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
CAMTA1	23261	broad.mit.edu	37	1	7797034	7797034	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7797034C>T	uc001aoi.2	+	14	3514	c.3307C>T	c.(3307-3309)CCC>TCC	p.P1103S	CAMTA1_uc010nzv.1_Missense_Mutation_p.P190S|CAMTA1_uc001aok.3_Missense_Mutation_p.P146S|CAMTA1_uc001aoj.2_Missense_Mutation_p.P59S	NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	1103					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)		GGAAGTTGACCCCTTGAATGT	0.488													61	265	---	---	---	---	PASS
FAM183A	440585	broad.mit.edu	37	1	43613612	43613612	+	5'UTR	SNP	A	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43613612A>T	uc009vwo.2	+	1						NM_001101376	NP_001094846	A6NL82	F183A_HUMAN	hCG23177											ovary(3)	3						GGCGCGTGGCAGCCCAAGGCC	0.622													14	33	---	---	---	---	PASS
TMEM59	9528	broad.mit.edu	37	1	54509109	54509109	+	Silent	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54509109G>A	uc001cwp.2	-	4	730	c.480C>T	c.(478-480)AGC>AGT	p.S160S	TMEM59_uc001cwn.2_Silent_p.S23S|TMEM59_uc001cwo.2_Silent_p.S23S|TMEM59_uc001cwq.2_Silent_p.S160S|TMEM59_uc001cwr.2_Silent_p.S93S|TMEM59_uc001cws.1_Silent_p.S171S	NM_004872	NP_004863	Q9BXS4	TMM59_HUMAN	thymic dendritic cell-derived factor 1	160	Extracellular (Potential).					Golgi membrane|integral to membrane					0						AGGTTATGAAGCTCTGTGCGG	0.398													47	118	---	---	---	---	PASS
TMEM59	9528	broad.mit.edu	37	1	54509110	54509110	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54509110C>T	uc001cwp.2	-	4	729	c.479G>A	c.(478-480)AGC>AAC	p.S160N	TMEM59_uc001cwn.2_Missense_Mutation_p.S23N|TMEM59_uc001cwo.2_Missense_Mutation_p.S23N|TMEM59_uc001cwq.2_Missense_Mutation_p.S160N|TMEM59_uc001cwr.2_Missense_Mutation_p.S93N|TMEM59_uc001cws.1_Missense_Mutation_p.S171N	NM_004872	NP_004863	Q9BXS4	TMM59_HUMAN	thymic dendritic cell-derived factor 1	160	Extracellular (Potential).					Golgi membrane|integral to membrane					0						GGTTATGAAGCTCTGTGCGGA	0.398													48	117	---	---	---	---	PASS
TRIM33	51592	broad.mit.edu	37	1	114968147	114968147	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114968147G>T	uc001eew.2	-	9	1703	c.1619C>A	c.(1618-1620)CCA>CAA	p.P540Q	TRIM33_uc010owr.1_Missense_Mutation_p.P130Q|TRIM33_uc010ows.1_Missense_Mutation_p.P148Q|TRIM33_uc001eex.2_Missense_Mutation_p.P540Q	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform	540					negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACAGGTGCTGGTGGTTGCTG	0.443			T	RET	papillary thyroid								7	487	---	---	---	---	PASS
CSDE1	7812	broad.mit.edu	37	1	115260583	115260583	+	3'UTR	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115260583T>C	uc001efk.2	-	20					NRAS_uc009wgu.2_5'Flank|CSDE1_uc001efi.2_3'UTR|CSDE1_uc001efj.2_RNA|CSDE1_uc001efl.2_3'UTR|CSDE1_uc001efm.2_3'UTR|CSDE1_uc009wgv.2_3'UTR|CSDE1_uc001efn.2_3'UTR	NM_001007553	NP_001007554	O75534	CSDE1_HUMAN	upstream of NRAS isoform 1						male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTTCCAGGCTGCAACTGTGC	0.333													3	12	---	---	---	---	PASS
WARS2	10352	broad.mit.edu	37	1	119576809	119576809	+	Silent	SNP	A	G	G	rs112701114		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119576809A>G	uc001ehn.2	-	5	571	c.543T>C	c.(541-543)GAT>GAC	p.D181D	WARS2_uc010oxf.1_Silent_p.D87D|WARS2_uc001ehm.2_Silent_p.D181D|WARS2_uc010oxg.1_Silent_p.D124D|WARS2_uc010oxh.1_Missense_Mutation_p.S153P|WARS2_uc010oxi.1_Missense_Mutation_p.S59P	NM_015836	NP_056651	Q9UGM6	SYWM_HUMAN	mitochondrial tryptophanyl tRNA synthetase 2	181					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)	GCTGGACTTGATCCTCCCCAA	0.438													6	307	---	---	---	---	PASS
NBPF7	343505	broad.mit.edu	37	1	120387017	120387017	+	Silent	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120387017G>A	uc010oxk.1	-	1	763	c.142C>T	c.(142-144)CTG>TTG	p.L48L		NM_001047980	NP_001041445	P0C2Y1	NBPF7_HUMAN	hypothetical protein LOC343505	48						cytoplasm				ovary(1)|skin(1)	2	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;3.66e-05)|Lung NSC(69;0.000192)|all_epithelial(167;0.0347)		Lung(183;0.0103)|LUSC - Lung squamous cell carcinoma(189;0.0544)		TTCTCTGCCAGCTGGGGGCGC	0.468											OREG0013730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	151	---	---	---	---	PASS
NOTCH2	4853	broad.mit.edu	37	1	120458045	120458045	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120458045A>G	uc001eik.2	-	34	7556	c.7300T>C	c.(7300-7302)TCT>CCT	p.S2434P		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	2434	Cytoplasmic (Potential).				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)		GACCAGTCAGAAGCAGAGTGG	0.587			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				9	33	---	---	---	---	PASS
ANKRD35	148741	broad.mit.edu	37	1	145558859	145558859	+	Missense_Mutation	SNP	G	A	A	rs150752253	byFrequency	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145558859G>A	uc001eob.1	+	7	586	c.478G>A	c.(478-480)GCA>ACA	p.A160T	NBPF10_uc001emp.3_Intron|ANKRD35_uc010oyx.1_Missense_Mutation_p.A3T	NM_144698	NP_653299	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	160	ANK 4.									ovary(4)|skin(1)	5	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCTGATGATCGCATCGCTGGG	0.577													4	29	---	---	---	---	PASS
LOC728855	728855	broad.mit.edu	37	1	149649002	149649002	+	Intron	SNP	G	A	A	rs116783842		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149649002G>A	uc009wlc.2	+						LOC728855_uc009wld.2_Intron|uc001eso.1_RNA					Homo sapiens mRNA, chromosome 1 specific transcript KIAA0493.												0						TTGGAATTCCGCTGTTCAGTT	0.428													7	393	---	---	---	---	PASS
RPRD2	23248	broad.mit.edu	37	1	150432538	150432538	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150432538G>T	uc009wlr.2	+	9	1357	c.1156G>T	c.(1156-1158)GAG>TAG	p.E386*	RPRD2_uc010pcc.1_Nonsense_Mutation_p.E360*|RPRD2_uc001eup.3_Nonsense_Mutation_p.E360*	NM_015203	NP_056018	Q5VT52	RPRD2_HUMAN	Regulation of nuclear pre-mRNA domain containing	386							protein binding			ovary(1)	1						TGAAACAGTCGAGGACAGGAA	0.408													5	280	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152188024	152188024	+	Silent	SNP	C	G	G	rs142170860		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152188024C>G	uc001ezt.1	-	3	6157	c.6081G>C	c.(6079-6081)TCG>TCC	p.S2027S		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	2027	22.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGCCACAGCTCGATGACTGTC	0.562													63	449	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152188367	152188367	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152188367T>C	uc001ezt.1	-	3	5814	c.5738A>G	c.(5737-5739)CAC>CGC	p.H1913R		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	1913	21.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTAGATCCGTGTTGTTCACC	0.557													8	529	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152283596	152283596	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152283596G>T	uc001ezu.1	-	3	3802	c.3766C>A	c.(3766-3768)CAA>AAA	p.Q1256K	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1256	Ser-rich.|Filaggrin 7.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCGATGATTGTTCCTGTCCC	0.572									Ichthyosis				27	161	---	---	---	---	PASS
SLC25A44	9673	broad.mit.edu	37	1	156177711	156177711	+	Silent	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156177711T>C	uc001fnp.2	+	3	982	c.660T>C	c.(658-660)CCT>CCC	p.P220P	SLC25A44_uc010phc.1_Silent_p.P111P|SLC25A44_uc009wrr.2_Silent_p.P228P|SLC25A44_uc010phd.1_RNA|SLC25A44_uc010phe.1_Intron	NM_014655	NP_055470	Q96H78	S2544_HUMAN	solute carrier family 25, member 44	220	Solcar 3.				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding			ovary(1)	1	Hepatocellular(266;0.158)					AGGAGTGCCCTCACATTGTCT	0.557													5	127	---	---	---	---	PASS
ATP1A2	477	broad.mit.edu	37	1	160091025	160091025	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160091025A>T	uc001fvc.2	+	3	293	c.161A>T	c.(160-162)CAA>CTA	p.Q54L	ATP1A2_uc001fvb.2_Missense_Mutation_p.Q54L|ATP1A2_uc010piz.1_5'Flank	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein	54	Cytoplasmic (Potential).				ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CGCAAATACCAAGTGGACCTG	0.423													16	100	---	---	---	---	PASS
ATF6	22926	broad.mit.edu	37	1	161789463	161789463	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161789463G>T	uc001gbr.2	+	8	1017	c.950G>T	c.(949-951)CGA>CTA	p.R317L	ATF6_uc001gbq.1_Missense_Mutation_p.R317L	NM_007348	NP_031374	P18850	ATF6A_HUMAN	activating transcription factor 6	317	Basic motif.|Cytoplasmic (Potential).				positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity	p.R317*(1)		ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)			ATAAAAAATCGAGAATCCGCT	0.378													4	145	---	---	---	---	PASS
SELE	6401	broad.mit.edu	37	1	169701065	169701065	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169701065G>A	uc001ggm.3	-	4	597	c.440C>T	c.(439-441)TCC>TTC	p.S147F	C1orf112_uc001ggj.2_Intron	NM_000450	NP_000441	P16581	LYAM2_HUMAN	selectin E precursor	147	EGF-like.|Extracellular (Potential).				actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity			ovary(3)|skin(2)	5	all_hematologic(923;0.208)					GCCACTGCAGGATGTATTGGT	0.443													52	90	---	---	---	---	PASS
PRRX1	5396	broad.mit.edu	37	1	170695367	170695367	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170695367T>C	uc001ghf.2	+	3	471	c.424T>C	c.(424-426)TTT>CTT	p.F142L	PRRX1_uc001ghe.2_Missense_Mutation_p.F142L	NM_022716	NP_073207	P54821	PRRX1_HUMAN	paired mesoderm homeobox 1 isoform pmx-1b	142	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCAGGTGTGGTTTCAGAACCG	0.448													6	37	---	---	---	---	PASS
CEP350	9857	broad.mit.edu	37	1	179989189	179989189	+	Silent	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179989189C>A	uc001gnt.2	+	12	2663	c.2280C>A	c.(2278-2280)TCC>TCA	p.S760S	CEP350_uc009wxl.2_Silent_p.S759S|CEP350_uc001gnu.2_Silent_p.S594S	NM_014810	NP_055625	Q5VT06	CE350_HUMAN	centrosome-associated protein 350	760						centrosome|nucleus|spindle				ovary(4)	4						GTTTACTCTCCCATCTCTTGA	0.403													5	301	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197072237	197072237	+	Silent	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197072237G>T	uc001gtu.2	-	18	6401	c.6144C>A	c.(6142-6144)GTC>GTA	p.V2048V	ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	2048	IQ 14.|IQ 15.				mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						ACTGTATAGTGACTGCTGCTT	0.323													4	118	---	---	---	---	PASS
PPP1CB	5500	broad.mit.edu	37	2	29004708	29004708	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29004708G>T	uc002rmg.2	+	5	680	c.520G>T	c.(520-522)GGA>TGA	p.G174*	PPP1CB_uc010ymj.1_Nonsense_Mutation_p.G146*|PPP1CB_uc010ymk.1_Missense_Mutation_p.G146C|PPP1CB_uc010yml.1_Nonsense_Mutation_p.G146*|PPP1CB_uc002rmh.2_Nonsense_Mutation_p.G174*|SPDYA_uc002rmi.2_5'Flank	NM_206876	NP_996759	P62140	PP1B_HUMAN	protein phosphatase 1, catalytic subunit, beta	174					cell cycle|cell division|glycogen metabolic process|triglyceride catabolic process	MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|myosin phosphatase activity|myosin-light-chain-phosphatase activity|protein binding			skin(1)	1	Acute lymphoblastic leukemia(172;0.155)					TTGTCATGGAGGTAGACTAGT	0.348													6	514	---	---	---	---	PASS
VIT	5212	broad.mit.edu	37	2	36982065	36982065	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36982065G>T	uc002rpl.2	+	5	498	c.277G>T	c.(277-279)GGT>TGT	p.G93C	VIT_uc002rpk.2_Missense_Mutation_p.G86C|VIT_uc010ynf.1_Missense_Mutation_p.G86C|VIT_uc002rpm.2_Missense_Mutation_p.G86C|VIT_uc010ezv.2_Missense_Mutation_p.G86C|VIT_uc010ezw.2_Missense_Mutation_p.G86C	NM_053276	NP_444506	Q6UXI7	VITRN_HUMAN	vitrin	93	LCCL.			G -> S (in Ref. 1; AAL18263).		proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)				TCTTCATAGTGGTGTGCTTGA	0.388													7	752	---	---	---	---	PASS
DNAH6	1768	broad.mit.edu	37	2	84924779	84924779	+	Silent	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84924779A>G	uc010fgb.2	+	47	7742	c.7605A>G	c.(7603-7605)GAA>GAG	p.E2535E	DNAH6_uc002sor.2_Silent_p.E507E	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	2535	AAA 4 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1						AAAAGGATGAACTGGAGCAGG	0.433													7	375	---	---	---	---	PASS
