral to plasma membrane	urea transmembrane transporter activity			central_nervous_system(1)|pancreas(1)	2						tgttttttggttttttttttt	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57490640	57490640	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57490640delT								CCBE1 (125996 upstream) : PMAIP1 (76552 downstream)																							TGTTGTTTGCTTTTTGTTTTG	0.413											OREG0025023	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58918977	58918977	+	IGR	DEL	A	-	-	rs75049303		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58918977delA								MC4R (878976 upstream) : CDH20 (82011 downstream)																							TGACAGTTGGAAAAAAAAAAT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62342867	62342868	+	IGR	DEL	CT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62342867_62342868delCT								C18orf20 (526607 upstream) : None (None downstream)																							GCCAGTACAACTCTCTCTCCAT	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73080936	73080936	+	IGR	DEL	C	-	-	rs117474209	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73080936delC								TSHZ1 (79036 upstream) : C18orf62 (40891 downstream)																							acggtcctgtccccgaaaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76423557	76423557	+	IGR	DEL	T	-	-	rs35573486		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76423557delT								None (None upstream) : SALL3 (316718 downstream)																							TATCCCCGGATTTTTTTGCTT	0.358													4	2	---	---	---	---	
BSG	682	broad.mit.edu	37	19	582927	582927	+	3'UTR	DEL	T	-	-	rs8259	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:582927delT	uc002loz.2	+	9					BSG_uc002loy.2_3'UTR|BSG_uc002lpa.2_3'UTR|BSG_uc002lpb.2_RNA|BSG_uc010drr.2_Frame_Shift_Del_p.F297fs|BSG_uc002lpc.2_3'UTR|BSG_uc002lpd.2_RNA	NM_001728	NP_001719	P35613	BASI_HUMAN	basigin isoform 1 precursor						blood coagulation|cell surface receptor linked signaling pathway|leukocyte migration|pyruvate metabolic process	Golgi membrane|integral to membrane|melanosome	lactate transmembrane transporter activity|mannose binding|protein binding				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)		GTTCCTTAGGTTTTTTTCCTT	0.507													4	2	---	---	---	---	
LINGO3	645191	broad.mit.edu	37	19	2301259	2301259	+	Intron	DEL	T	-	-	rs79783822		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2301259delT	uc010dsx.1	-						SPPL2B_uc010dsw.1_Intron	NM_001101391	NP_001094861	P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3							integral to membrane					0						AGATTTAGTGttttttttttt	0.303													3	5	---	---	---	---	
FSD1	79187	broad.mit.edu	37	19	4311683	4311683	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4311683delA	uc002lzy.2	+						FSD1_uc002lzz.2_Intron|FSD1_uc002maa.2_5'UTR	NM_024333	NP_077309	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing						cell division|mitosis	cleavage furrow|microtubule|microtubule organizing center|nucleus				skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		ctctgtctctaaaaaaaaaaa	0.264													9	4	---	---	---	---	
KDM4B	23030	broad.mit.edu	37	19	4966599	4966599	+	5'Flank	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4966599delT	uc002mbq.3	+						KDM4B_uc010xil.1_5'Flank	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1						ATGATTGCACttttttttttt	0.234													4	3	---	---	---	---	
OLFM2	93145	broad.mit.edu	37	19	10033916	10033916	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10033916delT	uc002mmp.2	-							NM_058164	NP_477512	O95897	NOE2_HUMAN	olfactomedin 2 precursor							extracellular region				large_intestine(1)|skin(1)	2						acagTGATAATTTTTTTTTTC	0.060													4	2	---	---	---	---	
DOCK6	57572	broad.mit.edu	37	19	11326767	11326767	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11326767delT	uc002mqs.3	-						DOCK6_uc010xlq.1_Intron	NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3						AAAAAAAAAAttttttttttt	0.214													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	16173084	16173084	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16173084delC								FLJ25328 (20169 upstream) : TPM4 (5233 downstream)																							ttcctgacttccacccaagac	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	22501503	22501503	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22501503delG								ZNF676 (121750 upstream) : ZNF98 (72396 downstream)																							CTACAAATGTGAAGAAAGTGG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30128506	30128507	+	IGR	DEL	TC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30128506_30128507delTC								POP4 (20344 upstream) : PLEKHF1 (27820 downstream)																							TTCTGAGGCTtctctctctctc	0.500													4	2	---	---	---	---	
