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
UBXN11	91544	broad.mit.edu	37	1	26609138	26609138	+	Splice_Site	SNP	A	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26609138A>C	uc001blw.2	-	15	1565	c.1292_splice	c.e15+1	p.R431_splice	UBXN11_uc001blz.1_Splice_Site_p.R398_splice|UBXN11_uc001blv.2_Splice_Site_p.R393_splice|UBXN11_uc001bly.2_Splice_Site_p.R311_splice|UBXN11_uc001blx.2_Splice_Site_p.R189_splice|UBXN11_uc001bma.2_Splice_Site_p.R398_splice|UBXN11_uc001bmb.1_Splice_Site_p.R431_splice	NM_183008	NP_892120	Q5T124	UBX11_HUMAN	socius isoform 2							cytoplasm|cytoskeleton				ovary(1)	1						CCCTGCACCCACCTGGCCTGC	0.632													23	32	---	---	---	---	PASS
MTF2	22823	broad.mit.edu	37	1	93575963	93575963	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93575963T>C	uc009wdj.2	+	2	474	c.182T>C	c.(181-183)TTT>TCT	p.F61S	MTF2_uc001dph.2_5'UTR|MTF2_uc010oth.1_5'UTR|MTF2_uc009wdk.2_Missense_Mutation_p.F61S|MTF2_uc001dpi.3_5'UTR|MTF2_uc010oti.1_Intron|MTF2_uc001dpj.3_5'UTR|MTF2_uc001dpl.3_5'UTR	NM_007358	NP_031384	Q9Y483	MTF2_HUMAN	metal response element binding transcription	61						nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)		GATGGCTTGTTTTATCTTGGC	0.343													8	559	---	---	---	---	PASS
SLC35A3	23443	broad.mit.edu	37	1	100488064	100488064	+	3'UTR	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100488064T>C	uc001dsp.1	+	8					SLC35A3_uc001dsq.1_3'UTR|SLC35A3_uc009wdy.1_3'UTR|SLC35A3_uc001dsr.1_3'UTR|SLC35A3_uc001dss.1_3'UTR	NM_012243	NP_036375	Q9Y2D2	S35A3_HUMAN	solute carrier family 35 member 3A						UDP-N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	sugar:hydrogen symporter activity|UDP-N-acetylglucosamine transmembrane transporter activity				0		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.124)|all cancers(265;0.198)|Lung(183;0.199)		TTTTTCACGATGGGGCACTAG	0.368													107	189	---	---	---	---	PASS
WARS2	10352	broad.mit.edu	37	1	119575670	119575670	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119575670G>C	uc001ehn.2	-	6	975	c.947C>G	c.(946-948)CCA>CGA	p.P316R	WARS2_uc010oxf.1_Missense_Mutation_p.P222R|WARS2_uc001ehm.2_3'UTR|WARS2_uc010oxg.1_Missense_Mutation_p.P259R|WARS2_uc010oxh.1_3'UTR	NM_015836	NP_056651	Q9UGM6	SYWM_HUMAN	mitochondrial tryptophanyl tRNA synthetase 2	316					tryptophanyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|tryptophan-tRNA ligase activity				0	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	ACGCTTAATTGGGGCAAACTT	0.498													75	123	---	---	---	---	PASS
ANP32E	81611	broad.mit.edu	37	1	150192837	150192837	+	3'UTR	SNP	A	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150192837A>C	uc001etw.2	-	7					ANP32E_uc010pbt.1_RNA|ANP32E_uc010pbu.1_3'UTR|ANP32E_uc010pbv.1_3'UTR|ANP32E_uc001etv.3_3'UTR	NM_030920	NP_112182	Q9BTT0	AN32E_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32							cytoplasmic membrane-bounded vesicle|nucleus	phosphatase inhibitor activity				0	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			ACTAGTTCTTATTTGGAATGA	0.289													37	38	---	---	---	---	PASS
RABGAP1L	9910	broad.mit.edu	37	1	174221599	174221599	+	Intron	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174221599T>C	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Missense_Mutation_p.I298T|RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.2_Intron	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						GTAATTCCTATTCCTTTTGAA	0.299													6	370	---	---	---	---	PASS
LIN9	286826	broad.mit.edu	37	1	226465541	226465541	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226465541A>G	uc001hqa.2	-	7	975	c.665T>C	c.(664-666)GTT>GCT	p.V222A	LIN9_uc001hqb.2_Missense_Mutation_p.V187A|LIN9_uc001hqc.2_Missense_Mutation_p.V154A|LIN9_uc009xel.1_Missense_Mutation_p.V187A	NM_173083	NP_775106	Q5TKA1	LIN9_HUMAN	lin-9 homolog	206	Sufficient for interaction with RB1.				cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		GAATTGTGAAACATCTGCAAC	0.358													7	554	---	---	---	---	PASS
OR2M2	391194	broad.mit.edu	37	1	248343839	248343839	+	Silent	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248343839A>G	uc010pzf.1	+	1	552	c.552A>G	c.(550-552)CTA>CTG	p.L184L		NM_001004688	NP_001004688	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M,	184	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TCCCTTCCCTACTAATCCTCT	0.413													5	328	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32728121	32728121	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32728121T>C	uc010ezu.2	+	49	9451	c.9317T>C	c.(9316-9318)CTC>CCC	p.L3106P		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	3106					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					GGTGTTCAGCTCATATGCAAT	0.323													10	747	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61575328	61575328	+	Silent	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61575328G>A	uc002sbe.2	-	15	1984	c.1962C>T	c.(1960-1962)TGC>TGT	p.C654C		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	654					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			AGTCCCCCAGGCAAATGCCTG	0.448													67	99	---	---	---	---	PASS
SCN3A	6328	broad.mit.edu	37	2	165946947	165946947	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165946947T>C	uc002ucx.2	-	28	6208	c.5716A>G	c.(5716-5718)ATC>GTC	p.I1906V	SCN3A_uc010zcy.1_Missense_Mutation_p.I389V|SCN3A_uc002ucy.2_Missense_Mutation_p.I1857V|SCN3A_uc002ucz.2_Missense_Mutation_p.I1857V	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	1906	IQ.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)	CGCTGAATGATAGCGGCAGAC	0.373													10	155	---	---	---	---	PASS
OSBPL6	114880	broad.mit.edu	37	2	179255817	179255817	+	Silent	SNP	T	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179255817T>G	uc002ulx.2	+	22	2697	c.2319T>G	c.(2317-2319)TCT>TCG	p.S773S	OSBPL6_uc002uly.2_Silent_p.S798S|OSBPL6_uc010zfe.1_Silent_p.S742S|OSBPL6_uc002ulz.2_Silent_p.S737S|OSBPL6_uc002uma.2_Silent_p.S777S	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	oxysterol-binding protein-like protein 6 isoform	773					lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			ATTGGAATTCTAACATGAATG	0.428													181	370	---	---	---	---	PASS
ITGA4	3676	broad.mit.edu	37	2	182347113	182347113	+	Silent	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182347113A>G	uc002unu.2	+	8	1630	c.867A>G	c.(865-867)AAA>AAG	p.K289K	ITGA4_uc010zfl.1_Silent_p.K289K	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor	289	FG-GAP 4.|Extracellular (Potential).				blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)	TTGATGAAAAAGAACTAAATA	0.308													6	409	---	---	---	---	PASS
ABCA12	26154	broad.mit.edu	37	2	215839587	215839587	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215839587T>A	uc002vew.2	-	35	5603	c.5383A>T	c.(5383-5385)AAT>TAT	p.N1795Y	ABCA12_uc002vev.2_Missense_Mutation_p.N1477Y|ABCA12_uc010zjn.1_Missense_Mutation_p.N722Y	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	1795					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GGGTGATAATTACTGCAATAT	0.398													118	211	---	---	---	---	PASS
APPL1	26060	broad.mit.edu	37	3	57291081	57291081	+	Splice_Site	SNP	T	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57291081T>A	uc003dio.2	+	14	1394	c.1247_splice	c.e14+2	p.G416_splice	APPL1_uc010hnb.2_Splice_Site_p.G416_splice|APPL1_uc011bey.1_Splice_Site_p.G399_splice	NM_012096	NP_036228	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH						apoptosis|cell cycle|cell proliferation|insulin receptor signaling pathway|regulation of apoptosis|regulation of establishment of protein localization in plasma membrane|regulation of glucose import	cytosol|early endosome membrane|microsome|nucleus|vesicle membrane	protein kinase B binding			breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		AGCAGCAGGGTAAGTTACCAC	0.448													48	79	---	---	---	---	PASS
KIAA1407	57577	broad.mit.edu	37	3	113723397	113723397	+	Intron	SNP	G	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113723397G>T	uc003eax.2	-						KIAA1407_uc011bin.1_RNA|KIAA1407_uc011bio.1_3'UTR	NM_020817	NP_065868	Q8NCU4	K1407_HUMAN	hypothetical protein LOC57577											ovary(2)	2						AAAACCTCAAGAGTTGCCAGA	0.473													42	77	---	---	---	---	PASS
UBA5	79876	broad.mit.edu	37	3	132389115	132389115	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132389115A>G	uc003epa.3	+	5	723	c.481A>G	c.(481-483)ATG>GTG	p.M161V	NPHP3_uc003eoz.1_Intron|UBA5_uc010htr.2_Missense_Mutation_p.M105V|UBA5_uc010htt.2_Missense_Mutation_p.M161V|UBA5_uc003epb.3_Missense_Mutation_p.M105V	NM_024818	NP_079094	Q9GZZ9	UBA5_HUMAN	ubiquitin-activating enzyme 5 isoform 1	161					protein ufmylation	aggresome|cytoplasm|cytoplasm|nucleus	ATP binding|cofactor binding|metal ion binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding|UFM1 activating enzyme activity			kidney(1)	1						TCAACATTTCATGGATAGAAT	0.259													99	195	---	---	---	---	PASS
CPB1	1360	broad.mit.edu	37	3	148559631	148559631	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148559631A>T	uc003ewl.2	+	6	519	c.496A>T	c.(496-498)AAG>TAG	p.K166*		NM_001871	NP_001862	P15086	CBPB1_HUMAN	pancreatic carboxypeptidase B1 preproprotein	166					proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			TGGACAAAATAAGCCTGCCAT	0.458													191	316	---	---	---	---	PASS
MECOM	2122	broad.mit.edu	37	3	168833662	168833662	+	Silent	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168833662A>G	uc003ffi.3	-	7	1703	c.1434T>C	c.(1432-1434)GCT>GCC	p.A478A	MECOM_uc010hwk.1_Silent_p.A501A|MECOM_uc003ffj.3_Silent_p.A543A|MECOM_uc011bpi.1_Silent_p.A479A|MECOM_uc003ffn.3_Silent_p.A478A|MECOM_uc003ffk.2_Silent_p.A478A|MECOM_uc003ffl.2_Silent_p.A638A|MECOM_uc011bpj.1_Silent_p.A666A|MECOM_uc011bpk.1_Silent_p.A468A|MECOM_uc010hwn.2_Silent_p.A666A	NM_005241	NP_005232	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform b	478					apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						CAGCAATAGAAGCAATAGCCT	0.408													8	867	---	---	---	---	PASS
USP13	8975	broad.mit.edu	37	3	179447988	179447988	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179447988A>G	uc003fkh.2	+	9	1181	c.1100A>G	c.(1099-1101)AAC>AGC	p.N367S	USP13_uc003fkf.2_Missense_Mutation_p.N367S	NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13	367					ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TATGTAGGAAACCTTCCCAGA	0.333													7	697	---	---	---	---	PASS
KLHL24	54800	broad.mit.edu	37	3	183390233	183390233	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183390233A>C	uc003flv.2	+	7	1858	c.1563A>C	c.(1561-1563)GAA>GAC	p.E521D	KLHL24_uc003flw.2_Missense_Mutation_p.E521D|KLHL24_uc003flx.2_Missense_Mutation_p.E521D	NM_017644	NP_060114	Q6TFL4	KLH24_HUMAN	DRE1 protein	521	Kelch 5.					axon|cytoplasm|perikaryon				ovary(1)	1	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)			ATCCAGTTGAAGATTACTGGA	0.393													62	104	---	---	---	---	PASS
ATP13A3	79572	broad.mit.edu	37	3	194182931	194182931	+	5'UTR	SNP	A	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194182931A>T	uc003fty.3	-	2						NM_024524	NP_078800	Q9H7F0	AT133_HUMAN	ATPase type 13A3						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)	1	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		CCTACAGTGGATTAAAGGTCC	0.418													143	247	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195509322	195509322	+	Silent	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195509322G>A	uc011bto.1	-	3	9205	c.8745C>T	c.(8743-8745)GTC>GTT	p.V2915V	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGTGTCGGTGACAGGAAGCG	0.612													3	15	---	---	---	---	PASS
TXK	7294	broad.mit.edu	37	4	48136175	48136175	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48136175A>G	uc003gxx.3	-	1	99	c.13T>C	c.(13-15)TCC>CCC	p.S5P	TXK_uc003gxy.1_Missense_Mutation_p.S5P	NM_003328	NP_003319	P42681	TXK_HUMAN	TXK tyrosine kinase	5						cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0						TACTCACAGGAGGAAAGGATC	0.443													8	464	---	---	---	---	PASS
PDGFRA	5156	broad.mit.edu	37	4	55156677	55156677	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55156677C>A	uc003han.3	+	22	3409	c.3078C>A	c.(3076-3078)GAC>GAA	p.D1026E	PDGFRA_uc003haa.2_Missense_Mutation_p.D786E	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	1026	Cytoplasmic (Potential).				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)	CTGACATTGACCCTGTCCCTG	0.572			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			49	72	---	---	---	---	PASS
POLR2B	5431	broad.mit.edu	37	4	57887152	57887152	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57887152G>A	uc003hcl.1	+	17	2454	c.2411G>A	c.(2410-2412)GGC>GAC	p.G804D	POLR2B_uc011cae.1_Missense_Mutation_p.G797D|POLR2B_uc011caf.1_Missense_Mutation_p.G729D|POLR2B_uc003hcm.1_Missense_Mutation_p.G297D	NM_000938	NP_000929	P30876	RPB2_HUMAN	DNA directed RNA polymerase II polypeptide B	804					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(2)	2	Glioma(25;0.08)|all_neural(26;0.181)					GTAGACCGCGGCTTCTTCAGG	0.353													142	196	---	---	---	---	PASS
GK2	2712	broad.mit.edu	37	4	80328227	80328227	+	Silent	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80328227T>C	uc003hlu.2	-	1	1146	c.1128A>G	c.(1126-1128)GCA>GCG	p.A376A		NM_033214	NP_149991	Q14410	GLPK2_HUMAN	glycerol kinase 2	376					glycerol-3-phosphate metabolic process	mitochondrial outer membrane	ATP binding|glycerol kinase activity			ovary(2)|skin(2)	4						GTATCCCTCTTGCACTGGGCT	0.423													6	294	---	---	---	---	PASS
DDIT4L	115265	broad.mit.edu	37	4	101108875	101108875	+	Missense_Mutation	SNP	G	C	C	rs148719835	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101108875G>C	uc003hvq.2	-	3	744	c.541C>G	c.(541-543)CTT>GTT	p.L181V		NM_145244	NP_660287	Q96D03	DDT4L_HUMAN	DNA-damage-inducible transcript 4-like	181					negative regulation of signal transduction	cytoplasm				ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;5.75e-09)		AGTGAGTAAAGTTTTTTCTTA	0.378													50	97	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13752256	13752256	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13752256C>T	uc003jfd.2	-	64	11057	c.11015G>A	c.(11014-11016)GGG>GAG	p.G3672E	DNAH5_uc003jfc.2_5'UTR	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3672	AAA 5 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					AAAGGTAGACCCAGTTTTAAT	0.403									Kartagener_syndrome				7	370	---	---	---	---	PASS
VCAN	1462	broad.mit.edu	37	5	82834255	82834255	+	Silent	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82834255T>C	uc003kii.3	+	8	5789	c.5433T>C	c.(5431-5433)AGT>AGC	p.S1811S	VCAN_uc003kij.3_Silent_p.S824S|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Silent_p.S475S	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	1811	GAG-beta.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)		AGCACAGCAGTATCCATCAAC	0.507													22	28	---	---	---	---	PASS
LY6G6F	259215	broad.mit.edu	37	6	31674688	31674688	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31674688C>T	uc003nwa.1	+	1	5	c.5C>T	c.(4-6)GCA>GTA	p.A2V	BAT5_uc011dnz.1_Intron|LY6G6F_uc003nwb.1_Missense_Mutation_p.A2V	NM_001003693	NP_001003693	Q5SQ64	LY66F_HUMAN	G6f protein precursor	2						integral to membrane|plasma membrane				breast(1)|central_nervous_system(1)	2						CTCCCCATGGCAGTCTTATTC	0.562													4	162	---	---	---	---	PASS
QKI	9444	broad.mit.edu	37	6	163991790	163991790	+	3'UTR	SNP	C	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163991790C>T	uc003qui.2	+	8					QKI_uc003quj.2_3'UTR	NM_006775	NP_006766	Q96PU8	QKI_HUMAN	quaking homolog, KH domain RNA binding isoform						mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)		ATGACCTGACCATGCCTGCCT	0.468													4	184	---	---	---	---	PASS
PRPS1L1	221823	broad.mit.edu	37	7	18066846	18066846	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18066846A>G	uc003stz.2	-	1	641	c.560T>C	c.(559-561)GTG>GCG	p.V187A		NM_175886	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like	187					nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			ovary(1)	1	Lung NSC(10;0.0385)|all_lung(11;0.0736)					AGCAAAGTCCACATTCAACTG	0.453													64	115	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48312610	48312610	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48312610A>G	uc003toq.2	+	17	3372	c.3347A>G	c.(3346-3348)GAG>GGG	p.E1116G	ABCA13_uc010kyr.2_Missense_Mutation_p.E619G	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	1116					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						TCAACAAGTGAGGAGTCTTCA	0.348													81	99	---	---	---	---	PASS
CCDC146	57639	broad.mit.edu	37	7	76908080	76908080	+	Silent	SNP	C	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76908080C>T	uc003uga.2	+	12	1579	c.1452C>T	c.(1450-1452)ACC>ACT	p.T484T	CCDC146_uc010ldp.2_Silent_p.T198T	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	484										ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				AAAAATACACCAACATTGTTA	0.299													6	474	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	148963737	148963737	+	RNA	SNP	G	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148963737G>T	uc003wfr.3	+	2		c.499G>T								Homo sapiens cDNA FLJ36716 fis, clone UTERU2010651.																		TGCAGAGGCGGCTGGAGAATG	0.652													14	16	---	---	---	---	PASS
REXO1L1	254958	broad.mit.edu	37	8	86786611	86786611	+	RNA	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86786611T>C	uc011lfx.1	-	1		c.2238A>G			REXO1L1_uc010mah.2_RNA	NM_172239	NP_758439	Q8IX06	GOR_HUMAN	exonuclease GOR							cytoplasm|nucleus	exonuclease activity|nucleic acid binding				0						ttcccggatatccttttttaa	0.000													3	9	---	---	---	---	PASS
INTS8	55656	broad.mit.edu	37	8	95892600	95892600	+	3'UTR	SNP	G	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95892600G>T	uc003yhb.2	+	27					INTS8_uc011lgq.1_RNA|INTS8_uc011lgr.1_RNA|INTS8_uc010mba.2_3'UTR|CCNE2_uc003yhc.2_3'UTR	NM_017864	NP_060334	Q75QN2	INT8_HUMAN	integrator complex subunit 8						snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)					ACAAATATTAGTTTAAAAACA	0.259													8	3	---	---	---	---	PASS
MPDZ	8777	broad.mit.edu	37	9	13137963	13137963	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13137963A>G	uc010mia.1	-	28	4250	c.4193T>C	c.(4192-4194)CTT>CCT	p.L1398P	MPDZ_uc003zky.3_5'Flank|MPDZ_uc010mib.2_Missense_Mutation_p.L103P|MPDZ_uc010mhx.2_Missense_Mutation_p.L220P|MPDZ_uc011lmm.1_Missense_Mutation_p.L257P|MPDZ_uc003zkz.3_Missense_Mutation_p.L91P|MPDZ_uc010mhy.2_Missense_Mutation_p.L1398P|MPDZ_uc010mhz.2_Missense_Mutation_p.L1365P|MPDZ_uc011lmn.1_Missense_Mutation_p.L1365P|MPDZ_uc003zlb.3_Missense_Mutation_p.L1398P	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1398	PDZ 8.				interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)		TACCTCTAGAAGCTCATCTGC	0.398													6	332	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79318764	79318764	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79318764T>C	uc010mpk.2	-	9	7889	c.7765A>G	c.(7765-7767)ACT>GCT	p.T2589A	PRUNE2_uc004akj.3_Missense_Mutation_p.T42A|PRUNE2_uc010mpl.1_Missense_Mutation_p.T42A	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	2589					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						GCTAACTGAGTTCCCTGCAGC	0.423													60	142	---	---	---	---	PASS
SVEP1	79987	broad.mit.edu	37	9	113169878	113169878	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113169878G>C	uc010mtz.2	-	38	8339	c.8002C>G	c.(8002-8004)CCT>GCT	p.P2668A	SVEP1_uc010mty.2_Missense_Mutation_p.P594A	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	2668	Sushi 21.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						TGTGTAGCAGGAGACTCCTTT	0.453													60	93	---	---	---	---	PASS
KIAA0368	23392	broad.mit.edu	37	9	114132845	114132845	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114132845A>T	uc004bfe.1	-	46	5378	c.5378T>A	c.(5377-5379)CTG>CAG	p.L1793Q		NM_001080398	NP_001073867			KIAA0368 protein												0						ACATTCCTTCAGAACAGCTTG	0.423													92	171	---	---	---	---	PASS
ODF2	4957	broad.mit.edu	37	9	131256871	131256871	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131256871A>G	uc011mbd.1	+	17	2146	c.1835A>G	c.(1834-1836)GAG>GGG	p.E612G	ODF2_uc011maz.1_Missense_Mutation_p.E612G|ODF2_uc011mbc.1_Missense_Mutation_p.E531G|ODF2_uc004bva.2_Missense_Mutation_p.E565G|ODF2_uc004bvb.2_Missense_Mutation_p.E588G|ODF2_uc011mbe.1_Missense_Mutation_p.E607G|ODF2_uc004bvc.2_Missense_Mutation_p.E588G|ODF2_uc011mbf.1_Missense_Mutation_p.E593G|ODF2_uc004bvd.3_Missense_Mutation_p.E612G|ODF2_uc004bve.2_Missense_Mutation_p.E593G|ODF2_uc004bvh.2_5'Flank	NM_002540	NP_002531	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2 isoform 1	612	Potential.				cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centriole|cilium|cytosol|microtubule|spindle pole	protein binding|structural molecule activity			ovary(1)	1						AAGCTGGCTGAGTGCCAAGAC	0.577													20	35	---	---	---	---	PASS
PDSS1	23590	broad.mit.edu	37	10	26994248	26994248	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26994248C>A	uc001isv.2	+	4	307	c.261C>A	c.(259-261)CAC>CAA	p.H87Q	PDSS1_uc001isw.2_Missense_Mutation_p.H87Q	NM_014317	NP_055132	Q5T2R2	DPS1_HUMAN	prenyl diphosphate synthase, subunit 1	87					isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	metal ion binding|protein heterodimerization activity				0						GTAAAACACACAGTGGTGAAA	0.368													100	221	---	---	---	---	PASS
FANK1	92565	broad.mit.edu	37	10	127683771	127683771	+	Intron	SNP	C	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127683771C>G	uc001ljh.3	+						FANK1_uc010quk.1_3'UTR|FANK1_uc009yan.2_Intron|FANK1_uc001lji.2_Intron	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				GGAAATGTCCCAAGCTTTAGG	0.318													5	8	---	---	---	---	PASS
DCHS1	8642	broad.mit.edu	37	11	6652328	6652328	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6652328G>T	uc001mem.1	-	9	4296	c.3886C>A	c.(3886-3888)CAA>AAA	p.Q1296K		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	1296	Cadherin 12.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGCTGCCTTGGTCATGAGCA	0.617													11	14	---	---	---	---	PASS
DENND5A	23258	broad.mit.edu	37	11	9192364	9192364	+	Intron	SNP	C	T	T	rs59591821		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9192364C>T	uc001mhl.2	-						DENND5A_uc001mhk.2_Translation_Start_Site|DENND5A_uc010rbw.1_Intron|DENND5A_uc010rbx.1_Intron	NM_015213	NP_056028	Q6IQ26	DEN5A_HUMAN	RAB6 interacting protein 1											liver(1)	1						cacacacacacataaatacac	0.199													4	110	---	---	---	---	PASS
FADS2	9415	broad.mit.edu	37	11	61624985	61624985	+	Missense_Mutation	SNP	G	A	A	rs140356378		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61624985G>A	uc001nsl.1	+	7	1015	c.865G>A	c.(865-867)GTC>ATC	p.V289I	FADS2_uc001nsj.2_Missense_Mutation_p.V267I|FADS2_uc010rlo.1_Missense_Mutation_p.V258I|FADS2_uc001nsk.2_Missense_Mutation_p.V289I	NM_004265	NP_004256	O95864	FADS2_HUMAN	fatty acid desaturase 2	289	Lumenal (Potential).				electron transport chain|transport|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	heme binding			ovary(1)|pancreas(1)	2					Alpha-Linolenic Acid(DB00132)	GACCATGATCGTCCATAAGAA	0.602													39	96	---	---	---	---	PASS
UBXN1	51035	broad.mit.edu	37	11	62445601	62445601	+	Intron	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62445601G>A	uc001nul.1	-						UBXN1_uc001nuj.2_Intron|UBXN1_uc001num.1_Intron|UBXN1_uc001nuk.2_Intron|UBXN1_uc010rme.1_Intron|UBXN1_uc010rmf.1_3'UTR	NM_015853	NP_056937	Q04323	UBXN1_HUMAN	UBX domain protein 1						negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process	cytoplasm	ATPase binding|K6-linked polyubiquitin binding				0						CTGTGTTGCCGAGGGAAAACA	0.483													41	53	---	---	---	---	PASS
OMP	4975	broad.mit.edu	37	11	76814080	76814080	+	Silent	SNP	C	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76814080C>T	uc010rsk.1	+	1	195	c.195C>T	c.(193-195)TTC>TTT	p.F65F	CAPN5_uc001oxx.2_Intron|CAPN5_uc009yup.2_Intron|CAPN5_uc009yuq.2_Intron|CAPN5_uc001oxy.2_Intron	NM_006189	NP_006180	P47874	OMP_HUMAN	olfactory marker protein	65					sensory perception of smell|synaptic transmission						0						GGCTACAGTTCGAGCGCTGGA	0.627													3	21	---	---	---	---	PASS
TPI1	7167	broad.mit.edu	37	12	6978057	6978057	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6978057A>G	uc001qrk.2	+	2	183	c.145A>G	c.(145-147)ATC>GTC	p.I49V	TPI1_uc010sfo.1_Translation_Start_Site	NM_000365	NP_000356	P60174	TPIS_HUMAN	triosephosphate isomerase 1 isoform 1	49					fatty acid biosynthetic process|gluconeogenesis|glycolysis|pentose-phosphate shunt	cytosol	triose-phosphate isomerase activity				0						TACTGCCTATATCGACTTCGC	0.512											OREG0021638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	108	166	---	---	---	---	PASS
HEBP1	50865	broad.mit.edu	37	12	13140039	13140039	+	Intron	SNP	C	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13140039C>G	uc001rbd.2	-						HEBP1_uc001rbf.2_3'UTR	NM_015987	NP_057071	Q9NRV9	HEBP1_HUMAN	heme binding protein 1						circadian rhythm	extracellular region				breast(1)	1		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		AGGAGTGGTACGGGAATCAAG	0.438													43	85	---	---	---	---	PASS
TFCP2	7024	broad.mit.edu	37	12	51495749	51495749	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51495749C>T	uc001rxw.2	-	11	1579	c.1120G>A	c.(1120-1122)GGA>AGA	p.G374R	TFCP2_uc001rxv.1_Missense_Mutation_p.G374R|TFCP2_uc009zlx.1_Missense_Mutation_p.G323R|TFCP2_uc001rxx.2_Intron|TFCP2_uc009zly.1_Missense_Mutation_p.G276R	NM_005653	NP_005644	Q12800	TFCP2_HUMAN	transcription factor CP2	374	DNA-binding.				regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						AGTCTGATTCCATCTGCAGGG	0.338													5	409	---	---	---	---	PASS
NXPH4	11247	broad.mit.edu	37	12	57619419	57619419	+	Silent	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57619419G>A	uc010srf.1	+	2	991	c.816G>A	c.(814-816)AAG>AAA	p.K272K	NXPH4_uc009zpj.2_Silent_p.K78K	NM_007224	NP_009155	O95158	NXPH4_HUMAN	neurexophilin 4 precursor	272	V (Cys-rich).				neuropeptide signaling pathway	extracellular region					0						TCTGTGCCAAGCCCTTCAAAG	0.577													18	35	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19442373	19442373	+	RNA	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19442373G>A	uc010tcj.1	-	1		c.3737C>T				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						GGCAATATCAGACCTAATATC	0.219													9	2	---	---	---	---	PASS
FARP1	10160	broad.mit.edu	37	13	99030151	99030151	+	Silent	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99030151T>C	uc001vnj.2	+	6	811	c.475T>C	c.(475-477)TTG>CTG	p.L159L	FARP1_uc001vnh.2_Silent_p.L159L	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1	159	FERM.				regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CGCAGCTCTCTTGATTTCACA	0.448													6	221	---	---	---	---	PASS
COL4A2	1284	broad.mit.edu	37	13	111125466	111125466	+	Silent	SNP	T	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111125466T>A	uc001vqx.2	+	29	2683	c.2394T>A	c.(2392-2394)CTT>CTA	p.L798L		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	798	Triple-helical region.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			TTAAAGGCCTTCCCGGAGACA	0.687													4	10	---	---	---	---	PASS
ARHGEF7	8874	broad.mit.edu	37	13	111953859	111953859	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111953859G>A	uc010tjo.1	+	19	2075	c.2023G>A	c.(2023-2025)GAA>AAA	p.E675K	ARHGEF7_uc001vrv.3_Missense_Mutation_p.E600K|ARHGEF7_uc001vrw.3_Missense_Mutation_p.E600K|ARHGEF7_uc001vrx.3_Missense_Mutation_p.E600K	NM_003899	NP_003890	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform a	Error:Variant_position_missing_in_Q14155_after_alignment					apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			ATTAAAGGATGAAGTTCAAGA	0.343													190	324	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22386695	22386695	+	Intron	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22386695A>G	uc001wbw.2	+						uc010tmg.1_Intron|uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aiy.2_RNA|uc001wch.2_Missense_Mutation_p.E36G					SubName: Full=Alpha-chain C region; Flags: Fragment;																		AGTGTCCAGGAGGGTGACAAC	0.433													7	323	---	---	---	---	PASS
ZC3H14	79882	broad.mit.edu	37	14	89042218	89042218	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89042218A>G	uc001xww.2	+	8	1282	c.1057A>G	c.(1057-1059)AAT>GAT	p.N353D	ZC3H14_uc010twd.1_Missense_Mutation_p.N353D|ZC3H14_uc010twe.1_Missense_Mutation_p.N353D|ZC3H14_uc001xwx.2_Missense_Mutation_p.N353D|ZC3H14_uc010twf.1_Missense_Mutation_p.N198D|ZC3H14_uc001xwy.2_Missense_Mutation_p.N319D|ZC3H14_uc010twg.1_Missense_Mutation_p.N198D|ZC3H14_uc001xxa.2_5'UTR	NM_024824	NP_079100	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14 isoform 1	353						cytoplasm|cytoplasm|nuclear speck	protein binding|RNA binding|zinc ion binding			ovary(2)|skin(1)	3						AGCTAACAAGAATCTGATTTT	0.328													7	540	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	20193209	20193209	+	RNA	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20193209T>C	uc010tyv.1	-	2		c.61A>G								Homo sapiens immunoglobulin heavy chain leader and variable region mRNA, partial cds.																		CAGCTGCACCTCACACTGGAC	0.537													5	140	---	---	---	---	PASS
SLC28A2	9153	broad.mit.edu	37	15	45559654	45559654	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45559654C>T	uc001zva.2	+	11	1009	c.944C>T	c.(943-945)ACA>ATA	p.T315I		NM_004212	NP_004203	O43868	S28A2_HUMAN	solute carrier family 28 (sodium-coupled	315					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)		TGTTTGTAGACAGAGGCACCT	0.547													54	131	---	---	---	---	PASS
EID1	23741	broad.mit.edu	37	15	49170357	49170357	+	5'UTR	SNP	G	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49170357G>C	uc001zxc.1	+	1					SHC4_uc010uey.1_5'Flank|SHC4_uc010uez.1_5'Flank|SHC4_uc001zxb.1_Intron	NM_014335	NP_055150	Q9Y6B2	EID1_HUMAN	CREBBP/EP300 inhibitor 1						cell cycle|cell differentiation|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	histone acetyltransferase binding|histone acetyltransferase regulator activity|transcription corepressor activity			liver(1)	1		all_lung(180;0.00455)		all cancers(107;2.73e-08)|GBM - Glioblastoma multiforme(94;9.58e-07)		TTTCCTAGAGGTTGAGCGGTT	0.597													27	66	---	---	---	---	PASS
TRPM7	54822	broad.mit.edu	37	15	50891477	50891477	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50891477T>C	uc001zyt.3	-	22	3269	c.3005A>G	c.(3004-3006)TAC>TGC	p.Y1002C	TRPM7_uc010bew.1_Missense_Mutation_p.Y1002C	NM_017672	NP_060142	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel,	1002	Helical; (Potential).				cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity			ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1)	10				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		CACTACAATGTAGAACATATT	0.333													90	192	---	---	---	---	PASS
CCPG1	9236	broad.mit.edu	37	15	55652924	55652924	+	Silent	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55652924T>C	uc002acv.1	-	8	1212	c.1047A>G	c.(1045-1047)AAA>AAG	p.K349K	CCPG1_uc002acy.2_Silent_p.K349K|CCPG1_uc002acu.1_Silent_p.K205K|CCPG1_uc002acw.1_Silent_p.K74K|CCPG1_uc002acx.2_Intron|CCPG1_uc010bfk.1_Silent_p.K349K|CCPG1_uc002acz.1_Silent_p.K349K	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2	349	Potential.|Lumenal (Potential).				cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)		TCTGATTTTCTTTAACTAATT	0.348													8	760	---	---	---	---	PASS
FAM63B	54629	broad.mit.edu	37	15	59146745	59146745	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59146745G>A	uc002afj.2	+	9	2004	c.1802G>A	c.(1801-1803)CGG>CAG	p.R601Q	FAM63B_uc002afi.2_Missense_Mutation_p.R600Q|FAM63B_uc002afk.2_RNA|FAM63B_uc002afl.2_RNA	NM_001040450	NP_001035540	Q8NBR6	FA63B_HUMAN	hypothetical protein LOC54629 isoform a	601										central_nervous_system(1)	1						GAACGTAAACGGAAGGAACCA	0.383													115	84	---	---	---	---	PASS
PALB2	79728	broad.mit.edu	37	16	23646730	23646730	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23646730C>G	uc002dlx.1	-	4	1337	c.1137G>C	c.(1135-1137)AAG>AAC	p.K379N		NM_024675	NP_078951	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	379					double-strand break repair via homologous recombination	nucleoplasm	DNA binding|protein binding			lung(3)|breast(3)|ovary(2)|skin(1)|kidney(1)|pancreas(1)	11				GBM - Glioblastoma multiforme(48;0.0167)		GGCTAAGACTCTTAGGTTGAC	0.393			F|N|Mis			Wilms tumor|medulloblastoma|AML ,breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia_type_N|Fanconi_Anemia|PALB2-associated_Familial_Breast_and_Pancreatic_Cancer|Pancreatic_Cancer_Familial_Clustering_of				16	509	---	---	---	---	PASS
BRD7	29117	broad.mit.edu	37	16	50357601	50357601	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50357601T>C	uc002egf.1	-	13	1407	c.1340A>G	c.(1339-1341)GAG>GGG	p.E447G	BRD7_uc002ege.1_Missense_Mutation_p.E447G	NM_013263	NP_037395	Q9NPI1	BRD7_HUMAN	bromodomain containing 7	447					cell cycle|negative regulation of cell proliferation|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of histone acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|nucleus	histone acetyl-lysine binding|p53 binding|transcription coactivator activity|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding				0		all_cancers(37;0.0127)				GGCCAAAAACTCATGGATGCT	0.463													96	154	---	---	---	---	PASS
TAF1C	9013	broad.mit.edu	37	16	84215642	84215642	+	Silent	SNP	G	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84215642G>T	uc002fhn.2	-	8	972	c.744C>A	c.(742-744)ACC>ACA	p.T248T	TAF1C_uc002fhm.2_Silent_p.T181T|TAF1C_uc010vnx.1_Silent_p.T248T|TAF1C_uc010vny.1_5'UTR|TAF1C_uc010vnz.1_5'UTR|TAF1C_uc002fho.2_5'UTR|TAF1C_uc010voa.1_5'UTR|TAF1C_uc002fhp.1_RNA|TAF1C_uc010vob.1_Silent_p.T248T	NM_005679	NP_005670	Q15572	TAF1C_HUMAN	TBP-associated factor 1C isoform 1	248					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding			ovary(1)	1						TGTCACCTGGGGTCAGAACGA	0.557													9	16	---	---	---	---	PASS
GEMIN4	50628	broad.mit.edu	37	17	649388	649388	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:649388A>T	uc002frs.1	-	2	2014	c.1895T>A	c.(1894-1896)ATG>AAG	p.M632K		NM_015721	NP_056536	P57678	GEMI4_HUMAN	gemin 4	632					rRNA processing|spliceosomal snRNP assembly	Cajal body|cytosol|nucleolus|small nuclear ribonucleoprotein complex|spliceosomal complex	protein binding			ovary(2)|kidney(1)|skin(1)	4		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CACGGGACTCATCAGGCAGTT	0.478													57	120	---	---	---	---	PASS
MAPK7	5598	broad.mit.edu	37	17	19283196	19283196	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19283196G>A	uc002gvn.2	+	3	720	c.334G>A	c.(334-336)GAC>AAC	p.D112N	B9D1_uc010cqm.1_5'Flank|B9D1_uc002gvl.3_5'Flank|MAPK7_uc002gvo.2_Intron|MAPK7_uc002gvq.2_Missense_Mutation_p.D112N|MAPK7_uc002gvp.2_Missense_Mutation_p.D112N	NM_139033	NP_620602	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7 isoform 1	112	Required for binding to MAP2K5 (By similarity).|Protein kinase.				cell cycle|cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase activity|protein binding			central_nervous_system(4)|lung(3)|stomach(1)|skin(1)	9	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					CTTTAAACACGACAACATCAT	0.537													3	54	---	---	---	---	PASS
SLC46A1	113235	broad.mit.edu	37	17	26723137	26723137	+	3'UTR	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26723137G>A	uc002hbf.1	-	6					SARM1_uc010waj.1_Intron|SARM1_uc010crl.1_Intron|SARM1_uc002hbe.1_Intron|SLC46A1_uc002hbg.1_3'UTR	NM_080669	NP_542400	Q96NT5	PCFT_HUMAN	proton-coupled folate transporter						cellular iron ion homeostasis|folic acid metabolic process	apical plasma membrane|cytoplasm|integral to membrane	folic acid binding|folic acid transporter activity|heme transporter activity				0	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)	AGCTCCCTCTGCCCAGCTGTC	0.602													13	15	---	---	---	---	PASS
DNAH17	8632	broad.mit.edu	37	17	76449445	76449445	+	Silent	SNP	C	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76449445C>T	uc010dhp.1	-	10	1731	c.1509G>A	c.(1507-1509)AGG>AGA	p.R503R	DNAH17_uc002jvs.2_RNA					SubName: Full=DNAH17 variant protein; Flags: Fragment;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TAATCGTGTTCCTGCCCAGTA	0.557													4	107	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3116378	3116378	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3116378T>C	uc002klp.2	-	21	3588	c.3254A>G	c.(3253-3255)GAC>GGC	p.D1085G	MYOM1_uc002klq.2_Missense_Mutation_p.D989G	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	1085	Fibronectin type-III 5.					striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						TCGCCACTGGTCTTCTTTGGC	0.522													6	206	---	---	---	---	PASS
ZNF519	162655	broad.mit.edu	37	18	14104777	14104777	+	3'UTR	SNP	A	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14104777A>C	uc002kst.1	-	3					ZNF519_uc002ksq.1_Intron|ZNF519_uc002ksr.1_Intron|ZNF519_uc010dlm.1_Intron	NM_145287	NP_660330	Q8TB69	ZN519_HUMAN	zinc finger protein 519						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GACACTTCTAATTTTTATTTA	0.294													29	88	---	---	---	---	PASS
LOC644669	644669	broad.mit.edu	37	18	15325895	15325895	+	RNA	SNP	C	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15325895C>A	uc002ktd.1	-	1		c.24G>T				NR_027417				Homo sapiens cDNA FLJ40312 fis, clone TESTI2029880.												0						CATTTACCTTCATCAGAGTTG	0.398													8	18	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8196481	8196481	+	Silent	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8196481G>A	uc002mjf.2	-	14	1968	c.1947C>T	c.(1945-1947)CAC>CAT	p.H649H		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	649	TB 3.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						CCCCAAAACCGTGGTCCGGAT	0.642													6	23	---	---	---	---	PASS
RTN2	6253	broad.mit.edu	37	19	45997582	45997582	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45997582G>A	uc002pcb.2	-	4	884	c.656C>T	c.(655-657)CCG>CTG	p.P219L	RTN2_uc002pcc.2_Missense_Mutation_p.P219L|RTN2_uc002pcd.2_RNA	NM_005619	NP_005610	O75298	RTN2_HUMAN	reticulon 2 isoform A	219						integral to endoplasmic reticulum membrane	signal transducer activity			ovary(3)	3		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00829)|Epithelial(262;0.184)|GBM - Glioblastoma multiforme(486;0.246)		GGATGGGGACGGAGTACCGGC	0.622													14	45	---	---	---	---	PASS
ZNF415	55786	broad.mit.edu	37	19	53612961	53612961	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53612961C>T	uc002qax.2	-	7	830	c.481G>A	c.(481-483)GCC>ACC	p.A161T	ZNF415_uc002qat.2_Missense_Mutation_p.A125T|ZNF415_uc002qaw.2_Missense_Mutation_p.A113T|ZNF415_uc010yds.1_Missense_Mutation_p.A113T|ZNF415_uc010ydt.1_Missense_Mutation_p.A113T|ZNF415_uc002qau.2_Missense_Mutation_p.A100T|ZNF415_uc002qav.2_Missense_Mutation_p.A125T|ZNF415_uc002qba.2_5'UTR|ZNF415_uc002qay.2_Missense_Mutation_p.A100T|ZNF415_uc002qaz.2_Missense_Mutation_p.A161T	NR_028343		Q09FC8	ZN415_HUMAN	RecName: Full=Zinc finger protein 415;	161					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleolus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.0191)		TCTTTTGGGGCCGTAGTCACT	0.383													5	313	---	---	---	---	PASS
LILRB3	11025	broad.mit.edu	37	19	54725980	54725980	+	Silent	SNP	G	A	A	rs150024950	byFrequency	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54725980G>A	uc002qef.1	-	4	489	c.378C>T	c.(376-378)CTC>CTT	p.L126L	LILRB3_uc002qee.1_Silent_p.L126L|LILRB3_uc002qeh.1_Silent_p.L126L|LILRB3_uc002qeg.1_RNA|LILRB3_uc002qei.1_Intron|LILRA6_uc002qek.1_Intron|LILRB3_uc010erh.1_Silent_p.L126L|LILRB3_uc002qej.1_Intron|LILRA6_uc002qel.1_Intron|LILRA6_uc002qem.1_Intron|LILRB3_uc002qen.1_Intron|LILRB3_uc002qeo.1_Intron|LILRB3_uc002qep.1_Silent_p.L126L|LILRB3_uc002qeq.1_Intron|LILRB3_uc002qer.1_Intron|LILRB3_uc002qes.1_Intron|LILRA6_uc010yep.1_Intron|LILRA6_uc010yeq.1_Intron	NM_006864	NP_006855	O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor,	126	Extracellular (Potential).|Ig-like C2-type 2.				cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	transmembrane receptor activity			skin(2)|ovary(1)	3	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCAGGGCTGAGAGGGTGGGTT	0.582													3	36	---	---	---	---	PASS
SLC27A5	10998	broad.mit.edu	37	19	59011001	59011001	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59011001G>A	uc002qtc.2	-	7	1635	c.1525C>T	c.(1525-1527)CGC>TGC	p.R509C	SLC27A5_uc002qtb.2_5'Flank	NM_012254	NP_036386	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid	509	Cytoplasmic (Probable).				bile acid and bile salt transport|bile acid biosynthetic process|very long-chain fatty acid metabolic process	endoplasmic reticulum membrane|integral to membrane	ATP binding|cholate-CoA ligase activity|long-chain fatty acid-CoA ligase activity				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		CGGGGGCCGCGGTAGCCCACG	0.657													6	7	---	---	---	---	PASS
SLC12A5	57468	broad.mit.edu	37	20	44663593	44663593	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44663593G>A	uc010zxl.1	+	2	204	c.128G>A	c.(127-129)GGC>GAC	p.G43D	SLC12A5_uc002xra.2_Missense_Mutation_p.G20D|SLC12A5_uc010zxm.1_RNA|SLC12A5_uc002xrb.2_Missense_Mutation_p.G20D	NM_001134771	NP_001128243	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	43	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	TCAGGTGATGGCAACCCCAAG	0.502													92	105	---	---	---	---	PASS
ZNF512B	57473	broad.mit.edu	37	20	62595905	62595905	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62595905T>C	uc002yhl.1	-	6	1253	c.1199A>G	c.(1198-1200)GAG>GGG	p.E400G		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	400					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTTCAGTGCCTCCATGCCCCC	0.687													4	31	---	---	---	---	PASS
NRIP1	8204	broad.mit.edu	37	21	16340088	16340088	+	Silent	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16340088A>G	uc002yjx.2	-	4	1024	c.426T>C	c.(424-426)TCT>TCC	p.S142S		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	142	Repression domain 1.				androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		TCTGCAGCCTAGAGCTGAATG	0.458													4	120	---	---	---	---	PASS
UMODL1	89766	broad.mit.edu	37	21	43533907	43533907	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43533907G>T	uc002zaf.1	+	13	2329	c.2329G>T	c.(2329-2331)GAA>TAA	p.E777*	UMODL1_uc002zad.1_Nonsense_Mutation_p.E705*|UMODL1_uc002zae.1_Nonsense_Mutation_p.E833*|UMODL1_uc002zag.1_Nonsense_Mutation_p.E905*	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor	777	Extracellular (Potential).|Fibronectin type-III 2.					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3						ATGTGGGAAAGAAGGTGCCAG	0.483													42	54	---	---	---	---	PASS
RBX1	9978	broad.mit.edu	37	22	41368620	41368620	+	3'UTR	SNP	G	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41368620G>T	uc003azk.2	+	5						NM_014248	NP_055063	P62877	RBX1_HUMAN	ring-box 1						DNA repair|interspecies interaction between organisms|protein neddylation|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	Cul3-RING ubiquitin ligase complex|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytosol|nucleus|SCF ubiquitin ligase complex	NEDD8 ligase activity|protein binding|zinc ion binding			skin(1)	1						TGCTGTTTCTGTAGCCATATT	0.348													26	176	---	---	---	---	PASS
MAGEE2	139599	broad.mit.edu	37	X	75003527	75003527	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75003527G>A	uc004ecj.1	-	1	1545	c.1360C>T	c.(1360-1362)CCA>TCA	p.P454S		NM_138703	NP_619648	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	454	MAGE 2.									ovary(1)|skin(1)	2						TAGGACAGTGGCCTGCATTCC	0.473													87	33	---	---	---	---	PASS
SMARCA1	6594	broad.mit.edu	37	X	128640071	128640071	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128640071A>G	uc004eun.3	-	8	1197	c.1084T>C	c.(1084-1086)TTT>CTT	p.F362L	SMARCA1_uc004eup.3_Missense_Mutation_p.F362L|SMARCA1_uc011muk.1_Missense_Mutation_p.F362L|SMARCA1_uc011mul.1_Missense_Mutation_p.F362L	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	362					ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding			ovary(3)|skin(1)	4						GCAGAATTAAAGACATCAGGC	0.348													7	270	---	---	---	---	PASS
C1orf86	199990	broad.mit.edu	37	1	2117162	2117162	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2117162delA	uc001aix.1	-						uc009vlc.1_5'Flank|C1orf86_uc001aiv.1_Intron|C1orf86_uc001aiw.1_Intron			Q6NZ36	CA086_HUMAN	SubName: Full=cDNA FLJ46112 fis, clone TESTI2035962;												0	all_cancers(77;0.000134)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		ACAGTAGACCAAAAAAGAGAA	0.473													4	2	---	---	---	---	
NPHP4	261734	broad.mit.edu	37	1	5954747	5954747	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5954747delA	uc001alq.1	-						NPHP4_uc001als.1_Intron|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron|NPHP4_uc009vlu.1_Intron	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin						actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		taagcagctcaaaaaaaaaat	0.000													3	3	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7263803	7263803	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7263803delT	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		gagttttctcttttttttttc	0.000													3	4	---	---	---	---	
SLC2A5	6518	broad.mit.edu	37	1	9126296	9126296	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9126296delT	uc001apo.2	-						SLC2A5_uc010nzz.1_Intron|SLC2A5_uc010oaa.1_Intron|SLC2A5_uc010oab.1_Intron|SLC2A5_uc010oac.1_Intron|SLC2A5_uc001app.3_Intron	NM_003039	NP_003030	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated						carbohydrate metabolic process	integral to membrane|plasma membrane	fructose transmembrane transporter activity|glucose transmembrane transporter activity			pancreas(2)|ovary(1)	3	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		CAATCCtttgttttttttttg	0.144													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	14410547	14410547	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14410547delG								PRDM2 (258975 upstream) : KAZ (514666 downstream)																							tgaggaggctggatagaaggc	0.020													4	2	---	---	---	---	