CD8B	926	broad.mit.edu	37	2	87073817	87073817	+	Missense_Mutation	SNP	G	C	C	rs149601403	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87073817G>C	uc002srz.2	-	4	623	c.573C>G	c.(571-573)ATC>ATG	p.I191M	RMND5A_uc002srs.3_Intron|CD8B_uc002srw.2_Missense_Mutation_p.I191M|CD8B_uc002srx.2_Missense_Mutation_p.I191M|CD8B_uc002sry.2_Intron|CD8B_uc010fgt.2_Intron|CD8B_uc002ssa.2_Missense_Mutation_p.I191M|CD8B_uc010yto.1_Missense_Mutation_p.I191M	NM_004931	NP_004922	P10966	CD8B_HUMAN	CD8b antigen isoform 5 precursor	191	Helical; (Potential).				immune response|regulation of defense response to virus by virus|regulation of immune response|T cell activation|transmembrane receptor protein tyrosine kinase signaling pathway|viral reproduction	early endosome|extracellular region|integral to plasma membrane|T cell receptor complex	coreceptor activity|MHC class I protein binding			upper_aerodigestive_tract(1)|skin(1)	2						AGCACAGGTGGATGGCCACTC	0.552													6	95	---	---	---	---	PASS
UXS1	80146	broad.mit.edu	37	2	106746130	106746130	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106746130C>A	uc002tdm.2	-	7	660	c.562G>T	c.(562-564)GGG>TGG	p.G188W	UXS1_uc002tdl.2_Missense_Mutation_p.G20W|UXS1_uc002tdn.2_Missense_Mutation_p.G193W|UXS1_uc002tdo.2_Missense_Mutation_p.G131W|UXS1_uc010ywh.1_Intron	NM_025076	NP_079352	Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1	188	Lumenal (Potential).				cellular metabolic process	Golgi cisterna membrane|integral to membrane	coenzyme binding|UDP-glucuronate decarboxylase activity			ovary(2)	2						GACAACTTACCCAACATGTTT	0.378													7	481	---	---	---	---	PASS
UGGT1	56886	broad.mit.edu	37	2	128917198	128917198	+	Silent	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128917198T>C	uc002tps.2	+	23	2644	c.2466T>C	c.(2464-2466)ACT>ACC	p.T822T	UGGT1_uc010fme.1_Silent_p.T697T|UGGT1_uc002tpr.2_Silent_p.T798T	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	822					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						AAACTCAGACTTCCAACGCTG	0.488													5	172	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152354253	152354253	+	Intron	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152354253C>A	uc010fnx.2	-						NEB_uc002txr.2_Intron|RIF1_uc002txp.2_Intron|NEB_uc010zbz.1_Intron|NEB_uc002txq.2_Intron|NEB_uc010zca.1_Intron|NEB_uc010zcb.1_Intron|NEB_uc002txt.3_3'UTR	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		AGAAAGCATCCAGAAAAACAA	0.398													6	418	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152364564	152364564	+	Silent	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152364564G>T	uc010fnx.2	-	134	18494	c.18303C>A	c.(18301-18303)ACC>ACA	p.T6101T	NEB_uc002txr.2_Silent_p.T2524T|NEB_uc010zca.1_5'Flank|NEB_uc010zcb.1_5'Flank|NEB_uc002txt.3_Silent_p.T606T	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	6101	Nebulin 167.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		GTATCTCTGGGGTGTCCAAAA	0.443													7	608	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178098960	178098960	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178098960C>G	uc002ulh.3	-	2	640	c.85G>C	c.(85-87)GAT>CAT	p.D29H	NFE2L2_uc002ulg.3_Missense_Mutation_p.D13H|NFE2L2_uc010zfa.1_Missense_Mutation_p.D13H|NFE2L2_uc002uli.3_Missense_Mutation_p.D13H|NFE2L2_uc010fra.2_Missense_Mutation_p.D13H|NFE2L2_uc010frb.2_Missense_Mutation_p.D13H	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	29					transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ACTCCAAGATCTATATCTTGC	0.363			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			75	157	---	---	---	---	PASS
PDE11A	50940	broad.mit.edu	37	2	178936671	178936671	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178936671G>A	uc002ulq.2	-	1	812	c.494C>T	c.(493-495)CCC>CTC	p.P165L	PDE11A_uc002ulr.2_Intron|PDE11A_uc002ult.1_Intron	NM_016953	NP_058649	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A isoform 4	165					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)			TGTGGTGGGGGGCAGGGAGCT	0.577									Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				14	40	---	---	---	---	PASS
TMEFF2	23671	broad.mit.edu	37	2	192814915	192814915	+	3'UTR	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192814915G>T	uc002utc.2	-	10						NM_016192	NP_057276	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two							extracellular region|integral to membrane				lung(2)|pancreas(1)|breast(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			TGTTTTCATTGGTGTAGATTA	0.308													4	118	---	---	---	---	PASS
KIF1A	547	broad.mit.edu	37	2	241724433	241724433	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241724433G>C	uc002vzy.2	-	7	839	c.693C>G	c.(691-693)GAC>GAG	p.D231E	KIF1A_uc010fzk.2_Missense_Mutation_p.D231E|KIF1A_uc002vzz.1_Missense_Mutation_p.D231E	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	231	Kinesin-motor.				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		TGGTCTCTGCGTCATGGCGCT	0.607													62	141	---	---	---	---	PASS
ITPR1	3708	broad.mit.edu	37	3	4683804	4683804	+	Silent	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4683804C>T	uc003bqa.2	+	7	742	c.394C>T	c.(394-396)CTA>TTA	p.L132L	ITPR1_uc010hbz.2_Silent_p.L132L|ITPR1_uc010hca.1_Silent_p.L132L|ITPR1_uc011asu.1_Silent_p.L132L|ITPR1_uc010hcb.1_Silent_p.L132L	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1	132	MIR 1.|Cytoplasmic (Potential).				activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		TAATAAATACCTAACAGTGAA	0.403													4	203	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47164273	47164273	+	Nonsense_Mutation	SNP	G	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47164273G>C	uc003cqs.2	-	3	1906	c.1853C>G	c.(1852-1854)TCA>TGA	p.S618*	SETD2_uc003cqv.2_Nonsense_Mutation_p.S607*	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	618					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TAATCGATTTGATGGAGCTGG	0.318			N|F|S|Mis		clear cell renal carcinoma								33	57	---	---	---	---	PASS
CACNA1D	776	broad.mit.edu	37	3	53777118	53777118	+	Silent	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53777118G>T	uc003dgv.3	+	22	3055	c.2892G>T	c.(2890-2892)GGG>GGT	p.G964G	CACNA1D_uc003dgu.3_Silent_p.G984G|CACNA1D_uc003dgy.3_Silent_p.G964G|CACNA1D_uc003dgw.3_Silent_p.G631G|CACNA1D_uc003dgx.1_Silent_p.G112G	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	964	Helical; Name=S3 of repeat III; (Potential).|III.				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)	TGGTGGTTGGGGTGTCTCTGG	0.433													203	267	---	---	---	---	PASS
SEC22A	26984	broad.mit.edu	37	3	122944129	122944129	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122944129G>T	uc003ege.2	+	4	605	c.526G>T	c.(526-528)GGT>TGT	p.G176C	SEC22A_uc003egf.2_Missense_Mutation_p.G176C	NM_012430	NP_036562	Q96IW7	SC22A_HUMAN	SEC22 vesicle trafficking protein homolog A	176	Cytoplasmic (Potential).				ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane	transporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0548)		TAAAGGTGCTGGTAAGATTTC	0.378													6	456	---	---	---	---	PASS
RASA2	5922	broad.mit.edu	37	3	141295907	141295907	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141295907G>A	uc003etz.1	+	15	1549	c.1549G>A	c.(1549-1551)GTA>ATA	p.V517I	RASA2_uc010huq.1_Missense_Mutation_p.V517I|RASA2_uc003eua.1_Missense_Mutation_p.V517I|RASA2_uc011bnc.1_Missense_Mutation_p.V109I	NM_006506	NP_006497	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	517	Ras-GAP.				intracellular signal transduction|negative regulation of Ras protein signal transduction	intracellular membrane-bounded organelle|intrinsic to internal side of plasma membrane|perinuclear region of cytoplasm	metal ion binding|Ras GTPase activator activity			ovary(2)|lung(2)|breast(1)|skin(1)	6						TGCTGTAGCCGTAGTATCACC	0.353													246	547	---	---	---	---	PASS
ATP11B	23200	broad.mit.edu	37	3	182575778	182575778	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182575778T>C	uc003flb.2	+	11	1221	c.964T>C	c.(964-966)TAT>CAT	p.Y322H		NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	322	Extracellular (Potential).				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)			TGAACCTTGGTATAACCAAAA	0.323													8	425	---	---	---	---	PASS
ACAP2	23527	broad.mit.edu	37	3	195016504	195016504	+	Silent	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195016504T>C	uc003fun.3	-	17	1846	c.1605A>G	c.(1603-1605)GAA>GAG	p.E535E		NM_012287	NP_036419	Q15057	ACAP2_HUMAN	centaurin, beta 2	535					regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2						GCCTCTTTTCTTCAGAACTTT	0.383													7	454	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195510785	195510785	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195510785C>T	uc011bto.1	-	2	8126	c.7666G>A	c.(7666-7668)GGT>AGT	p.G2556S	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)		GTGGCGTGACCTGTGGATGCT	0.577													4	139	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513468	195513468	+	Missense_Mutation	SNP	G	C	C	rs76596008		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513468G>C	uc011bto.1	-	2	5443	c.4983C>G	c.(4981-4983)CAC>CAG	p.H1661Q	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)		GAGGGGTGGCGTGACCTGTGG	0.587													10	32	---	---	---	---	PASS
ZNF595	152687	broad.mit.edu	37	4	53303	53303	+	5'UTR	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53303C>T	uc003fzv.1	+	1					ZNF595_uc003fzu.1_RNA|ZNF718_uc003fzt.3_5'UTR|ZNF595_uc010iay.1_RNA|ZNF595_uc011bus.1_5'UTR|ZNF595_uc011but.1_5'UTR	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TCAGCCACAGCCTCTGCCTCC	0.597													8	97	---	---	---	---	PASS
KIAA1530	57654	broad.mit.edu	37	4	1343562	1343562	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1343562G>A	uc003gde.3	+	3	796	c.349G>A	c.(349-351)GTG>ATG	p.V117M		NM_020894	NP_065945	Q2YD98	K1530_HUMAN	hypothetical protein LOC57654	117											0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)			CACCCGGGCCGTGGAAGGGTG	0.627													5	29	---	---	---	---	PASS
AFAP1	60312	broad.mit.edu	37	4	7780467	7780467	+	Intron	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7780467A>G	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron|LOC84740_uc003gkd.3_RNA	NM_198595	NP_940997	Q8N556	AFAP1_HUMAN	actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0						CCGGAATGCAAGACATCCGAT	0.577													4	45	---	---	---	---	PASS
SLIT2	9353	broad.mit.edu	37	4	20512749	20512749	+	Silent	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20512749T>C	uc003gpr.1	+	11	1251	c.1047T>C	c.(1045-1047)TCT>TCC	p.S349S	SLIT2_uc003gps.1_Silent_p.S349S	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	349	LRR 9.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						GACTACGCTCTCTGAATTCAC	0.383													39	185	---	---	---	---	PASS
SRP72	6731	broad.mit.edu	37	4	57349375	57349375	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57349375C>T	uc003hbv.2	+	9	936	c.896C>T	c.(895-897)TCC>TTC	p.S299F	SRP72_uc010ihe.2_Missense_Mutation_p.S238F|SRP72_uc003hbw.1_Intron	NM_006947	NP_008878	O76094	SRP72_HUMAN	signal recognition particle 72kDa	299					response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)					TTTAAGCTTTCCAAGAAACAA	0.348													115	250	---	---	---	---	PASS
RAP1GDS1	5910	broad.mit.edu	37	4	99313251	99313251	+	Intron	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99313251C>A	uc003htx.3	+						RAP1GDS1_uc003htu.2_3'UTR|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)		AGTCATGAACCACAAATGTAA	0.308			T	NUP98	T-ALL								5	361	---	---	---	---	PASS
QRFPR	84109	broad.mit.edu	37	4	122254089	122254089	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122254089C>A	uc010inj.1	-	4	1063	c.684G>T	c.(682-684)ATG>ATT	p.M228I	QRFPR_uc010ink.1_RNA|QRFPR_uc003ids.2_Missense_Mutation_p.M228I	NM_198179	NP_937822	Q96P65	QRFPR_HUMAN	G protein-coupled receptor 103	228	Helical; Name=5; (Potential).			VILFLLPLMVMLILYSKIGYELWIKKRVGDGSVLRTIHGKE MSKIAR -> SSSSSCLLW (in Ref. 1; AAL26488).		plasma membrane	neuropeptide Y receptor activity				0						TAAGCATCACCATAAGAGGCA	0.423													6	256	---	---	---	---	PASS
GK3P	2713	broad.mit.edu	37	4	166200549	166200549	+	Silent	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166200549G>T	uc003ird.3	-	1	627	c.249C>A	c.(247-249)TCC>TCA	p.S83S	KLHL2_uc003irb.2_Intron|KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron|KLHL2_uc010ira.2_Intron	NM_000167	NP_000158			glycerol kinase isoform b												0						CTTTTATGTTGGAAATACCAA	0.438													7	334	---	---	---	---	PASS
SH3RF1	57630	broad.mit.edu	37	4	170190302	170190302	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170190302G>A	uc003isa.1	-	2	397	c.62C>T	c.(61-63)GCT>GTT	p.A21V		NM_020870	NP_065921	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	21	RING-type.					Golgi apparatus|lamellipodium|perinuclear region of cytoplasm	ligase activity|zinc ion binding			breast(2)|lung(1)	3		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		CTTCGCAGAAGCATCAAGGCG	0.458													19	32	---	---	---	---	PASS