ZNF536	9745	broad.mit.edu	37	19	30895780	30895780	+	Intron	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30895780delC	uc002nsu.1	+						ZNF536_uc010edd.1_Intron	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					agttgcaagtccaggcctcac	0.000													4	2	---	---	---	---	
LOC400696	400696	broad.mit.edu	37	19	40173904	40173904	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40173904delT	uc010xve.1	+						LOC400696_uc010xvf.1_Intron	NM_207646	NP_997529			hypothetical protein LOC400696												0						gcctggctaattttttttttg	0.000													4	2	---	---	---	---	
RPS19	6223	broad.mit.edu	37	19	42366105	42366108	+	Intron	DEL	ACTA	-	-	rs149774805		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42366105_42366108delACTA	uc002ort.2	+							NM_001022	NP_001013	P39019	RS19_HUMAN	ribosomal protein S19						endocrine pancreas development|erythrocyte differentiation|gas transport|positive regulation of cellular component movement|response to extracellular stimulus|ribosomal small subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0						ACCGACCTTCACTAACTAAGGGGC	0.495									Diamond-Blackfan_Anemia				8	5	---	---	---	---	
ERF	2077	broad.mit.edu	37	19	42753474	42753474	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42753474delG	uc002ote.3	-	4	948	c.790delC	c.(790-792)CTCfs	p.L264fs	ERF_uc002otd.3_5'UTR	NM_006494	NP_006485	P50548	ERF_HUMAN	Ets2 repressor factor	264					cell proliferation|regulation of transcription from RNA polymerase II promoter	nucleus	ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			lung(1)|kidney(1)|central_nervous_system(1)|skin(1)	4		Prostate(69;0.00682)				GCCGGGGAGAGCTGAGGGGGC	0.711													11	18	---	---	---	---	
BBC3	27113	broad.mit.edu	37	19	47732436	47732437	+	Intron	DEL	AC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47732436_47732437delAC	uc002pgf.3	-						BBC3_uc010xyl.1_Intron|BBC3_uc010eky.2_Intron|BBC3_uc010ekz.2_Intron|hsa-mir-3191|MI0014236_5'Flank	NM_014417	NP_055232	Q9BXH1	BBC3_HUMAN	BCL2 binding component 3 isoform 4						activation of caspase activity|activation of pro-apoptotic gene products|cellular response to hypoxia|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|negative regulation of growth|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|positive regulation of thymocyte apoptosis|protein insertion into mitochondrial membrane involved in induction of apoptosis|reduction of endoplasmic reticulum calcium ion concentration|release of cytochrome c from mitochondria|release of sequestered calcium ion into cytosol	cytosol|mitochondrial outer membrane	protein binding|protein binding				0		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.000179)|OV - Ovarian serous cystadenocarcinoma(262;0.00029)|Epithelial(262;0.0103)|GBM - Glioblastoma multiforme(486;0.0234)		GCAAACACAAACACACACACAC	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19804031	19804031	+	IGR	DEL	G	-	-	rs35040175		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19804031delG								SLC24A3 (100491 upstream) : RIN2 (66179 downstream)																							TGCTCTGCCTGCTTTTTTTTT	0.393													4	2	---	---	---	---	
C20orf26	26074	broad.mit.edu	37	20	20243447	20243449	+	Intron	DEL	TGT	-	-	rs142947975		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20243447_20243449delTGT	uc002wru.2	+						C20orf26_uc010zse.1_Intron|C20orf26_uc002wrw.2_Intron|C20orf26_uc002wrv.2_Intron	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		CCTGTTTTTGTGTTTTTTTTTTT	0.232													5	3	---	---	---	---	
RALGAPA2	57186	broad.mit.edu	37	20	20636359	20636360	+	Intron	DEL	AC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20636359_20636360delAC	uc002wrz.2	-						RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						GGGGAGGTAGACACAGTCACTA	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	21267494	21267494	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21267494delC								PLK1S1 (40238 upstream) : XRN2 (16448 downstream)																							cttctcctggcccctctctcc	0.119													4	2	---	---	---	---	
TPX2	22974	broad.mit.edu	37	20	30382558	30382559	+	Intron	INS	-	GTGT	GTGT	rs10638647		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30382558_30382559insGTGT	uc002wwp.1	+						TPX2_uc010gdv.1_Intron	NM_012112	NP_036244	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated protein homolog						activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			tctgtcgcatagtgtgtgtgtg	0.045													3	3	---	---	---	---	