FHAD1	114827	broad.mit.edu	37	1	15655097	15655097	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15655097delA	uc001awb.2	+						FHAD1_uc001awa.1_Intron|uc001awc.1_RNA	NM_052929	NP_443161	B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding											skin(1)	1						CAAAGGGCCTAAAAAAATGCC	0.448													4	2	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16907639	16907646	+	Intron	DEL	AGAGAGGA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16907639_16907646delAGAGAGGA	uc009vos.1	-						NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Intron|NBPF1_uc010oce.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CATGGGAGCCAGAGAGGAAGAGAGCAGC	0.510													10	5	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16929805	16929808	+	Intron	DEL	CTTC	-	-	rs140610974		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16929805_16929808delCTTC	uc009vos.1	-						NBPF1_uc001aza.3_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		gtctctggatcttccTTGATGGGA	0.025													4	2	---	---	---	---	
HP1BP3	50809	broad.mit.edu	37	1	21083867	21083868	+	Intron	INS	-	A	A	rs148987896	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21083867_21083868insA	uc001bdw.1	-						HP1BP3_uc001bdv.1_Intron|HP1BP3_uc010odh.1_Intron|HP1BP3_uc001bdy.1_Intron|HP1BP3_uc001bdz.2_Intron|HP1BP3_uc001bea.2_Intron|HP1BP3_uc010odf.1_Intron|HP1BP3_uc010odg.1_Intron	NM_016287	NP_057371	Q5SSJ5	HP1B3_HUMAN	HP1-BP74						nucleosome assembly	nucleosome|nucleus	DNA binding			central_nervous_system(1)|skin(1)	2		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		TTATTATTAttttttttttttt	0.109													3	3	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21192411	21192411	+	Intron	DEL	C	-	-	rs5772920		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21192411delC	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		TAATTGTTTTCTAATAGTTGT	0.338													4	2	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21306670	21306670	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21306670delA	uc001bec.2	-						EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beg.2_Intron|EIF4G3_uc010odk.1_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		tttctggaagaaaaaaaaaaa	0.159													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30380809	30380810	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30380809_30380810insT								PTPRU (727494 upstream) : MATN1 (803316 downstream)																							AGTTTTTCATCTTTTTTTTTTT	0.441													4	2	---	---	---	---	
ZBTB8A	653121	broad.mit.edu	37	1	33005819	33005820	+	Intron	DEL	TT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33005819_33005820delTT	uc001bvn.2	+						ZBTB8A_uc001bvk.2_Intron|ZBTB8A_uc001bvm.2_Intron	NM_001040441	NP_001035531	Q96BR9	ZBT8A_HUMAN	zinc finger and BTB domain containing 8A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GGACCGCCTCTTTTGTGAGTTA	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	33535710	33535710	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33535710delT								AK2 (33218 upstream) : ADC (11004 downstream)																							ttgtgtcaacttttatccctc	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35295710	35295710	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35295710delC								GJA4 (34364 upstream) : C1orf212 (23414 downstream)																							AGATCACATACCCCCAACCAG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35887914	35887915	+	IGR	DEL	AA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35887914_35887915delAA								ZMYM4 (370 upstream) : KIAA0319L (11177 downstream)																							GTTCATTCTTAAGTATAAATAC	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37200162	37200163	+	IGR	DEL	TC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37200162_37200163delTC								CSF3R (251653 upstream) : GRIK3 (60965 downstream)																							tgtatcacaatctctctctctt	0.000													4	2	---	---	---	---	
RLF	6018	broad.mit.edu	37	1	40692354	40692355	+	Intron	INS	-	T	T	rs74972452	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40692354_40692355insT	uc001cfc.3	+							NM_012421	NP_036553	Q13129	RLF_HUMAN	rearranged L-myc fusion						chromosome organization|DNA integration|DNA mediated transformation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			ovary(2)|pancreas(1)	3	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			AGCTTTAAAAATTTTTTTTTTC	0.267													4	2	---	---	---	---	
ZSWIM5	57643	broad.mit.edu	37	1	45586317	45586317	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45586317delT	uc001cnd.2	-							NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM domain containing 5								zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)					tttttctttcttttttttttt	0.000													4	3	---	---	---	---	
MAST2	23139	broad.mit.edu	37	1	46270092	46270092	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46270092delA	uc001cov.2	+						MAST2_uc001cow.2_Intron	NM_015112	NP_055927	Q6P0Q8	MAST2_HUMAN	microtubule associated serine/threonine kinase						regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					TAAATAGAGTAAGATGTAAGT	0.433													4	2	---	---	---	---	
FAF1	11124	broad.mit.edu	37	1	51026824	51026824	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51026824delG	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron|FAF1_uc010onc.1_Intron	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		AATTACTTCTGGGGTATCACA	0.502													4	2	---	---	---	---	
C1orf185	284546	broad.mit.edu	37	1	51577808	51577808	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51577808delA	uc001csh.2	+							NM_001136508	NP_001129980	Q5T7R7	CA185_HUMAN	hypothetical protein LOC284546							integral to membrane					0						ACGGGAGGGGAAAAAAAAAAA	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56943201	56943201	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56943201delT								None (None upstream) : PPAP2B (17232 downstream)																							AACAAAACCCTTTTGCTGTGA	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	61253343	61253344	+	Intron	DEL	AA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61253343_61253344delAA	uc001czt.1	-											Homo sapiens cDNA FLJ39874 fis, clone SPLEN2015815.																		GAGATGGGAGAAAAAAAAACTA	0.282													4	2	---	---	---	---	
ROR1	4919	broad.mit.edu	37	1	64299338	64299338	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64299338delT	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19						TTCCTTTTCATTTTTTTTTTT	0.418													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	66935706	66935707	+	IGR	DEL	CA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66935706_66935707delCA								PDE4B (95445 upstream) : SGIP1 (64118 downstream)																							atgttcccaccacacacacata	0.000													4	2	---	---	---	---	
TYW3	127253	broad.mit.edu	37	1	75216918	75216919	+	Intron	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75216918_75216919delGT	uc001dgn.2	+						TYW3_uc010oqw.1_Intron|TYW3_uc010oqx.1_Intron|TYW3_uc010oqy.1_Intron	NM_138467	NP_612476	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog isoform						tRNA processing		methyltransferase activity			ovary(2)	2						tttcttgccagtgtgtgtgtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	78880224	78880224	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78880224delT								MGC27382 (45079 upstream) : PTGFR (76504 downstream)																							AATAGGCTTCTTTTTATTTCA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	81404178	81404178	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81404178delA								None (None upstream) : LPHN2 (367667 downstream)																							tttcaatcacaaaaaaaaatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	83832075	83832076	+	IGR	DEL	AT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83832075_83832076delAT								None (None upstream) : TTLL7 (502983 downstream)																							ctgtttgtgcatatatatatat	0.168													4	2	---	---	---	---	
COL24A1	255631	broad.mit.edu	37	1	86512992	86512992	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86512992delA	uc001dlj.2	-						COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron|COL24A1_uc009wcq.2_Intron	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		TATAGGAAATAAGCCTTAGGG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	87049185	87049185	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87049185delT								CLCA4 (2755 upstream) : CLCA3P (50774 downstream)																							gagtagggaatttatttatta	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88634408	88634408	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88634408delT								LMO4 (819805 upstream) : PKN2 (515514 downstream)																							CTTGTAGACATTTAAATCCTG	0.328													4	2	---	---	---	---	
LRRC8B	23507	broad.mit.edu	37	1	90001452	90001452	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90001452delT	uc001dni.2	+						LRRC8B_uc001dnh.2_Intron	NM_001134476	NP_001127948	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member							integral to membrane				ovary(2)	2		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		AGATTTGGGATTTTTTTTTTC	0.393													4	2	---	---	---	---	
PTBP2	58155	broad.mit.edu	37	1	97279080	97279080	+	3'UTR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97279080delT	uc001drq.2	+	14					PTBP2_uc001drn.2_3'UTR|PTBP2_uc001dro.2_3'UTR|PTBP2_uc010otz.1_3'UTR|PTBP2_uc001drp.2_RNA|PTBP2_uc009wdw.2_3'UTR|PTBP2_uc001drr.2_3'UTR|PTBP2_uc010oua.1_3'UTR|PTBP2_uc001dru.2_RNA|PTBP2_uc001drs.1_3'UTR|PTBP2_uc001drt.2_3'UTR	NM_021190	NP_067013	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2								nucleotide binding				0		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)		TTGGGGTTTCTTTTTTTTTTC	0.338													9	4	---	---	---	---	
HIAT1	64645	broad.mit.edu	37	1	100507933	100507933	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100507933delT	uc001dst.2	+							NM_033055	NP_149044	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1						transmembrane transport	integral to membrane|plasma membrane	transporter activity				0		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		GAGCACCAGATTTTTTTTTTC	0.393													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	103040045	103040047	+	IGR	DEL	ACT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103040045_103040047delACT								OLFM3 (577255 upstream) : COL11A1 (301977 downstream)																							gtatggcaggactacttattttc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	105430019	105430020	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105430019_105430020insT								None (None upstream) : None (None downstream)																							CTTACAGTTAGTTTTTTTTATT	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120149764	120149764	+	IGR	DEL	A	-	-	rs79524356		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120149764delA								HSD3B1 (92083 upstream) : ZNF697 (12236 downstream)																							GCACCATCTCAAAAAAAAAAA	0.428													3	4	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120592822	120592823	+	Intron	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120592822_120592823insA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAAGATTTAGAAAAAACACAC	0.337			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				3	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144947765	144947765	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144947765delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		tttaaaaagtaaaaaaaaaaa	0.000			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	146009450	146009450	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146009450delC	uc001emp.3	+							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)		GAAATCGGGGCCAGGAATCTA	0.572													4	2	---	---	---	---	
BCL9	607	broad.mit.edu	37	1	147011520	147011521	+	5'Flank	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147011520_147011521insG	uc001epq.2	+							NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9						Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					GAGCAAATTAAGGGGGAAAATA	0.356			T	IGH@|IGL@	B-ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152864387	152864387	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152864387delT								SMCP (6872 upstream) : IVL (16652 downstream)																							tctacatctattgagatgaac	0.000													4	2	---	---	---	---	
SNAPIN	23557	broad.mit.edu	37	1	153632223	153632224	+	Intron	DEL	TG	-	-	rs67464033		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153632223_153632224delTG	uc001fcq.2	+							NM_012437	NP_036569	O95295	SNAPN_HUMAN	SNAP-associated protein						intracellular protein transport|synaptic vesicle exocytosis	BLOC-1 complex|cell junction|perinuclear region of cytoplasm|synaptic vesicle membrane|synaptosome	SNARE binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TTTACATTCTTGTGTGTGTGTG	0.228													4	2	---	---	---	---	
THBS3	7059	broad.mit.edu	37	1	155169611	155169612	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155169611_155169612delCA	uc001fix.2	-	16	1886_1887	c.1863_1864delTG	c.(1861-1866)TGTGATfs	p.C621fs	RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Frame_Shift_Del_p.C612fs|THBS3_uc001fiz.2_Frame_Shift_Del_p.C584fs|THBS3_uc001fiy.2_Frame_Shift_Del_p.C150fs|THBS3_uc010pfu.1_Frame_Shift_Del_p.C501fs|THBS3_uc010pfv.1_RNA	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor	621_622	TSP type-3 6.				cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TCATTAGTATCACAGACATCCC	0.366													127	68	---	---	---	---	
SCAMP3	10067	broad.mit.edu	37	1	155232153	155232153	+	5'UTR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155232153delC	uc001fjs.2	-	1					RAG1AP1_uc010pey.1_Intron|SCAMP3_uc001fjr.2_5'Flank|SCAMP3_uc001fju.2_5'UTR|SCAMP3_uc001fjv.2_5'UTR|SCAMP3_uc001fjt.2_5'UTR	NM_005698	NP_005689	O14828	SCAM3_HUMAN	secretory carrier membrane protein 3 isoform 1						post-Golgi vesicle-mediated transport|protein transport	integral to membrane				ovary(3)	3	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GACGAAAGTGCCCCCACGTGA	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159485499	159485499	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159485499delT								OR10J1 (74989 upstream) : OR10J5 (19371 downstream)																							ttaatttttgtgcctaaccca	0.000													4	2	---	---	---	---	
OLFML2B	25903	broad.mit.edu	37	1	161968431	161968432	+	Intron	INS	-	A	A	rs149405717	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161968431_161968432insA	uc001gbu.2	-						OLFML2B_uc010pkq.1_Intron	NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B precursor											skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			TGGCTGGGAGTAAGTGAGTCAT	0.396													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	164280225	164280225	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164280225delA								NUF2 (954672 upstream) : PBX1 (248577 downstream)																							ACAACTTAAGAAAAAAAAAAG	0.423													4	2	---	---	---	---	
LOC400794	400794	broad.mit.edu	37	1	165537361	165537361	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165537361delT	uc001gdc.2	-						LOC400794_uc001gdd.2_Intron|LOC400794_uc009wvd.2_Intron	NR_026744				Homo sapiens cDNA FLJ35813 fis, clone TESTI2006067.												0						gtatcccgcattttagtaagt	0.259													4	2	---	---	---	---	
TMCO1	54499	broad.mit.edu	37	1	165787178	165787188	+	Intron	DEL	AAAAAAAAAAA	-	-	rs145106658		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165787178_165787188delAAAAAAAAAAA	uc001gdn.3	-									Q9UM00	TMCO1_HUMAN	Homo sapiens mRNA for putative membrane protein, complete cds.							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				central_nervous_system(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					gactccatctaaaaaaaaaaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166260957	166260957	+	IGR	DEL	T	-	-	rs72156784		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166260957delT								FAM78B (124751 upstream) : FMO9P (312196 downstream)																							GGGCTAAGTATTTTTTTTTTC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166610568	166610568	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166610568delA								FMO9P (16097 upstream) : POGK (198156 downstream)																							gagacgagggaaaaaaaaaac	0.010													3	4	---	---	---	---	
CD247	919	broad.mit.edu	37	1	167458337	167458337	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167458337delA	uc001gei.3	-						CD247_uc001gej.3_Intron|CD247_uc001gek.2_Intron	NM_198053	NP_932170	P20963	CD3Z_HUMAN	T-cell receptor zeta chain isoform 1 precursor						interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)			ACAAAAGACTAATAAAAATCC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	170798734	170798735	+	IGR	DEL	TA	-	-	rs112508533		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170798734_170798735delTA								PRRX1 (90194 upstream) : C1orf129 (105877 downstream)																							ttgttaattttatatgtcaact	0.000													4	4	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	172217220	172217220	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172217220delT	uc001gie.2	+						DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						GAATCTATGCTTTTTTTTGTA	0.264													4	2	---	---	---	---	
SEC16B	89866	broad.mit.edu	37	1	177933068	177933069	+	Intron	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177933068_177933069delTG	uc001gli.1	-						SEC16B_uc001glk.1_Intron|SEC16B_uc009wwz.1_Intron|SEC16B_uc001glj.1_Intron|SEC16B_uc001gll.3_Intron	NM_033127	NP_149118	Q96JE7	SC16B_HUMAN	leucine zipper transcription regulator 2						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4						TTCTTGATCCTGTCAATTTGAT	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	182069875	182069875	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182069875delC								ZNF648 (39028 upstream) : GLUL (281794 downstream)																							GTTATCTTGGCCAGTAAATTC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	182205857	182205858	+	IGR	DEL	CA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182205857_182205858delCA								ZNF648 (175010 upstream) : GLUL (145811 downstream)																							acacatacatcacacacacaca	0.099													4	2	---	---	---	---	
SMG7	9887	broad.mit.edu	37	1	183519210	183519210	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183519210delA	uc001gqg.2	+						SMG7_uc001gqf.2_Intron|SMG7_uc001gqh.2_Intron|SMG7_uc001gqi.2_Intron|SMG7_uc010poc.1_Intron	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						AAGGAAATAGAAAAAAAAAAA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	187345795	187345795	+	IGR	DEL	G	-	-	rs66547567		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187345795delG								PLA2G4A (387690 upstream) : None (None downstream)																							ttttgtttttgtttttgtttt	0.264													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193279811	193279811	+	IGR	DEL	T	-	-	rs67894413		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193279811delT								CDC73 (55871 upstream) : None (None downstream)																							AATAGGAAACTGCCCAGGCAG	0.403													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	195571044	195571044	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195571044delT								None (None upstream) : KCNT2 (623869 downstream)																							CTAACATTCATTTTTTTTTCC	0.289													4	2	---	---	---	---	
DYRK3	8444	broad.mit.edu	37	1	206843434	206843434	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206843434delT	uc001hek.2	+									O43781	DYRK3_HUMAN	Homo sapiens regulatory erythroid kinase long form (RED) mRNA, alternatively spliced product, complete cds.						erythrocyte differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|central_nervous_system(1)	3	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			CCTTTCTGCCTTTTTTGGTTG	0.393													4	2	---	---	---	---	
MAPKAPK2	9261	broad.mit.edu	37	1	206899242	206899242	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206899242delC	uc001hem.1	+						MAPKAPK2_uc001hel.1_Intron	NM_032960	NP_116584	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated						activation of MAPK activity|hormone biosynthetic process|innate immune response|leukotriene biosynthetic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|prostanoid metabolic process|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			tcttcttctgccccccactag	0.179													4	2	---	---	---	---	
NSL1	25936	broad.mit.edu	37	1	212912598	212912598	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212912598delT	uc001hjn.2	-						NSL1_uc001hjm.2_Intron|NSL1_uc010pti.1_Intron	NM_015471	NP_056286	Q96IY1	NSL1_HUMAN	NSL1, MIND kinetochore complex component isoform						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00597)|all cancers(67;0.00893)|GBM - Glioblastoma multiforme(131;0.0514)|Epithelial(68;0.102)		ttagctggtattattATCCAA	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222098224	222098224	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222098224delC								DUSP10 (182763 upstream) : HHIPL2 (597378 downstream)																							CATGTTTTTTCCAGTCTAGCC	0.323													4	2	---	---	---	---	
PCNXL2	80003	broad.mit.edu	37	1	233344662	233344662	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233344662delA	uc001hvl.2	-						PCNXL2_uc009xfu.2_Intron|PCNXL2_uc001hvp.1_Intron|PCNXL2_uc009xfv.1_Intron|PCNXL2_uc001hvq.1_Intron	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				TGAGACTATCAAAAAAAAAAT	0.224													4	2	---	---	---	---	
SLC35F3	148641	broad.mit.edu	37	1	234284599	234284599	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234284599delA	uc001hvy.1	+							NM_173508	NP_775779	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			agggaagaggaaaaaaaagaa	0.000													4	2	---	---	---	---	
AKT3	10000	broad.mit.edu	37	1	243754956	243754956	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243754956delA	uc001iab.1	-						AKT3_uc001hzz.1_Intron	NM_005465	NP_005456	Q9Y243	AKT3_HUMAN	AKT3 kinase isoform 1						signal transduction	Golgi apparatus|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|lung(1)|breast(1)|central_nervous_system(1)	4	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			ttgaaaatataaaaaatagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	1574285	1574286	+	IGR	INS	-	A	A	rs139418488	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1574285_1574286insA								TPO (27787 upstream) : PXDN (61374 downstream)																							GAGGCAAGGTGGGGGTTGCTAA	0.624													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	3892901	3892901	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3892901delC								ALLC (142643 upstream) : None (None downstream)																							GTTTCTGTTACCAAGCGAGAG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4840373	4840373	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4840373delT								None (None upstream) : SOX11 (992426 downstream)																							GGCTTCAGTCTTTTTTTTTTC	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	5645316	5645316	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5645316delT								None (None upstream) : SOX11 (187483 downstream)																							AACGTGACAGTTTTTACTCAG	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6404291	6404291	+	IGR	DEL	A	-	-	rs5829050		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6404291delA								LOC400940 (275927 upstream) : CMPK2 (576212 downstream)																							tgggtggaagaggctgccttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10404970	10404970	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10404970delT								C2orf48 (53114 upstream) : HPCAL1 (38070 downstream)																							CTGAGGGTCATTTCTCCAGTG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21043843	21043843	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21043843delT								C2orf43 (21016 upstream) : APOB (180459 downstream)																							aaccctctcattttacagatg	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21568483	21568483	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21568483delT								APOB (301538 upstream) : None (None downstream)																							TACCCAGCCATTTTTTAAATG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	22273922	22273922	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22273922delT								None (None upstream) : None (None downstream)																							ctcctcaaacttttttttcac	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23429880	23429880	+	IGR	DEL	C	-	-	rs34281647		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23429880delC								None (None upstream) : KLHL29 (325575 downstream)																							cttaacgagacgatactatat	0.159													3	3	---	---	---	---	
ATAD2B	54454	broad.mit.edu	37	2	24021374	24021374	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24021374delA	uc002rek.3	-						ATAD2B_uc010yki.1_Intron|ATAD2B_uc002rei.3_Intron|ATAD2B_uc002rej.3_Intron	NM_017552	NP_060022	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B								ATP binding|nucleoside-triphosphatase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGCCCCACCAAAAAAAAAAA	0.323													5	4	---	---	---	---	
HADHB	3032	broad.mit.edu	37	2	26503997	26503997	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26503997delT	uc002rgz.2	+						HADHB_uc010ykv.1_Intron|HADHB_uc010ykw.1_Intron|HADHB_uc002rha.2_Intron|HADHB_uc010ykx.1_Intron	NM_000183	NP_000174	P55084	ECHB_HUMAN	mitochondrial trifunctional protein, beta						fatty acid beta-oxidation	mitochondrial nucleoid	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acyltransferase activity|enoyl-CoA hydratase activity|protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGTTTTGTGTTTTTTTTTTA	0.109													4	3	---	---	---	---	
OTOF	9381	broad.mit.edu	37	2	26737983	26737983	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26737983delC	uc002rhk.2	-						OTOF_uc010ylb.1_Intron	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a						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)					CTCCGGCTCTCCCAGCAgcag	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35031939	35031939	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35031939delT								None (None upstream) : None (None downstream)																							CGTTGGTCAGTTTTTAAAAAT	0.299													4	2	---	---	---	---	
DHX57	90957	broad.mit.edu	37	2	39082580	39082591	+	Intron	DEL	CAATCAAAAGGA	-	-	rs72020623		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39082580_39082591delCAATCAAAAGGA	uc002rrf.2	-						DHX57_uc002rrd.3_5'Flank|DHX57_uc002rre.2_Intron|DHX57_uc002rrg.2_Intron	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				ATTTGCACTCCAATCAAAAGGACAATCAAATA	0.311													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	40874981	40874981	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40874981delT								SLC8A1 (135406 upstream) : None (None downstream)																							tacttatcacttttttttagg	0.000													4	3	---	---	---	---	
C2orf34	79823	broad.mit.edu	37	2	44730956	44730956	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44730956delA	uc002rum.2	+							NM_024766	NP_079042	Q7Z624	CMKMT_HUMAN	hypothetical protein LOC79823							cytoplasm	calmodulin-lysine N-methyltransferase activity				0		all_hematologic(82;0.0892)|Acute lymphoblastic leukemia(82;0.17)				ggaggctaggaaatctaagat	0.035													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46217747	46217747	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46217747delT	uc002rut.2	+							NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			cttcctctgcttttttttcta	0.000													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46248970	46248970	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46248970delT	uc002rut.2	+							NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			AGAATTTACCTTTTTGTGTGT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49405342	49405342	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49405342delA								FSHR (23712 upstream) : NRXN1 (740302 downstream)																							ATTAAAAAAGAAAAAAAAAAA	0.318													3	3	---	---	---	---	
APLF	200558	broad.mit.edu	37	2	68705429	68705429	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68705429delG	uc002sep.2	+						APLF_uc010fdf.2_Intron	NM_173545	NP_775816	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor						double-strand break repair|single strand break repair	cytosol|nucleus	3'-5' exonuclease activity|DNA-(apurinic or apyrimidinic site) lyase activity|endodeoxyribonuclease activity|metal ion binding|nucleotide binding|protein binding			ovary(2)	2						tgtaaaaaaaggaaaaggaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	69482811	69482811	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69482811delA								ANTXR1 (6354 upstream) : GFPT1 (64094 downstream)																							TCCCAGCTCCAAAACAAAACC	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	74266847	74266847	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74266847delA								DGUOK (80761 upstream) : TET3 (6603 downstream)																							ggaatcctcgaagggctcctt	0.000													4	2	---	---	---	---	
C2orf3	6936	broad.mit.edu	37	2	75915921	75915921	+	Intron	DEL	A	-	-	rs34774955		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75915921delA	uc002sno.2	-						C2orf3_uc010ffs.2_Intron|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						ACAAGAAGCTAAAAAAAAATG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82042420	82042420	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82042420delT								None (None upstream) : None (None downstream)																							AGATCTATCatttttttttta	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	86197426	86197426	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86197426delA								ST3GAL5 (81269 upstream) : LOC90784 (49913 downstream)																							tagtccctacaAAAAAAAAAA	0.005													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	88492406	88492406	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88492406delC								THNSL2 (6261 upstream) : FOXI3 (255320 downstream)																							GATGCGAAGACTTTGTCTCAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89579134	89579136	+	Intron	DEL	CTG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89579134_89579136delCTG	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		CTGGAGGATTctgctgctgctgc	0.399													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91739959	91739962	+	IGR	DEL	CTCA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91739959_91739962delCTCA								None (None upstream) : LOC654342 (65230 downstream)																							ttcatttcatctcatttttcatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91739974	91739975	+	IGR	INS	-	TC	TC			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91739974_91739975insTC								None (None upstream) : LOC654342 (65217 downstream)																							ttttcatctcatcatttttcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91768188	91768189	+	IGR	INS	-	T	T	rs138061050		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91768188_91768189insT								None (None upstream) : LOC654342 (37003 downstream)																							AGGACATATACtttattttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92095653	92095654	+	IGR	DEL	AC	-	-	rs148042328	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92095653_92095654delAC								GGT8P (125500 upstream) : FKSG73 (33505 downstream)																							CATCCAAAAAACAAAAAAagaa	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92194836	92194837	+	IGR	INS	-	T	T	rs145003390		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92194836_92194837insT								FKSG73 (64342 upstream) : None (None downstream)																							AGAGCAGGCTCTTGCCCACATC	0.495													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96527714	96527714	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96527714delA	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.																		atttcatagcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	97142988	97142988	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97142988delT								NCAPH (101714 upstream) : NEURL3 (20397 downstream)																							aaattgtatcttgttttttat	0.000													6	4	---	---	---	---	
TSGA10	80705	broad.mit.edu	37	2	99624473	99624473	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99624473delA	uc002szg.3	-						TSGA10_uc002szh.3_Intron|TSGA10_uc002szi.3_Intron|TSGA10_uc010fin.1_Intron	NM_182911	NP_878915	Q9BZW7	TSG10_HUMAN	testis specific, 10						spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2						agtcagttggaaaaagataaa	0.000													4	2	---	---	---	---	
AFF3	3899	broad.mit.edu	37	2	100623119	100623119	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100623119delT	uc002tag.2	-	6	1084	c.848delA	c.(847-849)AAGfs	p.K283fs	AFF3_uc002taf.2_Frame_Shift_Del_p.K308fs|AFF3_uc010fiq.1_Frame_Shift_Del_p.K283fs|AFF3_uc010yvr.1_Frame_Shift_Del_p.K437fs|AFF3_uc002tah.1_Frame_Shift_Del_p.K308fs|AFF3_uc010fir.1_Frame_Shift_Del_p.K360fs|AFF3_uc002tai.2_Frame_Shift_Del_p.K205fs	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1	283					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						GATGCTGAACTTGGAGAGCTT	0.532													42	27	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103016038	103016039	+	IGR	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103016038_103016039insG								IL18R1 (823 upstream) : IL18RAP (19215 downstream)																							TATAAGCCATTAAAAACAAATA	0.525													4	2	---	---	---	---	
IL18RAP	8807	broad.mit.edu	37	2	103035369	103035369	+	5'UTR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103035369delT	uc002tbx.2	+	1					IL18RAP_uc010fiz.2_5'Flank	NM_003853	NP_003844	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein						cell surface receptor linked signaling pathway|inflammatory response|innate immune response	integral to membrane	transmembrane receptor activity			skin(3)|ovary(2)	5						TTCCTTCCTCTTTTTTTTATG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105003138	105003138	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105003138delA	uc010ywf.1	-											SubName: Full=cDNA FLJ59030;																		ttcccatgtgaaaaaaaaaga	0.174													4	3	---	---	---	---	
NCK2	8440	broad.mit.edu	37	2	106475720	106475720	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106475720delG	uc002tdg.2	+						NCK2_uc002tdh.2_Intron|NCK2_uc002tdi.2_Intron	NM_003581	NP_003572	O43639	NCK2_HUMAN	NCK adaptor protein 2 isoform A						axon guidance|epidermal growth factor receptor signaling pathway|negative regulation of cell proliferation|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of epidermal growth factor receptor activity|regulation of translation|signal complex assembly|T cell activation	cytosol|endoplasmic reticulum	cytoskeletal adaptor activity|receptor signaling complex scaffold activity			ovary(1)|lung(1)	2						TTCTCTTTTCGGTGGTTAACA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107302015	107302015	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107302015delG								RGPD3 (217214 upstream) : ST6GAL2 (116043 downstream)																							CACCAAGGAAGGAGACCAATG	0.383													4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109946165	109946165	+	Intron	DEL	A	-	-	rs66661094		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109946165delA	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						AAGAAGTAAGAAAGCAGGAGG	0.498													4	2	---	---	---	---	
ACOXL	55289	broad.mit.edu	37	2	111579511	111579512	+	Intron	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111579511_111579512delTG	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0						cttctatcattgtgtgtgtgtg	0.000													4	2	---	---	---	---	
SLC35F5	80255	broad.mit.edu	37	2	114512514	114512515	+	Intron	INS	-	T	T	rs140278247	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114512514_114512515insT	uc002tku.1	-						SLC35F5_uc002tkt.2_Intron|SLC35F5_uc002tkv.2_Intron|SLC35F5_uc002tkw.2_Intron	NM_025181	NP_079457	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5						transport	integral to membrane					0						CATAGTCTCTCTAAGTAACCCT	0.282													10	5	---	---	---	---	
ACTR3	10096	broad.mit.edu	37	2	114684726	114684729	+	Intron	DEL	ATCT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114684726_114684729delATCT	uc002tkx.1	+						ACTR3_uc010yyc.1_Intron|ACTR3_uc010yyd.1_Intron	NM_005721	NP_005712	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog						cellular component movement|cilium morphogenesis	Arp2/3 protein complex	actin binding|ATP binding			skin(1)	1						TGAACCATCCATCTGACAATGCGT	0.275													6	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119259667	119259667	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119259667delA								INSIG2 (392071 upstream) : EN1 (340081 downstream)																							agaaagaaagaaagagagaga	0.065													4	2	---	---	---	---	
POTEF	728378	broad.mit.edu	37	2	130859424	130859424	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130859424delT	uc010fmh.2	-							NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on							cell cortex	ATP binding			skin(3)|ovary(2)	5						taaataaaaatattataagag	0.224													4	4	---	---	---	---	
POTEF	728378	broad.mit.edu	37	2	130859428	130859428	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130859428delA	uc010fmh.2	-							NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on							cell cortex	ATP binding			skin(3)|ovary(2)	5						taaaaatattataagagtatt	0.224													5	4	---	---	---	---	
POTEF	728378	broad.mit.edu	37	2	130859432	130859435	+	Intron	DEL	GAGT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130859432_130859435delGAGT	uc010fmh.2	-							NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on							cell cortex	ATP binding			skin(3)|ovary(2)	5						aatattataagagtattttaaatt	0.211													4	4	---	---	---	---	
ACMSD	130013	broad.mit.edu	37	2	135606842	135606843	+	Intron	INS	-	TTAT	TTAT	rs147569232	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135606842_135606843insTTAT	uc002ttz.2	+						ACMSD_uc002tua.2_Intron	NM_138326	NP_612199	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase						quinolinate metabolic process|tryptophan catabolic process	cytosol	aminocarboxymuconate-semialdehyde decarboxylase activity|metal ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.115)		CATCTACTGACTTATTTCCAGC	0.267													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	137270213	137270213	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137270213delT								CXCR4 (394488 upstream) : THSD7B (252902 downstream)																							atcttttgtctttttaacaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	144597204	144597204	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144597204delC								ARHGAP15 (71284 upstream) : GTDC1 (106379 downstream)																							GTCCTAACTTCCACTGTGCTT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	147110696	147110697	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147110696_147110697insA								None (None upstream) : PABPC1P2 (233928 downstream)																							tttccacaatgaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151176633	151176634	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151176633_151176634insA								MMADHC (732303 upstream) : RND3 (148078 downstream)																							GTTAAATCAGGATACATGACTC	0.361													4	2	---	---	---	---	
RBM43	375287	broad.mit.edu	37	2	152107578	152107581	+	Frame_Shift_Del	DEL	TCTC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152107578_152107581delTCTC	uc002txh.2	-	4	1061_1064	c.913_916delGAGA	c.(913-918)GAGAAAfs	p.E305fs		NM_198557	NP_940959	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	305_306							nucleotide binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(221;0.131)		ATCATTCTTTTCTCTCTATTTTCC	0.343													364	193	---	---	---	---	
RIF1	55183	broad.mit.edu	37	2	152331770	152331770	+	3'UTR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152331770delT	uc002txm.2	+	36					RIF1_uc002txl.2_3'UTR|RIF1_uc002txn.2_3'UTR|RIF1_uc002txo.2_3'UTR|RIF1_uc002txp.2_Intron|uc010fnw.1_5'Flank	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TGTAAGATCCTTTTTTTTTTC	0.303													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	160927325	160927328	+	IGR	DEL	CAAA	-	-	rs113175668		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160927325_160927328delCAAA								PLA2R1 (8204 upstream) : ITGB6 (28856 downstream)																							caaaacaacccaaacaaacaaaca	0.000													4	2	---	---	---	---	
ITGB6	3694	broad.mit.edu	37	2	161060926	161060926	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161060926delC	uc010fow.1	-									P18564	ITB6_HUMAN	Synthetic construct DNA, clone: pF1KB8424, Homo sapiens ITGB6 gene for integrin, beta 6, without stop codon, in Flexi system.						cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development	integrin complex	receptor activity			ovary(1)|lung(1)|skin(1)	3						TCTAGTATTTCACCAGTTACA	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162288207	162288208	+	IGR	INS	-	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162288207_162288208insC								TBR1 (6634 upstream) : SLC4A10 (192637 downstream)																							TTTTTTTTTTTTTCTCACGCTA	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162295406	162295406	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162295406delG								TBR1 (13833 upstream) : SLC4A10 (185439 downstream)																							atcctggggtgggatgatgta	0.104													4	2	---	---	---	---	
DPP4	1803	broad.mit.edu	37	2	162930287	162930304	+	Intron	DEL	GCCAGGGTCCTAGCAGAA	-	-	rs3216773		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162930287_162930304delGCCAGGGTCCTAGCAGAA	uc002ubz.2	-						DPP4_uc010fpb.2_Intron|DPP4_uc002uca.1_5'Flank|DPP4_uc002ucb.1_5'Flank	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	AAAGCTCGACGCCAGGGTCCTAGCAGAAGCCAGGGTCC	0.606													4	2	---	---	---	---	
SCN9A	6335	broad.mit.edu	37	2	167120834	167120834	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167120834delT	uc010fpl.2	-						uc002udp.2_Intron	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)	TGGAGTGTGCTTGGAGGGCTT	0.433													4	2	---	---	---	---	
SCN9A	6335	broad.mit.edu	37	2	167138537	167138537	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167138537delC	uc010fpl.2	-						uc002udp.2_Intron|SCN9A_uc002udr.1_Intron|SCN9A_uc002uds.1_Intron|SCN9A_uc002udt.1_Intron	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)	atagtgcttgcttcatattct	0.104													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	168175044	168175044	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168175044delA								XIRP2 (58785 upstream) : B3GALT1 (500138 downstream)																							GGAGGGAAGGAAAAAAAAATC	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173109613	173109614	+	IGR	DEL	AG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173109613_173109614delAG								DLX2 (142135 upstream) : ITGA6 (182468 downstream)																							TGACAGGAACAGAGAGAGAGAG	0.441													4	2	---	---	---	---	
ITGA6	3655	broad.mit.edu	37	2	173320553	173320554	+	Intron	DEL	AC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173320553_173320554delAC	uc002uhp.1	+						ITGA6_uc010fqk.1_Intron|ITGA6_uc010zdy.1_Intron|ITGA6_uc002uho.1_Intron	NM_001079818	NP_001073286	P23229	ITA6_HUMAN	integrin alpha chain, alpha 6 isoform a						blood coagulation|cell adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|positive regulation of apoptosis|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter	integrin complex	protein binding|receptor activity			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			AACTTAAAGTACACACACACCA	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174875012	174875012	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174875012delC								SP3 (44949 upstream) : OLA1 (62164 downstream)																							aagataaggaccaggtcttat	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177824500	177824500	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177824500delA								MIR1246 (358720 upstream) : HNRNPA3 (252922 downstream)																							ACCCTCTAACAAAAAGTACCA	0.448													4	2	---	---	---	---	
PDE11A	50940	broad.mit.edu	37	2	178787413	178787413	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178787413delC	uc002ulq.2	-						PDE11A_uc002ulr.2_Intron|PDE11A_uc002uls.1_Intron|PDE11A_uc002ult.1_Intron|PDE11A_uc002ulu.1_Intron	NM_016953	NP_058649	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A isoform 4						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)			cactccctcacccccactcca	0.000									Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	184243646	184243646	+	IGR	DEL	A	-	-	rs61006348		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184243646delA								NUP35 (217239 upstream) : None (None downstream)																							acacacacacacacccccaca	0.294													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	184243648	184243648	+	IGR	DEL	A	-	-	rs59751216		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184243648delA								NUP35 (217241 upstream) : None (None downstream)																							acacacacacacccccacaca	0.294													1	5	---	---	---	---	