SLC6A18	348932	broad.mit.edu	37	5	1244460	1244460	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1244460G>T	uc003jby.1	+	10	1591	c.1468G>T	c.(1468-1470)GGT>TGT	p.G490C		NM_182632	NP_872438	Q96N87	S6A18_HUMAN	solute carrier family 6, member 18	490	Helical; Name=10; (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CGAGGTTGTGGGTGTCGTTTA	0.582													5	188	---	---	---	---	PASS
C5orf42	65250	broad.mit.edu	37	5	37167182	37167182	+	Missense_Mutation	SNP	G	T	T	rs146595129		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37167182G>T	uc011cpa.1	-	35	7598	c.7367C>A	c.(7366-7368)CCT>CAT	p.P2456H	C5orf42_uc011coy.1_Missense_Mutation_p.P956H|C5orf42_uc003jks.2_RNA|C5orf42_uc011coz.1_Missense_Mutation_p.P1531H	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250	2456										ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TCTTACTTCAGGTGGTTCTAT	0.313													7	762	---	---	---	---	PASS
ZNF131	7690	broad.mit.edu	37	5	43123452	43123452	+	Intron	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43123452G>A	uc011cpw.1	+						ZNF131_uc010ivl.1_Intron|ZNF131_uc003jnj.3_Intron|ZNF131_uc003jnk.2_Intron|ZNF131_uc003jnn.3_Intron|ZNF131_uc003jnl.1_Intron|ZNF131_uc010ivm.1_Intron|ZNF131_uc003jnm.2_3'UTR	NM_003432	NP_003423	P52739	ZN131_HUMAN	zinc finger protein 131							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						ATAAATCAAAGAAGCCATTTT	0.299													10	275	---	---	---	---	PASS
CD180	4064	broad.mit.edu	37	5	66479930	66479930	+	Silent	SNP	A	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66479930A>C	uc003juy.2	-	3	889	c.741T>G	c.(739-741)ACT>ACG	p.T247T		NM_005582	NP_005573	Q99467	CD180_HUMAN	CD180 molecule precursor	247	Extracellular (Potential).				inflammatory response|innate immune response	integral to membrane|plasma membrane	receptor activity			ovary(1)	1		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		AGAGAGACTGAGTAGTAGAGT	0.428													13	242	---	---	---	---	PASS
ZFYVE16	9765	broad.mit.edu	37	5	79770481	79770481	+	Splice_Site	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79770481G>T	uc003kgr.3	+	18	4596	c.4294_splice	c.e18-1	p.V1432_splice	ZFYVE16_uc003kgq.3_Splice_Site_p.V1432_splice|ZFYVE16_uc003kgs.3_Splice_Site_p.V1432_splice|ZFYVE16_uc003kgt.3_Splice_Site_p.V520_splice|ZFYVE16_uc003kgu.3_Splice_Site_p.V184_splice	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16						BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		ATACATTTCAGGTGTTCTACT	0.328													5	292	---	---	---	---	PASS
PJA2	9867	broad.mit.edu	37	5	108719205	108719205	+	5'UTR	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108719205C>A	uc003kos.3	-	2						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)		acactatggacaagccgcaga	0.000													15	116	---	---	---	---	PASS
ZNF608	57507	broad.mit.edu	37	5	123984120	123984120	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123984120C>A	uc003ktq.1	-	4	2080	c.1957G>T	c.(1957-1959)GGT>TGT	p.G653C	ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Missense_Mutation_p.G653C|ZNF608_uc003ktt.1_Missense_Mutation_p.G653C	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	653						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)		GCTTTAGCACCAATAATGGAA	0.507													5	224	---	---	---	---	PASS
KIF3A	11127	broad.mit.edu	37	5	132070140	132070140	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132070140C>A	uc003kxo.2	-	2	191	c.37G>T	c.(37-39)GAT>TAT	p.D13Y	KIF3A_uc003kxn.2_5'UTR|KIF3A_uc011cxf.1_Missense_Mutation_p.D13Y|KIF3A_uc003kxp.2_Missense_Mutation_p.D13Y	NM_007054	NP_008985	Q9Y496	KIF3A_HUMAN	kinesin family member 3A	13	Kinesin-motor.				blood coagulation|organelle organization|plus-end-directed vesicle transport along microtubule	centrosome|cytosol|kinesin II complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|protein binding			pancreas(1)	1		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTCACATTATCGCAGCTTTCT	0.368													6	363	---	---	---	---	PASS
BRD8	10902	broad.mit.edu	37	5	137488441	137488441	+	Silent	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137488441G>A	uc003lcf.1	-	21	2641	c.2586C>T	c.(2584-2586)CAC>CAT	p.H862H	BRD8_uc003lcc.1_Intron	NM_139199	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8 isoform 2	862					cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			AAACCCACTCGTGTCCCATCT	0.443													8	153	---	---	---	---	PASS
PCDHB1	29930	broad.mit.edu	37	5	140433201	140433201	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140433201C>A	uc003lik.1	+	1	2223	c.2146C>A	c.(2146-2148)CAA>AAA	p.Q716K		NM_013340	NP_037472	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1 precursor	716	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACATGTCTACCAAAAGATTAA	0.348													6	475	---	---	---	---	PASS
PCDHB9	56127	broad.mit.edu	37	5	140569080	140569080	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140569080G>T	uc003liw.1	+	3	2189	c.2189G>T	c.(2188-2190)GGT>GTT	p.G730V	PCDHB10_uc003lix.2_5'Flank	NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	730	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTGCCCGAGGGTCCTTTTCCA	0.657													14	27	---	---	---	---	PASS
HMMR	3161	broad.mit.edu	37	5	162918133	162918133	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162918133A>G	uc003lzf.2	+	18	2320	c.2138A>G	c.(2137-2139)TAC>TGC	p.Y713C	HMMR_uc003lzh.2_Missense_Mutation_p.Y714C|HMMR_uc003lzg.2_Missense_Mutation_p.Y698C|HMMR_uc011dem.1_Missense_Mutation_p.Y627C|uc003lzi.2_Intron	NM_012484	NP_036616	O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor isoform b	713						cell surface|cytoplasm	hyaluronic acid binding				0	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)		ACAAACTGTTACCGAGCTCCT	0.318													8	813	---	---	---	---	PASS
CCDC99	54908	broad.mit.edu	37	5	169026150	169026150	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169026150A>C	uc003mae.3	+	10	1590	c.1311A>C	c.(1309-1311)AAA>AAC	p.K437N	CCDC99_uc010jjj.2_Missense_Mutation_p.K366N|CCDC99_uc011deq.1_Missense_Mutation_p.K254N|CCDC99_uc010jjk.2_Missense_Mutation_p.K163N	NM_017785	NP_060255	Q96EA4	SPDLY_HUMAN	coiled-coil domain containing 99	437	Potential.				cell division|establishment of mitotic spindle orientation|mitotic metaphase plate congression|mitotic prometaphase|protein localization to kinetochore	condensed chromosome outer kinetochore|cytosol|microtubule organizing center|nucleus|spindle pole	kinetochore binding|protein binding			ovary(1)|liver(1)	2	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGAAACTAAAATATGAACCTG	0.274													71	34	---	---	---	---	PASS
CANX	821	broad.mit.edu	37	5	179153702	179153702	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179153702C>T	uc003mkk.2	+	14	1844	c.1667C>T	c.(1666-1668)GCT>GTT	p.A556V	CANX_uc011dgp.1_Missense_Mutation_p.A591V|CANX_uc003mkl.2_Missense_Mutation_p.A556V|CANX_uc011dgq.1_Missense_Mutation_p.A448V	NM_001746	NP_001737	P27824	CALX_HUMAN	calnexin precursor	556	Cytoplasmic (Potential).				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein secretion	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane|melanosome	calcium ion binding|sugar binding|unfolded protein binding				0	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)	AAAAGTGATGCTGAAGAAGAT	0.373													5	401	---	---	---	---	PASS
MAML1	9794	broad.mit.edu	37	5	179201812	179201812	+	Silent	SNP	C	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179201812C>G	uc003mkm.2	+	5	3248	c.2985C>G	c.(2983-2985)TCC>TCG	p.S995S	MAML1_uc003mkn.1_Intron	NM_014757	NP_055572	Q92585	MAML1_HUMAN	mastermind-like 1	995					Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	peptide antigen binding|protein kinase binding|transcription coactivator activity			lung(4)|ovary(2)	6	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGATCGACTCCCTGCTGAAGA	0.537													23	43	---	---	---	---	PASS
UBR2	23304	broad.mit.edu	37	6	42650839	42650839	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42650839G>T	uc011dur.1	+	43	4765	c.4765G>T	c.(4765-4767)GAT>TAT	p.D1589Y	UBR2_uc011dus.1_Missense_Mutation_p.D1234Y|UBR2_uc003osh.2_RNA|UBR2_uc011dut.1_Missense_Mutation_p.D177Y	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	1589					cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding	p.D1589Y(1)		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)			AGGTGAAAGAGATGCTATAAG	0.363													6	445	---	---	---	---	PASS
CD2AP	23607	broad.mit.edu	37	6	47567071	47567071	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47567071T>A	uc003oyw.2	+	13	1765	c.1309T>A	c.(1309-1311)TTT>ATT	p.F437I		NM_012120	NP_036252	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	437					cell division|mitosis|protein complex assembly|signal transduction|substrate-dependent cell migration, cell extension	cytoplasm|filamentous actin|nucleolus|plasma membrane|ruffle	SH3 domain binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			TTCATCAAAATTTGAAACTGA	0.338													38	154	---	---	---	---	PASS
LMBRD1	55788	broad.mit.edu	37	6	70386388	70386388	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70386388C>A	uc003pfa.2	-	15	1578	c.1463G>T	c.(1462-1464)TGG>TTG	p.W488L	LMBRD1_uc003pey.2_Missense_Mutation_p.W284L|LMBRD1_uc003pez.2_Missense_Mutation_p.W415L|LMBRD1_uc010kal.2_Missense_Mutation_p.W415L|LMBRD1_uc003pfb.2_RNA	NM_018368	NP_060838	Q9NUN5	LMBD1_HUMAN	liver regeneration p-53 related protein	488	Helical; Name=9; (Potential).				interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1						ACTGAAGAACCAGAACTTGTG	0.383													5	264	---	---	---	---	PASS
HMGN3	9324	broad.mit.edu	37	6	79944289	79944289	+	5'UTR	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79944289C>A	uc003pit.2	-	1					HMGN3_uc003pis.2_5'UTR|HMGN3_uc003piu.1_5'UTR|uc003piv.1_RNA	NM_004242	NP_004233	Q15651	HMGN3_HUMAN	high mobility group nucleosomal binding domain 3						chromatin modification	chromatin|cytoplasm|nucleus	DNA binding|thyroid hormone receptor binding				0		all_cancers(76;0.000116)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0393)		BRCA - Breast invasive adenocarcinoma(397;0.125)		ATGACTATGTCGGTGAAGCAA	0.502													36	117	---	---	---	---	PASS
EPHA7	2045	broad.mit.edu	37	6	93953241	93953241	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93953241C>A	uc003poe.2	-	17	3141	c.2900G>T	c.(2899-2901)GGG>GTG	p.G967V	EPHA7_uc003pof.2_Missense_Mutation_p.G962V|EPHA7_uc011eac.1_Missense_Mutation_p.G963V	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	967	Cytoplasmic (Potential).|SAM.					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CAGTGTGATCCCTAAACTCAT	0.353													6	448	---	---	---	---	PASS
FNDC1	84624	broad.mit.edu	37	6	159660926	159660926	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159660926C>T	uc010kjv.2	+	14	4758	c.4558C>T	c.(4558-4560)CAC>TAC	p.H1520Y	FNDC1_uc010kjw.1_Missense_Mutation_p.H1405Y	NM_032532	NP_115921	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1520						extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CTTGGAACGGCACGACGATGA	0.318													4	64	---	---	---	---	PASS
PACRG	135138	broad.mit.edu	37	6	163149205	163149205	+	5'UTR	SNP	A	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163149205A>C	uc003qua.2	+	2					PARK2_uc003qtx.3_5'Flank|PARK2_uc003qty.3_5'Flank|PARK2_uc003qtz.3_5'Flank|PARK2_uc010kke.1_5'Flank|PACRG_uc003qub.2_5'UTR|PACRG_uc003quc.2_5'UTR	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		TCCTGCTCACATCCGTAAAGC	0.423													17	55	---	---	---	---	PASS
ZNF107	51427	broad.mit.edu	37	7	64167850	64167850	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64167850G>T	uc003ttd.2	+	7	1954	c.1168G>T	c.(1168-1170)GGC>TGC	p.G390C	ZNF107_uc003tte.2_Missense_Mutation_p.G390C	NM_016220	NP_057304	Q9UII5	ZN107_HUMAN	zinc finger protein 107	390	C2H2-type 12; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.00948)|all_lung(88;0.0249)				TGAAGAATGTGGCAAAGCTTT	0.323													5	147	---	---	---	---	PASS
SEMA3E	9723	broad.mit.edu	37	7	83277904	83277904	+	5'UTR	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83277904G>T	uc003uhy.1	-	1						NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor						axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)				CTTTAAGGAGGGTCTGAGTTT	0.552													4	76	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91641956	91641956	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91641956G>T	uc003ulg.2	+	9	3757	c.3532G>T	c.(3532-3534)GGT>TGT	p.G1178C	AKAP9_uc003ule.2_Missense_Mutation_p.G1190C|AKAP9_uc003ulf.2_Missense_Mutation_p.G1178C|AKAP9_uc003uli.2_Missense_Mutation_p.G803C	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	1190					G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ACAAGAAACAGGTAAAATGGT	0.348			T	BRAF	papillary thyroid								6	314	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94051214	94051214	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94051214A>G	uc003ung.1	+	39	2824	c.2353A>G	c.(2353-2355)ATG>GTG	p.M785V	COL1A2_uc011kib.1_Intron|COL1A2_uc010lfi.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	785			Missing (in OI2A).		axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CTCTTAGGGTATGACTGGTTT	0.443										HNSCC(75;0.22)			163	269	---	---	---	---	PASS