DHX35	60625	broad.mit.edu	37	20	37632714	37632714	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37632714delT	uc002xjh.2	+						DHX35_uc010zwa.1_Intron|DHX35_uc010zwb.1_Intron|DHX35_uc010zwc.1_Intron	NM_021931	NP_068750	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35							catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				TGAAGAtttcttttttttttg	0.159													5	3	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	40887246	40887246	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40887246delT	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)				CTGTGACTAATTTTTTTAAAT	0.368													4	2	---	---	---	---	
ZMYND8	23613	broad.mit.edu	37	20	45877747	45877748	+	Intron	INS	-	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45877747_45877748insA	uc002xta.1	-						ZMYND8_uc010ghq.1_Intron|ZMYND8_uc010ghr.1_Intron|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_Intron|ZMYND8_uc002xsw.1_Intron|ZMYND8_uc002xsx.1_Intron|ZMYND8_uc002xsy.1_Intron|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc002xtg.2_Intron|ZMYND8_uc010ghs.1_Intron	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			ACTCAGAGGATCCTCATTCTGC	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	51487687	51487687	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51487687delT								ZFP64 (679163 upstream) : TSHZ2 (101190 downstream)																							tgtgtctctctttttttttct	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58790250	58790250	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58790250delA	uc002ybl.2	+						uc010gjw.1_Intron					Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																		TTCCTTGGTCAGGGATCTGGT	0.557													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	59879832	59879833	+	Intron	DEL	TG	-	-	rs72496453		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59879832_59879833delTG	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)			tgtgtggggttgtgtgtgtgtg	0.084													3	4	---	---	---	---	
PRIC285	85441	broad.mit.edu	37	20	62191130	62191133	+	Intron	DEL	AGTC	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62191130_62191133delAGTC	uc002yfm.2	-						PRIC285_uc002yfl.1_Intron	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285						cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)			gtcagatgggagtcagtcagagtc	0.103													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9544374	9544374	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9544374delT								None (None upstream) : None (None downstream)																							ctcctggcactgaccttgccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9828206	9828207	+	IGR	INS	-	TA	TA			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9828206_9828207insTA								None (None upstream) : None (None downstream)																							ccactccctgttatagttgcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10707258	10707258	+	IGR	DEL	T	-	-	rs141818944		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10707258delT								None (None upstream) : TPTE (199485 downstream)																							ttctttgtgatttgtgatttc	0.000													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10773581	10773582	+	IGR	DEL	AG	-	-	rs112169104		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10773581_10773582delAG								None (None upstream) : TPTE (133161 downstream)																							ttctacaaaaagagagattcaa	0.000													5	6	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10951725	10951728	+	Intron	DEL	CTGT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10951725_10951728delCTGT	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)		TTAAAATCACCTGTCTGTTTACAA	0.279													3	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11030943	11030944	+	Intron	DEL	TA	-	-	rs143227624	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11030943_11030944delTA	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		agcaaacacttaattttttccc	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11031726	11031726	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11031726delA	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aacctgctacaagagtctact	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11039939	11039941	+	Intron	DEL	GTT	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11039939_11039941delGTT	uc002yit.1	-						TPTE_uc002yis.1_5'Flank	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GGATATAATCGTTGTTCTTCATC	0.320													7	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11059163	11059163	+	Intron	DEL	G	-	-	rs141258961		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11059163delG	uc002yit.1	-						BAGE_uc002yiw.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ATCTCTCTGTGGGAAATGACT	0.368													9	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11088127	11088127	+	Intron	DEL	T	-	-	rs139143393		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11088127delT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GAATAAGATATTTTTAAAATA	0.259													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	17414505	17414506	+	IGR	DEL	GA	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17414505_17414506delGA								USP25 (162128 upstream) : C21orf34 (28336 downstream)																							TGGGGCAGGGGAGAGAGAGAGA	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	20342180	20342181	+	IGR	INS	-	G	G	rs143981649	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20342180_20342181insG								TMPRSS15 (566210 upstream) : None (None downstream)																							ACTTAAGCCATGGTTTTTGTTT	0.257													4	2	---	---	---	---	