ITGAV	3685	broad.mit.edu	37	2	187504127	187504127	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187504127delG	uc002upq.2	+						ITGAV_uc010frs.2_Intron|ITGAV_uc010zfv.1_Intron	NM_002210	NP_002201	P06756	ITAV_HUMAN	integrin alpha-V isoform 1 precursor						angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)		CCATTTGTATGGCAGTCAAGA	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	189491986	189491986	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189491986delT								GULP1 (31336 upstream) : DIRC1 (106479 downstream)																							CTTTGCCCTCTTTTTTTTAAC	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	191501381	191501381	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191501381delC								TMEM194B (101913 upstream) : NAB1 (12467 downstream)																							AGAATATCTACCCCAGGGGCT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	192788682	192788683	+	IGR	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192788682_192788683delGT								SDPR (76701 upstream) : TMEFF2 (26066 downstream)																							TATATATGTAgtgtgtgtgtgt	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	192814332	192814332	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192814332delG								SDPR (102351 upstream) : TMEFF2 (417 downstream)																							GCACTTAACTGGGGGATTCTA	0.363													4	2	---	---	---	---	
HECW2	57520	broad.mit.edu	37	2	197121703	197121703	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197121703delG	uc002utm.1	-						HECW2_uc002utl.1_Intron	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						TGGCAACTATGGAATGGAGAA	0.373													4	2	---	---	---	---	
BMPR2	659	broad.mit.edu	37	2	203302661	203302661	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203302661delT	uc002uzf.3	+						BMPR2_uc010ftr.2_Intron|BMPR2_uc002uze.2_Intron	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II						anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9						aacgtacaaatttttttttgt	0.035													4	2	---	---	---	---	
INO80D	54891	broad.mit.edu	37	2	206884814	206884815	+	Intron	INS	-	G	G	rs67846134		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206884814_206884815insG	uc002vaz.3	-							NM_017759	NP_060229	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D						DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1						AGTATGTCTGTTTTTTTTTTTA	0.203													6	3	---	---	---	---	
CREB1	1385	broad.mit.edu	37	2	208430370	208430371	+	Intron	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208430370_208430371insG	uc002vcc.2	+						CREB1_uc010ziz.1_Intron|CREB1_uc002vcd.2_Intron|CREB1_uc010zja.1_Intron	NM_134442	NP_604391	P16220	CREB1_HUMAN	cAMP responsive element binding protein 1						activation of phospholipase C activity|axon guidance|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|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		protein dimerization activity|transcription cofactor activity		EWSR1/CREB1(42)	soft_tissue(42)|breast(1)|central_nervous_system(1)	44				LUSC - Lung squamous cell carcinoma(261;0.0768)|Epithelial(149;0.127)|Lung(261;0.145)	Adenosine monophosphate(DB00131)|Bromocriptine(DB01200)|Naloxone(DB01183)	CCAACTTGGAAGGGGGGTGTTC	0.386			T	EWSR1	clear cell sarcoma|angiomatoid fibrous histiocytoma								4	2	---	---	---	---	
PTH2R	5746	broad.mit.edu	37	2	209468316	209468317	+	Intron	INS	-	TG	TG	rs67154196		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209468316_209468317insTG	uc010fuo.1	+									P49190	PTH2R_HUMAN	Homo sapiens cDNA FLJ60238 complete cds, highly similar to Parathyroid hormone receptor precursor.							integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)		aatagtttaactacattttaaa	0.000													2	4	---	---	---	---	
C2orf67	151050	broad.mit.edu	37	2	211023889	211023889	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211023889delT	uc002vds.2	-						C2orf67_uc002vdt.2_Intron|C2orf67_uc002vdw.2_Intron|C2orf67_uc002vdy.1_Intron	NM_152519	NP_689732	A0AUZ9	CB067_HUMAN	hypothetical protein LOC151050											ovary(3)	3		Renal(323;0.202)		Epithelial(149;0.00435)|Lung(261;0.0529)|LUSC - Lung squamous cell carcinoma(261;0.0551)|all cancers(144;0.0696)		tcctgactactttgccttcta	0.030													4	2	---	---	---	---	
VWC2L	402117	broad.mit.edu	37	2	215425125	215425125	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215425125delC	uc002vet.2	+						VWC2L_uc010zjl.1_Intron	NM_001080500	NP_001073969	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain-containing							extracellular region					0						TAGTAATGTTCCACTTTGTTG	0.418													4	2	---	---	---	---	
FN1	2335	broad.mit.edu	37	2	216244327	216244327	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216244327delA	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_5'UTR|FN1_uc010zjp.1_Intron|FN1_uc002vfk.1_5'Flank|FN1_uc010fva.1_5'Flank|FN1_uc010fvb.1_5'Flank|FN1_uc010fvc.1_Intron|FN1_uc010fvd.1_Intron	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein						acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GCTTTCCCTTAAAAAAAAAAG	0.279													6	3	---	---	---	---	
RESP18	389075	broad.mit.edu	37	2	220195257	220195257	+	Intron	DEL	G	-	-	rs59436564		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220195257delG	uc002vlc.3	-						RESP18_uc002vlb.2_Intron|RESP18_uc010zle.1_Intron	NM_001007089	NP_001007090	Q5W5W9	RES18_HUMAN	regulated endocrine-specific protein 18							endoplasmic reticulum|extracellular region|Golgi apparatus					0						TTTCAGTTTTGTTTTTTTTTT	0.483													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221427370	221427370	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221427370delC								SLC4A3 (920669 upstream) : EPHA4 (855379 downstream)																							tcgatattgtccccacacttg	0.000													4	2	---	---	---	---	
EPHA4	2043	broad.mit.edu	37	2	222429297	222429297	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222429297delT	uc002vmq.2	-						EPHA4_uc002vmr.2_Intron|EPHA4_uc010zlm.1_Intron|EPHA4_uc010zln.1_Intron	NM_004438	NP_004429	P54764	EPHA4_HUMAN	ephrin receptor EphA4 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(6)|large_intestine(2)|central_nervous_system(2)|urinary_tract(1)|skin(1)	12		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		ATTGAGGAAGTTTTTTTTTTG	0.348													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	234797460	234797460	+	IGR	DEL	A	-	-	rs71832431		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234797460delA								MSL3L2 (20405 upstream) : TRPM8 (28583 downstream)																							gaatcagaagaaaaaaatgga	0.075													4	6	---	---	---	---	
ARL4C	10123	broad.mit.edu	37	2	235403251	235403251	+	3'UTR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235403251delT	uc002vvn.2	-	1					ARL4C_uc002vvm.3_3'UTR	NM_005737	NP_005728	P56559	ARL4C_HUMAN	ADP-ribosylation factor-like 4C						endocytic recycling|small GTPase mediated signal transduction	cytoplasm|filopodium|nucleus|plasma membrane	alpha-tubulin binding|GTP binding|GTPase activity			skin(1)	1		Breast(86;0.000596)|Renal(207;0.00339)|all_lung(227;0.00354)|all_hematologic(139;0.0494)|Lung NSC(271;0.0496)|Lung SC(224;0.164)|all_neural(83;0.173)		Epithelial(121;2.6e-19)|BRCA - Breast invasive adenocarcinoma(100;0.000296)|Lung(119;0.002)|LUSC - Lung squamous cell carcinoma(224;0.0048)		TGGGGTTTTATTTTTTTGGTG	0.363													4	2	---	---	---	---	
IQCA1	79781	broad.mit.edu	37	2	237355716	237355716	+	Intron	DEL	T	-	-	rs115490779	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237355716delT	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						CCCAGCCTCCTCCAGTGACTC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239914076	239914077	+	IGR	INS	-	T	T	rs72323584		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239914076_239914077insT								TWIST2 (81839 upstream) : HDAC4 (55788 downstream)																							tttcgtagaagttttttttttt	0.198													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	241772636	241772638	+	IGR	DEL	CCT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241772636_241772638delCCT								KIF1A (13012 upstream) : AGXT (35524 downstream)																							GCCTCTTCCCCCTCCTCCTCCAT	0.611													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	5968646	5968647	+	IGR	INS	-	TG	TG	rs141637536	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5968646_5968647insTG								EDEM1 (706997 upstream) : GRM7 (934155 downstream)																							gtttgtgtttctgtgtgtgtgt	0.109													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	19627171	19627171	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19627171delA								KCNH8 (50036 upstream) : EFHB (293797 downstream)																							AATCTTACCCAAAAAAAAGTA	0.348													4	2	---	---	---	---	
OXSR1	9943	broad.mit.edu	37	3	38283295	38283295	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38283295delT	uc003chy.2	+						OXSR1_uc010hhb.2_Intron	NM_005109	NP_005100	O95747	OXSR1_HUMAN	oxidative-stress responsive 1						intracellular protein kinase cascade|response to oxidative stress		ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity			skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AAGTTGTTTGTTTTTTTTTTT	0.209													4	2	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41787454	41787455	+	Intron	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41787454_41787455insG	uc003ckv.3	-							NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		agaaaaaaaaaactctaagaaa	0.000													4	2	---	---	---	---	
LTF	4057	broad.mit.edu	37	3	46482667	46482668	+	Intron	INS	-	GT	GT			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46482667_46482668insGT	uc003cpq.2	-						LTF_uc003fzr.2_Intron|LTF_uc010hjh.2_Intron|LTF_uc003cpr.2_Intron	NM_002343	NP_002334	P02788	TRFL_HUMAN	lactotransferrin precursor						cellular iron ion homeostasis|defense response to bacterium|humoral immune response|iron ion transport	extracellular region|stored secretory granule	ferric iron binding|heparin binding|protein binding|serine-type endopeptidase activity			central_nervous_system(2)|ovary(1)|lung(1)	4				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)	Pefloxacin(DB00487)	tgtgagagtgagtgtgtgtgtg	0.351													6	5	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54231974	54231974	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54231974delG	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		TTCTCTGTGAGGTGAAGCATC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	56730814	56730814	+	IGR	DEL	A	-	-	rs34144945		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56730814delA								C3orf63 (13679 upstream) : ARHGEF3 (30632 downstream)																							ACTGTTTTTTAAAAAAGGAGG	0.184													4	2	---	---	---	---	
FHIT	2272	broad.mit.edu	37	3	60065634	60065634	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60065634delA	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003	P49789	FHIT_HUMAN	fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		TTACACTATTAAAAAGGTACA	0.289			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	66627622	66627623	+	IGR	DEL	TC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66627622_66627623delTC								LRIG1 (76777 upstream) : KBTBD8 (421104 downstream)																							tttgtttccttctggccattga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	69198724	69198724	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69198724delA								LMOD3 (26978 upstream) : FRMD4B (20422 downstream)																							AAACAGAAGGAAAAAAAAAAA	0.398													4	2	---	---	---	---	
FOXP1	27086	broad.mit.edu	37	3	71120317	71120317	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71120317delA	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003doj.2_Intron|FOXP1_uc003dok.2_Intron	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		CCTTTTCTAGAAAAAAAGGTT	0.448			T	PAX5	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	72386851	72386851	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72386851delG								PROK2 (552494 upstream) : RYBP (36900 downstream)																							gtgtgtgtgtgGGGGGGAGGG	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	73905028	73905028	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73905028delT								PDZRN3 (230956 upstream) : CNTN3 (406694 downstream)																							ACTTTCTTTCTTTTTTTAACC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	78151202	78151202	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78151202delT								ROBO2 (454541 upstream) : ROBO1 (495186 downstream)																							GATGTTGATCTTTTTTTCTCT	0.388													4	2	---	---	---	---	
ROBO1	6091	broad.mit.edu	37	3	79392868	79392869	+	Intron	INS	-	AGA	AGA	rs138352860	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79392868_79392869insAGA	uc003dqe.2	-							NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		ATTTAAGTGGGAGAAGAAGAAA	0.366													4	3	---	---	---	---	
GBE1	2632	broad.mit.edu	37	3	81616307	81616307	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81616307delT	uc003dqg.2	-						GBE1_uc011bgm.1_Intron	NM_000158	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		tggcaacttatttgtcctcat	0.000									Glycogen_Storage_Disease_type_IV				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	84313331	84313332	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84313331_84313332insA								None (None upstream) : CADM2 (694801 downstream)																							TATacaaacagaaaaaaaaaga	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	84333668	84333668	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84333668delT								None (None upstream) : CADM2 (674465 downstream)																							AAATTGGAGATTTTTTGACAG	0.318													4	2	---	---	---	---	
EPHA3	2042	broad.mit.edu	37	3	89252484	89252485	+	Intron	DEL	AC	-	-	rs143074609		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89252484_89252485delAC	uc003dqy.2	+						EPHA3_uc003dqx.1_Intron|EPHA3_uc010hon.1_Intron	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor							extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TAaaaaaaaaacaaaacaaaac	0.252										TSP Lung(6;0.00050)			1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	97926080	97926080	+	IGR	DEL	T	-	-	rs5851109		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97926080delT								OR5H15 (37597 upstream) : OR5H6 (57049 downstream)																							AAATATATGATTTTTTTCCAT	0.308													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	98666973	98666973	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98666973delT								DCBLD2 (46440 upstream) : COL8A1 (690481 downstream)																							atcttttgtatttttttgttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105641973	105641973	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105641973delG								CBLB (53707 upstream) : LOC100302640 (913687 downstream)																							GTGGAATTTTGGGGGGATGCA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105779186	105779186	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105779186delG								CBLB (190920 upstream) : LOC100302640 (776474 downstream)																							ACACAATCCTGCAGTGGTGAG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	111254607	111254611	+	IGR	DEL	ATAAA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111254607_111254611delATAAA								PVRL3 (342234 upstream) : CD96 (6315 downstream)																							gtcttgatttataaaataagggagt	0.161													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117540336	117540336	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117540336delT								None (None upstream) : None (None downstream)																							GTGCGGCACATTTTGAGAGGG	0.333													4	2	---	---	---	---	
GSK3B	2932	broad.mit.edu	37	3	119748921	119748921	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119748921delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	ATCTAGTTGGAAAAAAAAAAT	0.259													3	3	---	---	---	---	
MUC13	56667	broad.mit.edu	37	3	124640001	124640002	+	Intron	INS	-	T	T	rs140184451	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124640001_124640002insT	uc003ehq.1	-							NM_033049	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, epithelial transmembrane							extracellular region|integral to membrane|plasma membrane					0						TCTCTACTTCCttttttttttc	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	124668425	124668425	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124668425delT								MUC13 (14845 upstream) : HEG1 (16130 downstream)																							ccaatgatgattaagtctatt	0.000													4	2	---	---	---	---	
PPP2R3A	5523	broad.mit.edu	37	3	135713492	135713492	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135713492delT	uc003eqv.1	+						PPP2R3A_uc011blz.1_Intron	NM_002718	NP_002709	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'',						protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(3)|pancreas(1)|lung(1)|breast(1)|skin(1)	7						gtctcctaggtttttgaagat	0.194													4	2	---	---	---	---	
STAG1	10274	broad.mit.edu	37	3	136347655	136347655	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136347655delA	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron|STAG1_uc003ere.2_Intron	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						CCCGGAATATAAAATGTAGTA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	138943798	138943799	+	IGR	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138943798_138943799delGT								BPESC1 (99795 upstream) : PISRT1 (8036 downstream)																							GTTGGTGTCAGTGTGTGTGTGT	0.252													4	2	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140169593	140169594	+	Intron	DEL	CA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140169593_140169594delCA	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						cacacacaagcacacacacCCC	0.287										HNSCC(16;0.037)			4	2	---	---	---	---	
TFDP2	7029	broad.mit.edu	37	3	141672056	141672056	+	Intron	DEL	A	-	-	rs140575104		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141672056delA	uc003eun.3	-						TFDP2_uc003euk.3_Intron|TFDP2_uc010hur.2_Intron|TFDP2_uc003eul.3_Intron|TFDP2_uc011bnf.1_Intron|TFDP2_uc011bng.1_Intron|TFDP2_uc003eum.3_Intron	NM_006286	NP_006277	Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1						TAAGAGCAGGAAAAAAAAAAT	0.373													4	4	---	---	---	---	
XRN1	54464	broad.mit.edu	37	3	142074095	142074096	+	Intron	INS	-	A	A	rs150539112	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142074095_142074096insA	uc003eus.2	-						XRN1_uc010huu.2_Intron|XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3						tgaaaTTATTTAAAAAAAGAAA	0.094													9	6	---	---	---	---	
ZIC4	84107	broad.mit.edu	37	3	147120982	147120982	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147120982delT	uc003ewd.1	-						ZIC4_uc011bno.1_Intron	NM_032153	NP_115529	Q8N9L1	ZIC4_HUMAN	zinc finger protein of the cerebellum 4							nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2						TTAACTGAAATTTAGTGAGGT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151917803	151917803	+	IGR	DEL	C	-	-	rs11292195		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151917803delC								SUCNR1 (318153 upstream) : LOC401093 (62610 downstream)																							GAGAAGTATGCCCCTGCCTAA	0.318													3	3	---	---	---	---	
KCNAB1	7881	broad.mit.edu	37	3	155858850	155858850	+	Intron	DEL	T	-	-	rs111752364		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155858850delT	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_5'Flank	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GTTTCTTTGCTTTtttttttt	0.224													4	2	---	---	---	---	
C3orf57	165679	broad.mit.edu	37	3	161081752	161081752	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161081752delA	uc003fee.2	-							NM_001040100	NP_001035189	Q8NFR3	SSPTB_HUMAN	ADMP						sphingolipid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	protein binding				0			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			ATGGTACATGAAAAAAAAAAT	0.274													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162884001	162884002	+	Intron	INS	-	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162884001_162884002insC	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																		tttctttatttcttcttcatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	164438364	164438365	+	IGR	INS	-	G	G	rs144105356	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164438364_164438365insG								MIR720 (379126 upstream) : SI (258322 downstream)																							AATTTGGCTCTGTTTTTTTTTC	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	164438365	164438366	+	IGR	INS	-	T	T	rs144105356	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164438365_164438366insT								MIR720 (379127 upstream) : SI (258321 downstream)																							ATTTGGCTCTGTTTTTTTTTCC	0.327													4	2	---	---	---	---	
FNDC3B	64778	broad.mit.edu	37	3	172041310	172041311	+	Intron	DEL	CA	-	-	rs149168084	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172041310_172041311delCA	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fia.2_Intron	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B							endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		ccttgtctcTCACACACACACA	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	182087569	182087570	+	IGR	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182087569_182087570delGT								SOX2OT (628566 upstream) : ATP11B (423721 downstream)																							GTGTCTTGGAgtgtgtgtgtgt	0.322													4	2	---	---	---	---	
ATP11B	23200	broad.mit.edu	37	3	182525154	182525154	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182525154delT	uc003flb.2	+						ATP11B_uc003fla.2_Intron	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B						aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TGATCAAGAGTTTCTAGTCCA	0.368													4	2	---	---	---	---	
TRA2B	6434	broad.mit.edu	37	3	185643007	185643007	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185643007delT	uc003fpv.2	-						TRA2B_uc003fpt.2_RNA|TRA2B_uc003fpu.2_Intron|TRA2B_uc010hym.2_Intron|TRA2B_uc003fpw.2_Intron	NM_004593	NP_004584	P62995	TRA2B_HUMAN	splicing factor, arginine/serine-rich 10						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|protein binding|RNA binding			ovary(2)	2						CAGTCGGAAGTTTTTTTTTTT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187263839	187263839	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187263839delT								RTP4 (174472 upstream) : SST (122857 downstream)																							ATGAATTAAATTTTTTATCAG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189074921	189074921	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189074921delA								TPRG1 (33651 upstream) : TP63 (274295 downstream)																							tcatcttcacaaaaattctgt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194299840	194299841	+	IGR	INS	-	T	T	rs143953400		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194299840_194299841insT								ATP13A3 (110872 upstream) : TMEM44 (8562 downstream)																							tctttcttttcttttttttttA	0.356													3	3	---	---	---	---	
LSG1	55341	broad.mit.edu	37	3	194366659	194366659	+	Intron	DEL	A	-	-	rs10621226		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194366659delA	uc003fui.2	-							NM_018385	NP_060855	Q9H089	LSG1_HUMAN	large subunit GTPase 1						nuclear export|protein transport	Cajal body|endoplasmic reticulum	GTP binding|hydrolase activity				0	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		TGTAGGAGACAAAAAAAGCCA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197058802	197058802	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197058802delG								DLG1 (32659 upstream) : BDH1 (177853 downstream)																							gttggatggtggggtaaattc	0.000													4	2	---	---	---	---	
ZFYVE28	57732	broad.mit.edu	37	4	2418574	2418574	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2418574delC	uc003gex.1	-						ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						GCAAGGGGCGCCCCATGTACC	0.637													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3855564	3855564	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3855564delC								ADRA2C (85313 upstream) : LOC348926 (88106 downstream)																							CCCTGCCCGGCCCCCAGCCCC	0.632													4	2	---	---	---	---	
JAKMIP1	152789	broad.mit.edu	37	4	6134752	6134752	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6134752delT	uc003giu.3	-						JAKMIP1_uc010idb.1_Intron|JAKMIP1_uc010idc.1_Intron|JAKMIP1_uc010idd.1_Intron|JAKMIP1_uc011bwc.1_Intron|JAKMIP1_uc003giv.3_Intron|JAKMIP1_uc010ide.2_Intron	NM_144720	NP_653321	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein						protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						GCAAGCCttattttttttaat	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6678589	6678589	+	IGR	DEL	G	-	-	rs35072066		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6678589delG								LOC93622 (815 upstream) : S100P (16977 downstream)																							ttctaggcacggggaacaagt	0.204													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10273301	10273301	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10273301delT								WDR1 (154728 upstream) : ZNF518B (168204 downstream)																							CTCAACGTCATTTTTTTTTCT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14490601	14490601	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14490601delA	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																		caatagctgcaaaaaaaaaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14532229	14532229	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14532229delA	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																		TGGATATATGAAAGCATGGAT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	17398887	17398887	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17398887delA								LDB2 (498463 upstream) : QDPR (89133 downstream)																							TGGTGGTAATAAATGTCACCA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	22622852	22622852	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22622852delA								GPR125 (105180 upstream) : GBA3 (71696 downstream)																							actccagatgaaaaaaaaagg	0.000													2	4	---	---	---	---	
PPARGC1A	10891	broad.mit.edu	37	4	23891999	23891999	+	5'Flank	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23891999delT	uc003gqs.2	-						PPARGC1A_uc003gqt.2_5'Flank|PPARGC1A_uc010ier.1_5'Flank|PPARGC1A_uc003gqu.3_5'Flank	NM_013261	NP_037393	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor						androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding			ovary(2)|lung(2)|kidney(2)|skin(2)	8		Breast(46;0.0503)				CCCTGCAATCTTTTTTTAATT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25623286	25623287	+	IGR	DEL	TC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25623286_25623287delTC								ANAPC4 (203167 upstream) : SLC34A2 (34148 downstream)																							CTAGGTGACTTCTGGATGACTG	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	26527078	26527079	+	IGR	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26527078_26527079delTG								CCKAR (35036 upstream) : TBC1D19 (58467 downstream)																							ccctacattttgtgtgtgtgtg	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	27768622	27768622	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27768622delT								STIM2 (742814 upstream) : None (None downstream)																							CTTTCTTTTCTTTTTTTTTTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	32205313	32205314	+	IGR	DEL	AA	-	-	rs72596009		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32205313_32205314delAA								None (None upstream) : None (None downstream)																							taatgatattaagagtttggac	0.084													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	37699579	37699579	+	IGR	DEL	A	-	-	rs67981500		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37699579delA								RELL1 (11580 upstream) : PGM2 (128703 downstream)																							GGTTTTTTGGAGACATCTCTA	0.299													5	3	---	---	---	---	
RPL9	6133	broad.mit.edu	37	4	39458973	39458974	+	Intron	INS	-	A	A	rs71643296		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39458973_39458974insA	uc003gub.2	-						RPL9_uc003guc.2_Intron|RPL9_uc011byk.1_Intron|RPL9_uc011byl.1_Intron|RPL9_uc003gud.1_3'UTR|LIAS_uc003gue.3_5'Flank|LIAS_uc011bym.1_5'Flank|LIAS_uc003guf.2_5'Flank|LIAS_uc003gug.2_5'Flank|LIAS_uc003guh.2_5'Flank	NM_001024921	NP_001020092	P32969	RL9_HUMAN	ribosomal protein L9						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|nucleolus|ribosome	rRNA binding|structural constituent of ribosome			skin(1)	1						cagccttgattaaaaaaaaaaa	0.178													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49220658	49220659	+	IGR	INS	-	C	C	rs58383135		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49220658_49220659insC								CWH43 (156565 upstream) : None (None downstream)																							ttccagaatctatgtccttatc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58808645	58808655	+	IGR	DEL	TTCCCACTAAT	-	-	rs77033843		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58808645_58808655delTTCCCACTAAT								IGFBP7 (832106 upstream) : None (None downstream)																							GGAATTGGGATTCCCACTAATGTATCTGTAT	0.289													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58808657	58808658	+	IGR	DEL	TA	-	-	rs61283673		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58808657_58808658delTA								IGFBP7 (832118 upstream) : None (None downstream)																							CCCACTAATGTATCTGTATTAG	0.277													4	3	---	---	---	---	
LPHN3	23284	broad.mit.edu	37	4	62395893	62395893	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62395893delA	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc010ihg.1_Intron	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						CTACAGAGAGAAAATTGCATA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63987008	63987009	+	IGR	INS	-	TTTTG	TTTTG	rs113031810		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63987008_63987009insTTTTG								None (None upstream) : None (None downstream)																							AATTTTCCTGTttttgttttgt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	67502218	67502219	+	IGR	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67502218_67502219insG								MIR1269 (359572 upstream) : CENPC1 (835770 downstream)																							AAAGAGCAGCTGGGGATGTGCA	0.500													4	2	---	---	---	---	
AFM	173	broad.mit.edu	37	4	74366103	74366104	+	Intron	INS	-	T	T	rs147401124	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74366103_74366104insT	uc003hhb.2	+							NM_001133	NP_001124	P43652	AFAM_HUMAN	afamin precursor						vitamin transport		vitamin E binding			ovary(2)|central_nervous_system(1)	3	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACAAGTGCATATTTTTTTTTTG	0.342													20	15	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	78167163	78167163	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78167163delG								CCNG2 (75953 upstream) : CXCL13 (265744 downstream)																							AGAGGGTGGTGGGGTTGAGAG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	83324308	83324308	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83324308delT								HNRNPD (29159 upstream) : HNRPDL (20041 downstream)																							AACAAAATGATTTTTTTTAAG	0.254													4	2	---	---	---	---	
COPS4	51138	broad.mit.edu	37	4	83967498	83967498	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83967498delT	uc003hoa.2	+						COPS4_uc003hob.2_Intron|COPS4_uc010ijw.2_Intron|COPS4_uc010ijx.2_Intron	NM_016129	NP_057213	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4						cullin deneddylation	cytoplasm|signalosome	protein binding			kidney(1)	1		Hepatocellular(203;0.114)				agaatgtaaattagttcagcc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84120307	84120307	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84120307delT								PLAC8 (84396 upstream) : COQ2 (62382 downstream)																							aaacgtatgatttttttttgc	0.050													8	4	---	---	---	---	
WDFY3	23001	broad.mit.edu	37	4	85648391	85648391	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85648391delA	uc003hpd.2	-						WDFY3_uc003hpe.1_Intron	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)		TACATTGTTTAAAAAAAAAAA	0.368													6	3	---	---	---	---	
WDFY3	23001	broad.mit.edu	37	4	85850365	85850365	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85850365delT	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)		actgggtcccttagttcaaca	0.000													4	2	---	---	---	---	
ARHGAP24	83478	broad.mit.edu	37	4	86593070	86593070	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86593070delT	uc003hpk.2	+						ARHGAP24_uc003hpi.1_Intron|ARHGAP24_uc003hpj.2_Intron	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		AAGTAGGTGCTTTTTTTTCCA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	88828350	88828350	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88828350delT								MEPE (60408 upstream) : SPP1 (68452 downstream)																							ATAAGCAATCTTAGTTTAAGT	0.338													4	2	---	---	---	---	
FAM13A	10144	broad.mit.edu	37	4	90026257	90026257	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90026257delC	uc003hsh.1	-									O94988	FA13A_HUMAN	Homo sapiens mRNA for KIAA0914 protein, partial cds.						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2						gtggacgggtcccctgtgagc	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	95651618	95651618	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95651618delT								PDLIM5 (62242 upstream) : BMPR1B (27510 downstream)																							ttgcactttcttttttttttt	0.000													4	2	---	---	---	---	
RAP1GDS1	5910	broad.mit.edu	37	4	99240137	99240138	+	Intron	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99240137_99240138insG	uc003htx.3	+						RAP1GDS1_uc003htu.2_Intron|RAP1GDS1_uc003htw.3_Intron|RAP1GDS1_uc003htv.3_Intron|RAP1GDS1_uc003htz.3_Intron|RAP1GDS1_uc003hty.3_Intron|RAP1GDS1_uc003hua.3_Intron	NM_001100427	NP_001093897	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1 isoform								binding|GTPase activator activity			ovary(1)|lung(1)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		tgTAGTTCTCTGGGGGGGGAAA	0.238			T	NUP98	T-ALL								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	101073137	101073138	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101073137_101073138insA								LOC256880 (199517 upstream) : DDIT4L (33891 downstream)																							TGTCCCTCTTGAAAAAAAAAAT	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	101603278	101603278	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101603278delC								EMCN (164028 upstream) : PPP3CA (341309 downstream)																							tcaaaagtatccctctgcaga	0.000													4	2	---	---	---	---	
BANK1	55024	broad.mit.edu	37	4	102455504	102455504	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102455504delA	uc003hvx.3	+							NM_001083907	NP_001077376	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		taatgaaatgaaaaaaaaaag	0.000													2	5	---	---	---	---	
SLC39A8	64116	broad.mit.edu	37	4	103225941	103225942	+	Intron	INS	-	A	A	rs143792636	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103225941_103225942insA	uc003hwb.1	-						SLC39A8_uc011ceo.1_Intron|SLC39A8_uc003hwa.1_Intron|SLC39A8_uc003hwc.2_Intron	NM_022154	NP_071437	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter),							integral to membrane|organelle membrane|plasma membrane	zinc ion transmembrane transporter activity				0		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		TGAAAAAAAACAAAAATAACCT	0.262													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	105845864	105845864	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105845864delA								CXXC4 (429806 upstream) : TET2 (222079 downstream)																							ctaaaaaaataaaaaaaaaat	0.005													5	3	---	---	---	---	
COL25A1	84570	broad.mit.edu	37	4	110104093	110104094	+	Intron	DEL	CA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110104093_110104094delCA	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzh.1_Intron	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		GAGGTCATAGCACACACACACA	0.371													4	2	---	---	---	---	
CCDC109B	55013	broad.mit.edu	37	4	110516891	110516893	+	Intron	DEL	GAG	-	-	rs138383728		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110516891_110516893delGAG	uc011cfs.1	+						CCDC109B_uc010imf.2_Intron	NM_017918	NP_060388	Q9NWR8	C109B_HUMAN	coiled-coil domain containing 109B							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)		gtgaatagctgaggagaagagca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111135955	111135955	+	IGR	DEL	T	-	-	rs113765269		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111135955delT								ELOVL6 (16135 upstream) : ENPEP (261274 downstream)																							agttttatcgttttTTTTTCT	0.164													4	2	---	---	---	---	
ANK2	287	broad.mit.edu	37	4	113880011	113880012	+	Intron	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113880011_113880012insT	uc003ibd.3	+						ANK2_uc003ibc.2_Intron	NM_001127493	NP_001120965	Q01484	ANK2_HUMAN	ankyrin 2 isoform 3						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		atttctttttctttttttttgg	0.084													4	2	---	---	---	---	
PDE5A	8654	broad.mit.edu	37	4	120444524	120444525	+	Intron	INS	-	TCTG	TCTG	rs10696044		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120444524_120444525insTCTG	uc003idh.2	-						uc003ide.3_Intron|PDE5A_uc003idf.2_Intron|PDE5A_uc003idg.2_Intron|uc003idi.3_Intron	NM_001083	NP_001074	O76074	PDE5A_HUMAN	phosphodiesterase 5A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|zinc ion binding				0					Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Vardenafil(DB00862)	GAACATGAAGATCTTTCAATAT	0.327													4	2	---	---	---	---	
LOC285419	285419	broad.mit.edu	37	4	124764685	124764685	+	Intron	DEL	G	-	-	rs144033398	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124764685delG	uc011cgn.1	+						LOC285419_uc003ifd.2_Intron	NR_027105				Homo sapiens mRNA; cDNA DKFZp686P12109 (from clone DKFZp686P12109).												0						tcagtacagcgggcatgccag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	125117348	125117348	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125117348delC								LOC285419 (265830 upstream) : ANKRD50 (468120 downstream)																							tgctctgcttccctccttaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	137010805	137010805	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137010805delT								None (None upstream) : None (None downstream)																							ACTTTGGTGCttttttttttt	0.070													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	138699725	138699725	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138699725delA								PCDH18 (246077 upstream) : SLC7A11 (385523 downstream)																							CATGGCACACAAAAAGTAGGA	0.368													4	2	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	143387748	143387748	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143387748delT	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011cho.1_Intron|INPP4B_uc003iiz.2_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					agaaaaagcatttttgagaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	148081853	148081853	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148081853delA								TTC29 (214819 upstream) : MIR548G (183928 downstream)																							TCTGAAGACCAAAAAAAAATA	0.303													3	3	---	---	---	---	
FAM160A1	729830	broad.mit.edu	37	4	152377224	152377224	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152377224delA	uc003imj.2	+							NM_001109977	NP_001103447	Q05DH4	F16A1_HUMAN	hypothetical protein LOC729830												0						TCATCTATGGAAAAAAAAGCT	0.318													4	2	---	---	---	---	
FHDC1	85462	broad.mit.edu	37	4	153889446	153889446	+	Intron	DEL	T	-	-	rs74930268		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153889446delT	uc003inf.2	+							NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1						actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)					GCCTGATATATTTTTTTTTTT	0.219													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	154050131	154050131	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154050131delT								FHDC1 (149283 upstream) : TRIM2 (24139 downstream)																							CTGTATTTACTTTTTTTTTTC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	155809696	155809696	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155809696delA								RBM46 (59732 upstream) : NPY2R (320085 downstream)																							TCTAGAGTATAAAAACTTCAG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	156243425	156243425	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156243425delC								NPY2R (105199 upstream) : MAP9 (20389 downstream)																							AGGAGATGGACCGTAAAAGGC	0.398													4	2	---	---	---	---	
GLRB	2743	broad.mit.edu	37	4	158043245	158043245	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158043245delA	uc003ipj.2	+							NM_000824	NP_000815	P48167	GLRB_HUMAN	glycine receptor, beta isoform A precursor						nervous system development|neuropeptide signaling pathway|startle response	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|protein binding|receptor activity			skin(2)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Glycine(DB00145)	ATTCTTCCTGaaaaaaaaaaa	0.214													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	160862588	160862589	+	IGR	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160862588_160862589insG								RAPGEF2 (581289 upstream) : None (None downstream)																							TGCTACAAAGTGGAAAAAAAAT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	164322165	164322165	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164322165delA								NPY5R (49081 upstream) : TKTL2 (70083 downstream)																							GAGGTCACACATTTTAACTTA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	165856075	165856075	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165856075delT								MARCH1 (550873 upstream) : TRIM61 (19525 downstream)																							TTTGGTGTTATttttctttct	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	166556491	166556491	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166556491delA								CPE (137010 upstream) : TLL1 (237919 downstream)																							accaaacatgaactttccttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	167062230	167062231	+	IGR	DEL	TG	-	-	rs111317945		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167062230_167062231delTG								TLL1 (37237 upstream) : SPOCK3 (592305 downstream)																							AGAAATGTTCtgtgtgtgtgtg	0.297													4	2	---	---	---	---	
CBR4	84869	broad.mit.edu	37	4	169898521	169898521	+	Intron	DEL	T	-	-	rs67561290	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169898521delT	uc011cjy.1	-									Q8N4T8	CBR4_HUMAN	Homo sapiens cDNA FLJ14431 fis, clone HEMBA1006521, weakly similar to 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE (EC 1.1.1.100).						fatty acid biosynthetic process|protein homotetramerization	mitochondrial matrix	NADPH binding|NADPH dehydrogenase (quinone) activity|protein binding|quinone binding				0		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)		gattttctacttactgctcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	174844359	174844361	+	IGR	DEL	TCT	-	-	rs149523632	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174844359_174844361delTCT								MORF4 (306565 upstream) : FBXO8 (313451 downstream)																							CCTTGAAAAATCTCCTCTCTTCA	0.424													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	175405382	175405382	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175405382delT								KIAA1712 (150851 upstream) : HPGD (5946 downstream)																							agcctactaattttttaatac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	176419235	176419236	+	IGR	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176419235_176419236delGT								ADAM29 (519905 upstream) : GPM6A (134853 downstream)																							TTTCAATTGCGTGTGTGTGTGT	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	187250819	187250819	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187250819delG	uc003izb.1	-											Homo sapiens coagulation factor XI (plasma thromboplastin antecedent), mRNA (cDNA clone IMAGE:4831055).																		CTTTGACTCTGGGGCTGCAGG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190614285	190614285	+	IGR	DEL	A	-	-	rs113246865		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190614285delA								None (None upstream) : FRG1 (247689 downstream)																							GAAGAGGTAGAAAAAAAAAAG	0.303													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190898573	190898574	+	IGR	INS	-	AA	AA	rs80185318		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190898573_190898574insAA								FRG1 (14215 upstream) : TUBB4Q (5105 downstream)																							ccaatatttgcaaaaatagaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	191037516	191037517	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:191037516_191037517insT								LOC653545 (27340 upstream) : None (None downstream)																							aggtaaacagattttttttatg	0.124													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	993903	993903	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:993903delT	uc003jbs.1	-											Homo sapiens cDNA FLJ44211 fis, clone THYMU3002661.																		TTTAAACCCATTTTTTCAGAC	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2811768	2811768	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2811768delC								C5orf38 (56256 upstream) : IRX1 (784400 downstream)																							TGGCTTGCAGCCCCCCAGACC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5329216	5329216	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5329216delA								ADAMTS16 (8805 upstream) : KIAA0947 (93591 downstream)																							gctacaattcaagatgagatt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7098522	7098522	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7098522delA								PAPD7 (341361 upstream) : ADCY2 (297821 downstream)																							GATGTGAGTTAAAATCAGAGC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	12634307	12634308	+	Intron	DEL	AC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12634307_12634308delAC	uc003jfb.1	+						uc010itv.1_Intron					Homo sapiens TAG1 mRNA, complete sequence.																		aaacattcatacacacacacac	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13308270	13308270	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13308270delT								None (None upstream) : DNAH5 (382167 downstream)																							tggattctactttggcttctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13622381	13622381	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13622381delT								None (None upstream) : DNAH5 (68056 downstream)																							agaggatatataagcttcaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17000447	17000447	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17000447delA								MYO10 (64062 upstream) : LOC285696 (129690 downstream)																							AAATGAGAGGAAAAAAAAATC	0.328													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	18976788	18976789	+	IGR	DEL	TT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18976788_18976789delTT								None (None upstream) : CDH18 (496368 downstream)																							acacggtctctttttcatcttc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	19347578	19347578	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19347578delG								None (None upstream) : CDH18 (125579 downstream)																							TAATTTCTTTGCTTCCTGTTG	0.259													4	2	---	---	---	---	