ZNF3	7551	broad.mit.edu	37	7	99668418	99668418	+	3'UTR	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99668418G>T	uc003usq.2	-	6					ZNF3_uc003usp.2_Intron|ZNF3_uc003usr.2_3'UTR|ZNF3_uc010lgj.2_3'UTR|ZNF3_uc003uss.2_3'UTR|ZNF3_uc003ust.3_3'UTR	NM_032924	NP_116313	P17036	ZNF3_HUMAN	zinc finger protein 3 isoform 2						cell differentiation|leukocyte activation|multicellular organismal development	nucleus	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			CTGACTACGCGGACTCCAACT	0.488													5	10	---	---	---	---	PASS
MCM7	4176	broad.mit.edu	37	7	99690954	99690954	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99690954G>T	uc003usw.1	-	14	2429	c.1919C>A	c.(1918-1920)TCA>TAA	p.S640*	MCM7_uc003usv.1_Nonsense_Mutation_p.S464*|MCM7_uc003usx.1_Nonsense_Mutation_p.S464*	NM_005916	NP_005907	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	640	Interaction with ATRIP.				cell cycle checkpoint|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|regulation of phosphorylation|response to DNA damage stimulus|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)				Atorvastatin(DB01076)	AGAGTCCTTTGACATCTCCAT	0.498													5	241	---	---	---	---	PASS
TFEC	22797	broad.mit.edu	37	7	115624530	115624530	+	5'UTR	SNP	A	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115624530A>T	uc003vhj.1	-	2					TFEC_uc003vhk.1_5'UTR|TFEC_uc003vhl.3_5'UTR|TFEC_uc011kmw.1_Missense_Mutation_p.L79Q	NM_012252	NP_036384	O14948	TFEC_HUMAN	transcription factor EC isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			large_intestine(1)	1			STAD - Stomach adenocarcinoma(10;0.00878)			GGCTTTCTGTAGCTGAGGCCT	0.428													108	149	---	---	---	---	PASS
SLC13A1	6561	broad.mit.edu	37	7	122765670	122765670	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122765670A>G	uc003vkm.2	-	11	1218	c.1193T>C	c.(1192-1194)CTT>CCT	p.L398P	SLC13A1_uc010lks.2_Missense_Mutation_p.L274P	NM_022444	NP_071889	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate	398	Helical; (Potential).					integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)	AGCTGGGATAAGAAAGAATAG	0.338													8	681	---	---	---	---	PASS
POT1	25913	broad.mit.edu	37	7	124493109	124493109	+	Silent	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124493109C>T	uc003vlm.2	-	10	1387	c.786G>A	c.(784-786)GAG>GAA	p.E262E	POT1_uc011koe.1_RNA|POT1_uc003vlk.2_RNA|POT1_uc003vll.2_RNA|POT1_uc003vlo.2_Silent_p.E131E|POT1_uc003vln.2_RNA	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1	262					DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						GAAGATGAAACTCTAAACTTA	0.358													212	368	---	---	---	---	PASS
EPHB6	2051	broad.mit.edu	37	7	142563322	142563322	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142563322G>A	uc011kst.1	+	8	1826	c.1039G>A	c.(1039-1041)GTT>ATT	p.V347I	EPHB6_uc011ksu.1_Missense_Mutation_p.V347I|EPHB6_uc003wbs.2_Missense_Mutation_p.V55I|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_Missense_Mutation_p.V55I|EPHB6_uc003wbv.2_5'Flank	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	347	Extracellular (Potential).|Cys-rich.					extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19	Melanoma(164;0.059)					AGCAGCCCCCGTTTGCCCCTG	0.652													13	25	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	144707224	144707224	+	IGR	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144707224C>A								TPK1 (174078 upstream) : None (None downstream)																							GTAATCTTACCCAGACACTTA	0.403													5	290	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	3566003	3566003	+	Silent	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3566003C>T	uc011kwk.1	-	7	1332	c.942G>A	c.(940-942)GCG>GCA	p.A314A		NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	314	Extracellular (Potential).					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)		TCAACTCAATCGCCTTTTTCA	0.433													6	179	---	---	---	---	PASS
LOC349196	349196	broad.mit.edu	37	8	7177474	7177474	+	Intron	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7177474A>G	uc010lrk.1	-						uc011kwo.1_Intron					Homo sapiens cDNA FLJ37516 fis, clone BRCAN2000832.												0						CTTGAAATGAAACTGAAACAA	0.313													4	47	---	---	---	---	PASS
SLC7A2	6542	broad.mit.edu	37	8	17409424	17409424	+	Silent	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17409424G>A	uc011kyc.1	+	6	1153	c.984G>A	c.(982-984)GCG>GCA	p.A328A	SLC7A2_uc011kyd.1_Silent_p.A368A|SLC7A2_uc011kye.1_Silent_p.A368A|SLC7A2_uc011kyf.1_Silent_p.A328A	NM_001008539	NP_001008539	P52569	CTR2_HUMAN	solute carrier family 7, member 2 isoform 2	328	Extracellular (Potential).				cellular amino acid metabolic process|ion transport	cytoplasm|integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity			ovary(2)|skin(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	TTCCTGTAGCGTTTGAATATG	0.502													138	242	---	---	---	---	PASS
ADRA1A	148	broad.mit.edu	37	8	26722260	26722260	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26722260G>C	uc003xfh.1	-	1	663	c.227C>G	c.(226-228)ACC>AGC	p.T76S	ADRA1A_uc003xfc.1_Missense_Mutation_p.T76S|ADRA1A_uc010lul.1_Missense_Mutation_p.T76S|ADRA1A_uc003xfd.1_RNA|ADRA1A_uc003xfe.1_Missense_Mutation_p.T76S|ADRA1A_uc010lum.1_Missense_Mutation_p.T76S|ADRA1A_uc003xff.1_RNA|ADRA1A_uc003xfg.1_Missense_Mutation_p.T76S	NM_000680	NP_000671	P35348	ADA1A_HUMAN	alpha-1A-adrenergic receptor isoform 1	76	Helical; Name=2; (By similarity).				activation of phospholipase C activity|aging|apoptosis|calcium ion transport into cytosol|cell-cell signaling|intracellular protein kinase cascade|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of synaptic transmission, GABAergic|positive regulation of action potential|positive regulation of cardiac muscle contraction|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase C signaling cascade|positive regulation of vasoconstriction|response to drug|response to hormone stimulus|response to stress|smooth muscle contraction	integral to plasma membrane	alpha1-adrenergic receptor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amphetamine(DB00182)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Carvedilol(DB01136)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Maprotiline(DB00934)|Mephentermine(DB01365)|Metaraminol(DB00610)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Nefazodone(DB01149)|Nicergoline(DB00699)|Nilutamide(DB00665)|Norepinephrine(DB00368)|Norgestrel(DB00506)|Oxymetazoline(DB00935)|Perphenazine(DB00850)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Prazosin(DB00457)|Promazine(DB00420)|Promethazine(DB01069)|Propericiazine(DB01608)|Propiomazine(DB00777)|Pseudoephedrine(DB00852)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioridazine(DB00679)|Tolazoline(DB00797)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Ziprasidone(DB00246)	CACCGTGGAGGTGAGCAGGAG	0.607													35	46	---	---	---	---	PASS
PURG	29942	broad.mit.edu	37	8	30854085	30854085	+	3'UTR	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30854085G>T	uc003xim.1	-	2						NM_001015508	NP_001015508	Q9UJV8	PURG_HUMAN	purine-rich element binding protein G isoform B							nucleus	DNA binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.0895)|Kidney(114;0.108)		TTTATTCTGAGGTGTAACATA	0.378													8	814	---	---	---	---	PASS
PENK	5179	broad.mit.edu	37	8	57354177	57354177	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57354177G>C	uc003xsz.2	-	2	539	c.458C>G	c.(457-459)TCC>TGC	p.S153C	PENK_uc003xta.3_Missense_Mutation_p.S153C	NM_006211	NP_006202	P01210	PENK_HUMAN	proenkephalin	153					neuropeptide signaling pathway	extracellular region	neuropeptide hormone activity|opioid peptide activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_lung(136;0.229)	Epithelial(17;0.000873)|all cancers(17;0.0069)			CAGGTCTGAGGAATTGGCCAG	0.527													17	100	---	---	---	---	PASS
CHD7	55636	broad.mit.edu	37	8	61720793	61720793	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61720793G>T	uc003xue.2	+	7	2937	c.2460G>T	c.(2458-2460)GAG>GAT	p.E820D		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	820	Chromo 1.				central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity	p.556_871dup(1)		ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CTGGAGAGGAGGTAGAAATTG	0.318													7	764	---	---	---	---	PASS
CHD7	55636	broad.mit.edu	37	8	61757864	61757864	+	Silent	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61757864C>T	uc003xue.2	+	23	5583	c.5106C>T	c.(5104-5106)AGC>AGT	p.S1702S		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1702					central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			AAGCCCAGAGCACACAGCCGG	0.507													19	81	---	---	---	---	PASS
RRS1	23212	broad.mit.edu	37	8	67342089	67342089	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67342089G>T	uc003xwa.2	+	1	827	c.723G>T	c.(721-723)AAG>AAT	p.K241N	ADHFE1_uc003xwb.3_5'Flank|ADHFE1_uc003xwd.3_5'Flank|ADHFE1_uc003xwc.3_5'Flank|ADHFE1_uc003xwe.3_5'Flank|ADHFE1_uc003xwf.3_5'Flank|ADHFE1_uc011les.1_5'Flank|ADHFE1_uc011leq.1_5'Flank|ADHFE1_uc011ler.1_5'Flank	NM_015169	NP_055984	Q15050	RRS1_HUMAN	homolog of yeast ribosome biogenesis regulatory	241					mitotic metaphase plate congression|ribosome biogenesis	condensed nuclear chromosome|nucleolus					0		Lung NSC(129;0.197)	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			GCCTCCCCAAGGAGAAGGTGC	0.607													10	10	---	---	---	---	PASS
ZHX1	11244	broad.mit.edu	37	8	124266181	124266181	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124266181G>T	uc003yqe.2	-	3	2436	c.2006C>A	c.(2005-2007)CCT>CAT	p.P669H	C8orf76_uc003yqd.2_Intron|ZHX1_uc003yqf.2_Missense_Mutation_p.P669H|ZHX1_uc003yqg.2_Intron|ZHX1_uc010mdi.2_Missense_Mutation_p.P669H	NM_007222	NP_009153	Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	669	Homeobox 4.				negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			CAGCTGCTCAGGTGTTTTTTT	0.468													6	341	---	---	---	---	PASS
ATAD2	29028	broad.mit.edu	37	8	124383950	124383950	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124383950C>A	uc003yqh.3	-	4	604	c.496G>T	c.(496-498)GGT>TGT	p.G166C	ATAD2_uc011lii.1_5'UTR|ATAD2_uc003yqi.3_RNA|ATAD2_uc003yqj.2_Missense_Mutation_p.G166C	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	166					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			TGGTTTACACCACTATAACGA	0.368													6	509	---	---	---	---	PASS
KIAA0196	9897	broad.mit.edu	37	8	126036702	126036702	+	3'UTR	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126036702C>T	uc003yrt.2	-	29					KIAA0196_uc011lir.1_3'UTR	NM_014846	NP_055661	Q12768	STRUM_HUMAN	strumpellin						cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			TAACTAATGCCATGAGATATA	0.303													23	56	---	---	---	---	PASS
CHMP5	51510	broad.mit.edu	37	9	33271188	33271188	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33271188G>T	uc003zsl.3	+	6	709	c.354G>T	c.(352-354)AAG>AAT	p.K118N	SUGT1P1_uc010mjq.1_Intron|CHMP5_uc003zsm.3_Missense_Mutation_p.K118N|CHMP5_uc011lnv.1_Missense_Mutation_p.K118N|CHMP5_uc003zsn.2_RNA	NM_016410	NP_057494	Q9NZZ3	CHMP5_HUMAN	chromatin modifying protein 5	118	Potential.				cellular membrane organization|protein transport	cytosol|endosome membrane	protein binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)			AAATGAAGAAGGCATACAAGC	0.353													5	308	---	---	---	---	PASS
PTPDC1	138639	broad.mit.edu	37	9	96860800	96860800	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96860800T>A	uc004auf.1	+	7	2130	c.1790T>A	c.(1789-1791)CTA>CAA	p.L597Q	PTPDC1_uc004aug.1_Missense_Mutation_p.L597Q|PTPDC1_uc004auh.1_Missense_Mutation_p.L649Q|PTPDC1_uc010mrj.1_Missense_Mutation_p.L651Q|PTPDC1_uc010mri.1_Missense_Mutation_p.L649Q	NM_177995	NP_818931	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	597							protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1						GCCAAAGCCCTAGCAAATTTA	0.388													14	62	---	---	---	---	PASS
SVEP1	79987	broad.mit.edu	37	9	113163140	113163140	+	Silent	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113163140T>C	uc010mtz.2	-	40	10153	c.9816A>G	c.(9814-9816)GAA>GAG	p.E3272E	SVEP1_uc010mty.2_Silent_p.E1198E	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	3272	Sushi 31.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						TTACCTCTAGTTCATAGCCAG	0.343													6	221	---	---	---	---	PASS