JAM2	58494	broad.mit.edu	37	21	27010942	27010942	+	5'Flank	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27010942delA	uc002ylp.1	+						JAM2_uc011ace.1_5'Flank|JAM2_uc002ylq.1_5'Flank|JAM2_uc011acf.1_5'Flank|JAM2_uc010glh.1_5'Flank|JAM2_uc002ylr.1_5'Flank|JAM2_uc010gli.1_5'Flank	NM_021219	NP_067042	P57087	JAM2_HUMAN	junctional adhesion molecule 2 precursor						blood coagulation|cell-cell adhesion|leukocyte migration	integral to plasma membrane|tight junction					0						TTCAACCTTTaaaaaaaaaca	0.303													4	2	---	---	---	---	
GART	2618	broad.mit.edu	37	21	34906683	34906683	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34906683delT	uc002yrx.2	-						GART_uc002yrz.2_Intron|GART_uc010gmd.2_Intron|GART_uc002yry.2_Intron|GART_uc002ysa.2_Intron	NM_000819	NP_000810	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase,						'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|metal ion binding|methyltransferase activity|phosphoribosylamine-glycine ligase activity|phosphoribosylformylglycinamidine cyclo-ligase activity|phosphoribosylglycinamide formyltransferase activity|protein binding			ovary(1)	1					Pemetrexed(DB00642)	catgcccggcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	39716948	39716949	+	IGR	INS	-	TA	TA	rs141314931	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39716948_39716949insTA								KCNJ15 (43204 upstream) : ERG (35003 downstream)																							GCCAAGAATCCTATATACCCAG	0.401													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	42282586	42282586	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42282586delG								DSCAM (63547 upstream) : C21orf130 (230841 downstream)																							AGGGCTTCATGGTCCTTGTCC	0.498													4	2	---	---	---	---	
UBASH3A	53347	broad.mit.edu	37	21	43826184	43826185	+	Intron	INS	-	TT	TT	rs117834816	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43826184_43826185insTT	uc002zbe.2	+						UBASH3A_uc002zbf.2_Intron|UBASH3A_uc010gpc.2_Intron|UBASH3A_uc010gpd.2_Intron|UBASH3A_uc010gpe.2_Intron	NM_018961	NP_061834	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing,							cytosol|nucleus				ovary(3)	3						GGGCTGAAGCGGGTAGCCAGGG	0.658													9	6	---	---	---	---	
DGCR2	9993	broad.mit.edu	37	22	19102589	19102591	+	Intron	DEL	GAG	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19102589_19102591delGAG	uc002zoq.1	-						DGCR2_uc002zor.1_Intron|DGCR2_uc011agr.1_Intron	NM_005137	NP_005128	P98153	IDD_HUMAN	integral membrane protein DGCR2 precursor						cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)					ACCGCAGGCAGAGGAGGAGGAGA	0.576													4	2	---	---	---	---	
GGT1	2678	broad.mit.edu	37	22	25016169	25016170	+	Intron	INS	-	T	T	rs28418841	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25016169_25016170insT	uc003aan.1	+						GGT1_uc003aas.1_Intron|GGT1_uc003aat.1_Intron|GGT1_uc003aau.1_Intron|GGT1_uc003aav.1_Intron|GGT1_uc003aaw.1_Intron|GGT1_uc003aax.1_Intron	NM_013430	NP_038347	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1 precursor						glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)	aaaaaaaaaaaaTCTTTCCTCC	0.277													7	4	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26185741	26185741	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26185741delA	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						CCACCCTGAGAAACCCACTGG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27858646	27858647	+	IGR	INS	-	T	T			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27858646_27858647insT								MIAT (743697 upstream) : MN1 (285619 downstream)																							tctttcttttcttttttttttA	0.386													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	34457267	34457267	+	IGR	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34457267delT								LARGE (138683 upstream) : None (None downstream)																							tttgcagctcttccaggagtc	0.000													4	2	---	---	---	---	