CDH18	1016	broad.mit.edu	37	5	19889415	19889415	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19889415delT	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					tgttagccaattttttttctg	0.000													4	2	---	---	---	---	
CDH18	1016	broad.mit.edu	37	5	19958219	19958220	+	Intron	DEL	TC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19958219_19958220delTC	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TTCCAAGGGATctctctcattg	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20759048	20759049	+	Intron	DEL	AA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20759048_20759049delAA	uc003jge.1	+											Homo sapiens cDNA FLJ36043 fis, clone TESTI2017582.																		TCATTTTGGCAAAAAAAAAATT	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	20792333	20792333	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20792333delC	uc003jge.1	+											Homo sapiens cDNA FLJ36043 fis, clone TESTI2017582.																		aaaaaaaaaacaaaaacaaaa	0.239													4	2	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21566449	21566450	+	Intron	INS	-	T	T	rs144794849	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21566449_21566450insT	uc003jgh.3	+							NR_027026				Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						cacatgtgtcctttttatatag	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23872412	23872412	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23872412delA								PRDM9 (343708 upstream) : CDH10 (614798 downstream)																							caacaacaacaaaaaaaaact	0.000													4	2	---	---	---	---	
CDH10	1008	broad.mit.edu	37	5	24553568	24553568	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24553568delC	uc003jgr.1	-						CDH10_uc011cnu.1_Intron	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		cctggcttttccctttaattt	0.000										HNSCC(23;0.051)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27796508	27796508	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27796508delG								CDH9 (757819 upstream) : None (None downstream)																							agcctttcaaggggcttgggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	29251501	29251504	+	IGR	DEL	TTGT	-	-	rs111402633		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29251501_29251504delTTGT								None (None upstream) : None (None downstream)																							AAATAACACATTGTTTGTTCCAAT	0.392													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30920114	30920114	+	IGR	DEL	A	-	-	rs72298333		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30920114delA								None (None upstream) : CDH6 (273682 downstream)																							AGCCAAGGGGAAAAAAATGAA	0.398													4	4	---	---	---	---	
CDH6	1004	broad.mit.edu	37	5	31284522	31284522	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31284522delA	uc003jhe.1	+						CDH6_uc003jhd.1_Intron	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7						CATGAATCTGAATCCACAGGG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	33517870	33517872	+	IGR	DEL	CAC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33517870_33517872delCAC								TARS (49676 upstream) : ADAMTS12 (9415 downstream)																							AGCTAATCAGCACCACCACAGTC	0.463													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38212845	38212845	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38212845delT								GDNF (373063 upstream) : EGFLAM (45688 downstream)																							TGGACAAGGCTTTTTTTGAGT	0.383													4	2	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38402075	38402075	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38402075delC	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron|EGFLAM_uc003jle.1_5'Flank|EGFLAM_uc003jlf.1_5'Flank|uc003jld.1_RNA	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					CACCATTTTTCCCAGAAGAGT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	39627636	39627636	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39627636delT								DAB2 (202301 upstream) : None (None downstream)																							acatggcctatttttttttaa	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40149232	40149232	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40149232delG								DAB2 (723897 upstream) : PTGER4 (530800 downstream)																							ATTCTGGGGTGGGGGGGAAAC	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	51617506	51617506	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51617506delA								ISL1 (926949 upstream) : ITGA1 (466268 downstream)																							CTGTGTTATCAAAAGAGCATT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	51648106	51648107	+	IGR	DEL	TC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51648106_51648107delTC								ISL1 (957549 upstream) : ITGA1 (435667 downstream)																							tgtgtcaagttctctctctctc	0.020													4	2	---	---	---	---	
SNX18	112574	broad.mit.edu	37	5	53841241	53841241	+	3'UTR	DEL	T	-	-	rs137909783		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53841241delT	uc003jpi.3	+	2					SNX18_uc011cqg.1_3'UTR	NM_001102575	NP_001096045	Q96RF0	SNX18_HUMAN	sorting nexin 18 isoform a						cell communication|endocytosis|positive regulation of GTPase activity|protein transport	endomembrane system|endosome membrane|extrinsic to internal side of plasma membrane	phosphatidylinositol binding|protein binding				0		Lung NSC(810;3.46e-05)|Breast(144;0.102)				GGTGGTTGGATTTTTTTTTTT	0.299													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	58171523	58171523	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58171523delT								RAB3C (24118 upstream) : PDE4D (93343 downstream)																							ACAGGTCAAGTTTTAGATCAG	0.343													4	2	---	---	---	---	
MAST4	375449	broad.mit.edu	37	5	66261152	66261152	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66261152delT	uc003jut.1	+						MAST4_uc003jur.3_Intron|MAST4_uc010iwz.2_Intron|MAST4_uc003jus.2_Intron|MAST4_uc003juu.1_Intron|MAST4_uc011cra.1_Intron	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TGTCCTGAACTTTTTTTCTTT	0.299													4	2	---	---	---	---	
MAST4	375449	broad.mit.edu	37	5	66437163	66437163	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66437163delG	uc003jut.1	+						MAST4_uc003juu.1_Intron|MAST4_uc011cra.1_Intron|MAST4_uc003juv.2_Intron|MAST4_uc003juw.2_Intron	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GTGTGCTGGTGGCAGGGCGGG	0.378													4	2	---	---	---	---	
S100Z	170591	broad.mit.edu	37	5	76208388	76208388	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76208388delA	uc003keq.3	+							NM_130772	NP_570128	Q8WXG8	S100Z_HUMAN	S100 calcium binding protein Z								calcium ion binding			ovary(1)	1		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;8.91e-51)|Epithelial(54;5.43e-45)|all cancers(79;1.82e-40)		gggaaagaggaaaaaaaaata	0.000													4	2	---	---	---	---	
PDE8B	8622	broad.mit.edu	37	5	76717418	76717419	+	Intron	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76717418_76717419delTG	uc003kfa.2	+						PDE8B_uc003kfb.2_Intron|PDE8B_uc003kfc.2_Intron|PDE8B_uc003kfd.2_Intron|PDE8B_uc003kfe.2_Intron	NM_003719	NP_003710	O95263	PDE8B_HUMAN	phosphodiesterase 8B isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)		TTTCAAACTCTGTGTGTGTGTG	0.342													4	3	---	---	---	---	
MSH3	4437	broad.mit.edu	37	5	80166386	80166387	+	Intron	INS	-	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80166386_80166387insC	uc003kgz.2	+							NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		GCACCTGTGTTTCTCAACTTTC	0.455								MMR					4	2	---	---	---	---	
SSBP2	23635	broad.mit.edu	37	5	80742368	80742369	+	Intron	INS	-	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80742368_80742369insC	uc003kho.2	-						RNU5E_uc011cto.1_Intron|SSBP2_uc010jar.2_Intron|SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		TTTATTCAGAAATTTTCTAAAT	0.277													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87328403	87328403	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87328403delA								CCNH (619567 upstream) : TMEM161B (162621 downstream)																							atataaacataaataaatgga	0.000													4	2	---	---	---	---	
CETN3	1070	broad.mit.edu	37	5	89707724	89707724	+	5'Flank	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89707724delT	uc003kjo.2	-							NM_004365	NP_004356	O15182	CETN3_HUMAN	centrin 3						cell division|centrosome cycle|mitosis	centriole	calcium ion binding				0		all_cancers(142;7.93e-09)|all_epithelial(76;2.13e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.42e-32)|Epithelial(54;1.45e-26)|all cancers(79;2.87e-23)		CTAAATTGAGTTTTTTTTTGT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	91935303	91935303	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91935303delG								None (None upstream) : FLJ42709 (809762 downstream)																							caagtctccagggaccacagg	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	92693235	92693235	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92693235delC								None (None upstream) : FLJ42709 (51830 downstream)																							TCTAGGTATTCCCATATTTTA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	103361789	103361790	+	IGR	DEL	TC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103361789_103361790delTC								NUDT12 (463299 upstream) : None (None downstream)																							ctatccagattctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	103957259	103957259	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103957259delA								None (None upstream) : RAB9BP1 (477916 downstream)																							TCACACACACAAAAAAAACTG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	106403165	106403165	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106403165delG								None (None upstream) : EFNA5 (309426 downstream)																							ATTTAAGGTAGGATAGGAAAG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	106480003	106480004	+	IGR	INS	-	A	A	rs72543191	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106480003_106480004insA								None (None upstream) : EFNA5 (232587 downstream)																							GCTATATTCCCGACCCTTTTCA	0.347													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	106491380	106491380	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106491380delA								None (None upstream) : EFNA5 (221211 downstream)																							CATAAGATAGAAAAAAATTAA	0.353													4	2	---	---	---	---	
EFNA5	1946	broad.mit.edu	37	5	106952907	106952910	+	Intron	DEL	ACAT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106952907_106952910delACAT	uc003kol.2	-						EFNA5_uc010jbr.1_Intron	NM_001962	NP_001953	P52803	EFNA5_HUMAN	ephrin-A5 precursor						cell-cell signaling	anchored to plasma membrane|caveola|extracellular space	ephrin receptor binding				0		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		TTACATGTGcacatacacacacac	0.221													4	2	---	---	---	---	
EFNA5	1946	broad.mit.edu	37	5	106952911	106952914	+	Intron	DEL	ACAC	-	-	rs72404386		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106952911_106952914delACAC	uc003kol.2	-						EFNA5_uc010jbr.1_Intron	NM_001962	NP_001953	P52803	EFNA5_HUMAN	ephrin-A5 precursor						cell-cell signaling	anchored to plasma membrane|caveola|extracellular space	ephrin receptor binding				0		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		ATGTGcacatacacacacacacac	0.230													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	107111842	107111842	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107111842delG								EFNA5 (105246 upstream) : FBXL17 (82898 downstream)																							ccaaagtgctgggattacagg	0.134													4	2	---	---	---	---	
PJA2	9867	broad.mit.edu	37	5	108674819	108674819	+	Intron	DEL	G	-	-	rs67731303		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108674819delG	uc003kos.3	-							NM_014819	NP_055634	O43164	PJA2_HUMAN	praja 2, RING-H2 motif containing						long-term memory|regulation of protein kinase A signaling cascade	cell junction|endoplasmic reticulum membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	ligase activity|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		GAAACAAGTTGGGGGTCTAAA	0.393													1	5	---	---	---	---	
MAN2A1	4124	broad.mit.edu	37	5	109175636	109175636	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109175636delT	uc003kou.1	+							NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		ATTTACATTCTTTTTTTTTTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	115764572	115764572	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115764572delT								COMMD10 (135594 upstream) : SEMA6A (14680 downstream)																							Caccctcttattttttttaca	0.184													4	3	---	---	---	---	
SEMA6A	57556	broad.mit.edu	37	5	115859629	115859629	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115859629delA	uc010jck.2	-						SEMA6A_uc003krx.3_Intron	NM_020796	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and						apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		GCCATGATTCAAAAACCTTTA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116051026	116051026	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116051026delA								SEMA6A (140475 upstream) : None (None downstream)																							tttgtttcctaagcagttggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	120297236	120297237	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120297236_120297237insT								PRR16 (274274 upstream) : FTMT (890413 downstream)																							catttctcaggttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	121553639	121553639	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121553639delC								ZNF474 (64382 upstream) : SNCAIP (93747 downstream)																							tggtttggctctgtgttccca	0.000													4	2	---	---	---	---	
SNCAIP	9627	broad.mit.edu	37	5	121684573	121684573	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121684573delA	uc003ksw.1	+						SNCAIP_uc011cwl.1_Intron|SNCAIP_uc010jct.2_Intron|SNCAIP_uc003ksx.1_Intron|SNCAIP_uc003ksy.1_Intron|SNCAIP_uc003ksz.1_Intron|SNCAIP_uc010jcu.2_Intron|SNCAIP_uc011cwm.1_Intron	NM_005460	NP_005451	Q9Y6H5	SNCAP_HUMAN	synuclein alpha interacting protein						cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		AGTTTTGTACAAAAAAAATAC	0.279													4	2	---	---	---	---	
ZNF608	57507	broad.mit.edu	37	5	124028745	124028745	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124028745delA	uc003ktq.1	-						ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Intron|ZNF608_uc003ktt.1_Intron	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608							intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		ctagggtgataaaaaatgttc	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124616726	124616727	+	IGR	DEL	AT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124616726_124616727delAT								ZNF608 (532226 upstream) : None (None downstream)																							AAAATGAAAAATAAAAAACACA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124664708	124664708	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124664708delG								ZNF608 (580208 upstream) : None (None downstream)																							gggctgccatggtgttattta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	126998678	126998680	+	IGR	DEL	CAA	-	-	rs34470549		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126998678_126998680delCAA								CTXN3 (4357 upstream) : FLJ33630 (277455 downstream)																							cctcaatagtcaacaacaagtgg	0.148													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	128421626	128421626	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128421626delT								SLC27A6 (52292 upstream) : ISOC1 (8816 downstream)																							aagagaattctttttttttca	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	128697882	128697882	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128697882delT								ISOC1 (248165 upstream) : ADAMTS19 (98221 downstream)																							GCCATCTCCCTTCTAATGTCA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	130309207	130309210	+	IGR	DEL	GTGT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130309207_130309210delGTGT								CHSY3 (786881 upstream) : HINT1 (185665 downstream)																							ttggtagttGgtgtgtgtgtgtgt	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	131688619	131688619	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131688619delC	uc003kwr.3	-											Homo sapiens hypothetical LOC553103, mRNA (cDNA clone IMAGE:5288197).																		attctgttagcccccagccaa	0.000													4	2	---	---	---	---	
FSTL4	23105	broad.mit.edu	37	5	132936113	132936113	+	Intron	DEL	G	-	-	rs67119987		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132936113delG	uc003kyn.1	-							NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTAGGATAAAGGGGGGGGGGA	0.204													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134434053	134434053	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134434053delT	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																		CTGTTTGCAATTTTTTTCCCT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134601933	134601934	+	Intron	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134601933_134601934delGT	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																		TCTTAGGACAGTGAAGGGGCGC	0.540													5	6	---	---	---	---	
SPOCK1	6695	broad.mit.edu	37	5	136424726	136424726	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136424726delG	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GGAGAGCACTGGGACTATTGC	0.562													4	2	---	---	---	---	
C5orf32	84418	broad.mit.edu	37	5	139576998	139576998	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139576998delG	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)			CCTTTCCTATGGATATACCCA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139991594	139991594	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139991594delT								SLC35A4 (42911 upstream) : CD14 (19723 downstream)																							AGAGAGCAAGTTTTTTTTGAG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	141559971	141559971	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141559971delA								NDFIP1 (25965 upstream) : SPRY4 (130021 downstream)																							AAATTTGGGTAAACATTCCCT	0.383													4	2	---	---	---	---	
SH3RF2	153769	broad.mit.edu	37	5	145440055	145440055	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145440055delA	uc003lnt.2	+						SH3RF2_uc011dbl.1_Intron|SH3RF2_uc003lnu.2_Intron|SH3RF2_uc011dbn.1_Intron|SH3RF2_uc011dbo.1_Intron	NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2								ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGTGGCTTGAAAaaaaagca	0.219													4	2	---	---	---	---	
RBM27	54439	broad.mit.edu	37	5	145638332	145638332	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145638332delT	uc003lnz.3	+						RBM27_uc003lny.2_Intron	NM_018989	NP_061862	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27						mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding			central_nervous_system(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATATTTATAAttttttttttt	0.124													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	147239561	147239561	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147239561delT								SPINK1 (28301 upstream) : SCGB3A2 (18713 downstream)																							aggaagtttgttagcccaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	147335218	147335218	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147335218delT								C5orf46 (49117 upstream) : SPINK5 (108317 downstream)																							AAATGGAAACTTTTTTTTGGC	0.284													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	147619208	147619208	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147619208delA								SPINK6 (24509 upstream) : SPINK13 (29074 downstream)																							cagagttaagaaaAAAAAAGG	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	152011049	152011050	+	Intron	INS	-	A	A	rs150643353	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152011049_152011050insA	uc003luw.1	-						uc003lux.1_Intron					Homo sapiens cDNA FLJ35529 fis, clone SPLEN2001912.																		CTGAGGAGCAGAAAAAAAAAAT	0.381													4	2	---	---	---	---	
GALNT10	55568	broad.mit.edu	37	5	153693442	153693442	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153693442delA	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.2_Intron|GALNT10_uc010jid.2_Intron	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			TCTACCCACTAAGACTCAGTT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154608406	154608407	+	IGR	INS	-	T	T	rs147431010	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154608406_154608407insT								KIF4B (210721 upstream) : SGCD (526656 downstream)																							atagctgcttattttttttttc	0.000													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155559250	155559251	+	Intron	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155559250_155559251delTG	uc003lwa.1	+							NM_172244	NP_758447	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 2						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGGgtgtgtttgtgtgtgtgtg	0.317													4	2	---	---	---	---	
HAVCR1	26762	broad.mit.edu	37	5	156482715	156482715	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156482715delA	uc010jij.1	-						HAVCR1_uc003lwi.2_Intron|HAVCR1_uc011ddm.1_Intron	NM_001099414	NP_001092884	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1						interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)|skin(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			gatctctactaaaaaaaaaat	0.000													4	2	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156699136	156699136	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156699136delT	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwp.2_Intron	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGGAAAGTCCTTTAGCCCCCA	0.507													4	2	---	---	---	---	
EBF1	1879	broad.mit.edu	37	5	158244578	158244579	+	Intron	INS	-	T	T	rs139483504	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158244578_158244579insT	uc010jip.2	-						EBF1_uc011ddw.1_Intron|EBF1_uc011ddx.1_Intron|EBF1_uc003lxl.3_Intron	NM_024007	NP_076870	Q9UH73	COE1_HUMAN	early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			accgtaagacataaactccttt	0.000			T	HMGA2	lipoma								3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	158971400	158971401	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158971400_158971401insA								LOC285627 (78116 upstream) : ADRA1B (372339 downstream)																							AAGATTTGGGGAAATGACTCAT	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	159320618	159320621	+	IGR	DEL	TTCT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159320618_159320621delTTCT								LOC285627 (427334 upstream) : ADRA1B (23119 downstream)																							AAAGATGCAATTCTTTCTTTCTTT	0.426													4	2	---	---	---	---	
ATP10B	23120	broad.mit.edu	37	5	160010280	160010281	+	Intron	INS	-	T	T	rs116488876	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160010280_160010281insT	uc003lym.1	-						ATP10B_uc010jit.1_Intron	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			tctgtatgggcttttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	161920885	161920885	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161920885delA								GABRG2 (338341 upstream) : CCNG1 (943692 downstream)																							attgctgatgaaaatggctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163631215	163631215	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163631215delT								MAT2B (684882 upstream) : None (None downstream)																							GCTGTCCTACTTTTTTTTCCC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163827852	163827852	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163827852delT	uc003lzn.2	+											Homo sapiens, clone IMAGE:4479080, mRNA, partial cds.																		GCTATTAGaatttttttttaa	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165622704	165622704	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165622704delT								None (None upstream) : None (None downstream)																							TTCCAGATGATTTTTTACGGT	0.159													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167298585	167298586	+	Intron	DEL	AC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167298585_167298586delAC	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		GAAAACACTTACACACACACCC	0.356													4	2	---	---	---	---	
WWC1	23286	broad.mit.edu	37	5	167882938	167882938	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167882938delT	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron|WWC1_uc003lzw.2_Intron|WWC1_uc010jjf.1_Intron	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		GTTTGTTTTGTTTTTTTTAAT	0.348													4	2	---	---	---	---	
DOCK2	1794	broad.mit.edu	37	5	169307076	169307076	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169307076delA	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron|FAM196B_uc003mag.2_Intron	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TAGAAGATATAAAAAAAGAAG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173700574	173700575	+	IGR	INS	-	AG	AG	rs139113400	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173700574_173700575insAG								HMP19 (164393 upstream) : MSX2 (451000 downstream)																							AGTGGGGGACAAGAGAGAGAGA	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	175060255	175060255	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175060255delA								SFXN1 (104634 upstream) : HRH2 (24785 downstream)																							ACAGTCAGGGAAAAAAAAAAA	0.488													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	175346494	175346494	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175346494delG								CPLX2 (35471 upstream) : THOC3 (40042 downstream)																							catagacatagggggaaatct	0.134													4	2	---	---	---	---	
SQSTM1	8878	broad.mit.edu	37	5	179241587	179241587	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179241587delA	uc011dgr.1	+						SQSTM1_uc011dgs.1_Intron	NM_001142298	NP_001135770	Q13501	SQSTM_HUMAN	sequestosome 1 isoform 2						anti-apoptosis|apoptosis|cell differentiation|endosome transport|induction of apoptosis by extracellular signals|intracellular signal transduction|macroautophagy|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein localization|regulation of I-kappaB kinase/NF-kappaB cascade|ubiquitin-dependent protein catabolic process	cytosol|late endosome|nucleoplasm	protein kinase C binding|receptor tyrosine kinase binding|SH2 domain binding|ubiquitin binding|zinc ion binding		SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(2)|ovary(1)	3	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ctacaggcataaccatgtgga	0.000									Paget_Disease_of_Bone				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	474505	474506	+	IGR	DEL	CA	-	-	rs140132321		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:474505_474506delCA								IRF4 (63063 upstream) : EXOC2 (10633 downstream)																							TTATCCGCTCCACACACACACA	0.550													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	1179858	1179858	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1179858delT								LOC285768 (78291 upstream) : FOXQ1 (132817 downstream)																							ACAAAATCTCTTACTAGGACT	0.413													4	2	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	2140049	2140050	+	Intron	INS	-	AT	AT			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2140049_2140050insAT	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		GTGTGTTAAAAATATATATATA	0.347													4	2	---	---	---	---	
LOC285780	285780	broad.mit.edu	37	6	6517269	6517269	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6517269delT	uc003mww.3	-						LOC285780_uc003mwx.2_Intron	NR_026970				Homo sapiens cDNA FLJ33708 fis, clone BRAWH2007862.												0						CAAAATGAACTTTTTTTTTTA	0.388													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	10377991	10377991	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10377991delT								None (None upstream) : TFAP2A (18926 downstream)																							CTCAATGGGATTTTTTTTTAC	0.284													4	2	---	---	---	---	
PHACTR1	221692	broad.mit.edu	37	6	13180408	13180408	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13180408delT	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron	NM_030948	NP_112210	Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			GAAAAACATGTTCAAAAAGAG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18055902	18055902	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18055902delT								KIF13A (68103 upstream) : NHLRC1 (64816 downstream)																							ATCTCCATGATTTTTTTTTTC	0.507													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18636440	18636440	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18636440delT	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																		TTCCTTAAAATTTTTTTTTCT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19690113	19690113	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19690113delA								None (None upstream) : ID4 (147504 downstream)																							ATACTGCAAGAAAAAAAAACG	0.348													4	2	---	---	---	---	
CDKAL1	54901	broad.mit.edu	37	6	21038028	21038028	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21038028delT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244	Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			CCACTAAAGATTATGCGATTT	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	21385221	21385221	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21385221delC								CDKAL1 (152589 upstream) : SOX4 (208751 downstream)																							CAATGAACCTCCCCCTCTCGA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	30984338	30984338	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30984338delG								MUC21 (26663 upstream) : HCG22 (37646 downstream)																							taggtaatgtgggttttacat	0.000													4	2	---	---	---	---	
ZNF76	7629	broad.mit.edu	37	6	35262831	35262831	+	Intron	DEL	A	-	-	rs113114842		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35262831delA	uc003oki.1	+						ZNF76_uc003okj.1_Intron|DEF6_uc003okk.2_5'Flank|DEF6_uc010jvs.2_5'Flank|DEF6_uc010jvt.2_5'Flank	NM_003427	NP_003418	P36508	ZNF76_HUMAN	zinc finger protein 76 (expressed in testis)						regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GGGGAGAGTCAAAAAAAAAAG	0.502													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	37555116	37555116	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37555116delT								C6orf129 (87416 upstream) : MDGA1 (45168 downstream)																							ttttcttttcttttttttttt	0.224													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	37723260	37723260	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37723260delT								MDGA1 (57494 upstream) : ZFAND3 (64047 downstream)																							AGGAGAGAAGTTTTGCCCTGG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	39144945	39144946	+	IGR	INS	-	CC	CC			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39144945_39144946insCC								C6orf64 (62080 upstream) : KCNK5 (11802 downstream)																							aaacaaaaaaaccccagccata	0.000													4	3	---	---	---	---	
UBR2	23304	broad.mit.edu	37	6	42529713	42529714	+	5'Flank	INS	-	T	T	rs142774222	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42529713_42529714insT	uc011dur.1	+						UBR2_uc003osf.2_5'Flank	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			AAGGGAAACAAtttttttttga	0.168													3	3	---	---	---	---	
UBR2	23304	broad.mit.edu	37	6	42583226	42583226	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42583226delC	uc011dur.1	+						UBR2_uc011dus.1_Intron|UBR2_uc010jxv.1_5'Flank|UBR2_uc003osh.2_5'Flank|UBR2_uc003osf.2_Intron	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			cactctgttgcccaggcaaca	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	43928503	43928503	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43928503delA								LOC100132354 (22560 upstream) : C6orf223 (39836 downstream)																							tgaaacacggaaaaaaaagag	0.000													4	2	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51490020	51490021	+	Intron	DEL	GA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51490020_51490021delGA	uc003pah.1	-							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)					CAAAGTGCTGGAGAGAGAGAGA	0.381													3	3	---	---	---	---	
IL17F	112744	broad.mit.edu	37	6	52110484	52110484	+	5'Flank	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52110484delT	uc003pam.1	-							NM_052872	NP_443104	Q96PD4	IL17F_HUMAN	interleukin 17F precursor						cartilage development|inflammatory response|lymphotoxin A biosynthetic process|negative regulation of angiogenesis|proteoglycan metabolic process|regulation of granulocyte macrophage colony-stimulating factor biosynthetic process|regulation of interleukin-2 biosynthetic process|regulation of interleukin-6 biosynthetic process|regulation of interleukin-8 biosynthetic process|regulation of transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|cytokine binding|protein homodimerization activity			ovary(1)	1	Lung NSC(77;0.116)					ctcttgggccttttatggagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	52754520	52754520	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52754520delT								GSTA5 (43627 upstream) : GSTA3 (6921 downstream)																							gtctcgggtatttttttatag	0.134													4	2	---	---	---	---	
GCM1	8521	broad.mit.edu	37	6	52994622	52994623	+	Intron	DEL	CT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52994622_52994623delCT	uc003pbp.2	-							NM_003643	NP_003634	Q9NP62	GCM1_HUMAN	glial cells missing homolog a							transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			central_nervous_system(1)	1	Lung NSC(77;0.0755)					TAAATCagacctctagaacacg	0.238													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57390643	57390644	+	Intron	DEL	CA	-	-	rs141634742		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57390643_57390644delCA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TTTAATGCTCCACACATTGCCT	0.401													6	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57436081	57436082	+	Intron	INS	-	T	T	rs149176852	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57436081_57436082insT	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)		cttttcttttcttttctttttg	0.129													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57455348	57455349	+	Intron	DEL	GA	-	-	rs144561408		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57455348_57455349delGA	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)		TGAGACCCTTGAGTGCACCCAA	0.436													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57538130	57538131	+	IGR	DEL	TG	-	-	rs67422833		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57538130_57538131delTG								PRIM2 (24755 upstream) : GUSBL2 (708028 downstream)																							CGAGTTTGACTGTTTTGGTTAG	0.386													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57562855	57562855	+	IGR	DEL	A	-	-	rs68009168		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57562855delA								PRIM2 (49480 upstream) : GUSBL2 (683304 downstream)																							aagctgtcacaaaaggagatg	0.025													4	3	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65105961	65105962	+	Intron	DEL	AT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65105961_65105962delAT	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						atgcacacacatgcacagacac	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	78535588	78535588	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78535588delT								HTR1B (362468 upstream) : None (None downstream)																							tatagtagggttaagtgctgt	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	81111607	81111607	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81111607delT								BCKDHB (55620 upstream) : None (None downstream)																							tctattcatatttttacaaat	0.000													4	2	---	---	---	---	
SYNCRIP	10492	broad.mit.edu	37	6	86346559	86346559	+	Intron	DEL	A	-	-	rs116240890	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86346559delA	uc003pla.2	-						SYNCRIP_uc003pku.2_Intron|SYNCRIP_uc003pkw.2_Intron|SYNCRIP_uc003pky.2_Intron|SYNCRIP_uc003pkv.2_Intron|SYNCRIP_uc003pkx.2_Intron|SYNCRIP_uc003pkz.2_Intron	NM_006372	NP_006363	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA						CRD-mediated mRNA stabilization|interspecies interaction between organisms	catalytic step 2 spliceosome|CRD-mediated mRNA stability complex|endoplasmic reticulum|histone pre-mRNA 3'end processing complex|microsome|nucleoplasm	nucleotide binding|protein binding			ovary(2)	2		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)		GTGATGTGGGAAAAAAAAAAC	0.353													6	3	---	---	---	---	
CASP8AP2	9994	broad.mit.edu	37	6	90565591	90565591	+	Intron	DEL	A	-	-	rs75192456		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90565591delA	uc003pnr.2	+						CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Intron|CASP8AP2_uc011dzz.1_Intron	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2						cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		gtaaaacaacaaaaaaaaaGT	0.114													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	100654174	100654174	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100654174delA								MCHR2 (212060 upstream) : SIM1 (182577 downstream)																							TAAGACATTTAAAAAAAACCT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	104707162	104707162	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104707162delA								None (None upstream) : HACE1 (468806 downstream)																							TCAATAGAGCAGGTTGAATTA	0.323													4	2	---	---	---	---	
HACE1	57531	broad.mit.edu	37	6	105219621	105219621	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105219621delA	uc003pqu.1	-						HACE1_uc010kcy.1_Intron|HACE1_uc010kcz.1_Intron|HACE1_uc010kcx.1_Intron|HACE1_uc003pqt.1_Intron	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		AGGTGTTTGGAAAAAAAAAAG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	125679204	125679205	+	IGR	INS	-	CTTT	CTTT			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125679204_125679205insCTTT								HDDC2 (55922 upstream) : HEY2 (389575 downstream)																							CAATTAAATGACTTCCTTCCCT	0.455													4	2	---	---	---	---	
EYA4	2070	broad.mit.edu	37	6	133756511	133756511	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133756511delT	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron|uc003qef.1_RNA	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)		AACAGCTTCCTTTCTTTATGC	0.542													4	2	---	---	---	---	
TMEM181	57583	broad.mit.edu	37	6	159003170	159003170	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159003170delT	uc003qrm.3	+						TMEM181_uc010kjr.1_Intron|TMEM181_uc003qri.1_Intron|TMEM181_uc003qrj.1_Intron|TMEM181_uc003qrk.1_Intron	NM_020823	NP_065874	Q9P2C4	TM181_HUMAN	G protein-coupled receptor 178						pathogenesis	integral to membrane	toxin binding			ovary(2)|central_nervous_system(1)	3		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)		GCATAGCCTGTTTTCACATTT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1370163	1370163	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1370163delC								UNCX (93551 upstream) : MICALL2 (103833 downstream)																							AACAGAATGGCCTCTGCCCTG	0.647													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	4113335	4113335	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4113335delC	uc003smx.2	+						SDK1_uc010kso.2_Intron	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TGTCTCAGTTCCCTTGCACAC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17496308	17496308	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17496308delG								AHR (110533 upstream) : SNX13 (334078 downstream)																							ATACTTGCCTGGGGCCCAAGT	0.438													4	2	---	---	---	---	
KLHL7	55975	broad.mit.edu	37	7	23169561	23169578	+	Intron	DEL	GCATGTATAAGAATGTAT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23169561_23169578delGCATGTATAAGAATGTAT	uc003svs.3	+						KLHL7_uc003svr.3_Intron|KLHL7_uc011jys.1_Intron|KLHL7_uc011jyt.1_Intron|KLHL7_uc003svt.2_Intron	NM_001031710	NP_001026880	Q8IXQ5	KLHL7_HUMAN	kelch-like 7 isoform 1							Golgi apparatus|nucleolus|plasma membrane					0						AAGAATGTAGGCATGTATAAGAATGTATGCATGTATAA	0.321													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	23531563	23531563	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23531563delT								RPS2P32 (534 upstream) : TRA2A (12839 downstream)																							GGAATGTATCttttttttttt	0.065													4	2	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23766572	23766572	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23766572delT	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						CCTTAAAAAATTTTTTTTTTT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24520054	24520054	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24520054delT								NPY (188577 upstream) : MPP6 (93031 downstream)																							TTAAAATTACTTCCATATTCA	0.448													4	2	---	---	---	---	
OSBPL3	26031	broad.mit.edu	37	7	24875354	24875354	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24875354delA	uc003sxf.2	-						OSBPL3_uc003sxd.2_Intron|OSBPL3_uc003sxe.2_Intron|OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron|OSBPL3_uc003sxj.1_Intron|OSBPL3_uc003sxk.1_Intron	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1						gtgcagccataaaaaagaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25762259	25762259	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25762259delT								NPVF (494154 upstream) : MIR148A (227280 downstream)																							TGTCAAGGGGTTTTTTGGCAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	30552676	30552677	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30552676_30552677insT								GGCT (8224 upstream) : GARS (81504 downstream)																							atttgggttgctttttttttat	0.010													4	2	---	---	---	---	
PDE1C	5137	broad.mit.edu	37	7	32077367	32077367	+	Intron	DEL	G	-	-	rs115197744	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32077367delG	uc003tcm.1	-						PDE1C_uc003tcn.1_Intron|PDE1C_uc003tco.1_Intron|PDE1C_uc003tcr.2_Intron|PDE1C_uc003tcs.2_Intron	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C						activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)			agctccttgagggcagaaacc	0.134													4	2	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	33060612	33060613	+	Intron	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33060612_33060613insA	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						ttcatatacttaaaaaaaaatt	0.030													4	2	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33218142	33218142	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33218142delG	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc011kan.1_Intron|BBS9_uc011kao.1_Intron	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			TAGAGGAGCTGGTGGTGCTGG	0.512									Bardet-Biedl_syndrome				4	2	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33606564	33606565	+	Intron	INS	-	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33606564_33606565insC	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc003tdr.1_Intron|BBS9_uc003tds.1_Intron|BBS9_uc003tdt.2_Intron	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			GAACTAAGTTTCCCCAGGTTGT	0.351									Bardet-Biedl_syndrome				4	2	---	---	---	---	
CCM2	83605	broad.mit.edu	37	7	45091843	45091843	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45091843delC	uc003tmo.2	+						CCM2_uc003tmn.2_Intron|CCM2_uc003tmp.2_Intron|CCM2_uc003tmq.2_Intron|CCM2_uc003tmr.2_Intron|CCM2_uc011kcb.1_Intron|CCM2_uc011kcc.1_Intron|CCM2_uc003tms.2_Intron	NM_031443	NP_113631	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2 isoform 2						endothelial tube morphogenesis|integrin-mediated signaling pathway|stress-activated MAPK cascade|vasculogenesis	cytoplasm	protein binding				0						ctgaagtattcagctggccag	0.040									Familial_Cerebral_Cavernous_Angioma				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	49767168	49767168	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49767168delA								CDC14C (800119 upstream) : VWC2 (46089 downstream)																							ACAAAAATATAAGAAATGAGG	0.368													4	2	---	---	---	---	