BAT2L1	84726	broad.mit.edu	37	9	134357757	134357757	+	Splice_Site	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134357757G>A	uc004can.3	+	20	5039	c.4984_splice	c.e20-1	p.Q1662_splice	BAT2L1_uc004cao.3_Intron|BAT2L1_uc004cap.3_5'Flank	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like								protein binding				0						GCTCTGCACAGCAGGGTTTTA	0.537													12	50	---	---	---	---	PASS
SETX	23064	broad.mit.edu	37	9	135202159	135202159	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135202159C>A	uc004cbk.2	-	10	5009	c.4826G>T	c.(4825-4827)GGT>GTT	p.G1609V	SETX_uc004cbj.2_Missense_Mutation_p.G1228V|SETX_uc010mzt.2_Missense_Mutation_p.G1228V	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	1609					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TTTAGAAAGACCAGCAATTCG	0.408													44	169	---	---	---	---	PASS
PHYH	5264	broad.mit.edu	37	10	13325777	13325777	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13325777G>T	uc001imf.2	-	7	829	c.741C>A	c.(739-741)CAC>CAA	p.H247Q	PHYH_uc001ime.2_Missense_Mutation_p.H147Q|PHYH_uc001img.2_Missense_Mutation_p.H230Q	NM_006214	NP_006205	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase isoform a precursor	247					fatty acid alpha-oxidation|nervous system development	peroxisomal matrix	electron carrier activity|L-ascorbic acid binding|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|phytanoyl-CoA dioxygenase activity|protein binding				0		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	CCATCACCAGGTGCACCCGGG	0.502													32	140	---	---	---	---	PASS
ARMC4	55130	broad.mit.edu	37	10	28250568	28250568	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28250568G>T	uc009xky.2	-	10	1413	c.1315C>A	c.(1315-1317)CAT>AAT	p.H439N	ARMC4_uc010qds.1_5'UTR|ARMC4_uc010qdt.1_Missense_Mutation_p.H131N|ARMC4_uc001itz.2_Missense_Mutation_p.H439N|ARMC4_uc010qdu.1_Missense_Mutation_p.H131N	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	439							binding			ovary(4)|skin(2)	6						TCCTGACGATGGTCAGGTGGT	0.398													5	203	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37430752	37430752	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37430752G>T	uc001iza.1	+	7	858	c.759G>T	c.(757-759)TTG>TTT	p.L253F		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	309						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						CTGCACCCTTGGTGGAAAGAA	0.502													4	86	---	---	---	---	PASS
B4GALNT4	338707	broad.mit.edu	37	11	379925	379925	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:379925C>T	uc001lpb.2	+	16	2557	c.2548C>T	c.(2548-2550)CGC>TGC	p.R850C		NM_178537	NP_848632	Q76KP1	B4GN4_HUMAN	beta	850	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCTGCACGCGCGCACCGGGGA	0.687													3	13	---	---	---	---	PASS
NAP1L4	4676	broad.mit.edu	37	11	2979729	2979729	+	Silent	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2979729G>T	uc001lxc.2	-	10	933	c.792C>A	c.(790-792)ACC>ACA	p.T264T	NAP1L4_uc009ydt.2_RNA|NAP1L4_uc010qxm.1_Silent_p.T264T|NAP1L4_uc010qxn.1_Silent_p.T264T	NM_005969	NP_005960	Q99733	NP1L4_HUMAN	nucleosome assembly protein 1-like 4	264					nucleosome assembly	chromatin assembly complex|cytoplasm	unfolded protein binding			ovary(1)	1		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)		TTTTCTTGATGGTTTTGACAG	0.393													6	565	---	---	---	---	PASS
SCUBE2	57758	broad.mit.edu	37	11	9091015	9091015	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9091015T>A	uc001mhh.1	-	5	625	c.545A>T	c.(544-546)CAC>CTC	p.H182L	SCUBE2_uc001mhi.1_Missense_Mutation_p.H182L|SCUBE2_uc001mhj.1_Missense_Mutation_p.H182L	NM_020974	NP_066025	Q9NQ36	SCUB2_HUMAN	CEGP1 protein precursor	182	EGF-like 4 (Potential).					extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		ACTACAGCCGTGATCCTTATT	0.577													12	36	---	---	---	---	PASS
DENND5A	23258	broad.mit.edu	37	11	9161237	9161237	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9161237A>G	uc001mhl.2	-	23	4100	c.3845T>C	c.(3844-3846)GTC>GCC	p.V1282A	DENND5A_uc001mhk.2_Missense_Mutation_p.V625A|DENND5A_uc010rbw.1_3'UTR	NM_015213	NP_056028	Q6IQ26	DEN5A_HUMAN	RAB6 interacting protein 1	1282	RUN 2.									liver(1)	1						GATGCCCTTGACAAGGGACGT	0.517													21	105	---	---	---	---	PASS
LYVE1	10894	broad.mit.edu	37	11	10580689	10580689	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10580689G>C	uc001miv.2	-	6	1224	c.938C>G	c.(937-939)ACT>AGT	p.T313S	uc001miu.2_Intron|LYVE1_uc010rca.1_Missense_Mutation_p.T209S	NM_006691	NP_006682	Q9Y5Y7	LYVE1_HUMAN	lymphatic vessel endothelial hyaluronan receptor	313	Cytoplasmic (Potential).				anatomical structure morphogenesis|cell-matrix adhesion|cellular component movement|response to wounding|transport	integral to plasma membrane|membrane fraction				central_nervous_system(1)|skin(1)	2				all cancers(16;7.22e-08)|Epithelial(150;1.03e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0609)		TCGCACGGTAGTTTTGCTTGG	0.468													16	763	---	---	---	---	PASS
FSHB	2488	broad.mit.edu	37	11	30255400	30255400	+	3'UTR	SNP	T	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30255400T>A	uc001msl.2	+	3					FSHB_uc001msm.2_3'UTR|FSHB_uc001msn.2_3'UTR	NM_000510	NP_000501	P01225	FSHB_HUMAN	follicle stimulating hormone, beta polypeptide						cellular nitrogen compound metabolic process|female gamete generation|female pregnancy|ovarian follicle development|peptide hormone processing|progesterone biosynthetic process|spermatogenesis|transforming growth factor beta receptor signaling pathway	cytoplasm|extracellular region|soluble fraction	follicle-stimulating hormone activity|protein heterodimerization activity			ovary(3)	3					Follitropin beta(DB00066)|Thyrotropin Alfa(DB00024)|Urofollitropin(DB00094)	ACCAAGATATTCAAAAAGTCT	0.507													5	13	---	---	---	---	PASS
GRM5	2915	broad.mit.edu	37	11	88781056	88781056	+	5'UTR	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88781056C>A	uc001pcq.2	-	1					GRM5_uc009yvm.2_5'UTR|GRM5_uc009yvn.1_5'UTR	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	GAAAGGAGTTCAAGCCAATAA	0.463													5	26	---	---	---	---	PASS
CASP1	834	broad.mit.edu	37	11	104897592	104897592	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104897592C>A	uc010rve.1	-	8	1110	c.1093G>T	c.(1093-1095)GAT>TAT	p.D365Y	CASP1_uc001pig.2_Missense_Mutation_p.D272Y|CASP1_uc001pik.2_Missense_Mutation_p.D328Y|CASP1_uc010rvf.1_Missense_Mutation_p.D272Y|CASP1_uc010rvg.1_Missense_Mutation_p.D344Y|CASP1_uc010rvh.1_Missense_Mutation_p.D224Y|CASP1_uc010rvi.1_Missense_Mutation_p.D49Y|CASP1_uc001pim.3_Missense_Mutation_p.D365Y|CASP1_uc009yxi.2_Missense_Mutation_p.D344Y|CASP1_uc010rvj.1_Missense_Mutation_p.D365Y|CASP1_uc009yxj.2_Missense_Mutation_p.D210Y|CASP1_uc010rvk.1_3'UTR	NM_033292	NP_150634	P29466	CASP1_HUMAN	caspase 1 isoform alpha precursor	365					cellular response to mechanical stimulus|cellular response to organic substance|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis|signal transduction	cytosol	caspase activator activity|cysteine-type endopeptidase activity|protein binding			ovary(2)	2		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)|Penicillamine(DB00859)	TCCTCCACATCACAGGAACAG	0.403													49	224	---	---	---	---	PASS
ST3GAL4	6484	broad.mit.edu	37	11	126276767	126276767	+	Intron	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126276767C>A	uc001qds.2	+						ST3GAL4_uc001qdt.2_Intron|ST3GAL4_uc009zcc.2_Intron|ST3GAL4_uc009zcd.2_Intron|ST3GAL4_uc001qdu.2_Intron|ST3GAL4_uc001qdv.2_Intron|ST3GAL4_uc009zce.2_Intron|ST3GAL4_uc001qdw.2_Intron|ST3GAL4_uc001qdx.1_Intron|ST3GAL4_uc001qdy.2_5'UTR|ST3GAL4_uc001qdz.2_5'Flank	NM_006278	NP_006269	Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase						post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)		TGGGAGAAGGCTTAGGCTGCC	0.532													14	67	---	---	---	---	PASS
CLEC12A	160364	broad.mit.edu	37	12	10137604	10137604	+	Silent	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10137604T>C	uc001qwr.3	+	6	965	c.777T>C	c.(775-777)TCT>TCC	p.S259S	CLEC12A_uc001qwq.2_Silent_p.S269S|CLEC12A_uc001qws.3_Silent_p.S226S|CLEC12A_uc001qwt.2_Silent_p.S188S	NM_138337	NP_612210	Q5QGZ9	CL12A_HUMAN	myeloid inhibitory C-type lectin-like receptor	259	Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity|sugar binding			skin(1)	1						agcttggttctacatatttta	0.065													5	205	---	---	---	---	PASS
CSDA	8531	broad.mit.edu	37	12	10854562	10854562	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10854562T>A	uc001qyt.2	-	8	1293	c.1050A>T	c.(1048-1050)AAA>AAT	p.K350N	CSDA_uc001qyu.2_Missense_Mutation_p.K281N	NM_003651	NP_003642	P16989	DBPA_HUMAN	cold shock domain protein A isoform a	350					negative regulation of transcription from RNA polymerase II promoter|response to cold	cytoplasm|nucleus	double-stranded DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|lung(1)|large_intestine(1)	4	Glioma(1;0.155)					GATTTACCTCTTTGCCATCTT	0.507													15	119	---	---	---	---	PASS
SLCO1C1	53919	broad.mit.edu	37	12	20890093	20890093	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20890093A>T	uc001rej.3	+	12	1790	c.1435A>T	c.(1435-1437)AGA>TGA	p.R479*	SLCO1C1_uc010sii.1_Nonsense_Mutation_p.R479*|SLCO1C1_uc010sij.1_Nonsense_Mutation_p.R430*|SLCO1C1_uc009zip.2_Nonsense_Mutation_p.R313*|SLCO1C1_uc001rei.2_Nonsense_Mutation_p.R479*|SLCO1C1_uc010sik.1_Nonsense_Mutation_p.R361*	NM_017435	NP_059131	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family,	479	Extracellular (Potential).|Kazal-like.				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(5)|pancreas(1)|skin(1)	7	Esophageal squamous(101;0.149)					TTGCAACTCAAGATGCAAATG	0.388													26	390	---	---	---	---	PASS
REP15	387849	broad.mit.edu	37	12	27850210	27850210	+	3'UTR	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27850210G>T	uc001rig.1	+	1						NM_001029874	NP_001025045	Q6BDI9	REP15_HUMAN	RAB15 effector protein							early endosome membrane				ovary(1)	1	Lung SC(9;0.0873)					TCTCTGACTTGGATATGTATT	0.388													6	402	---	---	---	---	PASS
KIF21A	55605	broad.mit.edu	37	12	39724585	39724585	+	Silent	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39724585A>G	uc001rly.2	-	23	3428	c.3282T>C	c.(3280-3282)AAT>AAC	p.N1094N	KIF21A_uc001rlv.2_Silent_p.N106N|KIF21A_uc001rlw.2_Silent_p.N411N|KIF21A_uc001rlx.2_Silent_p.N1081N|KIF21A_uc001rlz.2_Silent_p.N1058N|KIF21A_uc010skl.1_Silent_p.N1081N	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1094					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|pancreas(1)|lung(1)|skin(1)	7		Lung NSC(34;0.179)|all_lung(34;0.213)				CTAGCTCAGGATTTAATTCTG	0.363													12	599	---	---	---	---	PASS
LRRK2	120892	broad.mit.edu	37	12	40681178	40681178	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40681178G>T	uc001rmg.3	+	20	2647	c.2526G>T	c.(2524-2526)ATG>ATT	p.M842I	LRRK2_uc001rmh.1_Missense_Mutation_p.M464I	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	842					activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TAGCAAGAATGGTGATCAGAT	0.363													7	494	---	---	---	---	PASS
OSBPL8	114882	broad.mit.edu	37	12	76763548	76763548	+	Silent	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76763548G>T	uc001sye.1	-	20	2589	c.2109C>A	c.(2107-2109)ACC>ACA	p.T703T	OSBPL8_uc001syf.1_Silent_p.T661T|OSBPL8_uc001syg.1_Silent_p.T661T|OSBPL8_uc001syh.1_Silent_p.T678T	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform	703					lipid transport		lipid binding			ovary(1)	1						ACTTCTCTTGGGTAGCTTCAG	0.378													8	645	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19433111	19433111	+	RNA	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19433111G>A	uc010tcj.1	-	1		c.12999C>T				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						AAAAAGGAAAGAATAATCTGG	0.299													4	182	---	---	---	---	PASS
LOC374491	374491	broad.mit.edu	37	13	25168432	25168432	+	RNA	SNP	T	C	C	rs149337771	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25168432T>C	uc001upm.2	+	10		c.1104T>C			LOC374491_uc001upn.2_RNA|LOC374491_uc001upo.2_RNA					Homo sapiens mRNA; cDNA DKFZp434J0717 (from clone DKFZp434J0717).												0						TTGAAACAGCTGGTGTATTAA	0.373													6	162	---	---	---	---	PASS
CDK8	1024	broad.mit.edu	37	13	26927911	26927911	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26927911A>G	uc001uqr.1	+	4	376	c.350A>G	c.(349-351)AAC>AGC	p.N117S	CDK8_uc001uqs.1_Missense_Mutation_p.N117S|CDK8_uc001uqt.1_5'UTR	NM_001260	NP_001251	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	117	Protein kinase.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	mediator complex	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|large_intestine(1)|ovary(1)|skin(1)	5	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		TCTAAAGCAAACAAGAAGCCA	0.348													6	372	---	---	---	---	PASS