ELFN2	114794	broad.mit.edu	37	22	37803223	37803224	+	Intron	INS	-	C	C	rs149255878	by1000genomes	TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37803223_37803224insC	uc003asq.3	-							NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62							cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)					acaagagggctcgggactggga	0.089													2	4	---	---	---	---	
FAM83F	113828	broad.mit.edu	37	22	40405163	40405163	+	Intron	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40405163delG	uc003ayk.1	+							NM_138435	NP_612444	Q8NEG4	FA83F_HUMAN	hypothetical protein LOC113828											breast(1)	1						gggcaggtgtGGGAGGCGACT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	6772373	6772374	+	IGR	INS	-	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6772373_6772374insA								VCX3A (319214 upstream) : HDHD1A (194587 downstream)																							CAGAAAAAAAGAAAAAAAATCT	0.327													4	2	---	---	---	---	
STS	412	broad.mit.edu	37	X	7114248	7114248	+	Intron	DEL	T	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7114248delT	uc004crw.2	+						STS_uc011mhp.1_Intron|STS_uc004crx.1_Intron			P08842	STS_HUMAN	Homo sapiens cDNA, FLJ94694, highly similar to Homo sapiens steroid sulfatase (microsomal), arylsulfatase C,isozyme S (STS), mRNA.						female pregnancy|steroid catabolic process	endoplasmic reticulum membrane|endosome|Golgi apparatus|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			central_nervous_system(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)	gaagggacagttatggagaag	0.000									Ichthyosis				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	13565426	13565426	+	IGR	DEL	T	-	-	rs71934868		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13565426delT								ATXN3L (226908 upstream) : EGFL6 (22315 downstream)																							GTACTGAGGATTTTTTTTTCA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	20784318	20784319	+	IGR	INS	-	A	A			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20784318_20784319insA								RPS6KA3 (498795 upstream) : CNKSR2 (608661 downstream)																							ATTGTTCAGAGAAAAAAAAACC	0.376													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	39534359	39534359	+	IGR	DEL	A	-	-	rs76849931		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39534359delA								MID1IP1 (868578 upstream) : BCOR (376142 downstream)																							tcaggaagagaagatgggtgt	0.000													4	2	---	---	---	---	
CASK	8573	broad.mit.edu	37	X	41779227	41779227	+	Intron	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41779227delA	uc004dfl.3	-						CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron	NM_003688	NP_003679	O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein						cell adhesion	actin cytoskeleton|cytoplasm|nucleus|plasma membrane	ATP binding|calmodulin binding|guanylate kinase activity|protein serine/threonine kinase activity			ovary(3)|lung(2)|stomach(1)	6						ACCAAGGGGGAAAAAAACACA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	44573284	44573284	+	IGR	DEL	G	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44573284delG								FUNDC1 (171063 upstream) : DUSP21 (129965 downstream)																							ACCTTGAGCAGGAGGAATGAG	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	125587222	125587225	+	IGR	DEL	TGTG	-	-	rs112557964		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125587222_125587225delTGTG								DCAF12L2 (287288 upstream) : DCAF12L1 (96143 downstream)																							GTATCTATCAtgtgtgtgtgtgtg	0.034													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	125619757	125619757	+	IGR	DEL	C	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125619757delC								DCAF12L2 (319823 upstream) : DCAF12L1 (63611 downstream)																							agcagcccctcctttgcattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	155252987	155252988	+	In_Frame_Ins	INS	-	CAGCACCAC	CAGCACCAC			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155252987_155252988insCAGCACCAC	uc004fnw.1	+	7	1602_1603	c.943_944insCAGCACCAC	c.(943-945)ACA>ACAGCACCACCA	p.315_316insAPP	uc004fnx.3_In_Frame_Ins_p.101_102insAPP	NM_182905	NP_878908			WAS protein family homolog 1																		TGGGGTactaacaccaccccca	0.530													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9936396	9936396	+	IGR	DEL	A	-	-			TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9936396delA								TTTY22 (285542 upstream) : None (None downstream)																							TTTTCCTGACACTTCTCCTTG	0.478													13	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9936398	9936398	+	IGR	DEL	T	-	-	rs113260873		TCGA-B0-4852-01A-01D-1501-10	TCGA-B0-4852-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9936398delT								TTTY22 (285544 upstream) : None (None downstream)																							TTCCTGACACTTCTCCTTGTC	0.473													13	9	---	---	---	---	