EGFR	1956	broad.mit.edu	37	7	55170216	55170218	+	Intron	DEL	CTG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55170216_55170218delCTG	uc003tqk.2	+						EGFR_uc003tqh.2_Intron|EGFR_uc003tqi.2_Intron|EGFR_uc003tqj.2_Intron|EGFR_uc010kzg.1_Intron	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	ACTGCAGCGTCTGCTGCTTCTTG	0.379		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			4	2	---	---	---	---	
ZNF679	168417	broad.mit.edu	37	7	63721651	63721651	+	Intron	DEL	T	-	-	rs145025661		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63721651delT	uc003tsx.2	+							NM_153363	NP_699194	Q8IYX0	ZN679_HUMAN	zinc finger protein 679						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						CCATTAAAAATTTTTTTTTGC	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64960750	64960751	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64960750_64960751insT								ZNF92 (94753 upstream) : INTS4L2 (152026 downstream)																							ACATTCATTTATTTTTTTAGAC	0.351													2	4	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71743345	71743345	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71743345delA	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2							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)				CATTGGTGATAAAGACTCCGG	0.453													4	2	---	---	---	---	
WBSCR22	114049	broad.mit.edu	37	7	73111776	73111776	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73111776delA	uc003tyt.2	+						WBSCR22_uc003tyu.2_Intron|WBSCR22_uc003tyv.2_Intron|WBSCR22_uc003tyw.1_Intron	NM_017528	NP_059998	O43709	WBS22_HUMAN	Williams Beuren syndrome chromosome region 22							nucleus	methyltransferase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)				GGGTGTCCAGAGCGGGGAATT	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	73851336	73851336	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73851336delG								CLIP2 (31064 upstream) : GTF2IRD1 (16784 downstream)																							cattccgaaagggggaagtag	0.000													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78230050	78230051	+	Intron	DEL	GT	-	-	rs114449161	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78230050_78230051delGT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				acgaggggaggtgtgtgtgtgt	0.000													3	3	---	---	---	---	
KIAA1324L	222223	broad.mit.edu	37	7	86593997	86593997	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86593997delA	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)					AATAGATTTTAAAAAAAAATA	0.269													4	2	---	---	---	---	
LHFPL3	375612	broad.mit.edu	37	7	104269669	104269669	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104269669delT	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3							integral to membrane					0						TCACTGTCCCTTGTATTCACA	0.438													4	2	---	---	---	---	
SRPK2	6733	broad.mit.edu	37	7	104790498	104790498	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104790498delA	uc003vct.2	-						SRPK2_uc003vcu.2_Intron|SRPK2_uc003vcv.2_Intron|SRPK2_uc003vcw.1_Intron	NM_182691	NP_872633	P78362	SRPK2_HUMAN	serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6						GTAATTGGCCAAAAAAAAAAC	0.388													2	4	---	---	---	---	
PUS7	54517	broad.mit.edu	37	7	105127177	105127177	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105127177delT	uc003vcx.2	-						PUS7_uc010lji.2_Intron|PUS7_uc003vcy.2_Intron|PUS7_uc003vcz.1_Intron	NM_019042	NP_061915	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 homolog						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1						AGTTCTGTCCTTTTTTTTTTT	0.289													4	2	---	---	---	---	
CDHR3	222256	broad.mit.edu	37	7	105568816	105568816	+	Intron	DEL	C	-	-	rs140574042		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105568816delC	uc003vdk.2	+									Q6ZTQ4	CDHR3_HUMAN	RecName: Full=Cadherin-like protein 28; Flags: Precursor;						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1						TAATTAGGAACCCAATAACAC	0.393													1	6	---	---	---	---	
COG5	10466	broad.mit.edu	37	7	107183692	107183693	+	Intron	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107183692_107183693insG	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4						aaataaaaagaggcacattgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	108632679	108632679	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108632679delT								C7orf66 (108042 upstream) : EIF3IP1 (966605 downstream)																							TGCTGTTTCATTTTTTTTTCC	0.328													4	2	---	---	---	---	
IMMP2L	83943	broad.mit.edu	37	7	110998298	110998298	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110998298delT	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		ATGCATTATCTTACTACCCTC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	112134989	112134989	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112134989delT								C7orf53 (4054 upstream) : TMEM168 (270800 downstream)																							TCATTTTCTCTTTTTTTTCCC	0.368													4	2	---	---	---	---	
CAV1	857	broad.mit.edu	37	7	115927629	115927630	+	5'Flank	INS	-	C	C	rs146118236	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115927629_115927630insC	uc010lkd.1	+						CAV2_uc003vhv.2_5'Flank|CAV2_uc003vhw.2_5'Flank|CAV2_uc003vhx.2_5'Flank|CAV2_uc010lkb.1_5'Flank|CAV2_uc010lkc.2_5'Flank|CAV2_uc003vib.2_5'Flank|CAV2_uc003vhz.2_5'Flank|CAV2_uc003via.2_5'Flank|CAV1_uc010lke.1_5'Flank|uc003vhr.3_5'Flank|uc003vhu.1_5'Flank|uc003vhs.1_5'Flank|uc003vht.1_5'Flank|uc003vhy.1_5'Flank	NM_001753	NP_001744	Q03135	CAV1_HUMAN	caveolin 1						blood coagulation|calcium ion transport|caveola assembly|cellular response to starvation|cholesterol homeostasis|cytosolic calcium ion homeostasis|inactivation of MAPK activity|interspecies interaction between organisms|leukocyte migration|lipid storage|maintenance of protein location in cell|mammary gland involution|membrane depolarization|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of endothelial cell proliferation|negative regulation of epithelial cell differentiation|negative regulation of nitric oxide biosynthetic process|negative regulation of peptidyl-serine phosphorylation|negative regulation of protein binding|negative regulation of transcription from RNA polymerase II promoter|nitric oxide homeostasis|nitric oxide metabolic process|positive regulation of calcium ion transport into cytosol|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of metalloenzyme activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of vasoconstriction|protein homooligomerization|receptor internalization|regulation of blood coagulation|regulation of fatty acid metabolic process|regulation of nitric-oxide synthase activity|regulation of smooth muscle contraction|response to calcium ion|response to estrogen stimulus|response to hypoxia|response to progesterone stimulus|skeletal muscle tissue development|T cell costimulation|triglyceride metabolic process|vasculogenesis|vesicle organization	apical plasma membrane|basolateral plasma membrane|caveola|caveola|cytosol|endoplasmic reticulum|endosome|Golgi membrane|lipid particle|perinuclear region of cytoplasm	cholesterol binding|nitric-oxide synthase binding|peptidase activator activity|protein binding|protein complex scaffold|receptor binding				0	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			ATCAGAGACTATagggtctgct	0.035													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	121183754	121183754	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121183754delT								FAM3C (147332 upstream) : PTPRZ1 (329405 downstream)																							ATTCTTCTCATTTtttttttc	0.144													4	2	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122194239	122194242	+	Intron	DEL	TAAC	-	-	rs143235584		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122194239_122194242delTAAC	uc010lkp.2	-						CADPS2_uc003vkg.3_Intron|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						TATGGAAGTTTAACTATTTCTAGG	0.338													1	5	---	---	---	---	
MKLN1	4289	broad.mit.edu	37	7	130965969	130965969	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130965969delT	uc011kpl.1	+							NM_001145354	NP_001138826	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)					tgagttattcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	131768048	131768048	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131768048delG								PODXL (526672 upstream) : PLXNA4 (40044 downstream)																							TGGGGGCTCTGGGGGGACCAG	0.607													4	2	---	---	---	---	
CHRM2	1129	broad.mit.edu	37	7	136595548	136595549	+	Intron	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136595548_136595549delGT	uc003vtf.1	+						CHRM2_uc003vtg.1_Intron|CHRM2_uc003vtj.1_Intron|CHRM2_uc003vtk.1_Intron|CHRM2_uc003vtl.1_Intron|CHRM2_uc003vtm.1_Intron|CHRM2_uc003vti.1_Intron|CHRM2_uc003vto.1_Intron|CHRM2_uc003vtn.1_Intron|uc003vtp.1_Intron	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2						activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)	TTAAAATTAAgtgtgtgtgtgt	0.287													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	137881317	137881319	+	IGR	DEL	AGA	-	-	rs58468215		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137881317_137881319delAGA								AKR1D1 (78267 upstream) : TRIM24 (263760 downstream)																							aagcagaagcagaagcagaagca	0.133													5	3	---	---	---	---	
HIPK2	28996	broad.mit.edu	37	7	139425768	139425768	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139425768delA	uc003vvf.3	-						HIPK2_uc003vvd.3_Intron	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)					CAGCCAAAGGAAAAATGAGGG	0.398													4	2	---	---	---	---	
LOC100124692	100124692	broad.mit.edu	37	7	141885945	141885945	+	Intron	DEL	T	-	-	rs111646116		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141885945delT	uc003vxa.2	+							NR_003717				Homo sapiens cDNA FLJ16351 fis, clone TESTI2039060, moderately similar to Maltase-glucoamylase, intestinal.												0						CTTGGTTGTCTTTTTTTTTTT	0.229													5	3	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	145988191	145988191	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145988191delA	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)			AGACTAAGATAAAACATGATG	0.289										HNSCC(39;0.1)			4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146746859	146746860	+	Intron	DEL	AG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146746859_146746860delAG	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)			CCAGAAAACTAGAGAGAGAGAG	0.450										HNSCC(39;0.1)			5	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158332705	158332705	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158332705delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|uc003wnu.1_RNA|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CTGGAGCTGGTGACGGCTGGG	0.632													4	2	---	---	---	---	
ARHGEF10	9639	broad.mit.edu	37	8	1850428	1850428	+	Intron	DEL	G	-	-	rs57084797		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1850428delG	uc003wpr.2	+						ARHGEF10_uc003wpq.1_Intron|ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc003wpt.2_Intron|ARHGEF10_uc003wpv.2_Intron|ARHGEF10_uc010lre.2_Intron	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		GTTCACGTTTGCCCCTTCAGC	0.323													4	2	---	---	---	---	
ARHGEF10	9639	broad.mit.edu	37	8	1892818	1892818	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1892818delT	uc003wpr.2	+						ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc010lre.2_Intron	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		ATCACTTTACTTTAGATAACT	0.458													4	2	---	---	---	---	
MYOM2	9172	broad.mit.edu	37	8	2056080	2056080	+	Intron	DEL	T	-	-	rs72314617		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2056080delT	uc003wpx.3	+						MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		tcttctttccttttttttttt	0.124													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2152121	2152122	+	IGR	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2152121_2152122delGT								MYOM2 (58742 upstream) : CSMD1 (640754 downstream)																							ATTCATGCAGGTGTGTGTGTGC	0.178													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3951093	3951093	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3951093delA	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CACCACATTGAAAAAAAGTGG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	6105045	6105046	+	IGR	INS	-	C	C	rs138420093	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6105045_6105046insC								None (None upstream) : MCPH1 (159075 downstream)																							TCTCTATCCTTACCCACTTTGG	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	8798474	8798475	+	IGR	DEL	CA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8798474_8798475delCA								MFHAS1 (47343 upstream) : ERI1 (61839 downstream)																							acctcctcctcacacagaggcc	0.144													4	2	---	---	---	---	
SGCZ	137868	broad.mit.edu	37	8	14533855	14533856	+	Intron	INS	-	TG	TG	rs145238741	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14533855_14533856insTG	uc003wwq.2	-							NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		aatgaaatagatgtgtgtgtgt	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	15680365	15680365	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15680365delC								TUSC3 (58372 upstream) : MSR1 (285023 downstream)																							tagtgaccttcgcagtatcag	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	16095260	16095260	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16095260delC								MSR1 (44960 upstream) : FGF20 (755074 downstream)																							gggtctttctccgggctcttg	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23763363	23763364	+	IGR	DEL	AC	-	-	rs66754675		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23763363_23763364delAC								STC1 (51043 upstream) : ADAM28 (388216 downstream)																							Gcacacacaaacacacacacac	0.035													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	24509735	24509736	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24509735_24509736insT								ADAM7 (125254 upstream) : NEFM (261538 downstream)																							attttccttgCTTTTTTTTTCC	0.297													4	2	---	---	---	---	
SCARA5	286133	broad.mit.edu	37	8	27842617	27842617	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27842617delC	uc003xgj.2	-						SCARA5_uc010luz.2_Intron|SCARA5_uc003xgk.2_Intron|SCARA5_uc003xgl.2_Intron	NM_173833	NP_776194	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		ctactgtggtccagcctatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	29668054	29668055	+	IGR	DEL	AA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29668054_29668055delAA								C8orf75 (62429 upstream) : LOC286135 (110974 downstream)																							AGAGGGCATGAAAAAGAGAGCT	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	30078707	30078708	+	IGR	DEL	CA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30078707_30078708delCA								DCTN6 (37648 upstream) : RBPMS (163236 downstream)																							gtttcagagtcacacacacaca	0.000													4	2	---	---	---	---	
WHSC1L1	54904	broad.mit.edu	37	8	38170725	38170726	+	Intron	INS	-	TG	TG			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38170725_38170726insTG	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron	NM_023034	NP_075447	Q9BZ95	NSD3_HUMAN	WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			gtgtgtgtatttgtgtgtgtgt	0.223			T	NUP98	AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	39917458	39917458	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39917458delT								IDO2 (43548 upstream) : C8orf4 (93531 downstream)																							CGAGATTCCCTTTTTTGAGAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	40204567	40204567	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40204567delA								C8orf4 (191746 upstream) : ZMAT4 (183549 downstream)																							cttcaccaagaaaaaaaaaac	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43688865	43688865	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43688865delC								POTEA (470537 upstream) : None (None downstream)																							tttgtagaatccgcaaaggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54486661	54486661	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54486661delC								OPRK1 (322467 upstream) : ATP6V1H (141455 downstream)																							gttacagagacctaaaacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58200344	58200344	+	IGR	DEL	T	-	-	rs79518077		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58200344delT								C8orf71 (3056 upstream) : FAM110B (706769 downstream)																							GGGACATGAATTTTTTTTTTG	0.398													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58336208	58336208	+	IGR	DEL	A	-	-	rs5891654		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58336208delA								C8orf71 (138920 upstream) : FAM110B (570905 downstream)																							tttaaaaattaaaaaaaaaaa	0.299													4	2	---	---	---	---	
NKAIN3	286183	broad.mit.edu	37	8	63734591	63734591	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63734591delT	uc010lyq.1	+							NM_173688	NP_775959	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)				AAAAAATCCCTCCAGGATACA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65406505	65406505	+	IGR	DEL	A	-	-	rs145813923		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65406505delA								MIR124-2 (114691 upstream) : LOC401463 (80363 downstream)																							ccagactaagaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	67172299	67172299	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67172299delA								CRH (81601 upstream) : RRS1 (168964 downstream)																							tccacagtggaaaaaaaaata	0.000													4	2	---	---	---	---	
C8orf34	116328	broad.mit.edu	37	8	69635478	69635478	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69635478delT	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			aacctaatcctttttacaatt	0.090													4	2	---	---	---	---	
TRPA1	8989	broad.mit.edu	37	8	72963342	72963342	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72963342delA	uc003xza.2	-						uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1							integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	TGGCTATTATAATCATTGTTC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	89994682	89994683	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89994682_89994683insA								MMP16 (654965 upstream) : RIPK2 (775292 downstream)																							ggacttagcctaaaaaaaattg	0.158													4	2	---	---	---	---	
KIAA1429	25962	broad.mit.edu	37	8	95517090	95517090	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95517090delA	uc003ygo.1	-						KIAA1429_uc010maz.1_Intron	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1						mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			gctaaaAGGGAAAAAGGGAAT	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102083589	102083589	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102083589delC								YWHAZ (117966 upstream) : ZNF706 (125679 downstream)																							ATGAATTCTTCAGCGTGGAGG	0.517													4	2	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	103128530	103128531	+	Intron	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103128530_103128531delTG	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			aaacCTCTACTGTGTGTCAAGG	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	108570599	108570599	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108570599delA								ANGPT1 (60345 upstream) : RSPO2 (340946 downstream)																							CCCAAACCACAAAGGCCTTAC	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	110004283	110004283	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110004283delT								TMEM74 (204513 upstream) : TRHR (95456 downstream)																							TAGACAGAGCTTTTTTTTAAT	0.303													4	2	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	114150289	114150290	+	Intron	INS	-	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114150289_114150290insC	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						GCTCTTTTTTTCCCTAATGTAA	0.297										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	118692489	118692489	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118692489delA								MED30 (139990 upstream) : EXT1 (119113 downstream)																							AAAGTCAAAGAAAAAACGATT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120422284	120422284	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120422284delA								MAL2 (164373 upstream) : NOV (6268 downstream)																							caaaattattaaaaagctgtg	0.149													4	2	---	---	---	---	
SNTB1	6641	broad.mit.edu	37	8	121794656	121794656	+	Intron	DEL	C	-	-	rs67722207		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121794656delC	uc010mdg.2	-						SNTB1_uc003ype.2_Intron	NM_021021	NP_066301	Q13884	SNTB1_HUMAN	basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			TTAAAAGAAACCTTTTTTTAA	0.224													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	122596993	122596993	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122596993delG								SNTB1 (772684 upstream) : HAS2 (28278 downstream)																							tttcttagttggtaaaattgt	0.104													4	2	---	---	---	---	
FER1L6	654463	broad.mit.edu	37	8	124927031	124927031	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124927031delT	uc003yqw.2	+							NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CATGGGTTAATTTAGACTTAA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	126794644	126794644	+	IGR	DEL	T	-	-	rs71875267		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126794644delT								TRIB1 (344002 upstream) : FAM84B (770043 downstream)																							aaaaagatggttttttttttc	0.000													3	3	---	---	---	---	
FAM49B	51571	broad.mit.edu	37	8	130989785	130989785	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130989785delT	uc003ysw.2	-						FAM49B_uc003ysx.2_Intron|FAM49B_uc003ysy.1_Intron	NM_016623	NP_057707	Q9NUQ9	FA49B_HUMAN	hypothetical protein LOC51571												0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			GTCCTCACTCttttttttttt	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	135468763	135468764	+	IGR	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135468763_135468764delTG								ST3GAL1 (884580 upstream) : ZFAT (21269 downstream)																							TTGCTGGGTTTGTGTGTGTGTG	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136194498	136194498	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136194498delT								MIR30D (377310 upstream) : LOC286094 (51876 downstream)																							atcccagtcattttttatttc	0.000													4	2	---	---	---	---	
JRK	8629	broad.mit.edu	37	8	143753319	143753319	+	5'Flank	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143753319delC	uc003ywo.2	-						JRK_uc003ywp.2_5'Flank	NM_001077527	NP_001070995			jerky isoform b												0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ctcttcctcaccctcccttgc	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144849516	144849517	+	IGR	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144849516_144849517delGT								FAM83H (33602 upstream) : SCRIB (23573 downstream)																							tgttttatgagtgtgtgtgtgt	0.000													4	2	---	---	---	---	
RCL1	10171	broad.mit.edu	37	9	4880901	4880901	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4880901delT	uc003ziv.1	+									Q9Y2P8	RCL1_HUMAN	Homo sapiens cDNA FLJ11677 fis, clone HEMBA1004778.						ribosome biogenesis|RNA processing	nucleolus	RNA-3'-phosphate cyclase activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0206)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0244)		tcaacatatctttttttaggg	0.169													4	2	---	---	---	---	
CD274	29126	broad.mit.edu	37	9	5455678	5455678	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5455678delA	uc003zje.2	+						C9orf46_uc003zjd.2_Intron|CD274_uc011lmb.1_Intron|CD274_uc010mhn.2_5'Flank|CD274_uc003zjf.2_5'Flank	NM_014143	NP_054862	Q9NZQ7	PD1L1_HUMAN	CD274 molecule precursor						cell proliferation|cell surface receptor linked signaling pathway|immune response|T cell costimulation	endomembrane system|integral to membrane	receptor activity			lung(1)|central_nervous_system(1)	2	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)		CTGTAGGGGGAAAAAGCATTG	0.418			T	CIITA	PMBL|Hodgkin Lymphona|								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	7233112	7233112	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7233112delA								KDM4C (57465 upstream) : C9orf123 (563381 downstream)																							ataaaaagttAAaaaaatttt	0.085													4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	10095128	10095128	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10095128delA	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TTTGCTGTTCAAAAAAAAATC	0.269										TSP Lung(15;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	10794172	10794173	+	IGR	DEL	AG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10794172_10794173delAG								PTPRD (181449 upstream) : None (None downstream)																							tgggatgggaagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	22208061	22208062	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22208061_22208062insT								CDKN2BAS (86970 upstream) : DMRTA1 (238778 downstream)																							TTATCTTGAACTTTTTTCTTTT	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	22419996	22419996	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22419996delA								CDKN2BAS (298905 upstream) : DMRTA1 (26844 downstream)																							TTTCTTCATTAAAAAAAACTG	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	30174452	30174452	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30174452delT								None (None upstream) : None (None downstream)																							GATTTGATCATTTACTCAGTG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	31252321	31252321	+	IGR	DEL	A	-	-	rs111550545		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31252321delA								None (None upstream) : None (None downstream)																							GTCTAGCAAGAAAAAAAAAAA	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	32870241	32870241	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32870241delC								TMEM215 (81044 upstream) : APTX (102368 downstream)																							ATGTCTTTTTCTTGCTCATAT	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33206936	33206936	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33206936delA								B4GALT1 (39580 upstream) : SUGT1P1 (12134 downstream)																							TTAGGAAGACAAAAAAAATGG	0.398													4	2	---	---	---	---	
AQP7	364	broad.mit.edu	37	9	33395917	33395917	+	Intron	DEL	C	-	-	rs33962618		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33395917delC	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_5'Flank|AQP7_uc010mjt.2_5'Flank|AQP7_uc011lnx.1_Intron|AQP7_uc011lny.1_Intron|AQP7_uc003zss.3_Intron|AQP7_uc011lnz.1_Intron|AQP7_uc011loa.1_Intron	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		agtagatgtgcaataagtatt	0.085													4	3	---	---	---	---	
FRMPD1	22844	broad.mit.edu	37	9	37736856	37736857	+	Intron	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37736856_37736857delGT	uc004aag.1	+						FRMPD1_uc004aah.1_Intron|FRMPD1_uc011lqm.1_Intron|FRMPD1_uc011lqn.1_Intron	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1							cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		gtgcgtgagagtgtgtgtgtgt	0.366													6	3	---	---	---	---	
CNTNAP3	79937	broad.mit.edu	37	9	39146774	39146774	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39146774delT	uc004abi.2	-						CNTNAP3_uc004abj.2_Intron|CNTNAP3_uc011lqr.1_Intron|CNTNAP3_uc004abk.1_Intron|CNTNAP3_uc011lqs.1_Intron|CNTNAP3_uc004abl.1_Intron	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3 precursor						cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		CCCATTGCTATTTTTTGTGTA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66515952	66515952	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66515952delT	uc010mnh.1	-											Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																		TTTCCACACATTTTTTTTACT	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68389317	68389317	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68389317delT								FAM27B (595128 upstream) : MIR1299 (612922 downstream)																							cctattcagatttttttatgg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90681011	90681011	+	5'Flank	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90681011delT	uc004apv.1	-											full-length cDNA clone CS0DI004YC05 of Placenta Cot 25-normalized of Homo sapiens (human).																		CAGAAAAttcttttttttttt	0.159													3	3	---	---	---	---	
IARS	3376	broad.mit.edu	37	9	94990569	94990570	+	Intron	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94990569_94990570insT	uc004art.1	-						IARS_uc004ars.1_Intron|IARS_uc004aru.3_Intron|IARS_uc010mqr.2_Intron|IARS_uc010mqt.2_Intron	NM_013417	NP_038203	P41252	SYIC_HUMAN	isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			ovary(1)|skin(1)	2					L-Isoleucine(DB00167)	aggacataatcttttttttttc	0.104													4	2	---	---	---	---	
C9orf3	84909	broad.mit.edu	37	9	97717973	97717973	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97717973delA	uc004ava.2	+						C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron|C9orf3_uc004avc.2_Intron	NM_032823	NP_116212	Q8N6M6	AMPO_HUMAN	aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		AACCAAGTCCAAACAAAAATG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	101854625	101854625	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101854625delA								COL15A1 (21557 upstream) : TGFBR1 (12787 downstream)																							AAGCGCCTAGAAAAAAAAAAG	0.423													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	105864161	105864161	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105864161delT								CYLC2 (83391 upstream) : SMC2 (992380 downstream)																							TTGTTTGTGGTTTTATTTTTA	0.363													4	2	---	---	---	---	
PALM2-AKAP2	445815	broad.mit.edu	37	9	112704100	112704100	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112704100delA	uc004bei.2	+						PALM2_uc004bef.2_Intron|PALM2_uc004beg.2_Intron|PALM2_uc004beh.3_Intron|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						gggcaaggggagggggagacc	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	117709902	117709902	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117709902delA								TNFSF8 (17132 upstream) : TNC (72904 downstream)																							ttctgagattaaaaaaaactt	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120990746	120990747	+	IGR	DEL	CA	-	-	rs12236665		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120990746_120990747delCA								TLR4 (510982 upstream) : DBC1 (938161 downstream)																							catacacacgcacacacacaca	0.015													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	121133862	121133862	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121133862delC								TLR4 (654098 upstream) : DBC1 (795046 downstream)																							taacttctctcccatgcatct	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	123494588	123494589	+	IGR	INS	-	TCTTC	TCTTC	rs148745431	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123494588_123494589insTCTTC								MEGF9 (17976 upstream) : FBXW2 (24665 downstream)																							TCAGGAACTGAtcttctcttct	0.257													3	3	---	---	---	---	
DAB2IP	153090	broad.mit.edu	37	9	124480282	124480282	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124480282delG	uc004bln.2	+							NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform						activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2						CCTTGCTGGTGGTCTCCCTGT	0.592													4	2	---	---	---	---	
RBM18	92400	broad.mit.edu	37	9	125010064	125010065	+	Intron	INS	-	T	T	rs34974193		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125010064_125010065insT	uc004bma.2	-						RBM18_uc004blz.2_Intron|RBM18_uc010mvy.2_Intron|RBM18_uc011lyp.1_Intron	NM_033117	NP_149108	Q96H35	RBM18_HUMAN	RNA binding motif protein 18								nucleotide binding|RNA binding				0						tttttttgttgttttttttttt	0.149													6	3	---	---	---	---	
ZNF79	7633	broad.mit.edu	37	9	130196390	130196390	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130196390delA	uc004bqw.3	+						ZNF79_uc011maf.1_Intron|ZNF79_uc011mag.1_Intron	NM_007135	NP_009066	Q15937	ZNF79_HUMAN	zinc finger protein 79						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1						gccatttcctaaacacacgag	0.000													4	2	---	---	---	---	
FNBP1	23048	broad.mit.edu	37	9	132673126	132673127	+	Intron	INS	-	TG	TG	rs142696317	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132673126_132673127insTG	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc011mbu.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848	Q96RU3	FNBP1_HUMAN	formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		TGACTCTCTAAtgtgtgtgtgt	0.342			T	MLL	AML								9	9	---	---	---	---	
RXRA	6256	broad.mit.edu	37	9	137261749	137261749	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137261749delC	uc004cfb.2	+						RXRA_uc004cfa.1_Intron	NM_002957	NP_002948	P19793	RXRA_HUMAN	retinoid X receptor, alpha						cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)	GGTGCATGAGCCCAGCATGTG	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137909649	137909650	+	IGR	DEL	GA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137909649_137909650delGA								FCN1 (99840 upstream) : OLFM1 (57439 downstream)																							GAGGTGGCGGGAGAGAGAGAGA	0.460													4	2	---	---	---	---	
GLT6D1	360203	broad.mit.edu	37	9	138517099	138517100	+	Intron	DEL	GC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138517099_138517100delGC	uc010nbd.1	-							NM_182974	NP_892019	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1						carbohydrate metabolic process	integral to membrane	transferase activity, transferring hexosyl groups			ovary(1)	1		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		AAGAAAGGGAGCAGGAGCTAAA	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2056818	2056819	+	5'Flank	INS	-	G	G	rs149009459	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2056818_2056819insG	uc001igo.1	-											Homo sapiens cDNA FLJ40155 fis, clone TESTI2014362.																		GTGTTTTATTTTTGTTGTTGTT	0.366													2	5	---	---	---	---	
PITRM1	10531	broad.mit.edu	37	10	3188323	3188323	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3188323delA	uc010qah.1	-						PITRM1_uc001igr.1_Intron|PITRM1_uc001igs.1_5'Flank|PITRM1_uc001igt.1_Intron|PITRM1_uc009xhv.1_Intron|PITRM1_uc001igu.1_Intron|PITRM1_uc010qai.1_Intron|uc001igv.1_RNA			E7ES23	E7ES23_HUMAN	SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;						proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1						TATAAACTGCAAAAAAATACC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3333612	3333612	+	IGR	DEL	T	-	-	rs142878578		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3333612delT								PITRM1 (118609 upstream) : KLF6 (484577 downstream)																							ATTTTTAAGGTTTTTTTTTTC	0.338													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3502524	3502525	+	Intron	INS	-	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3502524_3502525insC	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																		TCCTTCGGTTTCCCAGTTGCCC	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4042488	4042488	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4042488delT								KLF6 (215015 upstream) : LOC100216001 (578956 downstream)																							TTCAGATTTCTTTTTTTTTTC	0.318													4	6	---	---	---	---	
TAF3	83860	broad.mit.edu	37	10	7925187	7925187	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7925187delC	uc010qbd.1	+							NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140						maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						tttagttcttcaatctagaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8170991	8170992	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8170991_8170992insT								GATA3 (53829 upstream) : None (None downstream)																							ATTCGTACTAATTTTTTTTTGT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10266644	10266644	+	IGR	DEL	C	-	-	rs78447990		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10266644delC								None (None upstream) : SFTA1P (559758 downstream)																							GGGAATATTTCCCTTTCTGTG	0.532													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	26116045	26116046	+	IGR	DEL	TC	-	-	rs2437402	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26116045_26116046delTC								GPR158 (224890 upstream) : MYO3A (106956 downstream)																							aatgagtttttcttttaattcc	0.000													4	2	---	---	---	---	
MYO3A	53904	broad.mit.edu	37	10	26438094	26438094	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26438094delT	uc001isn.2	+						MYO3A_uc009xko.1_Intron|MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA						protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						gagaagttactttttttttta	0.040													4	2	---	---	---	---	
YME1L1	10730	broad.mit.edu	37	10	27410625	27410625	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27410625delT	uc001iti.2	-						YME1L1_uc001itj.2_Intron|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_Intron	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1						protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						gactaatttattttttattta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42654253	42654255	+	IGR	DEL	TAT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42654253_42654255delTAT								None (None upstream) : LOC441666 (173060 downstream)																							caaatttgcatattattactaat	0.034													4	2	---	---	---	---	
ARHGAP22	58504	broad.mit.edu	37	10	49831130	49831130	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49831130delC	uc010qgm.1	-						ARHGAP22_uc001jgv.2_Intron	NM_021226	NP_067049	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 2						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity			ovary(1)	1						TCAAAATGTGCCTCTGTGACC	0.453													4	2	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	52877918	52877918	+	Intron	DEL	A	-	-	rs11296841		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52877918delA	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		AGTTAAGAGCAGAGCAGCAAT	0.095													4	2	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53778733	53778734	+	Intron	INS	-	A	A	rs140507007	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53778733_53778734insA	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		aatttatgaagaaaagggttca	0.000													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	60212483	60212483	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60212483delG								TFAM (56587 upstream) : BICC1 (60421 downstream)																							atcagagtcagggcataaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	67606912	67606912	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67606912delA								None (None upstream) : CTNNA3 (72813 downstream)																							ACCCATACATAAAAAAAAATA	0.368													4	2	---	---	---	---	
MYST4	23522	broad.mit.edu	37	10	76650889	76650889	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76650889delT	uc001jwn.1	+						MYST4_uc001jwm.1_Intron|MYST4_uc001jwo.1_Intron|MYST4_uc001jwp.1_Intron	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic						histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)					CCTTGTTACCTTTGCTATAGT	0.398			T	CREBBP	AML								4	2	---	---	---	---	
C10orf11	83938	broad.mit.edu	37	10	78037277	78037278	+	Intron	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78037277_78037278insT	uc001jxi.2	+							NM_032024	NP_114413	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)					agctatttggatttttttttct	0.074													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	84475169	84475169	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84475169delG	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		TACTTTCAGTGGTGtctctga	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	86973608	86973608	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86973608delC								FAM190B (695332 upstream) : GRID1 (385704 downstream)																							tatctccttgccacagcttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	90792630	90792630	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90792630delT								FAS (17089 upstream) : CH25H (173066 downstream)																							TGGATAAAGATCCAGAATATG	0.403													4	2	---	---	---	---	
TNKS2	80351	broad.mit.edu	37	10	93600113	93600113	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93600113delA	uc001khp.2	+							NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related						positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)				ataataagacaaaaaaaaaGG	0.174													6	3	---	---	---	---	
CPEB3	22849	broad.mit.edu	37	10	93911964	93911964	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93911964delT	uc001khw.1	-						CPEB3_uc001khu.1_Intron|CPEB3_uc001khv.1_Intron|CPEB3_uc010qnn.1_Intron	NM_014912	NP_055727	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0		Colorectal(252;0.0869)				gcctcaagccttttTTTAAAG	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	95316951	95316951	+	IGR	DEL	G	-	-	rs76916254		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95316951delG								CEP55 (28104 upstream) : GPR120 (9471 downstream)																							AGGATTTTTTGTTTTGTTTTG	0.358													4	2	---	---	---	---	
ENTPD1	953	broad.mit.edu	37	10	97497147	97497147	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97497147delT	uc001kli.3	+						ENTPD1_uc001kle.1_Intron	NM_001098175	NP_001091645	P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1						cell adhesion	integral to plasma membrane	ATP binding			ovary(3)	3		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		AAATTAAAACttttttttttt	0.154													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102981268	102981269	+	IGR	DEL	CA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102981268_102981269delCA								TLX1 (83723 upstream) : LBX1 (5465 downstream)																							CTGCACACCTCACACACCCTGG	0.480													4	2	---	---	---	---	
C10orf76	79591	broad.mit.edu	37	10	103716105	103716106	+	Intron	DEL	TC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103716105_103716106delTC	uc009xwy.1	-						C10orf76_uc009xwx.1_Intron	NM_024541	NP_078817	Q5T2E6	CJ076_HUMAN	hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		GCCTCCCTATTCTCTCTCTCTC	0.446													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	103827952	103827953	+	IGR	DEL	TT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103827952_103827953delTT								HPS6 (160 upstream) : LDB1 (39374 downstream)																							tctactcatctttatataatcc	0.109													4	2	---	---	---	---	
RBM20	282996	broad.mit.edu	37	10	112430779	112430779	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112430779delC	uc001kzf.2	+							NM_001134363	NP_001127835	Q5T481	RBM20_HUMAN	RNA binding motif protein 20							nucleus	nucleotide binding|RNA binding|zinc ion binding				0						ATTGGCGCTGCCAAAGAAAGT	0.418													4	2	---	---	---	---	
ABLIM1	3983	broad.mit.edu	37	10	116204072	116204072	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116204072delA	uc010qsg.1	-						ABLIM1_uc010qsh.1_Intron|ABLIM1_uc010qsi.1_Intron|ABLIM1_uc010qsk.1_Intron|ABLIM1_uc009xyp.2_Intron|ABLIM1_uc010qsf.1_Intron|ABLIM1_uc009xyn.2_Intron|ABLIM1_uc010qsj.1_Intron|ABLIM1_uc009xyo.2_Intron	NM_002313	NP_002304	O14639	ABLM1_HUMAN	actin-binding LIM protein 1 isoform a						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		TTGGGACCCTAAACCCTCTTA	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	116578164	116578164	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116578164delT								ABLIM1 (50145 upstream) : FAM160B1 (3339 downstream)																							atcctcaggctttggtaccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	118629277	118629277	+	Intron	DEL	C	-	-	rs59520145		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118629277delC	uc001lcw.2	+											SubName: Full=Putative uncharacterized protein C10orf134;																		TTTACTACTACTTTTTCTTTT	0.343													2	4	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126770242	126770242	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126770242delA	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		agttaaagggaaaaaaaAAAT	0.159													2	5	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127575513	127575516	+	Intron	DEL	TCTT	-	-	rs143617895		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127575513_127575516delTCTT	uc001ljg.1	-							NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TTTCCCCATGTCTTTCTGTCTCTT	0.412													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130262707	130262707	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130262707delC								MKI67 (338239 upstream) : None (None downstream)																							tcctccccatccttccctcta	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132684555	132684555	+	IGR	DEL	C	-	-	rs78070882		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132684555delC								GLRX3 (701771 upstream) : TCERG1L (206101 downstream)																							gtggtttgcacccccggctcc	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	1128157	1128157	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1128157delA								MUC2 (23740 upstream) : MUC5B (14317 downstream)																							agtgtacaataaaaattacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	6121092	6121093	+	IGR	DEL	TG	-	-	rs149849422		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6121092_6121093delTG								OR56A1 (72158 upstream) : OR56B4 (7916 downstream)																							ttttaaactctgtggatacaga	0.079													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	6161845	6161846	+	IGR	INS	-	A	A	rs146407335	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6161845_6161846insA								OR56B4 (31879 upstream) : OR52B2 (28740 downstream)																							GATAAGACTTTAAAAAAAAAAC	0.064													4	3	---	---	---	---	