PDS5B	23047	broad.mit.edu	37	13	33233417	33233417	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33233417G>T	uc010abf.2	+	6	782	c.624G>T	c.(622-624)AAG>AAT	p.K208N	PDS5B_uc001uuo.2_Missense_Mutation_p.K208N|PDS5B_uc010abg.2_RNA	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog	208					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)		CTGCTCATAAGGTGAGTAGCA	0.363													6	355	---	---	---	---	PASS
CLN5	1203	broad.mit.edu	37	13	77574621	77574621	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77574621G>T	uc001vkc.2	+	4	769	c.741G>T	c.(739-741)TGG>TGT	p.W247C		NM_006493	NP_006484	O75503	CLN5_HUMAN	ceroid-lipofuscinosis, neuronal 5	198					brain development|cell death|lysosomal lumen acidification|neuron maturation|protein catabolic process	endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|perinuclear region of cytoplasm	protein binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0503)		TGGCAAAGTGGGTGAAACAGG	0.343													4	94	---	---	---	---	PASS
UGGT2	55757	broad.mit.edu	37	13	96665676	96665676	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96665676G>T	uc001vmt.2	-	5	715	c.545C>A	c.(544-546)CCA>CAA	p.P182Q	UGGT2_uc010afo.2_RNA|UGGT2_uc001vmv.2_Missense_Mutation_p.P182Q|UGGT2_uc010afp.2_Missense_Mutation_p.P182Q	NM_020121	NP_064506	Q9NYU1	UGGG2_HUMAN	UDP-glucose ceramide glucosyltransferase-like 2	182					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3						AATCACCACTGGTAAGTTCTC	0.323													6	402	---	---	---	---	PASS
CLYBL	171425	broad.mit.edu	37	13	100543598	100543598	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100543598G>A	uc001vok.2	+	8	968	c.954G>A	c.(952-954)ATG>ATA	p.M318I		NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like precursor	318					cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AAGGGAGTATGATCGACATGC	0.443													59	253	---	---	---	---	PASS
COL4A2	1284	broad.mit.edu	37	13	111144511	111144511	+	Silent	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111144511T>C	uc001vqx.2	+	38	3838	c.3549T>C	c.(3547-3549)GCT>GCC	p.A1183A		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	1183	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)			GGCCGGGAGCTCCGGGCTTAC	0.652													12	49	---	---	---	---	PASS
RALGAPA1	253959	broad.mit.edu	37	14	36094594	36094594	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36094594T>C	uc001wti.2	-	34	5775	c.5384A>G	c.(5383-5385)GAA>GGA	p.E1795G	RALGAPA1_uc010amp.2_RNA|RALGAPA1_uc001wtj.2_Missense_Mutation_p.E1795G|RALGAPA1_uc010tpv.1_Missense_Mutation_p.E1808G|RALGAPA1_uc010tpw.1_Missense_Mutation_p.E1842G	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1	1795	Minimal domain that binds to TCF3/E12 (By similarity).				activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						GTTCCTAAGTTCTCTAAGTAG	0.343													6	276	---	---	---	---	PASS
AHSA1	10598	broad.mit.edu	37	14	77928560	77928560	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77928560A>G	uc001xtw.2	+	3	489	c.329A>G	c.(328-330)GAT>GGT	p.D110G	AHSA1_uc010tvk.1_Missense_Mutation_p.D110G	NM_012111	NP_036243	O95433	AHSA1_HUMAN	activator of heat shock 90kDa protein ATPase	110					protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		AATTTGTCTGATGAAAACAGC	0.428													6	354	---	---	---	---	PASS
CLMN	79789	broad.mit.edu	37	14	95669872	95669872	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95669872A>G	uc001yef.2	-	9	1930	c.1814T>C	c.(1813-1815)CTA>CCA	p.L605P		NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin	605						integral to membrane	actin binding				0				Epithelial(152;0.193)		CCTTTTACCTAGTTTTTCAGC	0.428													35	140	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	29084045	29084045	+	RNA	SNP	T	G	G	rs75345913	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29084045T>G	uc001zcj.2	+	3		c.396T>G								Homo sapiens, Similar to hect domain and RLD 2, clone IMAGE:4581928, mRNA.																		TTATTCGTATTTTTTGGTAAC	0.229													5	26	---	---	---	---	PASS
MTMR10	54893	broad.mit.edu	37	15	31260141	31260141	+	Missense_Mutation	SNP	T	C	C	rs67546733		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31260141T>C	uc001zfh.1	-	6	645	c.547A>G	c.(547-549)AAA>GAA	p.K183E	MTMR10_uc010azx.1_5'UTR|MTMR10_uc001zfi.1_Intron|MTMR10_uc001zfj.2_Missense_Mutation_p.K101E|MTMR10_uc001zfk.2_Intron|MTMR10_uc010ubl.1_Intron	NM_017762	NP_060232	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	183							phosphatase activity			ovary(1)	1		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		TGGTATTTTTTCCCAACATAT	0.328													92	261	---	---	---	---	PASS
TRPM1	4308	broad.mit.edu	37	15	31342634	31342634	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31342634C>T	uc001zfm.2	-	11	1477	c.1349G>A	c.(1348-1350)CGG>CAG	p.R450Q	TRPM1_uc010azy.2_Missense_Mutation_p.R357Q|TRPM1_uc001zfl.2_RNA	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	450	Extracellular (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CTCTATCTTCCGGGGGTCAGT	0.378													5	368	---	---	---	---	PASS
ZNF280D	54816	broad.mit.edu	37	15	56946413	56946413	+	Silent	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56946413A>G	uc002adu.2	-	19	2413	c.2196T>C	c.(2194-2196)ACT>ACC	p.T732T	ZNF280D_uc002adv.2_Silent_p.T719T|ZNF280D_uc010bfq.2_Silent_p.T732T|ZNF280D_uc002adw.1_Intron|ZNF280D_uc010bfp.2_RNA	NM_017661	NP_060131	Q6N043	Z280D_HUMAN	suppressor of hairy wing homolog 4 isoform 1	732					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		GGTGCTCAGAAGTTGGGATAC	0.284													6	375	---	---	---	---	PASS
PIF1	80119	broad.mit.edu	37	15	65114788	65114788	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65114788G>A	uc002ant.2	-	3	646	c.580C>T	c.(580-582)CCT>TCT	p.P194S	PIF1_uc002anr.2_5'Flank|PIF1_uc002ans.2_5'Flank|PIF1_uc010uiq.1_Missense_Mutation_p.P194S|PIF1_uc002anu.2_Missense_Mutation_p.P194S	NM_025049	NP_079325	Q9H611	PIF1_HUMAN	DNA helicase homolog PIF1	194	Hydrolyzes ATP in the presence of both magnesium and single-stranded DNA; weak activity in the presence of RNA or double-stranded DNA; No unwinding activity.				negative regulation of telomerase activity|regulation of telomere maintenance|viral genome replication	nuclear chromosome, telomeric region	ATP binding|ATP-dependent 5'-3' DNA helicase activity|ATP-dependent 5'-3' DNA/RNA helicase activity|magnesium ion binding|single-stranded DNA-dependent ATP-dependent DNA helicase activity|telomeric DNA binding				0						CTCTTCACAGGCAGGGGCCAC	0.607													10	32	---	---	---	---	PASS
ARNT2	9915	broad.mit.edu	37	15	80762712	80762712	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80762712G>T	uc002bfr.2	+	4	514	c.348G>T	c.(346-348)ATG>ATT	p.M116I	ARNT2_uc002bfq.2_Missense_Mutation_p.M116I|ARNT2_uc010unm.1_Missense_Mutation_p.M105I|ARNT2_uc002bfs.2_Missense_Mutation_p.M105I	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator	116	Helix-loop-helix motif.				central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)			TGAAGTCCATGAGGGGTACAG	0.592													17	48	---	---	---	---	PASS
ABHD2	11057	broad.mit.edu	37	15	89744770	89744770	+	3'UTR	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89744770A>G	uc002bnj.2	+	16					ABHD2_uc002bnk.2_3'UTR	NM_007011	NP_008942	P08910	ABHD2_HUMAN	alpha/beta hydrolase domain containing protein							integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)					TACTCTTTTCATTCGGATCAT	0.423													98	236	---	---	---	---	PASS
ZC3H7A	29066	broad.mit.edu	37	16	11858940	11858940	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11858940G>T	uc002dbk.2	-	14	1987	c.1789C>A	c.(1789-1791)CCG>ACG	p.P597T	ZC3H7A_uc002dbj.2_RNA|ZC3H7A_uc002dbl.2_Missense_Mutation_p.P597T|ZC3H7A_uc002dbm.1_Missense_Mutation_p.P507T	NM_014153	NP_054872	Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	597						nucleus	nucleic acid binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						TTTGTAACCGGGTGAGAACAA	0.284													10	635	---	---	---	---	PASS
PARN	5073	broad.mit.edu	37	16	14711480	14711480	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14711480G>A	uc010uzd.1	-	6	497	c.355C>T	c.(355-357)CAG>TAG	p.Q119*	PARN_uc010uzc.1_Nonsense_Mutation_p.Q58*|PARN_uc010uze.1_Nonsense_Mutation_p.Q73*|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_RNA	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation	119					female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						TCAAATCCCTGGCTTGCTAGA	0.368													126	266	---	---	---	---	PASS
SMG1	23049	broad.mit.edu	37	16	18882733	18882733	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18882733A>G	uc002dfm.2	-	16	2618	c.2255T>C	c.(2254-2256)TTC>TCC	p.F752S	SMG1_uc010bwb.2_Missense_Mutation_p.F612S	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	752	Interaction with SMG8 and SMG9.				DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						CGGAAGAGAGAATAAAGGTGC	0.333													8	350	---	---	---	---	PASS
ACSM3	6296	broad.mit.edu	37	16	20803412	20803412	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20803412G>T	uc002dhr.2	+	11	1602	c.1415G>T	c.(1414-1416)TGG>TTG	p.W472L	ACSM3_uc010vba.1_Missense_Mutation_p.W501L|ERI2_uc002dhs.2_Intron	NM_005622	NP_005613	Q53FZ2	ACSM3_HUMAN	SA hypertension-associated homolog isoform 1	472					regulation of blood pressure	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			ovary(1)	1						GGGTATTTCTGGTTTGTTGCA	0.378													7	814	---	---	---	---	PASS
RRN3P3	100131998	broad.mit.edu	37	16	22444123	22444123	+	RNA	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22444123G>A	uc002dkp.2	-	4		c.1060C>T			RRN3P3_uc010vbu.1_RNA	NR_027460				Homo sapiens cDNA FLJ31180 fis, clone KIDNE2000266.												0						ATCACTATCCGCTCAAAATTC	0.333													4	35	---	---	---	---	PASS
CTCF	10664	broad.mit.edu	37	16	67662302	67662302	+	Silent	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67662302C>T	uc002etl.2	+	9	1838	c.1548C>T	c.(1546-1548)ACC>ACT	p.T516T	CTCF_uc010cek.2_Silent_p.T188T|CTCF_uc002etm.1_Silent_p.T5T	NM_006565	NP_006556	P49711	CTCF_HUMAN	CCCTC-binding factor	516	C2H2-type 9.				chromatin modification|chromosome segregation|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|regulation of centromeric sister chromatid cohesion|regulation of molecular function, epigenetic	chromosome, centromeric region|condensed chromosome|nucleolus|nucleoplasm	chromatin insulator sequence binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		ACAAGCGCACCCACACCGGGG	0.597													4	73	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													6	45	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268081	70268081	+	RNA	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268081G>A	uc010cfp.1	-	3		c.334C>T								Homo sapiens cDNA, FLJ98908.																		TCTTACTGTTGGCTAAAAGGC	0.373													4	47	---	---	---	---	PASS
RPAIN	84268	broad.mit.edu	37	17	5331651	5331651	+	Intron	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5331651G>A	uc002gbq.2	+						RPAIN_uc010vsz.1_3'UTR|RPAIN_uc002gbp.1_3'UTR|RPAIN_uc010vta.1_3'UTR|RPAIN_uc010vtb.1_Intron|RPAIN_uc002gbs.2_Intron|RPAIN_uc002gbt.2_Intron|RPAIN_uc002gbu.2_Intron|RPAIN_uc002gbv.2_Intron|RPAIN_uc002gbr.2_Intron|RPAIN_uc002gbw.2_Intron|RPAIN_uc002gbx.1_5'Flank	NM_001033002	NP_001028174	Q86UA6	RIP_HUMAN	RPA interacting protein isoform b						DNA recombination|DNA repair|DNA-dependent DNA replication|protein import into nucleus|response to UV	cytoplasm|cytoplasm|nucleolus|PML body|PML body	metal ion binding|protein complex binding				0						ATTATCTGAGGAATTTACCTG	0.408													15	91	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10399327	10399327	+	Silent	SNP	C	T	T	rs149731873	byFrequency	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10399327C>T	uc002gmo.2	-	35	5203	c.5109G>A	c.(5107-5109)AGG>AGA	p.R1703R	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1703	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						CTGCGATTTTCCTGCTCCTCT	0.542													6	106	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	34235676	34235676	+	RNA	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34235676C>A	uc010ctx.1	-	1		c.1278G>T								Homo sapiens cDNA FLJ43944 fis, clone TESTI4014392.																		CAGACTGCACCAGTGAATTCT	0.453													3	6	---	---	---	---	PASS
GIP	2695	broad.mit.edu	37	17	47036046	47036046	+	3'UTR	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47036046T>C	uc002iol.1	-	6						NM_004123	NP_004114	P09681	GIP_HUMAN	gastric inhibitory polypeptide preproprotein						energy reserve metabolic process|signal transduction	extracellular region|soluble fraction	hormone activity			skin(1)	1						CAGAATCCAGTCCTGAGCTGG	0.517													38	194	---	---	---	---	PASS
MYO5B	4645	broad.mit.edu	37	18	47376016	47376016	+	Silent	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47376016C>A	uc002leb.2	-	32	4524	c.4236G>T	c.(4234-4236)CTG>CTT	p.L1412L	MYO5B_uc002ldz.2_5'UTR|MYO5B_uc002lea.2_Silent_p.L527L	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	1412	Potential.				protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		GCTTTTCTACCAGTTCTTTAA	0.498													6	268	---	---	---	---	PASS
ATP8B1	5205	broad.mit.edu	37	18	55399206	55399206	+	5'Flank	SNP	C	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55399206C>G	uc002lgw.2	-						uc002lgv.1_RNA	NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1						ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(5)|ovary(2)|central_nervous_system(2)|lung(1)	10		Colorectal(73;0.229)				CCAAATTCAACTTGACATGAA	0.338									Byler_disease				6	36	---	---	---	---	PASS
SAFB2	9667	broad.mit.edu	37	19	5613494	5613494	+	Silent	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5613494C>T	uc002mcd.2	-	5	800	c.588G>A	c.(586-588)TTG>TTA	p.L196L	SAFB2_uc010xio.1_Silent_p.L196L|SAFB2_uc010xip.1_RNA	NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	196					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		CTTTGAAGTTCAACGATGAAG	0.418													70	231	---	---	---	---	PASS
COL5A3	50509	broad.mit.edu	37	19	10087919	10087919	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10087919C>T	uc002mmq.1	-	44	3360	c.3274G>A	c.(3274-3276)GAT>AAT	p.D1092N		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	1092	Triple-helical region.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)			TCTCCTTTATCGCCTTTACTC	0.607													5	71	---	---	---	---	PASS
MRPL4	51073	broad.mit.edu	37	19	10370469	10370469	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10370469G>T	uc002mnm.2	+	10	1070	c.916G>T	c.(916-918)GCC>TCC	p.A306S	MRPL4_uc002mnn.2_Missense_Mutation_p.A306S|MRPL4_uc002mno.2_3'UTR	NM_146387	NP_666499	Q9BYD3	RM04_HUMAN	mitochondrial ribosomal protein L4 isoform a	306					translation	mitochondrion|ribosome	structural constituent of ribosome	p.A306fs>4(1)		ovary(1)	1		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)		GGGCCCAGCGGCCACCCCGTA	0.667													5	30	---	---	---	---	PASS
ZNF257	113835	broad.mit.edu	37	19	22271975	22271975	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22271975A>T	uc010ecx.2	+	4	1592	c.1423A>T	c.(1423-1425)ACT>TCT	p.T475S	ZNF257_uc010ecy.2_Missense_Mutation_p.T443S	NM_033468	NP_258429	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	475	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.0961)|Lung NSC(12;0.103)				TTCACACCTTACTCAACATAA	0.393													4	98	---	---	---	---	PASS
MLL4	9757	broad.mit.edu	37	19	36221724	36221724	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36221724C>G	uc010eei.2	+	27	5393	c.5393C>G	c.(5392-5394)GCA>GGA	p.A1798G		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	1798					chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTGGAGGCTGCAGAGGAGAAC	0.592													15	26	---	---	---	---	PASS
BIRC8	112401	broad.mit.edu	37	19	53793290	53793290	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53793290G>T	uc002qbk.2	-	1	1586	c.338C>A	c.(337-339)CCT>CAT	p.P113H		NM_033341	NP_203127	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat-containing 8	113					apoptosis		zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(134;0.00304)		TTGTAGCATAGGATTAGGGAA	0.373													7	782	---	---	---	---	PASS
ZNF765	91661	broad.mit.edu	37	19	53879109	53879109	+	5'UTR	SNP	G	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53879109G>A	uc010ydx.1	+	3					ZNF525_uc010eqn.2_5'UTR|ZNF525_uc002qbl.2_RNA	NM_001040185	NP_001035275	Q7L2R6	ZN765_HUMAN	zinc finger protein 765						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00379)		CTCTATACAGGGACGTGATGC	0.463													6	170	---	---	---	---	PASS
ZNF331	55422	broad.mit.edu	37	19	54080261	54080261	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54080261T>G	uc002qbx.1	+	7	1881	c.447T>G	c.(445-447)CAT>CAG	p.H149Q	ZNF331_uc002qby.1_Missense_Mutation_p.H149Q|ZNF331_uc002qbz.1_Missense_Mutation_p.H149Q|ZNF331_uc002qca.1_Missense_Mutation_p.H149Q|ZNF331_uc010eqr.1_Missense_Mutation_p.H149Q|ZNF331_uc002qcb.1_Missense_Mutation_p.H149Q|ZNF331_uc002qcc.1_Missense_Mutation_p.H149Q|ZNF331_uc002qcd.1_Missense_Mutation_p.H149Q	NM_018555	NP_061025	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	149	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)	6				GBM - Glioblastoma multiforme(134;0.00555)		TTAGTCAACATCAGAAAATCC	0.413			T	?	follicular thyroid adenoma								28	76	---	---	---	---	PASS
CACNG7	59284	broad.mit.edu	37	19	54444778	54444778	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54444778T>C	uc002qcr.1	+	4	494	c.479T>C	c.(478-480)GTC>GCC	p.V160A	CACNG7_uc010era.1_Missense_Mutation_p.V160A	NM_031896	NP_114102	P62955	CCG7_HUMAN	voltage-dependent calcium channel gamma-7	160					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(1)	1	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		AACGACGAGGTCATGAACAGG	0.562													6	173	---	---	---	---	PASS
ZNF805	390980	broad.mit.edu	37	19	57752278	57752278	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57752278G>T	uc010ygt.1	+	1	226	c.19G>T	c.(19-21)GAC>TAC	p.D7Y	ZNF805_uc010ygu.1_5'UTR	NM_001023563	NP_001018857	Q5CZA5	ZN805_HUMAN	zinc finger protein 805 isoform 1	7					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GGCTTTGACGGACCCGGCGCA	0.682													9	41	---	---	---	---	PASS
NCOA6	23054	broad.mit.edu	37	20	33329342	33329342	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33329342G>T	uc002xav.2	-	12	7289	c.4718C>A	c.(4717-4719)CCA>CAA	p.P1573Q	NCOA6_uc002xaw.2_Missense_Mutation_p.P1573Q	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1573					brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding			ovary(3)|breast(3)|central_nervous_system(1)	7						AGGGATGCTTGGTGCAACGTT	0.443													5	265	---	---	---	---	PASS
FAM83D	81610	broad.mit.edu	37	20	37580832	37580832	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37580832A>T	uc002xjg.2	+	4	1558	c.1517A>T	c.(1516-1518)AAG>ATG	p.K506M		NM_030919	NP_112181	Q9H4H8	FA83D_HUMAN	hypothetical protein LOC81610	476	Ser-rich.				cell division|mitosis	cytoplasm|spindle pole		p.K506N(1)		ovary(3)	3		Myeloproliferative disorder(115;0.00878)				TCCAGTTTGAAGTCTTCCTCC	0.488													5	196	---	---	---	---	PASS
NCOA3	8202	broad.mit.edu	37	20	46282198	46282198	+	3'UTR	SNP	A	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46282198A>G	uc002xtk.2	+	23					NCOA3_uc002xtl.2_3'UTR|NCOA3_uc002xtm.2_3'UTR|NCOA3_uc002xtn.2_3'UTR|NCOA3_uc010zyc.1_3'UTR	NM_181659	NP_858045	Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5						AAACCACTGTACAAATGACAC	0.393													5	434	---	---	---	---	PASS
SLCO4A1	28231	broad.mit.edu	37	20	61299368	61299368	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61299368A>T	uc002ydb.1	+	9	1848	c.1643A>T	c.(1642-1644)TAC>TTC	p.Y548F	SLCO4A1_uc002ydc.1_Intron|LOC100127888_uc002ydd.2_5'Flank|SLCO4A1_uc002yde.1_Intron	NM_016354	NP_057438	Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family	548	Extracellular (Potential).|Kazal-like.				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(1)	1	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)			TCCCAGGTGTACCGAGACTGT	0.582													184	319	---	---	---	---	PASS
ITSN1	6453	broad.mit.edu	37	21	35094892	35094892	+	Splice_Site	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35094892G>T	uc002yta.1	+	4	390	c.122_splice	c.e4-1	p.G41_splice	DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Splice_Site|ITSN1_uc002ysz.2_Splice_Site_p.G41_splice|ITSN1_uc010gmg.2_Splice_Site_p.G41_splice|ITSN1_uc010gmh.2_Splice_Site|ITSN1_uc002ysw.2_Splice_Site_p.G41_splice|ITSN1_uc010gmi.2_Splice_Site_p.G41_splice|ITSN1_uc010gmj.2_Splice_Site|ITSN1_uc002ysy.2_Splice_Site_p.G41_splice|ITSN1_uc002ysx.2_Splice_Site_p.G41_splice|ITSN1_uc002ytb.1_Splice_Site_p.G41_splice|ITSN1_uc002ytc.1_Splice_Site_p.G41_splice|ITSN1_uc002ytd.2_Splice_Site|ITSN1_uc010gmk.2_Splice_Site_p.G41_splice|ITSN1_uc010gml.2_Splice_Site|ITSN1_uc002ytj.2_Splice_Site_p.G41_splice|ITSN1_uc010gmm.1_Splice_Site|ITSN1_uc002yte.2_5'Flank	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4						TTAATTTACAGGTGATCAAGC	0.299													6	414	---	---	---	---	PASS
ENTHD1	150350	broad.mit.edu	37	22	40140024	40140024	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40140024G>T	uc003ayg.2	-	7	1735	c.1484C>A	c.(1483-1485)CCA>CAA	p.P495Q		NM_152512	NP_689725	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	495										ovary(2)|skin(1)	3	Melanoma(58;0.0749)					AGAGTTATTTGGAAGAATTCC	0.433													4	131	---	---	---	---	PASS
SLC7A3	84889	broad.mit.edu	37	X	70147708	70147708	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70147708A>C	uc004dyn.2	-	6	1141	c.983T>G	c.(982-984)ATT>AGT	p.I328S	SLC7A3_uc004dyo.2_Missense_Mutation_p.I328S	NM_032803	NP_116192	Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid	328	Extracellular (Potential).				cellular nitrogen compound metabolic process	integral to membrane|plasma membrane				ovary(1)|kidney(1)	2	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	AGCCCATCCAATGTAGAGAAA	0.493													6	59	---	---	---	---	PASS
RAB33A	9363	broad.mit.edu	37	X	129306194	129306194	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129306194C>T	uc004evl.2	+	1	422	c.158C>T	c.(157-159)ACC>ATC	p.T53I	RAB33A_uc010nre.2_RNA	NM_004794	NP_004785	Q14088	RB33A_HUMAN	Ras-related protein Rab-33A	53					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding				0						ACCTGCCTGACCTTCCGCTTC	0.572													17	11	---	---	---	---	PASS
FAM122B	159090	broad.mit.edu	37	X	133915948	133915948	+	Splice_Site	SNP	C	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133915948C>A	uc004exr.2	-	8	653	c.503_splice	c.e8-1	p.G168_splice	FAM122B_uc004exq.2_Splice_Site_p.G187_splice|FAM122B_uc004exs.2_Splice_Site_p.G169_splice|FAM122B_uc004ext.2_Splice_Site_p.G116_splice|FAM122B_uc004exu.2_Splice_Site|FAM122B_uc011mvp.1_Splice_Site_p.G135_splice|FAM122B_uc004exv.2_Splice_Site_p.G187_splice	NM_145284	NP_660327	Q7Z309	F122B_HUMAN	hypothetical protein LOC159090												0	Acute lymphoblastic leukemia(192;0.000127)					TCCATTTCACCTAAAACAGAA	0.403													6	268	---	---	---	---	PASS
PASD1	139135	broad.mit.edu	37	X	150842545	150842545	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150842545G>T	uc004fev.3	+	15	2394	c.2062G>T	c.(2062-2064)GAT>TAT	p.D688Y		NM_173493	NP_775764	Q8IV76	PASD1_HUMAN	PAS domain containing 1	688						nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					GACCCCACAGGATTACATCCG	0.498													11	55	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	6367	6367	+	5'UTR	SNP	T	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:6367T>C	uc011mfh.1	+	1					uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		CCTAGCAGGTGTCTCCTCTAT	0.493													53	16	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	5722764	5722766	+	Intron	DEL	CAG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5722764_5722766delCAG	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																		CCTGGGCCTCCAGCAGCAGCAGA	0.591													4	2	---	---	---	---	
RERE	473	broad.mit.edu	37	1	8541778	8541779	+	Intron	DEL	TA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8541778_8541779delTA	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc010nzx.1_Intron|RERE_uc001aph.1_Intron	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		cttaaggtcctatgactggctc	0.084													4	2	---	---	---	---	
CASZ1	54897	broad.mit.edu	37	1	10711096	10711097	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10711096_10711097insG	uc001aro.2	-	12	3037_3038	c.2717_2718insC	c.(2716-2718)CCGfs	p.P906fs	CASZ1_uc001arp.1_Frame_Shift_Ins_p.P906fs	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	906					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		TCACTTGGGCCGGGGGGAACCT	0.698													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	14764374	14764376	+	IGR	DEL	AGG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14764374_14764376delAGG								PRDM2 (612802 upstream) : KAZ (160837 downstream)																							AGAAAGAAAAAGGAGGAGGAGGA	0.458													4	2	---	---	---	---	
ALDH4A1	8659	broad.mit.edu	37	1	19214305	19214305	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19214305delT	uc001bbb.2	-						ALDH4A1_uc010ocu.1_Intron|ALDH4A1_uc001bbc.2_Intron	NM_170726	NP_733844	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4A1 isoform a precursor						proline biosynthetic process|proline catabolic process	mitochondrial matrix	1-pyrroline-5-carboxylate dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	NADH(DB00157)	attaagctggtcccccacttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59408397	59408400	+	IGR	DEL	CCCA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59408397_59408400delCCCA								JUN (158612 upstream) : LOC729467 (189210 downstream)																							GAatttaattcccacagccactct	0.108													4	2	---	---	---	---	