PPFIBP2	8495	broad.mit.edu	37	11	7559611	7559611	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7559611delC	uc001mfj.3	+							NM_003621	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2						cell communication|DNA integration	intracellular	DNA binding|integrase activity|protein binding			ovary(2)|breast(2)	4				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		TGTTGCTGCTCTTTGCCTTCT	0.542													4	2	---	---	---	---	
TEAD1	7003	broad.mit.edu	37	11	12783493	12783493	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12783493delG	uc001mkj.3	+							NM_021961	NP_068780	P28347	TEAD1_HUMAN	TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		agcactgaatgggggTGGTTG	0.229													4	2	---	---	---	---	
MRGPRX1	259249	broad.mit.edu	37	11	18958849	18958849	+	5'Flank	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18958849delT	uc001mpg.2	-							NM_147199	NP_671732	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1						acute-phase response	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(2)|central_nervous_system(1)	3						AGAGTAGCAGTTTTTGGAATT	0.458													4	2	---	---	---	---	
RCN1	5954	broad.mit.edu	37	11	31901758	31901759	+	Intron	INS	-	AAT	AAT			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31901758_31901759insAAT	uc010rea.1	+							NM_002901	NP_002892	Q15293	RCN1_HUMAN	reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)					gaggtagttggaataaatgacc	0.104													4	2	---	---	---	---	
QSER1	79832	broad.mit.edu	37	11	32977178	32977178	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32977178delT	uc001mty.2	+						QSER1_uc001mtz.1_Intron|QSER1_uc001mua.2_Intron	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1											ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					ATTGTTTAACTTTTTTTTTTA	0.259													4	3	---	---	---	---	
CD44	960	broad.mit.edu	37	11	35188800	35188801	+	Intron	DEL	TG	-	-	rs35130248		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35188800_35188801delTG	uc001mvu.2	+						CD44_uc001mvv.2_Intron|CD44_uc001mvw.2_Intron|CD44_uc001mvx.2_Intron|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Intron|CD44_uc010rer.1_Intron|CD44_uc009ykh.2_Intron	NM_000610	NP_000601	P16070	CD44_HUMAN	CD44 antigen isoform 1 precursor						cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity			pancreas(1)	1	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronidase(DB00070)	CACTGAGTTTTGTGTGTGTGTG	0.332													4	2	---	---	---	---	
PRR5L	79899	broad.mit.edu	37	11	36462906	36462906	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36462906delG	uc001mwo.3	+						PRR5L_uc001mwp.2_Intron|PRR5L_uc009ykk.2_Intron|PRR5L_uc010rfc.1_Intron	NM_001160167	NP_001153639	Q6MZQ0	PRR5L_HUMAN	protor-2 isoform a											ovary(1)	1						ccaaaagaaagggacagcagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	38474747	38474747	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38474747delT								None (None upstream) : None (None downstream)																							GCATGCATTATTTTTTTTCCT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	38855717	38855718	+	IGR	DEL	GG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38855717_38855718delGG								None (None upstream) : None (None downstream)																							ATGAATTCCTGGGTGTTATTAA	0.317													4	2	---	---	---	---	
HSD17B12	51144	broad.mit.edu	37	11	43877353	43877353	+	3'UTR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43877353delA	uc001mxq.3	+	11						NM_016142	NP_057226	Q53GQ0	DHB12_HUMAN	hydroxysteroid (17-beta) dehydrogenase 12						long-chain fatty-acyl-CoA biosynthetic process|steroid biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	estradiol 17-beta-dehydrogenase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity				0						AAGGGTAGCTAATGACATGAA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44671432	44671432	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44671432delT								CD82 (30119 upstream) : TSPAN18 (210447 downstream)																							cctcagctcattttTTTTTTA	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44874076	44874077	+	IGR	INS	-	GAAA	GAAA	rs139799846	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44874076_44874077insGAAA								CD82 (232763 upstream) : TSPAN18 (7802 downstream)																							TGTTGGCTTCTGAGTTAATTCA	0.351													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49302476	49302477	+	IGR	DEL	TG	-	-	rs112159452		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49302476_49302477delTG								FOLH1 (72254 upstream) : LOC440040 (277603 downstream)																							tcatcttttatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49380451	49380451	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49380451delG								FOLH1 (150229 upstream) : LOC440040 (199629 downstream)																							TCTGCCATGTGGGCTGCTTTT	0.458													4	2	---	---	---	---	
OR8H2	390151	broad.mit.edu	37	11	55872313	55872314	+	5'Flank	INS	-	T	T	rs35552904		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55872313_55872314insT	uc010riy.1	+							NM_001005200	NP_001005200	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	Esophageal squamous(21;0.00693)					TAAACAGAAAGtttttttttgt	0.114										HNSCC(53;0.14)			8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59681131	59681131	+	IGR	DEL	T	-	-	rs71831362		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59681131delT								TCN1 (47090 upstream) : PLAC1L (126617 downstream)																							TTTAACCTACttttttttttc	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	61441794	61441795	+	IGR	DEL	AT	-	-	rs57489677		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61441794_61441795delAT								RPLP0P2 (34873 upstream) : DAGLA (6115 downstream)																							ggataagtggatggatggatgg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	61441797	61441798	+	IGR	DEL	GA	-	-	rs57512837		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61441797_61441798delGA								RPLP0P2 (34876 upstream) : DAGLA (6112 downstream)																							taagtggatggatggatggatg	0.040													4	2	---	---	---	---	
GANAB	23193	broad.mit.edu	37	11	62403059	62403059	+	Intron	DEL	A	-	-	rs74843001		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62403059delA	uc001nub.2	-						GANAB_uc001nua.2_Intron|GANAB_uc001nuc.2_Intron|GANAB_uc010rma.1_Intron|GANAB_uc010rmb.1_Intron	NM_198334	NP_938148	Q14697	GANAB_HUMAN	neutral alpha-glucosidase AB isoform 2						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|Golgi apparatus|melanosome	carbohydrate binding|glucan 1,3-alpha-glucosidase activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5						tccatataggaaaaaaaatga	0.035													3	3	---	---	---	---	
SLC22A10	387775	broad.mit.edu	37	11	63065426	63065427	+	Intron	INS	-	T	T	rs137941419	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63065426_63065427insT	uc009yor.2	+						SLC22A10_uc010rmo.1_Intron|SLC22A10_uc001nwu.3_Intron|SLC22A10_uc010rmp.1_Intron	NM_001039752	NP_001034841	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10							integral to membrane	transmembrane transporter activity			ovary(2)	2						ATGATTCCATCTTTTTTTTACT	0.292													4	5	---	---	---	---	
POLA2	23649	broad.mit.edu	37	11	65043865	65043865	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65043865delT	uc001odj.2	+						POLA2_uc009yqf.1_Intron|POLA2_uc010rod.1_Intron	NM_002689	NP_002680	Q14181	DPOA2_HUMAN	DNA-directed DNA polymerase alpha 2						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	nucleoplasm	DNA binding				0					Dacarbazine(DB00851)	TCATCTAAAGTTTTTTTTTTT	0.328													3	3	---	---	---	---	
CATSPER1	117144	broad.mit.edu	37	11	65794034	65794034	+	5'Flank	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65794034delC	uc001ogt.2	-							NM_053054	NP_444282	Q8NEC5	CTSR1_HUMAN	sperm-associated cation channel 1						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	protein binding			ovary(2)	2						GGGCCTCATTCCCAAATGCCT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	66185285	66185285	+	IGR	DEL	A	-	-	rs147472496		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66185285delA								SLC29A2 (45640 upstream) : NPAS4 (3190 downstream)																							AGTTGGAGACAAAAAAAAAAG	0.393											OREG0021106	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
SUV420H1	51111	broad.mit.edu	37	11	67974267	67974267	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67974267delA	uc001onm.1	-						SUV420H1_uc001onn.1_Intron|SUV420H1_uc009ysf.2_Intron|SUV420H1_uc001ono.1_Intron|SUV420H1_uc001onp.2_Intron|SUV420H1_uc010rqa.1_Intron|SUV420H1_uc001onq.2_Intron	NM_017635	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			ovary(2)|kidney(1)	3						CTCACACATGAAAAAAAAAAT	0.358													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	68987065	68987066	+	IGR	DEL	GA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68987065_68987066delGA								TPCN2 (57158 upstream) : MYEOV (74556 downstream)																							TAAAAGTTGGGAGAGAGAGAGA	0.342													4	2	---	---	---	---	
RNF169	254225	broad.mit.edu	37	11	74467806	74467806	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74467806delG	uc001ovl.3	+							NM_001098638	NP_001092108	Q8NCN4	RN169_HUMAN	ring finger protein 169								zinc ion binding			ovary(1)	1						ggaagcatgtgggactgcaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74722880	74722881	+	IGR	DEL	TT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74722880_74722881delTT								NEU3 (4139 upstream) : OR2AT4 (76916 downstream)																							AGGAGTTAACTTTTTTTTTTTC	0.401													2	4	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	79036154	79036155	+	Intron	DEL	AG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79036154_79036155delAG	uc001ozl.3	-							NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						GGCACGTGGAAGAGAGAGAGAG	0.485													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83580348	83580348	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83580348delA	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)				CATTAGCTTTAAAAAAAAAGC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109794535	109794535	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109794535delT								C11orf87 (494697 upstream) : ZC3H12C (169391 downstream)																							agacagtggctttttattgaa	0.000													4	2	---	---	---	---	
IL18	3606	broad.mit.edu	37	11	112037337	112037337	+	5'Flank	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112037337delT	uc001pnb.1	-						IL18_uc009yym.1_5'Flank|TEX12_uc001pnc.2_5'Flank|TEX12_uc001pnd.2_5'Flank	NM_001562	NP_001553	Q14116	IL18_HUMAN	interleukin 18 proprotein						angiogenesis|cell-cell signaling|chemokine biosynthetic process|granulocyte macrophage colony-stimulating factor biosynthetic process|interferon-gamma biosynthetic process|interleukin-13 biosynthetic process|interleukin-2 biosynthetic process|positive regulation of activated T cell proliferation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma production|positive regulation of interleukin-17 production|positive regulation of natural killer cell proliferation|positive regulation of NK T cell proliferation|regulation of cell adhesion|sleep|T-helper 1 type immune response|type 2 immune response	cytosol|extracellular space	cytokine activity|signal transducer activity				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		GGTAATTTGCTTTTTTTTTTC	0.363													2	4	---	---	---	---	
BCO2	83875	broad.mit.edu	37	11	112052730	112052730	+	Intron	DEL	A	-	-	rs35381587		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112052730delA	uc001pnf.2	+						BCO2_uc001pne.1_Intron|BCO2_uc001png.2_Intron|BCO2_uc001pnh.2_Intron|BCO2_uc010rwt.1_Intron|BCO2_uc009yyn.2_Intron|BCO2_uc001pni.2_Intron	NM_031938	NP_114144	Q9BYV7	BCDO2_HUMAN	beta-carotene dioxygenase 2 isoform a						carotene metabolic process|retinal metabolic process|retinoic acid metabolic process		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						aatttacaagaaaaaaatcaa	0.035													4	3	---	---	---	---	
C11orf71	54494	broad.mit.edu	37	11	114270517	114270518	+	3'UTR	INS	-	ACG	ACG			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114270517_114270518insACG	uc001pou.3	-	1					C11orf71_uc001pot.1_Intron|RBM7_uc001pov.2_5'Flank|RBM7_uc001pow.2_5'Flank|RBM7_uc001pox.2_5'Flank	NM_019021	NP_061894	Q6IPW1	CK071_HUMAN	hypothetical protein LOC54494												0		all_cancers(61;1.15e-11)|all_epithelial(67;5.3e-06)|all_hematologic(158;0.000303)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.6e-06)|Epithelial(105;4.31e-05)|all cancers(92;0.00036)		AAATCAATCAACTGTTACACTT	0.401													4	2	---	---	---	---	
BUD13	84811	broad.mit.edu	37	11	116622446	116622446	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116622446delT	uc001ppn.2	-						BUD13_uc001ppo.2_Intron	NM_032725	NP_116114	Q9BRD0	BUD13_HUMAN	BUD13 homolog isoform 1											large_intestine(1)|pancreas(1)	2	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)		GTTTTTTACCTTGGAAATAAG	0.333													4	2	---	---	---	---	
DSCAML1	57453	broad.mit.edu	37	11	117435898	117435898	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117435898delA	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	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)		cttctgttttaaaaatcaatg	0.000													4	2	---	---	---	---	
HMBS	3145	broad.mit.edu	37	11	118962250	118962251	+	Intron	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118962250_118962251insT	uc001puz.1	+						HMBS_uc009zao.1_Intron|HMBS_uc001pvc.1_Intron|HMBS_uc009zap.1_Intron|HMBS_uc001pva.1_Intron|HMBS_uc001pvb.1_Intron|HMBS_uc001pvd.1_Intron|HMBS_uc001pve.1_Intron|HMBS_uc001pvf.1_Intron	NM_000190	NP_000181	P08397	HEM3_HUMAN	hydroxymethylbilane synthase isoform 1						peptidyl-pyrromethane cofactor linkage	cytosol	hydroxymethylbilane synthase activity				0	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		GGGCCTGCCCCTATCCTCTCCC	0.460									Porphyria_Acute_Intermittent				19	11	---	---	---	---	
GRIK4	2900	broad.mit.edu	37	11	120660021	120660021	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120660021delC	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)	TCCTCTCTATCCCCCTGTATT	0.403													4	2	---	---	---	---	
FAM118B	79607	broad.mit.edu	37	11	126131050	126131051	+	Intron	INS	-	AAATGTA	AAATGTA	rs78366918		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126131050_126131051insAAATGTA	uc001qdf.2	+						FAM118B_uc009zca.2_Intron|FAM118B_uc001qdg.2_Intron	NM_024556	NP_078832	Q9BPY3	F118B_HUMAN	hypothetical protein LOC79607												0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		GCCTGTatgtgaaatgtaaaat	0.381													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	131115624	131115624	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131115624delG								SNX19 (329242 upstream) : NTM (124747 downstream)																							TGCCCACTGTGAGGCCATGGG	0.473													4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131593723	131593724	+	Intron	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131593723_131593724delTG	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						tgtgtgtgcatgtgtgtgtgtg	0.153													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132639992	132639992	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132639992delA	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		TAGAGGAAAGAAAAAAAATAA	0.259													3	3	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132786236	132786236	+	Intron	DEL	G	-	-	rs75771691	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132786236delG	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		CCATGACTCTGGGGTTCCATG	0.502													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133090860	133090860	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133090860delG	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		ACGGCTGTATGGCCCTTCCAT	0.453													4	2	---	---	---	---	
LOC100288778	100288778	broad.mit.edu	37	12	84447	84448	+	Intron	INS	-	GTT	GTT			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84447_84448insGTT	uc010scy.1	+						uc010scx.1_Intron|LOC100288778_uc010scz.1_Intron|LOC100288778_uc010sdb.1_Intron					SubName: Full=Actin nucleation promoting factor; Flags: Fragment;												0						AAAGTGATGCAGTTTAtggaat	0.282													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	2140187	2140188	+	IGR	INS	-	TC	TC	rs139881300	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2140187_2140188insTC								DCP1B (26510 upstream) : CACNA1C (22228 downstream)																							GGCAAGACAGGTCTCTACAGGT	0.441													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	9631896	9631900	+	IGR	DEL	GAAAG	-	-	rs68022474		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9631896_9631900delGAAAG								DDX12 (31128 upstream) : KLRB1 (115971 downstream)																							CACTACAGATGAAAGGAAACATTCA	0.283													3	3	---	---	---	---	
CLECL1	160365	broad.mit.edu	37	12	9888285	9888288	+	5'Flank	DEL	TTGT	-	-	rs35880460		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9888285_9888288delTTGT	uc001qwj.2	-							NM_172004	NP_742001	Q8IZS7	CLCL1_HUMAN	type II transmembrane protein DCAL1							integral to membrane|plasma membrane	sugar binding				0						cttgctgaacttgtttattacctc	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16658182	16658183	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16658182_16658183insA								MGST1 (134840 upstream) : LMO3 (43124 downstream)																							tccacaagaataaaaaaaatgc	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16954080	16954080	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16954080delG								LMO3 (191322 upstream) : None (None downstream)																							TCGCCCATCTGGTTTTTTTTT	0.448													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	17183185	17183185	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17183185delA								LMO3 (420427 upstream) : None (None downstream)																							TTGTGAGCTTAAAAAAAAGTA	0.294													4	2	---	---	---	---	
SOX5	6660	broad.mit.edu	37	12	23979634	23979634	+	Intron	DEL	A	-	-	rs34746862		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23979634delA	uc001rfw.2	-						SOX5_uc001rfx.2_Intron|SOX5_uc001rfy.2_Intron|SOX5_uc010siv.1_Intron|SOX5_uc010siw.1_Intron|SOX5_uc001rfz.1_Intron|SOX5_uc001rga.2_Intron	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						ATTAGGGCTTAAAAAAAAAAA	0.388													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	28912587	28912587	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28912587delC								CCDC91 (209489 upstream) : FAR2 (389645 downstream)																							GTCAGTTCTACCAAGTTGCAT	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	28928632	28928633	+	IGR	DEL	CA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28928632_28928633delCA								CCDC91 (225534 upstream) : FAR2 (373599 downstream)																							caagcccaatcacacacacacg	0.035													4	2	---	---	---	---	
DENND5B	160518	broad.mit.edu	37	12	31712411	31712414	+	Intron	DEL	CAGA	-	-	rs112484826		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31712411_31712414delCAGA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc001rkj.2_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2						GAGTTATCTCCAGACAAAGAGTAA	0.304													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31757312	31757315	+	IGR	DEL	TTTG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31757312_31757315delTTTG								DENND5B (13360 upstream) : C12orf72 (42779 downstream)																							ctaatgtttctttgtttgtttgtt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	39517164	39517164	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39517164delT								CPNE8 (217744 upstream) : KIF21A (169867 downstream)																							tctatctttattccctctgcc	0.090													6	3	---	---	---	---	
SLC2A13	114134	broad.mit.edu	37	12	40411238	40411239	+	Intron	INS	-	CG	CG			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40411238_40411239insCG	uc010skm.1	-						SLC2A13_uc001rmf.2_Intron	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)				TTTCTCCCTCTTCTTTAAGGAT	0.257										HNSCC(50;0.14)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47934548	47934549	+	IGR	INS	-	CCACAT	CCACAT	rs145314665	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47934548_47934549insCCACAT								FAM113B (304107 upstream) : RPAP3 (121167 downstream)																							AATTCTCATGACCACATCCCAT	0.515													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47987292	47987292	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47987292delT								FAM113B (356851 upstream) : RPAP3 (68424 downstream)																							AGCCCTACCCTCCCCCAACAA	0.383													4	2	---	---	---	---	
FAIM2	23017	broad.mit.edu	37	12	50283590	50283590	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50283590delG	uc001rvj.1	-						FAIM2_uc001rvi.1_Intron|FAIM2_uc001rvk.1_Intron	NM_012306	NP_036438	Q9BWQ8	FAIM2_HUMAN	Fas apoptotic inhibitory molecule 2						anti-apoptosis|apoptosis	cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|ovary(1)|skin(1)	3						GAGTGGGAGTGGGGAGGGGTT	0.552													4	2	---	---	---	---	
ACVR1B	91	broad.mit.edu	37	12	52368293	52368294	+	Intron	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52368293_52368294delGT	uc001rzn.2	+						ACVR1B_uc001rzl.2_Intron|ACVR1B_uc001rzm.2_Intron|ACVR1B_uc010snn.1_Intron	NM_004302	NP_004293	P36896	ACV1B_HUMAN	activin A receptor, type IB isoform a precursor						G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway	cell surface	activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding			pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1)	9				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	AAAAAAATTCGTGTGTGTGTGT	0.396													0	6	---	---	---	---	
ATF7	11016	broad.mit.edu	37	12	54001435	54001436	+	Intron	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54001435_54001436insA	uc001sdz.2	-						ATF7_uc010sok.1_Intron|ATF7_uc010sol.1_Intron|ATF7_uc001sea.3_Intron|ATF7_uc001seb.3_Intron	NM_006856	NP_006847	P17544	ATF7_HUMAN	activating transcription factor 7 isoform 2						interspecies interaction between organisms	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2						tgttaaatgggaaaaaaaaaca	0.000													4	2	---	---	---	---	
HOXC4	3221	broad.mit.edu	37	12	54422129	54422130	+	Intron	INS	-	T	T	rs150694870	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54422129_54422130insT	uc001seu.2	+						HOXC6_uc001ses.2_Intron|HOXC5_uc001set.2_Intron|HOXC6_uc001sev.2_5'Flank	NM_014620	NP_055435	P09017	HXC4_HUMAN	homeobox C4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						AGCAGAAGCGATTTTTTTCCCC	0.396													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	57206807	57206807	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57206807delT								HSD17B6 (25233 upstream) : SDR9C7 (110812 downstream)																							atttcttctattttttttttg	0.045													2	4	---	---	---	---	
SRGAP1	57522	broad.mit.edu	37	12	64539668	64539668	+	3'UTR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64539668delG	uc010ssp.1	+	22					SRGAP1_uc001srv.2_3'UTR	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)		TGTGCAATTTGGGGAGGGGAG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	64626407	64626407	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64626407delC	uc001srx.2	+											Homo sapiens mRNA; cDNA DKFZp434A0326 (from clone DKFZp434A0326).																		cccaatcctgcccctgcttcc	0.000													4	2	---	---	---	---	
MSRB3	253827	broad.mit.edu	37	12	65722027	65722027	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65722027delT	uc001ssn.2	+						MSRB3_uc001ssm.2_Intron|MSRB3_uc009zqp.2_Intron	NM_198080	NP_932346	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		AACTACAGGCTTTTTTTTTTA	0.308													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	70097155	70097156	+	IGR	INS	-	GGG	GGG			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70097155_70097156insGGG								BEST3 (3959 upstream) : RAB3IP (35475 downstream)																							gaggaggaggaggaggaAAGAG	0.193													4	2	---	---	---	---	
ZFC3H1	196441	broad.mit.edu	37	12	72032609	72032609	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72032609delA	uc001swo.2	-							NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2						RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5						AAAAACAAACAAAAAAAAACA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	72444654	72444654	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72444654delT								TPH2 (18433 upstream) : LOC283392 (211674 downstream)																							cctcagtttctttttgtgtat	0.050													4	2	---	---	---	---	
TRHDE	29953	broad.mit.edu	37	12	72916564	72916564	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72916564delA	uc001sxa.2	+							NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme						cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3						TGCCTTCTATAAACCCGATGG	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	75964344	75964344	+	IGR	DEL	C	-	-	rs71440406		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75964344delC								KRR1 (58926 upstream) : PHLDA1 (454884 downstream)																							atgatcagaaCATGTGAGATT	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	76344581	76344581	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76344581delG								KRR1 (439163 upstream) : PHLDA1 (74647 downstream)																							TTACCTCTCTGGATGGAAGAG	0.259													4	2	---	---	---	---	
NAV3	89795	broad.mit.edu	37	12	78392511	78392511	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78392511delT	uc001syp.2	+						NAV3_uc001syo.2_Intron	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						AAACAGGTCCTTCCAAATGCA	0.264										HNSCC(70;0.22)			4	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82658541	82658541	+	IGR	DEL	G	-	-	rs78254122		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82658541delG								PPFIA2 (505432 upstream) : CCDC59 (87549 downstream)																							ataaaattgaggaagaaaaag	0.149													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	85842108	85842108	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85842108delA								ALX1 (146549 upstream) : RASSF9 (356223 downstream)																							gaacaacaacaaaaaaagaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	86086959	86086959	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86086959delG								ALX1 (391400 upstream) : RASSF9 (111372 downstream)																							ggtaatctctgatccggcatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	87502868	87502868	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87502868delA								MGAT4C (270187 upstream) : C12orf50 (870948 downstream)																							tgaacacagtaaaaaaaatca	0.000													4	2	---	---	---	---	
CEP290	80184	broad.mit.edu	37	12	88514013	88514013	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88514013delT	uc001tar.2	-	15	1744	c.1400delA	c.(1399-1401)AATfs	p.N467fs	CEP290_uc001tat.2_Frame_Shift_Del_p.N229fs|CEP290_uc009zsl.1_RNA	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	467	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						GTTTTTACAATTCTTTATTTC	0.249													504	290	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92543992	92543992	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92543992delA	uc001tca.2	+											Homo sapiens cDNA clone IMAGE:4828106.																		TAGTAGTAGGAAAAAAAAAAT	0.279													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92717567	92717567	+	IGR	DEL	T	-	-	rs34279195		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92717567delT								BTG1 (177894 upstream) : CLLU1OS (96303 downstream)																							taccttgttgttttttttttt	0.000													4	2	---	---	---	---	
C12orf63	374467	broad.mit.edu	37	12	97073209	97073209	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97073209delA	uc001tet.1	+							NM_198520	NP_940922	Q6ZTY8	CL063_HUMAN	hypothetical protein LOC374467											skin(6)|ovary(1)	7						ATACTAAAAGAAAAAAAAAAT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97656649	97656650	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97656649_97656650insT								NEDD1 (309188 upstream) : RMST (202149 downstream)																							AAAGAGTCAGATTTTTTTTTCT	0.297													4	2	---	---	---	---	
APAF1	317	broad.mit.edu	37	12	99106462	99106462	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99106462delT	uc001tfz.2	+						APAF1_uc001tfy.2_Intron|APAF1_uc001tga.2_Intron|APAF1_uc001tgb.2_Intron|APAF1_uc001tgc.2_Intron|APAF1_uc009zto.2_Intron	NM_181861	NP_863651	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1 isoform						activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)	gcccgactaattttttttttt	0.000													4	2	---	---	---	---	
SLC17A8	246213	broad.mit.edu	37	12	100767232	100767232	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100767232delC	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						TCCACCAATTCCATTCAGTTG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108644569	108644570	+	IGR	DEL	AG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108644569_108644570delAG								WSCD2 (258 upstream) : CMKLR1 (37252 downstream)																							agagagagacagagagagagag	0.351													4	2	---	---	---	---	
CMKLR1	1240	broad.mit.edu	37	12	108724609	108724610	+	Intron	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108724609_108724610insG	uc001tmw.2	-						CMKLR1_uc001tmv.2_Intron|CMKLR1_uc009zuv.2_Intron	NM_001142343	NP_001135815	Q99788	CML1_HUMAN	chemokine-like receptor 1 isoform a						chemotaxis|immune response|negative regulation of interleukin-12 production|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage chemotaxis|regulation of calcium-mediated signaling|skeletal system development	integral to plasma membrane	chemokine receptor activity			lung(3)|ovary(1)|pancreas(1)	5						AACAGCTGAATGGGGGCTGCAG	0.525													4	2	---	---	---	---	
C12orf76	400073	broad.mit.edu	37	12	110510754	110510754	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110510754delA	uc001tqe.1	-						uc001tqf.1_Intron			Q8N812	CL076_HUMAN	Homo sapiens cDNA FLJ11385 fis, clone HEMBA1000520.											large_intestine(1)	1						acttcatctcaaaaaaaaaaa	0.119													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112760182	112760182	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112760182delA								C12orf51 (16144 upstream) : RPL6 (82813 downstream)																							ctcaaaaaagaaaaaaaaaag	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	121743229	121743229	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121743229delC								CAMKK2 (7118 upstream) : ANAPC5 (2821 downstream)																							TCCTTTTTTTCCCCCCACCAA	0.408													4	2	---	---	---	---	
BCL7A	605	broad.mit.edu	37	12	122464747	122464747	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122464747delG	uc001ubp.2	+						BCL7A_uc001ubo.2_Intron	NM_001024808	NP_001019979	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A isoform b						negative regulation of transcription, DNA-dependent					ovary(1)|lung(1)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		CCTTGGACCTGGACACAGGAG	0.527			T	MYC	BNHL								4	2	---	---	---	---	
TMEM132C	92293	broad.mit.edu	37	12	129055847	129055847	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129055847delT	uc001uhs.3	+							NM_001136103	NP_001129575	Q8N3T6	T132C_HUMAN	transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1						ccagtctgagtttaggtttct	0.045													4	2	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129997967	129997967	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129997967delT	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)		tggggaccaattttTTTTTAA	0.090													4	2	---	---	---	---	
CRYL1	51084	broad.mit.edu	37	13	21075667	21075667	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21075667delT	uc001une.2	-						CRYL1_uc001unf.2_Intron|CRYL1_uc001ung.2_Intron	NM_015974	NP_057058	Q9Y2S2	CRYL1_HUMAN	lambda-crystallin						fatty acid metabolic process	cytosol	3-hydroxyacyl-CoA dehydrogenase activity|L-gulonate 3-dehydrogenase activity|NAD+ binding|protein homodimerization activity				0		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)		CCCAAGGGGATTTCTGGCAGG	0.468													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21541085	21541085	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21541085delA								XPO4 (64172 upstream) : LATS2 (6093 downstream)																							aaactaagttaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22465062	22465062	+	IGR	DEL	C	-	-	rs55872907		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22465062delC								FGF9 (186422 upstream) : None (None downstream)																							tgcacacacacatgcacacat	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27054953	27054954	+	IGR	INS	-	TTT	TTT			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27054953_27054954insTTT								CDK8 (76384 upstream) : WASF3 (76886 downstream)																							GAATATAGGGATTTTCCCCCAT	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27914194	27914194	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27914194delA								RASL11A (66367 upstream) : GTF3A (84487 downstream)																							gtcccaaaggaaaaaaaaaGT	0.249													4	2	---	---	---	---	
GTF3A	2971	broad.mit.edu	37	13	28007859	28007859	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28007859delG	uc001ure.2	+						GTF3A_uc001urf.2_Intron|GTF3A_uc001urg.2_Intron	NM_002097	NP_002088	Q92664	TF3A_HUMAN	transcription factor IIIA						regulation of transcription, DNA-dependent|rRNA transcription|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|protein binding|RNA binding|zinc ion binding				0		Lung SC(185;0.0156)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.11)|OV - Ovarian serous cystadenocarcinoma(117;0.158)		GGAAAATAGAGGCGAGGATAG	0.502													4	2	---	---	---	---	
FLT3	2322	broad.mit.edu	37	13	28642370	28642370	+	Intron	DEL	A	-	-	rs78763053		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28642370delA	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)	CACTGACAGGAAAAAAAAAAC	0.368			Mis|O		AML|ALL								4	2	---	---	---	---	
PAN3	255967	broad.mit.edu	37	13	28834855	28834855	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28834855delT	uc001urz.2	+						PAN3_uc010tdo.1_Intron|PAN3_uc001ury.2_Intron|PAN3_uc001urx.2_Intron	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		GAAACCTGTCTTTTAAAAAAA	0.249													6	7	---	---	---	---	
MTUS2	23281	broad.mit.edu	37	13	29989117	29989117	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29989117delG	uc001usl.3	+							NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						gtttcggtttggggggttttt	0.000													4	2	---	---	---	---	
PDS5B	23047	broad.mit.edu	37	13	33275759	33275760	+	Intron	DEL	AT	-	-	rs36089979	byFrequency	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33275759_33275760delAT	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		agacacacacatatatatatat	0.243													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	33528108	33528108	+	IGR	DEL	A	-	-	rs112783556		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33528108delA								PDS5B (175953 upstream) : KL (62093 downstream)																							TACCAAAGTTAAAAAAAAAAT	0.378													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	35349676	35349676	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35349676delA								RFC3 (808982 upstream) : NBEA (166780 downstream)																							TCGTGCTTCTAAAAAAAACCG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	37041470	37041470	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37041470delT								CCNA1 (24452 upstream) : C13orf36 (206579 downstream)																							ttttttcagattttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	37971450	37971450	+	IGR	DEL	A	-	-	rs112113436		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37971450delA								CSNK1A1L (291649 upstream) : POSTN (165270 downstream)																							tggaaaacagaaaaaaaaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	38071268	38071268	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38071268delG								CSNK1A1L (391467 upstream) : POSTN (65452 downstream)																							atcagatgttggaccctggga	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	40689345	40689345	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40689345delA								COG6 (323543 upstream) : LOC646982 (231928 downstream)																							AAAGCTAGCCAGATGGTGTTG	0.343													4	2	---	---	---	---	
FOXO1	2308	broad.mit.edu	37	13	41117540	41117540	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41117540delA	uc010acc.1	-							NM_002015	NP_002006	Q12778	FOXO1_HUMAN	forkhead box O1						anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|lung(1)|central_nervous_system(1)	948		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		ctttatccataatagtcaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	41359671	41359672	+	IGR	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41359671_41359672insT								MRPS31 (14324 upstream) : SLC25A15 (3875 downstream)																							GCCCTTTTGCCttttttttgag	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	46843347	46843348	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46843347_46843348insA								LCP1 (86888 upstream) : C13orf18 (72791 downstream)																							aaataaatctgaaaaaaaaaaa	0.000													4	3	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	49033658	49033658	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49033658delC	uc001vcb.2	+							NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(6)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	tcataataaaccagtaaacat	0.124		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			22	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	53864873	53864873	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53864873delT								OLFM4 (238687 upstream) : None (None downstream)																							AAAAATTCCATTTAGGAATAA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	58174444	58174445	+	IGR	DEL	TT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58174444_58174445delTT								PRR20B (430092 upstream) : PCDH17 (31344 downstream)																							TGGTATAttctttttttttttc	0.203													4	2	---	---	---	---	
PCDH17	27253	broad.mit.edu	37	13	58228536	58228537	+	Intron	DEL	TT	-	-	rs146806619		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58228536_58228537delTT	uc001vhq.1	+						PCDH17_uc010aec.1_Intron	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		ATTTCTTAAGTTTTTTTTTTCA	0.193													4	2	---	---	---	---	
DIAPH3	81624	broad.mit.edu	37	13	60470677	60470677	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60470677delA	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron|DIAPH3_uc001vhv.2_Intron	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		GATGTTTTATAATATCTCAGG	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	64846625	64846625	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64846625delT								OR7E156P (529924 upstream) : None (None downstream)																							TTGTTGTTTATTTGGGTTTGG	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	66192151	66192151	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66192151delT								None (None upstream) : PCDH9 (684816 downstream)																							AAGTGTTTGATTTTTTTCGAT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71852315	71852315	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71852315delT								None (None upstream) : DACH1 (159783 downstream)																							GTCATTGAAATTTTTTTTGAA	0.328													4	2	---	---	---	---	
DACH1	1602	broad.mit.edu	37	13	72271379	72271379	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72271379delA	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937	Q9UI36	DACH1_HUMAN	dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		ttattaaatgaaAAAAAATGA	0.179													4	2	---	---	---	---	
DACH1	1602	broad.mit.edu	37	13	72287222	72287222	+	Intron	DEL	T	-	-	rs111368443		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72287222delT	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937	Q9UI36	DACH1_HUMAN	dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		tttcttcttcttttttttttt	0.338													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	72540304	72540304	+	IGR	DEL	G	-	-	rs113097594		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72540304delG								DACH1 (98974 upstream) : C13orf37 (742191 downstream)																							TGAGGTTTTTGTTTTTGTTGG	0.403													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	72540310	72540310	+	IGR	DEL	G	-	-	rs61407727		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72540310delG								DACH1 (98980 upstream) : C13orf37 (742185 downstream)																							TTTTGTTTTTGTTGGCATTTT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78063345	78063346	+	IGR	DEL	TT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78063345_78063346delTT								MYCBP2 (162168 upstream) : SCEL (46463 downstream)																							atggttaggattttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78097172	78097172	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78097172delT								MYCBP2 (195995 upstream) : SCEL (12637 downstream)																							TCCTATGGGGTTTTTTTTACC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78569047	78569048	+	Intron	INS	-	T	T	rs4885504	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78569047_78569048insT	uc001vks.2	+						uc001vkt.1_5'Flank					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																		TTTTTTTCTGGTTTTTTTTTGT	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	81905912	81905912	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81905912delC								SPRY2 (990826 upstream) : None (None downstream)																							tgatcaaaatccaaaacactt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	82923866	82923866	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82923866delA								None (None upstream) : None (None downstream)																							gattatgaataaagctgttat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	91852451	91852452	+	IGR	DEL	AC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91852451_91852452delAC								LOC144776 (273600 upstream) : MIR17HG (147622 downstream)																							tgataattatacacacacacac	0.099													4	2	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	93160092	93160092	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93160092delT	uc010tif.1	+							NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				GTTTACCTTATTTTTTTTTGC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	98306170	98306170	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98306170delA								RAP2A (185919 upstream) : IPO5 (299759 downstream)																							ATGAAATTGCAAAATTGTGCT	0.473													4	2	---	---	---	---	
NALCN	259232	broad.mit.edu	37	13	101791956	101791956	+	Intron	DEL	T	-	-	rs71760356		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101791956delT	uc001vox.1	-							NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GGCTGGGTGGTTTTTTTTTTT	0.418													2	4	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102383464	102383464	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102383464delC	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)					CAATGTACAGCAGCAAGAACC	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	104665027	104665028	+	IGR	INS	-	GT	GT	rs137890462	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104665027_104665028insGT								SLC10A2 (945831 upstream) : None (None downstream)																							tctcttggtgcgtgtgtgtgtg	0.198													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106279333	106279334	+	IGR	INS	-	CA	CA	rs149089628	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106279333_106279334insCA								DAOA (135951 upstream) : EFNB2 (862764 downstream)																							TGTAATAATATcacacacacac	0.228													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	109186898	109186898	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109186898delT								TNFSF13B (227534 upstream) : MYO16 (61602 downstream)																							AAAATTGCAGTTTTTTTTTTC	0.388													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112068824	112068824	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112068824delC								C13orf16 (72231 upstream) : SOX1 (653089 downstream)																							AAAGTGCTGACCCCCGGGCCT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20674562	20674562	+	IGR	DEL	G	-	-	rs144285934		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20674562delG								OR11G2 (8032 upstream) : OR11H6 (17307 downstream)																							TATTTAGAGTGGGATGCTCAC	0.353													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26256469	26256469	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26256469delT								STXBP6 (737298 upstream) : NOVA1 (658621 downstream)																							atttaattgatttttttaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26866389	26866389	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26866389delA								None (None upstream) : NOVA1 (48701 downstream)																							TCGGTTCCCCATTCCTGGGCC	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	33379833	33379833	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33379833delT								AKAP6 (77566 upstream) : NPAS3 (28626 downstream)																							TTAGCTAAGCTTTCCTAGACC	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	34507955	34507955	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34507955delT								EGLN3 (87668 upstream) : C14orf147 (394190 downstream)																							ACAGGCAGCCTTTTTTTCCCT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35127091	35127091	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35127091delA								SNX6 (27725 upstream) : CFL2 (52497 downstream)																							cttacatggcaaaagggaatt	0.035													4	2	---	---	---	---	
RALGAPA1	253959	broad.mit.edu	37	14	36221018	36221018	+	Intron	DEL	C	-	-	rs57282578		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36221018delC	uc001wti.2	-						RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron|RALGAPA1_uc001wtk.1_Intron	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						acaacaacaacaaaaaaaaac	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	45162454	45162454	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45162454delA								FSCB (185955 upstream) : C14orf28 (204053 downstream)																							TACACACACCAAAAAAAAAGC	0.249													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	45211142	45211142	+	IGR	DEL	A	-	-	rs77349794		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45211142delA								FSCB (234643 upstream) : C14orf28 (155365 downstream)																							ACTGAGTTTCaaaaaaaaaaa	0.289													2	4	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50061826	50061826	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50061826delT	uc010anj.1	-							NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		ttctccagtcttttttttCCC	0.154													4	2	---	---	---	---	
SOCS4	122809	broad.mit.edu	37	14	55510990	55510991	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55510990_55510991insT	uc001xbo.2	+	3	1796_1797	c.1231_1232insT	c.(1231-1233)ATTfs	p.I411fs	SOCS4_uc001xbp.2_Frame_Shift_Ins_p.I411fs	NM_199421	NP_955453	Q8WXH5	SOCS4_HUMAN	suppressor of cytokine signaling 4	411	SOCS box.				intracellular signal transduction|negative regulation of signal transduction|regulation of growth					ovary(1)|kidney(1)	2						TGCCCTTCCAATTCCTTCTTCT	0.371													187	97	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	55688196	55688197	+	IGR	INS	-	GT	GT	rs147776527	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55688196_55688197insGT								DLGAP5 (29800 upstream) : FBXO34 (49824 downstream)																							tgtgttgtggggtgtgtgtgtg	0.262													4	4	---	---	---	---	
FBXO34	55030	broad.mit.edu	37	14	55811039	55811039	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55811039delT	uc001xbu.2	+						FBXO34_uc010aoo.2_Intron	NM_017943	NP_060413	Q9NWN3	FBX34_HUMAN	F-box only protein 34											ovary(2)|lung(2)|skin(1)	5						TTTTACAGACTTTtttttttt	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	57522104	57522104	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57522104delG								OTX2 (244920 upstream) : EXOC5 (147092 downstream)																							AGACACCCCTGGGGGGAAACA	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	58447368	58447369	+	IGR	INS	-	TAGG	TAGG	rs139643274	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58447368_58447369insTAGG								SLC35F4 (383753 upstream) : C14orf37 (23440 downstream)																							AAGAAAATGGCTGTGTTTGTGT	0.347													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	59602880	59602880	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59602880delG								DACT1 (487844 upstream) : DAAM1 (52519 downstream)																							CCTTTCACCAGGCCCTTCCCA	0.547													4	2	---	---	---	---	
C14orf179	112752	broad.mit.edu	37	14	76485679	76485679	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76485679delT	uc010asm.1	+						C14orf179_uc001xsf.2_Intron|C14orf179_uc010asl.1_Intron|C14orf179_uc001xsg.2_Intron|C14orf179_uc010tve.1_Intron|C14orf179_uc001xse.2_Intron	NM_001102564	NP_001096034	Q96FT9	IFT43_HUMAN	hypothetical protein LOC112752 isoform 2						cilium morphogenesis|intraflagellar retrograde transport						0				BRCA - Breast invasive adenocarcinoma(234;0.0199)		ttctccttcatttttgaataa	0.000													4	2	---	---	---	---	
C14orf145	145508	broad.mit.edu	37	14	81319652	81319652	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81319652delA	uc001xux.2	-						C14orf145_uc001xuz.2_Intron|C14orf145_uc001xuy.1_Intron	NM_152446	NP_689659	Q6ZU80	CE128_HUMAN	hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)		gcaataagataaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	85899918	85899919	+	IGR	INS	-	AC	AC	rs145086436	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85899918_85899919insAC								None (None upstream) : FLRT2 (96569 downstream)																							GATATATGTATacacacacaca	0.277													4	2	---	---	---	---	
FLRT2	23768	broad.mit.edu	37	14	86056601	86056601	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86056601delC	uc001xvr.2	+						FLRT2_uc010atd.2_Intron	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2						cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)		ggcaaaactgccccctttaga	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	87393652	87393652	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87393652delA								None (None upstream) : GALC (910512 downstream)																							CAAGCATTGCAATGGCTTTGT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88166998	88166998	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88166998delT								None (None upstream) : GALC (137166 downstream)																							AGAATCCGGATTTTTTTTTCA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88800181	88800181	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88800181delT								KCNK10 (6925 upstream) : SPATA7 (51831 downstream)																							CGTGTTTAACttttttttttt	0.204													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	90226278	90226278	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90226278delT								FOXN3 (140784 upstream) : C14orf143 (37193 downstream)																							GAGAGTTAGATATATAATTAT	0.343													4	2	---	---	---	---	
BTBD7	55727	broad.mit.edu	37	14	93709547	93709547	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93709547delT	uc001ybo.2	-						BTBD7_uc010aur.2_Intron|BTBD7_uc010two.1_Intron|BTBD7_uc001ybp.2_Intron	NM_001002860	NP_001002860	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7 isoform 1											pancreas(1)	1		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		tctgtttttgttttttttttt	0.119													4	3	---	---	---	---	
KIAA1409	57578	broad.mit.edu	37	14	94115301	94115302	+	Intron	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94115301_94115302delGT	uc001ybv.1	+						KIAA1409_uc001ybs.1_Intron	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578							integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		aagcagcaaggtgtgtgtgtgc	0.015													4	2	---	---	---	---	
PRIMA1	145270	broad.mit.edu	37	14	94200409	94200409	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94200409delT	uc001ybw.1	-						PRIMA1_uc001ybx.1_Intron	NM_178013	NP_821092	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1 precursor						neurotransmitter catabolic process	cell junction|integral to membrane|synapse				large_intestine(1)|skin(1)	2		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		CACAGTCCCCTCTTGTCATTA	0.373													4	2	---	---	---	---	
TRAF3	7187	broad.mit.edu	37	14	103363418	103363418	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103363418delA	uc001ymc.1	+						TRAF3_uc001yme.1_Intron|TRAF3_uc001ymd.1_Intron|TRAF3_uc010txy.1_Intron	NM_145725	NP_663777	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3 isoform 1						apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion	signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		tctagaggggaaaaaaaagaa	0.149													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20446341	20446341	+	IGR	DEL	C	-	-	rs57325753		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20446341delC								None (None upstream) : GOLGA6L6 (290753 downstream)																							tttttcttttctttttttttg	0.129													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20502809	20502809	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20502809delT								None (None upstream) : GOLGA6L6 (234285 downstream)																							TCAGGAACTGTTTTTTAATTA	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20514646	20514648	+	IGR	DEL	ATG	-	-	rs137979527	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20514646_20514648delATG								None (None upstream) : GOLGA6L6 (222446 downstream)																							atgagatgaaatgatgagatgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20555519	20555519	+	IGR	DEL	G	-	-	rs112475595		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20555519delG								None (None upstream) : GOLGA6L6 (181575 downstream)																							AAGAGTGCCCGCCCCTGCCCT	0.662													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20573875	20573875	+	IGR	DEL	A	-	-	rs150151593		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20573875delA								None (None upstream) : GOLGA6L6 (163219 downstream)																							AGAAAAGTGGAAAAAAAAGTC	0.308													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22693374	22693375	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22693374_22693375insA								MIR1268 (180094 upstream) : GOLGA8DP (8910 downstream)																							ttagccacactaaaaaaaaaac	0.000													4	3	---	---	---	---	
TUBGCP5	114791	broad.mit.edu	37	15	22836591	22836591	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22836591delA	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron	NM_052903	NP_443135	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		cacagaacttaaaaaaaaaaa	0.065											OREG0022987	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23940034	23940034	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23940034delC								NDN (7584 upstream) : PWRN2 (469892 downstream)																							aagtgtgtgacccccaacaag	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24520036	24520036	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24520036delA								PWRN2 (104941 upstream) : PWRN1 (258803 downstream)																							tccccagctgaaacttcactt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26256501	26256501	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26256501delA								ATP10A (146184 upstream) : GABRB3 (532194 downstream)																							tatattccttaaattgcatat	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	27883699	27883699	+	IGR	DEL	A	-	-	rs71982160		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27883699delA								GABRG3 (105565 upstream) : OCA2 (116326 downstream)																							caagagaaataaaaaaaacac	0.030													4	2	---	---	---	---	
OCA2	4948	broad.mit.edu	37	15	28200746	28200746	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28200746delT	uc001zbh.3	-						OCA2_uc010ayv.2_Intron	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II						eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		ATGAGGGCACTGAACCTATAC	0.388									Oculocutaneous_Albinism				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	29892150	29892150	+	IGR	DEL	T	-	-	rs111464916		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29892150delT								FAM189A1 (29223 upstream) : TJP1 (100209 downstream)																							TGTCTCTATGTTTTTTTTATT	0.189													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	31036796	31036796	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31036796delT	uc001zev.2	+											Homo sapiens hypothetical LOC440261, mRNA (cDNA clone IMAGE:7479697), complete cds.																		ATATTTTATCTTAAAGGCACC	0.438													4	2	---	---	---	---	
OTUD7A	161725	broad.mit.edu	37	15	31802582	31802582	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31802582delT	uc001zfq.2	-						OTUD7A_uc001zfr.2_Intron	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		gtgtttttgcttttttttttc	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	32494119	32494120	+	Intron	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32494119_32494120insA	uc001zfv.1	-											Homo sapiens cDNA FLJ43588 fis, clone SKNSH2009991.																		tgaagaatgttaaaaaaaaaaa	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	32617841	32617842	+	Intron	INS	-	T	T	rs144109950		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32617841_32617842insT	uc001zfv.1	-											Homo sapiens cDNA FLJ43588 fis, clone SKNSH2009991.																		ctatgaaggtattttttagatg	0.010													5	4	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	33712871	33712871	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33712871delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ttTCCTTCGATTTTTTTTTTA	0.169													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37523782	37523783	+	IGR	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37523782_37523783delTG								MEIS2 (130282 upstream) : TMCO5A (703044 downstream)																							tgtgtgtttatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37650012	37650013	+	IGR	DEL	TT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37650012_37650013delTT								MEIS2 (256512 upstream) : TMCO5A (576814 downstream)																							AAAATCCATATTTTCCCCATTG	0.401													4	2	---	---	---	---	
C15orf54	400360	broad.mit.edu	37	15	39540433	39540435	+	5'Flank	DEL	CTT	-	-	rs72358671		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39540433_39540435delCTT	uc001zkg.2	+							NM_207445	NP_997328	Q8N8G6	CO054_HUMAN	hypothetical protein LOC400360												0		all_cancers(109;5.39e-14)|all_epithelial(112;3.14e-12)|Lung NSC(122;9.74e-10)|all_lung(180;2.23e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;1.19e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0706)		TCCTTGTCTCCTTCATCTTCCTT	0.414													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39765175	39765175	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39765175delA								C15orf54 (218127 upstream) : THBS1 (108105 downstream)																							GTCATCTGGGAATGCTCAGAG	0.507													4	2	---	---	---	---	
EIF2AK4	440275	broad.mit.edu	37	15	40225593	40225594	+	5'Flank	INS	-	G	G	rs138423864	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40225593_40225594insG	uc001zkm.1	+						EIF2AK4_uc001zkl.2_5'Flank	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha						translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		GGAAGGAGGGTGGGGGGGGTCA	0.490													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	42934987	42934987	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42934987delT	uc001zqg.2	+						uc001zqh.2_Intron					Homo sapiens cDNA FLJ16106 fis, clone THYMU1000496, moderately similar to KINESIN-LIKE PROTEIN KIF1C.																		gaaggaccagttttttttGTG	0.030													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	47081439	47081440	+	IGR	DEL	AA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47081439_47081440delAA								None (None upstream) : SEMA6D (394963 downstream)																							ATCATTTAAGAAAAAAAAGACA	0.361													4	2	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	47761539	47761540	+	Intron	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47761539_47761540delGT	uc001zvw.2	+							NM_020858	NP_065909	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		acgcatgtgcgtgtgtgtgtgt	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	48103373	48103373	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48103373delA								SEMA6D (36954 upstream) : SLC24A5 (309796 downstream)																							CTGCTGGCTGAAGGGACAATT	0.473													4	2	---	---	---	---	
FBN1	2200	broad.mit.edu	37	15	48732649	48732649	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48732649delA	uc001zwx.1	-						FBN1_uc010beo.1_Intron	NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor						heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		AGGCCAAGCCAAAGGCACACA	0.443													4	2	---	---	---	---	
FBN1	2200	broad.mit.edu	37	15	48769465	48769465	+	Intron	DEL	T	-	-	rs79034823	byFrequency	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48769465delT	uc001zwx.1	-							NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor						heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		AATTTACAACTTTAGAAAGTG	0.299													4	2	---	---	---	---	
MYO5A	4644	broad.mit.edu	37	15	52602052	52602053	+	3'UTR	DEL	TG	-	-	rs35770130		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52602052_52602053delTG	uc002aby.2	-	41					MYO5A_uc002abx.3_3'UTR|MYO5A_uc010ugd.1_3'UTR	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		tgtgtgtgtatgtgtgtgtgtg	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	53509962	53509962	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53509962delT								ONECUT1 (427753 upstream) : WDR72 (295976 downstream)																							TTATGGTGCCTTCTGCCATTT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	55065650	55065650	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55065650delT								UNC13C (144845 upstream) : RSL24D1 (407871 downstream)																							TGTGTGTGGGTTTTTTTTTTT	0.328													6	3	---	---	---	---	
PRTG	283659	broad.mit.edu	37	15	55946258	55946266	+	Intron	DEL	AAAACTAAT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55946258_55946266delAAAACTAAT	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)		CAAACACTGAAAAACTAATACGAAAGTGA	0.330													2	4	---	---	---	---	
TCF12	6938	broad.mit.edu	37	15	57299347	57299348	+	Intron	INS	-	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57299347_57299348insC	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		GTGAAACATTTCCTCAGTTTCT	0.277			T	TEC	extraskeletal myxoid chondrosarcoma								4	2	---	---	---	---	
GCOM1	145781	broad.mit.edu	37	15	57925426	57925426	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57925426delG	uc002aei.2	+						GCOM1_uc002aej.2_Intron|GCOM1_uc002aek.2_Intron|GCOM1_uc002ael.2_Intron|GCOM1_uc002aem.2_Intron|GCOM1_uc002aeq.2_Intron|GCOM1_uc002aen.2_Intron|GCOM1_uc010bfy.2_Intron|GCOM1_uc002aeo.2_Intron|GCOM1_uc002aep.2_Intron|GCOM1_uc010bfx.2_Intron	NM_001018100	NP_001018110	P0CAP1	GCOM1_HUMAN	GRINL1A upstream protein isoform 7						intracellular signal transduction	extrinsic to internal side of plasma membrane|I band				ovary(1)	1						ATTGCATTATGGGAGAAGGAT	0.413													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	61279525	61279525	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61279525delC	uc002agx.2	-							NM_134261	NP_599023	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						aagacagactccagattatcc	0.114													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	61447223	61447223	+	Intron	DEL	A	-	-	rs34780771		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61447223delA	uc002agx.2	-							NM_134261	NP_599023	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						gtggagttctaatatacagta	0.139													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62609191	62609191	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62609191delA								C2CD4B (151709 upstream) : MGC15885 (320180 downstream)																							atgttgaaacaaaaaaagtta	0.015													4	2	---	---	---	---	
TLE3	7090	broad.mit.edu	37	15	70389205	70389206	+	5'UTR	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70389205_70389206insG	uc002asm.2	-	1					TLE3_uc002ask.2_5'Flank|TLE3_uc002asl.2_5'Flank|TLE3_uc010ukd.1_5'Flank|TLE3_uc010bik.1_Intron|TLE3_uc010bil.1_5'UTR|TLE3_uc002asn.2_5'UTR|TLE3_uc002asp.2_5'UTR|TLE3_uc002aso.2_5'UTR	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						GGTGCGGGGGAGGGGGGAGCCG	0.728													14	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70830947	70830947	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70830947delT								TLE3 (440691 upstream) : UACA (115948 downstream)																							TATTCATCTCTGCCTGGGGTG	0.368													2	5	---	---	---	---	
THSD4	79875	broad.mit.edu	37	15	71633456	71633456	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71633456delT	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2						tctctctcccttttttttttc	0.154													4	2	---	---	---	---	
ARIH1	25820	broad.mit.edu	37	15	72818139	72818139	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72818139delT	uc002aut.3	+							NM_005744	NP_005735	Q9Y4X5	ARI1_HUMAN	ariadne ubiquitin-conjugating enzyme E2 binding						ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding				0						CTCCACATTCTTTTTtttttt	0.095													4	2	---	---	---	---	
C15orf59	388135	broad.mit.edu	37	15	74033240	74033241	+	Intron	DEL	GA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74033240_74033241delGA	uc002avy.2	-							NM_001039614	NP_001034703	Q2T9L4	CO059_HUMAN	hypothetical protein LOC388135											pancreas(1)	1						TGCCCTGGGGGAGAGGGAACTG	0.579													4	2	---	---	---	---	
SCAPER	49855	broad.mit.edu	37	15	76673074	76673074	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76673074delA	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_3'UTR	NM_020843	NP_065894	Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3						TTCCTACATGAAAAAAAAAAT	0.333													4	2	---	---	---	---	
RASGRF1	5923	broad.mit.edu	37	15	79347921	79347922	+	Intron	INS	-	AT	AT			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79347921_79347922insAT	uc002beq.2	-						RASGRF1_uc002bep.2_Intron|RASGRF1_uc010blm.1_Intron|RASGRF1_uc002ber.3_Intron	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine						activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6						GAGacacacacacacacacaca	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79714236	79714236	+	IGR	DEL	G	-	-	rs151203408		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79714236delG								TMED3 (9902 upstream) : KIAA1024 (10622 downstream)																							gcctggtggtgggaacttgcc	0.000													1	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	81836587	81836587	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81836587delA								TMC3 (170169 upstream) : MEX3B (497541 downstream)																							cTACCGTTGTAATGACTTTGG	0.239													4	2	---	---	---	---	
FSD2	123722	broad.mit.edu	37	15	83471234	83471234	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83471234delC	uc002bjd.2	-						FSD2_uc010uol.1_Intron|FSD2_uc010uom.1_Intron	NM_001007122	NP_001007123	A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing											central_nervous_system(1)	1						CCTTCACACTCCTGTATGTCA	0.463													4	2	---	---	---	---	
SH3GL3	6457	broad.mit.edu	37	15	84160416	84160416	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84160416delC	uc002bjw.2	+						SH3GL3_uc010bms.2_Intron|SH3GL3_uc010uot.1_Intron|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						AGAATCGATGCCATCTTCAGA	0.463													4	2	---	---	---	---	
ADAMTSL3	57188	broad.mit.edu	37	15	84582289	84582289	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84582289delT	uc002bjz.3	+						ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)			TTTTTCTTTCTTTTTTTTTTG	0.303													4	2	---	---	---	---	
AKAP13	11214	broad.mit.edu	37	15	86280548	86280548	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86280548delC	uc002blv.1	+						AKAP13_uc002blu.1_Intron|AKAP13_uc002blw.1_Intron|AKAP13_uc002blx.1_Intron	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						CCCCATCCCACCCCCAGGACT	0.403													4	2	---	---	---	---	
KLHL25	64410	broad.mit.edu	37	15	86320282	86320282	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86320282delC	uc002bly.2	-							NM_022480	NP_071925	Q9H0H3	ENC2_HUMAN	BTB/POZ KELCH domain protein							cytoplasm				ovary(2)	2						AACCTCCCAGCCCTCAGCCTC	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87710497	87710498	+	IGR	INS	-	T	T	rs5814279		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87710497_87710498insT								AGBL1 (138214 upstream) : NCRNA00052 (409662 downstream)																							CTGCAAACTGCTTAGATAGGAA	0.406													3	4	---	---	---	---	
SEMA4B	10509	broad.mit.edu	37	15	90767638	90767638	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90767638delA	uc002boy.2	+						SEMA4B_uc002boz.2_Intron|SEMA4B_uc010uqd.1_Intron|SEMA4B_uc002bpa.2_Intron|SEMA4B_uc010bnv.1_Intron	NM_020210	NP_064595			semaphorin 4B precursor											ovary(1)|breast(1)|kidney(1)	3	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			tatacgtgccaaatagtttat	0.134													4	2	---	---	---	---	
PRC1	9055	broad.mit.edu	37	15	91528452	91528452	+	Intron	DEL	T	-	-	rs11357808		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91528452delT	uc002bqm.2	-						PRC1_uc002bqn.2_Intron|PRC1_uc002bqo.2_Intron|PRC1_uc010uqs.1_Intron|PRC1_uc010uqt.1_Intron	NM_003981	NP_003972	O43663	PRC1_HUMAN	protein regulator of cytokinesis 1 isoform 1						cytokinesis|mitotic spindle elongation	cytoplasm|nucleus|spindle microtubule|spindle pole	protein binding			ovary(1)|skin(1)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)					TTTTTTGGTGttttttttttg	0.164													4	2	---	---	---	---	
SLCO3A1	28232	broad.mit.edu	37	15	92414103	92414103	+	Intron	DEL	T	-	-	rs72473667		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92414103delT	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc010boc.1_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)			atctacaatcttttttttttc	0.000													2	4	---	---	---	---	
FAM174B	400451	broad.mit.edu	37	15	93262561	93262562	+	Intron	INS	-	A	A	rs147162297	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93262561_93262562insA	uc002bsl.3	-									Q3ZCQ3	F174B_HUMAN	Homo sapiens cDNA PSEC0264 fis, clone NT2RP3002337.							integral to membrane					0						tacagatgcagaaaaaaacaaa	0.347													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94408604	94408604	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94408604delC	uc002bte.1	-											Homo sapiens cDNA clone IMAGE:5266107.																		TTTCTTCAGTCCCCAGATAGC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95555838	95555838	+	IGR	DEL	A	-	-	rs34516732		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95555838delA								MCTP2 (528658 upstream) : LOC145820 (420484 downstream)																							atgattcaggaaaaaaaaaag	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98721686	98721686	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98721686delT								ARRDC4 (204619 upstream) : FAM169B (258705 downstream)																							CTTTCTTTTGTTTTTTTTTCA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	100094733	100094733	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100094733delT								LRRC28 (167453 upstream) : MEF2A (11400 downstream)																							tatttattccttttttgaatt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	101333134	101333135	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101333134_101333135insA								ASB7 (141232 upstream) : ALDH1A3 (86874 downstream)																							AATTTCTACAgaaaaaaaaata	0.069													4	2	---	---	---	---	
NPRL3	8131	broad.mit.edu	37	16	160308	160308	+	Intron	DEL	A	-	-	rs11316789		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:160308delA	uc002cfr.2	-						NPRL3_uc010uua.1_Intron|NPRL3_uc002cfp.1_Intron|NPRL3_uc002cfq.2_Intron|NPRL3_uc010uub.1_Intron|NPRL3_uc010uuc.1_Intron|NPRL3_uc002cfs.1_Intron	NM_001077350	NP_001070818	Q12980	NPRL3_HUMAN	conserved gene telomeric to alpha globin cluster								protein binding			ovary(1)	1						AAAAATAAACAAAAAAAAACG	0.274													2	4	---	---	---	---	
SOLH	6650	broad.mit.edu	37	16	588295	588295	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:588295delT	uc002chi.2	+						SOLH_uc002chg.2_RNA|SOLH_uc002chh.1_Intron	NM_005632	NP_005623	O75808	CAN15_HUMAN	small optic lobes						proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)	2		Hepatocellular(780;0.00335)				cagagtattgttttttttttt	0.199													4	2	---	---	---	---	
CREBBP	1387	broad.mit.edu	37	16	3837470	3837470	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3837470delC	uc002cvv.2	-						CREBBP_uc002cvw.2_Intron	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a						cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TCCTTGCTGTCCCCCATCCCA	0.517			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	7896795	7896795	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7896795delT								A2BP1 (133455 upstream) : TMEM114 (722708 downstream)																							AGTTGTTTTATTTTTTTTTCT	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8548153	8548153	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8548153delT								A2BP1 (784813 upstream) : TMEM114 (71350 downstream)																							GACATTAGCCTTTTAAAAAGT	0.328													4	2	---	---	---	---	
ATF7IP2	80063	broad.mit.edu	37	16	10542563	10542563	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10542563delT	uc002czu.2	+						ATF7IP2_uc002czv.2_Intron|ATF7IP2_uc010uyo.1_Intron|ATF7IP2_uc010uyp.1_Intron|ATF7IP2_uc002czw.2_Intron|ATF7IP2_uc010uyq.1_Intron	NM_024997	NP_079273	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						tctcaatctattttagatgta	0.000													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12290243	12290244	+	Intron	INS	-	A	A	rs145922360	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12290243_12290244insA	uc002dby.3	+						SNX29_uc010uyx.1_Intron	NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						TTAAGTGCCCTACTCAGAGGCA	0.297													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	13465774	13465774	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13465774delC								SHISA9 (131502 upstream) : ERCC4 (548240 downstream)																							CTCAAACCCACCCAGAGTCAC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	13634051	13634052	+	IGR	DEL	CA	-	-	rs147225114		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13634051_13634052delCA								SHISA9 (299779 upstream) : ERCC4 (379962 downstream)																							CATACATGCCcacacacacaca	0.213													4	2	---	---	---	---	
XYLT1	64131	broad.mit.edu	37	16	17521494	17521494	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17521494delA	uc002dfa.2	-							NM_022166	NP_071449	Q86Y38	XYLT1_HUMAN	xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4						AAGGTTGCCCAAATGTGCACA	0.323													4	2	---	---	---	---	
TMC5	79838	broad.mit.edu	37	16	19455155	19455158	+	Intron	DEL	GTAC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19455155_19455158delGTAC	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1						gaatggatgggtacatggatggat	0.000													6	3	---	---	---	---	
ACSM2A	123876	broad.mit.edu	37	16	20483373	20483374	+	Intron	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20483373_20483374delGT	uc010bwe.2	+						ACSM2A_uc010bwd.1_Intron|ACSM2A_uc010vax.1_Intron|ACSM2A_uc002dhf.3_Intron|ACSM2A_uc002dhg.3_Intron|ACSM2A_uc010vay.1_Intron	NM_001010845	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			skin(2)|breast(1)	3						GCTCTCATGAGTGTGTGTGTGT	0.342													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20621035	20621035	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20621035delT								ACSM2B (33340 upstream) : ACSM1 (13524 downstream)																							GTCAAAAGTATTTTTTTTTTT	0.299													7	4	---	---	---	---	
LOC641298	641298	broad.mit.edu	37	16	22491715	22491716	+	Intron	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22491715_22491716insT	uc010bxf.2	+						LOC641298_uc002dkt.1_5'Flank	NR_027154				Homo sapiens cDNA FLJ54878 complete cds, highly similar to Serine/threonine-protein kinase SMG1 (EC 2.7.11.1).												0						TAAGACTCTGGTTTTTTTTTTC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22654595	22654596	+	IGR	INS	-	GA	GA			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22654595_22654596insGA								LOC653786 (66409 upstream) : HS3ST2 (171264 downstream)																							gagtgagggatgagagagagag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22710281	22710281	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22710281delC								LOC653786 (122095 upstream) : HS3ST2 (115579 downstream)																							Acttccccctccacctttctc	0.085													4	2	---	---	---	---	
EARS2	124454	broad.mit.edu	37	16	23561234	23561234	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23561234delC	uc002dlt.3	-						EARS2_uc002dlr.3_Intron|EARS2_uc002dls.3_Intron|EARS2_uc002dlu.2_Intron	NM_001083614	NP_001077083	Q5JPH6	SYEM_HUMAN	glutamyl-tRNA synthetase 2 precursor						glutamyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|glutamate-tRNA ligase activity|RNA binding				0				GBM - Glioblastoma multiforme(48;0.0353)	L-Glutamic Acid(DB00142)	ccccaggtcaccacggggctg	0.000													4	2	---	---	---	---	
HS3ST4	9951	broad.mit.edu	37	16	25803851	25803851	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25803851delA	uc002dof.2	+							NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)		cagttttgctaaattgtgttt	0.000													4	2	---	---	---	---	
HS3ST4	9951	broad.mit.edu	37	16	25894718	25894719	+	Intron	DEL	AT	-	-	rs149425027	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25894718_25894719delAT	uc002dof.2	+							NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)		AACAAAAAAAATACCCCACACT	0.218													3	3	---	---	---	---	
BCKDK	10295	broad.mit.edu	37	16	31123613	31123614	+	3'UTR	DEL	GA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31123613_31123614delGA	uc002eaw.3	+	12					BCKDK_uc002eav.3_3'UTR|BCKDK_uc010cah.2_RNA|BCKDK_uc010cai.2_3'UTR	NM_005881	NP_005872	O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase						branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation	mitochondrial alpha-ketoglutarate dehydrogenase complex	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|ATP binding|protein binding|protein serine/threonine kinase activity|two-component sensor activity			stomach(1)|breast(1)	2						CTGCTCACCCGACCAGCCTGGG	0.663													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33045448	33045450	+	IGR	DEL	AAT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33045448_33045450delAAT								SLC6A10P (148985 upstream) : MIR1826 (920058 downstream)																							TGGAGAACAGaataatattttta	0.222													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33576631	33576633	+	IGR	DEL	ATG	-	-	rs143259411	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33576631_33576633delATG								SLC6A10P (680168 upstream) : MIR1826 (388875 downstream)																							atgaaatgaaatgatgaaatgat	0.000													4	2	---	---	---	---	
NKD1	85407	broad.mit.edu	37	16	50633819	50633819	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50633819delT	uc002egg.1	+							NM_033119	NP_149110	Q969G9	NKD1_HUMAN	naked cuticle homolog 1						Wnt receptor signaling pathway	cytoplasm|plasma membrane	calcium ion binding|protein binding				0		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		GTGTTTTGGGTTTTTTTTCCC	0.453													4	2	---	---	---	---	
RBL2	5934	broad.mit.edu	37	16	53481212	53481213	+	Intron	INS	-	TTCTCTTA	TTCTCTTA	rs147359000	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53481212_53481213insTTCTCTTA	uc002ehi.3	+						RBL2_uc010vgv.1_Intron|RBL2_uc002ehj.2_Intron|RBL2_uc010vgw.1_5'Flank	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)						cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						ATATCCAAATCTTCTCTTATTA	0.282													7	6	---	---	---	---	
CIAPIN1	57019	broad.mit.edu	37	16	57462928	57462928	+	3'UTR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57462928delC	uc002ell.1	-	9					CIAPIN1_uc002elk.1_RNA|CIAPIN1_uc002elm.1_3'UTR|CIAPIN1_uc002eln.1_3'UTR|CIAPIN1_uc010cda.1_3'UTR|CIAPIN1_uc002elo.1_3'UTR	NM_020313	NP_064709	Q6FI81	CPIN1_HUMAN	cytokine induced apoptosis inhibitor 1						anti-apoptosis|apoptosis	cytoplasm|nucleolus					0						CACCACTGTGCCCCCCAGCCA	0.512													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	60030337	60030337	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60030337delT								None (None upstream) : None (None downstream)																							gacttttacatttttaaggca	0.129													4	2	---	---	---	---	
PRMT7	54496	broad.mit.edu	37	16	68374883	68374884	+	Intron	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68374883_68374884insA	uc002evy.1	+						PRMT7_uc002evx.1_Intron|PRMT7_uc010vlg.1_Intron|PRMT7_uc002evz.1_Intron	NM_019023	NP_061896	Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7						cell differentiation|DNA methylation involved in gamete generation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|spliceosomal snRNP assembly|transcription, DNA-dependent	cytosol|nucleus	[myelin basic protein]-arginine N-methyltransferase activity|histone methyltransferase activity (H4-R3 specific)|protein-arginine omega-N monomethyltransferase activity|protein-arginine omega-N symmetric methyltransferase activity|ribonucleoprotein binding				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		CTGGTGTTAGTAAAAATAGGAA	0.238													4	2	---	---	---	---	
DDX19A	55308	broad.mit.edu	37	16	70351678	70351678	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70351678delA	uc002eys.2	+						DDX19B_uc010vly.1_Intron|DDX19B_uc010vlv.1_Intron|DDX19B_uc010vlw.1_Intron|DDX19B_uc002eyo.2_Intron|DDX19B_uc002eyp.2_Intron|DDX19B_uc002eyq.2_Intron|DDX19B_uc002eyr.2_Intron|DDX19B_uc010vlx.1_Intron|uc002eyt.2_Intron	NM_007242	NP_009173	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform						mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)				ctgtctcaacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ZFHX3	463	broad.mit.edu	37	16	72896736	72896736	+	Intron	DEL	A	-	-	rs79473866	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72896736delA	uc002fck.2	-						ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A						muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				gcaaggaaggaaaaaaaaaag	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77283549	77283549	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77283549delT								SYCE1L (36573 upstream) : ADAMTS18 (32477 downstream)																							GGGGTGTATATTTCCTGGAGA	0.363													4	2	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	78173916	78173916	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78173916delC	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron|WWOX_uc002ffj.1_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		tgtgcaagtgccaagcaggtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87981003	87981003	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87981003delT								CA5A (10891 upstream) : BANP (3235 downstream)																							tggacttttctttttttttga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88211068	88211069	+	IGR	DEL	TA	-	-	rs113456699		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88211068_88211069delTA								BANP (100145 upstream) : ZNF469 (282810 downstream)																							ATCAGGATATTAGTTATATTTG	0.490													4	2	---	---	---	---	
C16orf55	124045	broad.mit.edu	37	16	89736114	89736114	+	3'UTR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89736114delC	uc002fnw.1	+	3					C16orf55_uc010vpk.1_3'UTR|C16orf55_uc002fny.1_RNA	NM_153025	NP_694570	Q96N06	CP055_HUMAN	hypothetical protein LOC124045												0		all_lung(18;0.000665)|all_hematologic(23;0.0355)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		GAAGCCGTGGCCCCCTTCTCC	0.677													5	3	---	---	---	---	
NXN	64359	broad.mit.edu	37	17	814235	814235	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:814235delT	uc002fsa.2	-							NM_022463	NP_071908	Q6DKJ4	NXN_HUMAN	nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		CTTTTTTAGCTTTTTTTTAAA	0.428													4	2	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2786878	2786878	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2786878delT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						tcctgttttctttttttttcC	0.284													4	2	---	---	---	---	
SPATA22	84690	broad.mit.edu	37	17	3378542	3378543	+	Intron	INS	-	C	C			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3378542_3378543insC	uc010vrg.1	-						ASPA_uc010ckg.2_Intron|ASPA_uc002fvq.2_5'Flank	NM_032598	NP_115987	Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22												0						CCCTAATAAGACCCCTTTTTGA	0.426													4	2	---	---	---	---	
MINK1	50488	broad.mit.edu	37	17	4763780	4763783	+	Intron	DEL	AATC	-	-	rs147930934		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4763780_4763783delAATC	uc010vsl.1	+						MINK1_uc010vsk.1_Intron|MINK1_uc010vsm.1_Intron|MINK1_uc010vsn.1_Intron|MINK1_uc010vso.1_Intron	NM_153827	NP_722549	Q8N4C8	MINK1_HUMAN	misshapen-like kinase 1 isoform 3						JNK cascade	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)|skin(1)	6						CTTGGGAAATAATCAAACCCTTTG	0.431													1	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	7871410	7871411	+	IGR	DEL	AC	-	-	rs66958109		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7871410_7871411delAC								CNTROB (18515 upstream) : GUCY2D (34577 downstream)																							tctcactccaacacacacacac	0.094													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	8203694	8203696	+	IGR	DEL	TCC	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8203694_8203696delTCC								SLC25A35 (5524 upstream) : ARHGEF15 (9894 downstream)																							ctttcttctttcctcctcctcct	0.000													4	2	---	---	---	---	
PIK3R6	146850	broad.mit.edu	37	17	8732683	8732684	+	Intron	DEL	AT	-	-	rs149430519		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8732683_8732684delAT	uc002glq.1	-						PIK3R6_uc002glr.1_Intron|PIK3R6_uc002gls.1_Intron	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6						platelet activation	cytosol					0						acacacacacatgcatggatac	0.000													3	3	---	---	---	---	
WDR16	146845	broad.mit.edu	37	17	9487916	9487917	+	Intron	INS	-	TCAAATATAC	TCAAATATAC	rs151267827	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9487916_9487917insTCAAATATAC	uc002gly.2	+						WDR16_uc002glz.2_Intron|WDR16_uc010coc.2_Intron	NM_145054	NP_659491	Q8N1V2	WDR16_HUMAN	WD40-repeat protein upregulated in HCC isoform							cytoplasm|intracellular membrane-bounded organelle	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4						tttagcagattaatgcagtatt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	12502672	12502672	+	Intron	DEL	A	-	-	rs12452207	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12502672delA	uc002gnl.1	+						uc002gnm.1_Intron					Homo sapiens cDNA FLJ34690 fis, clone MESAN2000894.																		GTCATTGTAGAAAAAAAAATC	0.274													4	2	---	---	---	---	
CYTSB	92521	broad.mit.edu	37	17	20174786	20174786	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20174786delT	uc002gwq.2	+						CYTSB_uc002gws.2_Intron|CYTSB_uc002gwv.2_Intron|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gww.2_Intron	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0						cagctttttcttttacacaac	0.000													4	2	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21211921	21211921	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21211921delT	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		tcaattaaaattttttttttt	0.363													4	2	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21311305	21311306	+	Intron	INS	-	C	C	rs145540266		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21311305_21311306insC	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	cacccatccatcatccatccat	0.134										Prostate(3;0.18)			6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25301871	25301871	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25301871delA								None (None upstream) : WSB1 (319235 downstream)																							CTGAGAGTCTAAAAAAATAAA	0.353													5	3	---	---	---	---	
UTP6	55813	broad.mit.edu	37	17	30212964	30212964	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30212964delT	uc002hgr.2	-						UTP6_uc002hgq.2_Intron|UTP6_uc010cst.2_Intron|UTP6_uc010wbw.1_Intron	NM_018428	NP_060898	Q9NYH9	UTP6_HUMAN	hepatocellular carcinoma-associated antigen 66						rRNA processing	nucleolus	binding			ovary(1)	1		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				AATGTTTCACTTTCCTACCAA	0.318													110	62	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	34444257	34444257	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34444257delA								CCL4 (11243 upstream) : TBC1D3B (48804 downstream)																							tttgttgtgcaaaaaaaaatg	0.139													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	38274412	38274412	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38274412delG								NR1D1 (17439 upstream) : MSL1 (4378 downstream)																							acattgtagtgggggaggata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39114595	39114595	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39114595delG								KRT23 (20759 upstream) : KRT39 (74 downstream)																							CCATCTTCCTGGGTGCTTACA	0.443													4	2	---	---	---	---	
OSBPL7	114881	broad.mit.edu	37	17	45895345	45895345	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45895345delT	uc002ilx.1	-						OSBPL7_uc002ilw.1_5'Flank	NM_145798	NP_665741	Q9BZF2	OSBL7_HUMAN	oxysterol-binding protein-like protein 7						lipid transport		lipid binding				0						AGCACACCCCTTCCCTGGCGC	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	45922192	45922192	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45922192delC								SCRN2 (3493 upstream) : SP6 (88 downstream)																							GAAGCATCCACCCCACTCTGT	0.542											OREG0024503	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SKAP1	8631	broad.mit.edu	37	17	46408187	46408187	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46408187delA	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						CAGGGGGCGGAAAAAAAAAAA	0.428													3	3	---	---	---	---	
SKAP1	8631	broad.mit.edu	37	17	46467828	46467828	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46467828delA	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0						TTCACGTATTAAAAAAAAAGG	0.353													3	3	---	---	---	---	
C17orf93	360205	broad.mit.edu	37	17	46801384	46801385	+	Intron	DEL	TA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46801384_46801385delTA	uc002inz.1	+						PRAC_uc002iny.2_5'Flank	NR_024103				Homo sapiens PRAC2 mRNA, partial sequence.												0						TTTTCCGGAGTATATGTGTGTG	0.500											OREG0024525	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	17	47960847	47960848	+	IGR	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47960847_47960848delTG								TAC4 (35468 upstream) : DLX4 (85714 downstream)																							GTGGTCACTCTGTGTGTGTGTG	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	50355472	50355472	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50355472delA								CA10 (118095 upstream) : None (None downstream)																							agaataggagaaaaaaaaacc	0.000													4	2	---	---	---	---	
DDX5	1655	broad.mit.edu	37	17	62495653	62495653	+	3'UTR	DEL	C	-	-	rs60647527		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62495653delC	uc002jek.2	-	13					POLG2_uc002jei.2_5'Flank|POLG2_uc010deg.1_5'Flank|DDX5_uc010deh.2_3'UTR|DDX5_uc002jej.2_3'UTR|DDX5_uc010wqa.1_3'UTR	NM_004396	NP_004387	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5						cell growth|regulation of alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA helicase activity|transcription cofactor activity			ovary(2)|lung(1)	3	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			Aaaaaaaaaaccaaacaaaaa	0.264			T	ETV4	prostate								4	3	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	63828537	63828538	+	Intron	DEL	AA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63828537_63828538delAA	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			tgttttttggaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ABCA5	23461	broad.mit.edu	37	17	67310577	67310577	+	5'UTR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67310577delA	uc002jif.2	-	1					ABCA5_uc002jig.2_Intron|ABCA5_uc002jih.2_Intron|ABCA5_uc010dfe.2_Intron	NM_018672	NP_061142	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5						cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)					TAAACCTATTAAAGAGGAAAA	0.313													266	122	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76618042	76618043	+	IGR	INS	-	C	C	rs144900632	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76618042_76618043insC								DNAH17 (149186 upstream) : CYTH1 (52088 downstream)																							ACCTCCCCAGGCCAGGATGCCC	0.619													4	2	---	---	---	---	
CARD14	79092	broad.mit.edu	37	17	78172745	78172745	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78172745delT	uc002jxw.1	+						CARD14_uc002jxt.1_Intron|CARD14_uc002jxv.2_Intron|CARD14_uc010wud.1_Intron	NM_024110	NP_077015	Q9BXL6	CAR14_HUMAN	caspase recruitment domain protein 14 isoform 1						activation of NF-kappaB-inducing kinase activity|positive regulation of protein phosphorylation|regulation of apoptosis	aggresome|cytoplasm|plasma membrane	CARD domain binding			ovary(4)|skin(1)	5	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			Cttttctttctttttttttgt	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	78281802	78281802	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78281802delT	uc002jyf.2	+						uc002jyg.1_Intron	NM_020954	NP_066005			hypothetical protein LOC57714																		GCGTTCTGCATTTTTTTAATA	0.343													4	2	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78840306	78840306	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78840306delT	uc002jyt.1	+						RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						gaacaaaacatttttttaaaa	0.000													4	2	---	---	---	---	
COLEC12	81035	broad.mit.edu	37	18	408485	408486	+	Intron	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:408485_408486insA	uc002kkm.2	-							NM_130386	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12						carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				TTCATAAACAGAAAAAAAAATG	0.332													5	3	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3903856	3903856	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3903856delA	uc010wyz.1	-							NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				AGCAATATTGAAATGGCAAAG	0.358													4	2	---	---	---	---	
EPB41L3	23136	broad.mit.edu	37	18	5466782	5466782	+	Intron	DEL	T	-	-	rs71368795		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5466782delT	uc002kmt.1	-						EPB41L3_uc010wzh.1_Intron|EPB41L3_uc002kmu.1_Intron|EPB41L3_uc010dkq.1_Intron|EPB41L3_uc010dks.1_Intron|EPB41L3_uc002kmv.1_Intron	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						ATGTAGAAACTTTTCCTAGGA	0.383													4	2	---	---	---	---	
PTPRM	5797	broad.mit.edu	37	18	8356206	8356225	+	Intron	DEL	AAGCTTAGCTCTGCAGGGAA	-	-	rs35185651		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8356206_8356225delAAGCTTAGCTCTGCAGGGAA	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)				GACTTGACAGAAGCTTAGCTCTGCAGGGAAAAGAGAGGAG	0.445													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	8542713	8542713	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8542713delG								PTPRM (135855 upstream) : RAB12 (66722 downstream)																							CCCTAAGTGTGGCACATGAAG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	8960466	8960466	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8960466delC								KIAA0802 (127691 upstream) : NDUFV2 (142209 downstream)																							gcctcggcctcccaaagtgct	0.100													4	2	---	---	---	---	
RAB31	11031	broad.mit.edu	37	18	9752099	9752100	+	Intron	INS	-	AT	AT			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9752099_9752100insAT	uc002kog.2	+							NM_006868	NP_006859	Q13636	RAB31_HUMAN	RAB31, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			skin(1)	1						AGCCTCTACTCATACAGCTTTG	0.530													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14184631	14184631	+	3'UTR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14184631delT	uc010xag.1	+	3					uc002ksv.1_Intron					RecName: Full=Putative ankyrin repeat domain-containing protein 20A5;																		CTATGAAGAGTTTTTTTTTTC	0.363													4	2	---	---	---	---	
ROCK1	6093	broad.mit.edu	37	18	18611105	18611105	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18611105delG	uc002kte.2	-							NM_005406	NP_005397	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein						actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)					cgcaagccctgggggaaagag	0.000													4	3	---	---	---	---	
ESCO1	114799	broad.mit.edu	37	18	19113137	19113137	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19113137delA	uc002kth.1	-						ESCO1_uc002kti.1_Intron	NM_052911	NP_443143	Q5FWF5	ESCO1_HUMAN	establishment of cohesion 1 homolog 1						cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding				0						CAATCTCTTTAAAAAAAAAAT	0.313													4	2	---	---	---	---	
CABLES1	91768	broad.mit.edu	37	18	20758177	20758178	+	Intron	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20758177_20758178insT	uc002kuc.2	+						CABLES1_uc002kub.2_Intron|CABLES1_uc002kud.2_Intron	NM_001100619	NP_001094089	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1 isoform 2						blood coagulation|cell cycle|cell division|regulation of cell cycle|regulation of cell division	cytosol|nucleus	cyclin-dependent protein kinase regulator activity|protein binding			breast(1)	1	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TCGGATCCTGATTTTTTTTTTT	0.495													4	2	---	---	---	---	
C18orf45	85019	broad.mit.edu	37	18	20916966	20916967	+	Intron	INS	-	GT	GT	rs145502809	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20916966_20916967insGT	uc002kuf.2	-						C18orf45_uc010xaq.1_Intron|C18orf45_uc010xar.1_Intron|C18orf45_uc002kug.2_Intron|C18orf45_uc002kuh.2_Intron	NM_032933	NP_116322	Q24JQ0	CR045_HUMAN	hypothetical protein LOC85019							integral to membrane					0	all_cancers(21;0.000238)|all_epithelial(16;5.29e-06)|Lung NSC(20;0.00925)|Colorectal(14;0.0202)|all_lung(20;0.0255)|Ovarian(20;0.127)					TTTCCCCTGTAgtgtgtgtgtg	0.327													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	22205511	22205511	+	5'Flank	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22205511delG	uc002kvj.1	+											Homo sapiens cDNA FLJ42358 fis, clone UTERU2023262.																		TGAGCTCCAAGGGATGCTTGG	0.448													4	2	---	---	---	---	
ZNF521	25925	broad.mit.edu	37	18	22869970	22869970	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22869970delA	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					AATACAGTGCAAAAAAAAGAC	0.299			T	PAX5	ALL								4	2	---	---	---	---	
ZNF521	25925	broad.mit.edu	37	18	22930508	22930509	+	Intron	DEL	AG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22930508_22930509delAG	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					AACACACAACAGAAACTTTTTC	0.361			T	PAX5	ALL								4	2	---	---	---	---	
KCTD1	284252	broad.mit.edu	37	18	24142940	24142940	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24142940delA	uc010xbk.1	-							NM_198991	NP_945342	Q719H9	KCTD1_HUMAN	potassium channel tetramerisation domain						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|voltage-gated potassium channel complex	transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity			ovary(1)	1	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			atttgggaggaacacagttcc	0.209													4	2	---	---	---	---	
CDH2	1000	broad.mit.edu	37	18	25546844	25546844	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25546844delA	uc002kwg.2	-						CDH2_uc010xbn.1_Intron	NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4						AGTTCCCACTAAAAAAAAAGT	0.368													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	30142181	30142182	+	IGR	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30142181_30142182insA								WBP11P1 (47585 upstream) : KLHL14 (110452 downstream)																							ATATTATTTTGAAAAAAAACCC	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	30230147	30230147	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30230147delT								WBP11P1 (135551 upstream) : KLHL14 (22487 downstream)																							tactttttaattttttttcaa	0.000													4	2	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34121528	34121528	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34121528delT	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron|FHOD3_uc002kzu.1_5'Flank	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				TATACATTTATTTTTTTGCTT	0.154													4	2	---	---	---	---	
CELF4	56853	broad.mit.edu	37	18	35145787	35145788	+	5'UTR	DEL	CG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35145787_35145788delCG	uc002lae.2	-	1					CELF4_uc010dnd.1_5'UTR|CELF4_uc002lag.2_5'UTR|CELF4_uc002laf.2_5'UTR|CELF4_uc002lai.2_5'UTR	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						ctcgctcgctcgcgctcgcgct	0.168													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	37470878	37470878	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37470878delT								LOC647946 (90596 upstream) : None (None downstream)																							aatgcttgtgtttttttctgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	37745343	37745344	+	IGR	INS	-	T	T	rs150821642	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37745343_37745344insT								LOC647946 (365061 upstream) : None (None downstream)																							gtccttttttcttttttttaca	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38505653	38505654	+	IGR	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38505653_38505654delTG								None (None upstream) : KC6 (554584 downstream)																							tgtgtgtgcatgtgtgtgtgtg	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	41193637	41193638	+	IGR	INS	-	T	T	rs144697604	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41193637_41193638insT								SYT4 (336022 upstream) : None (None downstream)																							gagccaaaggattttttttttc	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	42063664	42063664	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42063664delA	uc002lax.3	-											Homo sapiens cDNA clone IMAGE:5265929.																		gtcttgaaagaaaaaaaaatt	0.000													6	3	---	---	---	---	
SETBP1	26040	broad.mit.edu	37	18	42641988	42641989	+	Intron	DEL	TG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42641988_42641989delTG	uc010dni.2	+							NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		tgtgcccatttgtgtgtgtgtg	0.366									Schinzel-Giedion_syndrome				6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	43263723	43263723	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43263723delC								SLC14A2 (665 upstream) : SLC14A1 (40369 downstream)																							GAGGGGTTTTCCATGGTCAAG	0.433													4	2	---	---	---	---	
HAUS1	115106	broad.mit.edu	37	18	43702865	43702865	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43702865delT	uc002lbu.2	+						HAUS1_uc002lbv.2_Intron	NM_138443	NP_612452	Q96CS2	HAUS1_HUMAN	coiled-coil domain containing 5						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole				ovary(1)	1						GTAGCTCCTCTTTACTGTGTT	0.209													4	2	---	---	---	---	
KIAA0427	9811	broad.mit.edu	37	18	46372815	46372818	+	Intron	DEL	TGGA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46372815_46372818delTGGA	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron|KIAA0427_uc002lde.3_Intron	NM_014772	NP_055587	O43310	CTIF_HUMAN	hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0						TGTTGCCGAGtggatggatggatg	0.167													2	5	---	---	---	---	
KIAA0427	9811	broad.mit.edu	37	18	46372868	46372869	+	Intron	INS	-	GATG	GATG	rs58256324		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46372868_46372869insGATG	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron|KIAA0427_uc002lde.3_Intron	NM_014772	NP_055587	O43310	CTIF_HUMAN	hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0						atgaaaggatagatggatggat	0.079													4	2	---	---	---	---	
DYM	54808	broad.mit.edu	37	18	46865423	46865424	+	Intron	INS	-	A	A	rs144426917	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46865423_46865424insA	uc002ldi.1	-						DYM_uc010xdf.1_Intron	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin							Golgi apparatus					0						aactctgctagaaaaaaaaaat	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	48050101	48050101	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48050101delC								SKA1 (129567 upstream) : MAPK4 (36383 downstream)																							TGGTGTAATTCCATGGACAGA	0.468													4	2	---	---	---	---	
MAPK4	5596	broad.mit.edu	37	18	48176768	48176768	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48176768delG	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)		cccCTAGCCTGGGCCTGCACC	0.318													4	2	---	---	---	---	
ME2	4200	broad.mit.edu	37	18	48462244	48462244	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48462244delA	uc002ley.2	+						ME2_uc010dpd.2_Intron	NM_002396	NP_002387	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial						malate metabolic process	mitochondrial matrix	electron carrier activity|malate dehydrogenase (decarboxylating) activity|malate dehydrogenase (oxaloacetate-decarboxylating) activity|metal ion binding|NAD binding				0		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)	NADH(DB00157)	gaccaaaaagaaaaaaaaata	0.000													3	3	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50157019	50157019	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50157019delT	uc002lfe.1	+							NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GACGGTGAGATTTTTTTTTTT	0.373													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	52285936	52285936	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52285936delC								C18orf26 (19212 upstream) : RAB27B (209904 downstream)																							tttgcagacacaaaaaacacg	0.169													4	2	---	---	---	---	
TCF4	6925	broad.mit.edu	37	18	53194385	53194385	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53194385delC	uc002lfz.2	-						TCF4_uc010xdx.1_Intron|TCF4_uc010dph.1_Intron|TCF4_uc010xdy.1_Intron|TCF4_uc002lga.2_Intron|TCF4_uc010dpi.2_Intron	NM_003199	NP_003190	P15884	ITF2_HUMAN	transcription factor 4 isoform b						positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GTCTGCAAAGCCCACCACAAA	0.468													4	2	---	---	---	---	
ONECUT2	9480	broad.mit.edu	37	18	55115667	55115668	+	Intron	INS	-	A	A			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55115667_55115668insA	uc002lgo.2	+							NM_004852	NP_004843	O95948	ONEC2_HUMAN	one cut domain, family member 2						organ morphogenesis	nucleus	sequence-specific DNA binding			ovary(2)|central_nervous_system(1)	3		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		ATTTGATGTTGAAAAAAATTGT	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	56318734	56318734	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56318734delT								ALPK2 (22545 upstream) : MALT1 (19884 downstream)																							ctatgatttcttttttttttt	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57469274	57469274	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57469274delG								CCBE1 (104630 upstream) : PMAIP1 (97918 downstream)																							Tctatcaggtggtatgttaca	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58554234	58554234	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58554234delT								MC4R (514233 upstream) : CDH20 (446754 downstream)																							TTCTCAATGCTTTAAGTCTTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62860795	62860795	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62860795delC								None (None upstream) : CDH7 (556693 downstream)																							TAAGGAAAGTCATATCTGATT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	63701953	63701953	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63701953delC								CDH7 (153779 upstream) : CDH19 (469368 downstream)																							ataaaagtctccagtctccag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65042307	65042307	+	IGR	DEL	T	-	-	rs75002100		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65042307delT								CDH19 (771091 upstream) : DSEL (131512 downstream)																							gtcttcttcattttttttttt	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65531519	65531520	+	IGR	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65531519_65531520delGT								DSEL (347552 upstream) : TMX3 (809407 downstream)																							gtgtgtgtgcgtgtgtgtgtgt	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65623022	65623022	+	IGR	DEL	A	-	-	rs77732978		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65623022delA								DSEL (439055 upstream) : TMX3 (717905 downstream)																							AAGCTATTAGAAAAAAAATGG	0.328													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65994935	65994935	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65994935delT								DSEL (810968 upstream) : TMX3 (345992 downstream)																							AGCAAATGTATTTAATATGCC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	66200208	66200212	+	IGR	DEL	ACATA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66200208_66200212delACATA								None (None upstream) : TMX3 (140715 downstream)																							TGTGTTTTTTACATAAATACAAGcc	0.220													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	67029331	67029331	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67029331delT								CCDC102B (306905 upstream) : DOK6 (38960 downstream)																							attaaactacttttttttttc	0.090													5	3	---	---	---	---	
SOCS6	9306	broad.mit.edu	37	18	67979561	67979561	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67979561delT	uc002lkr.1	+						SOCS6_uc010dqq.2_5'Flank	NM_004232	NP_004223	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6						defense response|JAK-STAT cascade|negative regulation of signal transduction|regulation of growth	cytoplasm				large_intestine(1)|lung(1)	2		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				TTTTGTTTTGTTTTTTTTTCA	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68221708	68221708	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68221708delA								SOCS6 (224274 upstream) : None (None downstream)																							ATTTTTAGTGAAAAAAAAAGT	0.308													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68436724	68436724	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68436724delA								SOCS6 (439290 upstream) : None (None downstream)																							taaattaaataaaaaaaaAAA	0.134													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68456274	68456275	+	IGR	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68456274_68456275delGT								SOCS6 (458840 upstream) : None (None downstream)																							ACTAGTAATAGTGTGTGTGTGT	0.302													4	2	---	---	---	---	
MBP	4155	broad.mit.edu	37	18	74802348	74802348	+	Intron	DEL	T	-	-	rs138753422		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74802348delT	uc010xfd.1	-						MBP_uc002lmr.2_Intron	NM_001025101	NP_001020272	P02686	MBP_HUMAN	Golli-mbp isoform 1						central nervous system development|immune response|synaptic transmission	plasma membrane	structural constituent of myelin sheath			haematopoietic_and_lymphoid_tissue(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)		ggatccatgctttcaccagct	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76007917	76007917	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76007917delA								None (None upstream) : SALL3 (732358 downstream)																							ATTATTCTAGAAAAAAAAAAG	0.413													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76774721	76774722	+	IGR	INS	-	A	A	rs138638914		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76774721_76774722insA								SALL3 (16530 upstream) : ATP9B (54675 downstream)																							GATCAGTTCCCCCCTTACTACT	0.485													4	2	---	---	---	---	
SPPL2B	56928	broad.mit.edu	37	19	2350159	2350160	+	Intron	DEL	CG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2350159_2350160delCG	uc002lvs.2	+						SPPL2B_uc002lvr.2_Intron	NM_152988	NP_694533	Q8TCT7	PSL1_HUMAN	signal peptide peptidase-like 2B isoform 2							Golgi membrane|integral to membrane	aspartic-type endopeptidase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACACACTCACGCGCTCTCATT	0.520													4	2	---	---	---	---	
VAV1	7409	broad.mit.edu	37	19	6835862	6835862	+	Intron	DEL	T	-	-	rs75839924		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6835862delT	uc002mfu.1	+						VAV1_uc010xjh.1_Intron|VAV1_uc010dva.1_Intron|VAV1_uc002mfv.1_Intron	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16						tttgaaggactttttttttgt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29977539	29977539	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29977539delC	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		TGCTCAGGTTCCCATTTCATT	0.279													4	2	---	---	---	---	
CATSPERG	57828	broad.mit.edu	37	19	38851361	38851361	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38851361delC	uc002oih.3	+						CATSPERG_uc002oig.3_Intron|CATSPERG_uc002oif.3_Intron|CATSPERG_uc010efw.2_Intron	NM_021185	NP_067008	Q6ZRH7	CTSRG_HUMAN	cation channel, sperm-associated, gamma						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(1)|skin(1)	2						GCCCTGCCTTCCCCCTGCAGC	0.612													14	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42327060	42327060	+	IGR	DEL	A	-	-	rs34576342		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42327060delA								CEACAM3 (11469 upstream) : LYPD4 (14090 downstream)																							ccacaaaagtaaaaaaaaaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	45231304	45231304	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45231304delT								CEACAM16 (17320 upstream) : BCL3 (20674 downstream)																							cttcctatgctccatctccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	46930887	46930887	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46930887delT								CCDC8 (13968 upstream) : PNMAL1 (38862 downstream)																							CCACCCTCCCTTGCATTACCC	0.522													4	2	---	---	---	---	
PLA2G4C	8605	broad.mit.edu	37	19	48591632	48591632	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48591632delA	uc002phx.2	-						PLA2G4C_uc002phw.2_Intron|PLA2G4C_uc010elr.2_Intron|PLA2G4C_uc010xzd.1_Intron	NM_003706	NP_003697	Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC isoform 1 precursor						arachidonic acid metabolic process|glycerophospholipid catabolic process|inflammatory response|intracellular signal transduction|parturition	cytosol|membrane	calcium-independent phospholipase A2 activity|phospholipid binding			ovary(1)|skin(1)	2		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		cggaaaaaagaaaaaaaaaac	0.000													2	4	---	---	---	---	
ZNF808	388558	broad.mit.edu	37	19	53035995	53035996	+	Intron	INS	-	GCC	GCC	rs77897069		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53035995_53035996insGCC	uc010epq.1	+						ZNF808_uc002pzq.2_Intron	NM_001039886	NP_001034975	Q8N4W9	ZN808_HUMAN	zinc finger protein 808						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		GTAAAGTATTTATTAAGTATTT	0.307													3	3	---	---	---	---	
ZNF808	388558	broad.mit.edu	37	19	53035999	53036001	+	Intron	DEL	AAG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53035999_53036001delAAG	uc010epq.1	+						ZNF808_uc002pzq.2_Intron	NM_001039886	NP_001034975	Q8N4W9	ZN808_HUMAN	zinc finger protein 808						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		AGTATTTATTAAGTATTTATTAA	0.305													3	3	---	---	---	---	
ZNF845	91664	broad.mit.edu	37	19	53835689	53835690	+	5'Flank	DEL	CC	-	-	rs74723251		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53835689_53835690delCC	uc010ydv.1	+						ZNF845_uc010ydw.1_5'Flank	NM_138374	NP_612383	Q96IR2	ZN845_HUMAN	zinc finger protein 845						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						agcttaataacccccatggatg	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	126653	126653	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:126653delT								DEFB126 (262 upstream) : DEFB127 (11533 downstream)																							cagaaacacctggagagatgg	0.159													4	2	---	---	---	---	
SIRPB2	284759	broad.mit.edu	37	20	1457133	1457133	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1457133delC	uc002wfg.2	-						SIRPB2_uc002wfh.3_Intron	NM_001122962	NP_001116434	Q5JXA9	SIRB2_HUMAN	signal-regulatory protein beta 2 isoform 1							integral to membrane					0						TCAAAGACCACCCTTCCCTCT	0.502													4	3	---	---	---	---	
UBOX5	22888	broad.mit.edu	37	20	3110095	3110095	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3110095delA	uc002whw.2	-						uc002whv.1_Intron|UBOX5_uc002whx.2_Intron|UBOX5_uc002why.1_Intron	NM_014948	NP_055763	O94941	RNF37_HUMAN	U-box domain containing 5 isoform a							nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2						ATCAGGTGATAACCATAATTT	0.428													4	2	---	---	---	---	
C20orf194	25943	broad.mit.edu	37	20	3320971	3320972	+	Intron	INS	-	C	C	rs58672154		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3320971_3320972insC	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron|C20orf194_uc010gay.1_Intron	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943												0						CCTAGTTTGTACTATAAAAAAA	0.302													5	4	---	---	---	---	
HSPA12B	116835	broad.mit.edu	37	20	3711153	3711153	+	5'Flank	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3711153delG	uc002wjd.2	+						HSPA12B_uc010zqi.1_5'Flank|HSPA12B_uc002wje.2_5'Flank|HSPA12B_uc010zqj.1_5'Flank	NM_052970	NP_443202	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B								ATP binding				0						TGGGCTCACTGGGGCTATTTG	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	10810808	10810808	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10810808delA								JAG1 (156114 upstream) : None (None downstream)																							TTTGTGGGCTAAAAAAGAAAG	0.264													4	2	---	---	---	---	
SEC23B	10483	broad.mit.edu	37	20	18490242	18490242	+	Intron	DEL	A	-	-	rs6081176	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18490242delA	uc002wqz.1	+						SEC23B_uc002wra.1_Intron|SEC23B_uc002wrb.1_Intron|SEC23B_uc010zsb.1_Intron|SEC23B_uc002wrc.1_Intron	NM_006363	NP_006354	Q15437	SC23B_HUMAN	Sec23 homolog B						ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1						CACAGTCTTCAtttttttttt	0.189													2	4	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19675254	19675254	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19675254delA	uc002wrl.2	+							NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						GATTTGGGGGACAGTGTTGGC	0.493													4	2	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19691645	19691673	+	Intron	DEL	ATGCAGTCTCACTGCCTCCCAGTATGCAC	-	-	rs74215532		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19691645_19691673delATGCAGTCTCACTGCCTCCCAGTATGCAC	uc002wrl.2	+							NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						GCCCTTTGCTATGCAGTCTCACTGCCTCCCAGTATGCACATGCAGTCTC	0.371													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22033829	22033829	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22033829delT								PAX1 (337209 upstream) : LOC284788 (347142 downstream)																							gctaaaagaattgcttaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22194692	22194692	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22194692delC								PAX1 (498072 upstream) : LOC284788 (186279 downstream)																							GACTGATGCACCATGGAGGCA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25937358	25937358	+	Intron	DEL	C	-	-	rs111987729		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25937358delC	uc002wvf.2	+											Homo sapiens cDNA clone IMAGE:5298175.																		ttggctgagacagaaagaaaa	0.000													6	6	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29648244	29648244	+	Intron	DEL	T	-	-	rs113515738		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29648244delT	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						aaacattgcatcccctaatcc	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31267061	31267061	+	IGR	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31267061delG								C20orf203 (5318 upstream) : COMMD7 (23433 downstream)																							tttcagagatggggaaaccgt	0.075													4	2	---	---	---	---	
CEP250	11190	broad.mit.edu	37	20	34096147	34096147	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34096147delT	uc002xcm.2	+						CEP250_uc010zve.1_Intron	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2						centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			attaagtttgttttttttttt	0.090													9	4	---	---	---	---	
RPRD1B	58490	broad.mit.edu	37	20	36686215	36686223	+	Intron	DEL	TCAGTATGT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36686215_36686223delTCAGTATGT	uc002xho.3	+							NM_021215	NP_067038	Q9NQG5	RPR1B_HUMAN	Regulation of nuclear pre-mRNA domain containing											pancreas(1)	1						ATGGCAGGTGTCAGTATGTCTTTGCGTGC	0.459											OREG0025919	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37949321	37949322	+	IGR	DEL	GA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37949321_37949322delGA								LOC339568 (95930 upstream) : None (None downstream)																							gaaggagtgtgagagagaaggC	0.282													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41285561	41285561	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41285561delT	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)				CACCCATCACTCCAACACTGA	0.254													4	2	---	---	---	---	
C20orf111	51526	broad.mit.edu	37	20	42832335	42832336	+	Intron	DEL	CA	-	-	rs79208015		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42832335_42832336delCA	uc002xlk.2	-							NM_016470	NP_057554	Q9NX31	CT111_HUMAN	oxidative stress responsive 1												0		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			agacttttttcacacacacaca	0.109													3	3	---	---	---	---	
STK4	6789	broad.mit.edu	37	20	43620303	43620303	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43620303delT	uc002xnb.2	+						STK4_uc010ggx.2_Intron|STK4_uc010ggy.2_Intron|STK4_uc010ggw.1_Intron	NM_006282	NP_006273	Q13043	STK4_HUMAN	serine/threonine kinase 4						apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)				AATGTTGTACttttttttttt	0.129													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	44614351	44614351	+	IGR	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44614351delC								ZNF335 (13518 upstream) : MMP9 (23196 downstream)																							CAAGCTGCCTCCCAGaggaag	0.229													4	2	---	---	---	---	
CDH22	64405	broad.mit.edu	37	20	44908549	44908550	+	Intron	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44908549_44908550insT	uc010ghk.1	-							NM_021248	NP_067071	Q9UJ99	CAD22_HUMAN	cadherin 22 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)				ttgacggagcattttttttaac	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55630463	55630464	+	IGR	DEL	CA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55630463_55630464delCA								TFAP2C (416127 upstream) : BMP7 (113345 downstream)																							AGTGCAGGGCCACACACACCCG	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59236413	59236413	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59236413delT								MIR646 (352788 upstream) : CDH4 (591146 downstream)																							ATTTGTGAGATTACAGTCTAG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9414623	9414624	+	IGR	INS	-	G	G			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9414623_9414624insG								None (None upstream) : None (None downstream)																							CATTGAAAAAAAGTTTAGAGAT	0.233													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10527958	10527958	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10527958delA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		AAATGAGCTGAAAAAAAAATG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10853708	10853712	+	IGR	DEL	GAATG	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10853708_10853712delGAATG								None (None upstream) : TPTE (53031 downstream)																							gaatggaatagaatggaatggaatg	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11087112	11087113	+	Intron	INS	-	C	C	rs138881683		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11087112_11087113insC	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)		catctcaaaaaaaaattaataa	0.000													4	2	---	---	---	---	
USP25	29761	broad.mit.edu	37	21	17196722	17196722	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17196722delT	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		AAATTCAGAATTTTAAAAAAT	0.219													4	2	---	---	---	---	
NCAM2	4685	broad.mit.edu	37	21	22422455	22422455	+	Intron	DEL	A	-	-	rs146653242		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22422455delA	uc002yld.1	+						NCAM2_uc011acb.1_Intron	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor						neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		TGTAAAGTGCAAAAAAAAAAA	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	24331950	24331950	+	IGR	DEL	C	-	-	rs5843029		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24331950delC								None (None upstream) : None (None downstream)																							aaatgacaatcacaaataaac	0.169													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	24810977	24810977	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24810977delT								None (None upstream) : None (None downstream)																							GCAGAACCTGTTTTTTTTTTT	0.254													4	2	---	---	---	---	
TIAM1	7074	broad.mit.edu	37	21	32857802	32857803	+	Intron	DEL	GA	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32857802_32857803delGA	uc002yow.1	-						TIAM1_uc002yox.1_Intron	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10						TGAGAGTGTGGAGAGAGGAGGC	0.406													4	2	---	---	---	---	
URB1	9875	broad.mit.edu	37	21	33756019	33756019	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33756019delA	uc002ypn.2	-							NM_014825	NP_055640	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog							nucleolus	protein binding				0						AAGGAAAAAGAAAAAAAAAAG	0.328													5	3	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37348174	37348175	+	Intron	DEL	CT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37348174_37348175delCT	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						CATACTTTGCCTCTCTCTCTCA	0.351			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				2	4	---	---	---	---	
ERG	2078	broad.mit.edu	37	21	39870560	39870560	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39870560delT	uc010gnw.2	-						ERG_uc002yxa.2_5'Flank|ERG_uc011aek.1_5'Flank|ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc011aem.1_5'Flank|ERG_uc002yxc.3_Intron|ERG_uc010gnz.2_Intron	NM_001136155	NP_001129627	P11308	ERG_HUMAN	ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)				AGCCAGGAGattttttttttt	0.453													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40380722	40380722	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40380722delT								ETS2 (183846 upstream) : PSMG1 (166668 downstream)																							GGTGGAAACCTTTTTTTCTTT	0.512													4	2	---	---	---	---	
IGSF5	150084	broad.mit.edu	37	21	41134555	41134555	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41134555delT	uc002yyo.2	+							NM_001080444	NP_001073913	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily 5 like							integral to membrane|tight junction					0		Prostate(19;5.35e-06)				cagaaggtaatttaccccatg	0.000													4	2	---	---	---	---	
CECR5	27440	broad.mit.edu	37	22	17621478	17621478	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17621478delA	uc002zmf.2	-						CECR5_uc002zmd.2_Intron|CECR5_uc002zme.2_Intron|CECR5_uc002zmg.2_Intron|CECR5_uc002zmh.2_Intron	NM_033070	NP_149061	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5								hydrolase activity				0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				ctgtccccgcaaaaaaaacaa	0.174													4	2	---	---	---	---	
MICAL3	57553	broad.mit.edu	37	22	18374023	18374023	+	Intron	DEL	A	-	-	rs11313720		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18374023delA	uc002zng.3	-						MICAL3_uc011agl.1_Intron|MICAL3_uc002znh.2_Intron|MICAL3_uc002znj.1_Intron|MICAL3_uc002znk.1_Intron|MICAL3_uc002znl.1_Intron|MICAL3_uc002znm.2_Intron|MICAL3_uc010grf.2_Intron	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		aTAGGAGCACAAAAAAAAAAA	0.144													4	2	---	---	---	---	
KREMEN1	83999	broad.mit.edu	37	22	29480045	29480046	+	Intron	INS	-	T	T			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29480045_29480046insT	uc011akm.1	+						KREMEN1_uc003ael.2_Intron	NM_032045	NP_114434	Q96MU8	KREM1_HUMAN	kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5						gagggatcctcttttttttagg	0.000													4	2	---	---	---	---	
THOC5	8563	broad.mit.edu	37	22	29939718	29939718	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29939718delA	uc003afr.2	-						THOC5_uc003afs.2_Intron|THOC5_uc003aft.2_Intron|THOC5_uc003afu.2_Intron|THOC5_uc010gvo.2_Intron|THOC5_uc003afv.1_Intron|THOC5_uc003afw.1_5'Flank	NM_001002878	NP_001002878	Q13769	THOC5_HUMAN	THO complex 5						intronless viral mRNA export from host nucleus|monocyte differentiation|mRNA processing|primitive hemopoiesis|RNA splicing	cytoplasm|intermediate filament cytoskeleton|THO complex part of transcription export complex	protein binding|RNA binding			breast(3)	3						AATCTCGGGCAAAAAAAAGTA	0.423													4	2	---	---	---	---	
SYN3	8224	broad.mit.edu	37	22	33296531	33296532	+	Intron	DEL	AG	-	-	rs71835045		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33296531_33296532delAG	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						cTATATTTTAAGAGACATCCTT	0.114													0	6	---	---	---	---	
SYN3	8224	broad.mit.edu	37	22	33296536	33296537	+	Intron	INS	-	T	T	rs144298242	by1000genomes	TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33296536_33296537insT	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						TTTTAAGAGACATCCTTTTTTG	0.114													0	6	---	---	---	---	
RBM9	23543	broad.mit.edu	37	22	36418425	36418425	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36418425delA	uc003aon.3	-						RBM9_uc003aoo.3_Intron	NM_001082578	NP_001076047	O43251	RFOX2_HUMAN	RNA binding motif protein 9 isoform 5						estrogen receptor signaling pathway|mRNA processing|negative regulation of transcription, DNA-dependent|regulation of cell proliferation|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding|transcription corepressor activity|transcription factor binding				0						CGTGATAGTGAAAAAAAAATG	0.393													3	3	---	---	---	---	
LOC646851	646851	broad.mit.edu	37	22	38993014	38993014	+	Intron	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38993014delA	uc011anw.1	-							NM_001013647	NP_001013669	B7Z7C6	B7Z7C6_HUMAN	hypothetical protein LOC646851												0						TTGTAGTTAGAAAAAAAAAAT	0.269													6	3	---	---	---	---	
ENTHD1	150350	broad.mit.edu	37	22	40165639	40165639	+	Intron	DEL	G	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40165639delG	uc003ayg.2	-							NM_152512	NP_689725	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1											ovary(2)|skin(1)	3	Melanoma(58;0.0749)					aaatggaactggtcaccaagg	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	42664973	42664973	+	5'Flank	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42664973delA	uc003bcl.2	+											Homo sapiens hypothetical gene supported by BC039496, mRNA (cDNA clone IMAGE:5549330), partial cds.																		AATGAGAGATAAAAAAGCAAA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48037874	48037874	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48037874delT	uc003bik.1	+						uc003bij.2_RNA					Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																		ttttaaaaaataaccactcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48879626	48879626	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48879626delT								None (None upstream) : FAM19A5 (5662 downstream)																							tctgtattccttttgcttgtc	0.080													4	2	---	---	---	---	
LMF2	91289	broad.mit.edu	37	22	50942709	50942710	+	Intron	INS	-	CT	CT	rs61419617		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50942709_50942710insCT	uc003blp.2	-						LMF2_uc010hba.2_Intron|LMF2_uc003blo.2_Intron	NM_033200	NP_149977	Q9BU23	LMF2_HUMAN	lipase maturation factor 2							endoplasmic reticulum membrane|integral to membrane				breast(1)	1		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCACACCCCCCGGTGCCCGGCC	0.421													3	7	---	---	---	---	
ARHGAP6	395	broad.mit.edu	37	X	11355171	11355171	+	Intron	DEL	C	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11355171delC	uc004cup.1	-						ARHGAP6_uc004cuo.1_Intron|ARHGAP6_uc004cur.1_Intron|ARHGAP6_uc004cun.1_Intron|ARHGAP6_uc011mif.1_Intron	NM_013427	NP_038286	O43182	RHG06_HUMAN	Rho GTPase activating protein 6 isoform 1						actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2						GCCCACCTGTCCCCAGGCTCT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	40480324	40480324	+	IGR	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40480324delT								ATP6AP2 (14437 upstream) : CXorf38 (7961 downstream)																							ATGTCCAAAGttttttttttc	0.234													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	50696831	50696831	+	IGR	DEL	A	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50696831delA								BMP15 (37225 upstream) : NUDT10 (378252 downstream)																							ttgaagacataatggccaaaa	0.000													4	2	---	---	---	---	
ARMCX1	51309	broad.mit.edu	37	X	100802598	100802598	+	5'Flank	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100802598delT	uc004ehv.2	+						ARMCX1_uc004ehw.2_5'Flank	NM_016608	NP_057692	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1							integral to membrane	binding			ovary(3)|pancreas(1)	4						GTCTGTGTTGTTTTTGCTCAC	0.259													4	2	---	---	---	---	
COL4A5	1287	broad.mit.edu	37	X	107849730	107849730	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107849730delT	uc004enz.1	+						COL4A5_uc011mso.1_Intron|COL4A5_uc004eob.1_Intron	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor						axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4						GCTCTCTCAGTTTTTTTTTTT	0.234									Alport_syndrome_with_Diffuse_Leiomyomatosis				5	3	---	---	---	---	
WDR44	54521	broad.mit.edu	37	X	117490350	117490350	+	Intron	DEL	T	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117490350delT	uc004eqn.2	+						WDR44_uc004eqo.2_Intron|WDR44_uc011mtr.1_Intron	NM_019045	NP_061918	Q5JSH3	WDR44_HUMAN	WD repeat domain 44 protein							cytosol|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm				lung(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5						TAATCCCAGATTTTTTTTTTT	0.353													4	3	---	---	---	---	
GPC3	2719	broad.mit.edu	37	X	132871468	132871469	+	Intron	DEL	GT	-	-			TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132871468_132871469delGT	uc004exe.1	-						GPC3_uc004exd.1_Intron|GPC3_uc010nrn.1_Intron|GPC3_uc011mvh.1_Intron|GPC3_uc010nro.1_Intron|GPC3_uc010nrp.1_Intron	NM_004484	NP_004475	P51654	GPC3_HUMAN	glypican 3 isoform 2 precursor							extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)					gtgagggagggtgtgtgtgtgg	0.010			T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13540952	13540953	+	IGR	INS	-	TC	TC	rs113976452		TCGA-CW-5585-01A-01D-1534-10	TCGA-CW-5585-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13540952_13540953insTC								None (None upstream) : None (None downstream)																							Gatattaaatttatttttaaaa	0.213													6	3	---	---	---	---	