CYP2J2	1573	broad.mit.edu	37	1	60367587	60367587	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60367587delC	uc001czq.2	-							NM_000775	NP_000766	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J,						epoxygenase P450 pathway|linoleic acid metabolic process|regulation of heart contraction|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	arachidonic acid 11,12-epoxygenase activity|arachidonic acid 14,15-epoxygenase activity|aromatase activity|electron carrier activity|heme binding|linoleic acid epoxygenase activity			ovary(1)	1	all_cancers(7;0.000396)					acctccacagcccccactgct	0.000													4	2	---	---	---	---	
NFIA	4774	broad.mit.edu	37	1	61694806	61694806	+	Intron	DEL	A	-	-	rs71789347		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61694806delA	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145	Q12857	NFIA_HUMAN	nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2						AGGGTAAAAGAAAAAAAAAAA	0.279													6	3	---	---	---	---	
UBE2U	148581	broad.mit.edu	37	1	64686318	64686318	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64686318delT	uc001dbn.1	+							NM_152489	NP_689702	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)								ATP binding|protein binding|ubiquitin-protein ligase activity				0						catcaagcagttttttttttc	0.000													9	4	---	---	---	---	
SERBP1	26135	broad.mit.edu	37	1	67890362	67890362	+	Intron	DEL	A	-	-	rs3838405		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67890362delA	uc001ddv.2	-						SERBP1_uc001ddx.2_Intron|SERBP1_uc001ddy.2_Intron|SERBP1_uc001ddw.2_Intron	NM_001018067	NP_001018077	Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1 isoform 1						regulation of mRNA stability	nucleus|perinuclear region of cytoplasm	mRNA 3'-UTR binding|protein binding			skin(1)	1						TATGGGGGGGAAAAAATGAGT	0.318													6	4	---	---	---	---	
LHX8	431707	broad.mit.edu	37	1	75620283	75620283	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75620283delT	uc001dgo.2	+						LHX8_uc001dgq.2_Intron	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN	LIM homeobox 8							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						TGGTTCCCCCTTACACATTGG	0.463													4	2	---	---	---	---	
ST6GALNAC3	256435	broad.mit.edu	37	1	76845831	76845831	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76845831delA	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_Intron|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541	Q8NDV1	SIA7C_HUMAN	sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5						AAGTATTCTTaaaatgggcag	0.174													4	2	---	---	---	---	
AK5	26289	broad.mit.edu	37	1	77895816	77895816	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77895816delA	uc001dhn.2	+						AK5_uc001dho.2_Intron	NM_174858	NP_777283	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5 isoform 1						ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1						tatggagttcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
GBP1	2633	broad.mit.edu	37	1	89522242	89522242	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89522242delT	uc001dmx.2	-							NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,						interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		tttctttgtgtttggctagaa	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91160493	91160494	+	IGR	INS	-	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91160493_91160494insA								ZNF326 (666399 upstream) : BARHL2 (17086 downstream)																							AGGTAGAAGGGAAAAAAAAACA	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98866545	98866547	+	IGR	DEL	AGG	-	-	rs72103370		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98866545_98866547delAGG								MIR137 (354818 upstream) : SNX7 (260689 downstream)																							aagcagaatcaggagaaggccat	0.000													1	5	---	---	---	---	
RNPC3	55599	broad.mit.edu	37	1	104073565	104073565	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104073565delC	uc010oul.1	+						RNPC3_uc010oum.1_Intron|RNPC3_uc010oun.1_Intron	NM_017619	NP_060089	Q96LT9	RBM40_HUMAN	RNA-binding region (RNP1, RRM) containing 3						mRNA processing	U12-type spliceosomal complex	nucleotide binding|protein binding|RNA binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Lung(183;0.111)|Epithelial(280;0.122)|all cancers(265;0.125)|Colorectal(144;0.163)		gtacctgtcacccaagcaata	0.010													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145092769	145092769	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145092769delG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						GCAGAACTGTGGGGAGCAGGA	0.313													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148901093	148901093	+	Intron	DEL	T	-	-	rs113935923		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148901093delT	uc009wkv.1	+											Homo sapiens cDNA, FLJ17483.																		TTTTCCATCATTTTTTTTTTT	0.458													4	2	---	---	---	---	
TMOD4	29765	broad.mit.edu	37	1	151146702	151146702	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151146702delA	uc001exc.3	-						TMOD4_uc001exb.2_5'Flank|TMOD4_uc001exd.2_Intron|TMOD4_uc010pct.1_Intron	NM_013353	NP_037485	Q9NZQ9	TMOD4_HUMAN	tropomodulin 4 (muscle)						muscle contraction	cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			aaacaaaaagaaaaaaaaaag	0.234													3	3	---	---	---	---	
KIRREL	55243	broad.mit.edu	37	1	158044555	158044555	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158044555delC	uc001frn.3	+						KIRREL_uc010pib.1_Intron|KIRREL_uc009wsq.2_5'Flank	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor							integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)					AGACTAGGATCCCACTTCTGT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159648516	159648519	+	IGR	DEL	ACAC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159648516_159648519delACAC								APCS (89856 upstream) : CRP (33561 downstream)																							GTCTTTACTTACACACACACACGC	0.127													4	2	---	---	---	---	
COPA	1314	broad.mit.edu	37	1	160293327	160293327	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160293327delA	uc009wti.2	-						COPA_uc001fvv.3_Intron|COPA_uc009wtj.1_Intron	NM_004371	NP_004362	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha isoform						COPI coating of Golgi vesicle|intracellular protein transport|pancreatic juice secretion|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|extracellular space|microsome|soluble fraction	hormone activity|structural molecule activity			ovary(1)|skin(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GACCCTGTAGAAAAGAGTGGT	0.423													105	53	---	---	---	---	
ADAMTS4	9507	broad.mit.edu	37	1	161165724	161165725	+	Intron	INS	-	AC	AC	rs143918790	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161165724_161165725insAC	uc001fyt.3	-							NM_005099	NP_005090	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis|skeletal system development	extracellular space|proteinaceous extracellular matrix	metalloendopeptidase activity|protease binding|zinc ion binding			ovary(4)|central_nervous_system(1)	5	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			cacacacacagacacacacaca	0.347													5	3	---	---	---	---	
POGK	57645	broad.mit.edu	37	1	166807003	166807006	+	5'Flank	DEL	TGTG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166807003_166807006delTGTG	uc001gdt.1	+						POGK_uc010ple.1_5'Flank|POGK_uc010plf.1_5'Flank	NM_017542	NP_060012	Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain						multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1						tgtgtgtgtctgtgtgtgtgtgtg	0.333													4	2	---	---	---	---	
KIFAP3	22920	broad.mit.edu	37	1	169930005	169930006	+	Intron	INS	-	A	A	rs140237252	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169930005_169930006insA	uc001ggv.2	-						KIFAP3_uc010plx.1_Intron	NM_014970	NP_055785	Q92845	KIFA3_HUMAN	kinesin-associated protein 3						blood coagulation|plus-end-directed vesicle transport along microtubule|protein complex assembly|signal transduction	centrosome|condensed nuclear chromosome|cytosol|endoplasmic reticulum|kinesin II complex|spindle microtubule	kinesin binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GACTAACTTGGAAAAAAAAATG	0.292													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	179789664	179789665	+	IGR	INS	-	G	G	rs148739247	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179789664_179789665insG								FAM163A (4338 upstream) : TOR1AIP2 (24289 downstream)																							ttggcctgtgtctagggatgag	0.040													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	195091853	195091854	+	IGR	DEL	GG	-	-	rs150151405	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195091853_195091854delGG								None (None upstream) : None (None downstream)																							ttattaggctgggactatccct	0.000													4	2	---	---	---	---	
KIF21B	23046	broad.mit.edu	37	1	200994851	200994851	+	5'Flank	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200994851delG	uc001gvs.1	-						KIF21B_uc001gvr.1_5'Flank|KIF21B_uc009wzl.1_5'Flank|KIF21B_uc010ppn.1_5'Flank|uc001gvu.2_RNA	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6						TCTGACTTCCGACAGTAGATG	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	203490718	203490718	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203490718delG								OPTC (12641 upstream) : ATP2B4 (105210 downstream)																							acgccactctgattctctgag	0.095													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	206116903	206116903	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206116903delT								SLC26A9 (204315 upstream) : FAM72A (22008 downstream)																							CTGTGGGTTATTTTTTTTTTA	0.393													4	5	---	---	---	---	
CNIH3	149111	broad.mit.edu	37	1	224838780	224838783	+	Intron	DEL	CACG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224838780_224838783delCACG	uc001hos.1	+							NM_152495	NP_689708	Q8TBE1	CNIH3_HUMAN	cornichon homolog 3						intracellular signal transduction|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic shaft|postsynaptic membrane					0	Breast(184;0.218)			GBM - Glioblastoma multiforme(131;0.073)		cacacacacacacgcacaaacaca	0.407													4	2	---	---	---	---	
CABC1	56997	broad.mit.edu	37	1	227154174	227154174	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227154174delA	uc001hqm.1	+						CABC1_uc001hqn.1_Intron|CABC1_uc009xeq.1_Intron|CABC1_uc010pvq.1_Intron|CABC1_uc010pvr.1_Intron	NM_020247	NP_064632	Q8NI60	ADCK3_HUMAN	chaperone, ABC1 activity of bc1 complex like						cell death	mitochondrion	ATP binding|protein serine/threonine kinase activity				0		Prostate(94;0.0771)				GGTACACTCTAAGTTAGTTAC	0.438													4	2	---	---	---	---	
OBSCN	84033	broad.mit.edu	37	1	228424535	228424535	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228424535delT	uc009xez.1	+						OBSCN_uc001hsn.2_Intron	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				ggaatgttgattttttttttc	0.000													4	2	---	---	---	---	
GALNT2	2590	broad.mit.edu	37	1	230258362	230258363	+	Intron	DEL	TG	-	-	rs5781568		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230258362_230258363delTG	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				AGGGTGGCTCtgtgtgtgtgtg	0.292													2	4	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	232125424	232125424	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232125424delG	uc001huz.2	+						TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				CTACAGAGTTGGGAAGATCGA	0.259													4	2	---	---	---	---	
PCNXL2	80003	broad.mit.edu	37	1	233234262	233234262	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233234262delT	uc001hvl.2	-						PCNXL2_uc001hvm.1_Intron|PCNXL2_uc009xfu.2_Intron|PCNXL2_uc001hvp.1_Intron|PCNXL2_uc009xfv.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)				CTATGCCTTCTTTTTTTTTTC	0.368													3	3	---	---	---	---	
SLC35F3	148641	broad.mit.edu	37	1	234456331	234456331	+	Intron	DEL	A	-	-	rs74147434	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234456331delA	uc001hwa.1	+						SLC35F3_uc001hvy.1_Intron	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)			GATGTAGCAGAAAAAAAATGT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	242116697	242116698	+	IGR	INS	-	A	A	rs146028908	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242116697_242116698insA								EXO1 (63650 upstream) : MAP1LC3C (42094 downstream)																							atcaataaattaaaaaaaaTAG	0.183													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244509476	244509476	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244509476delT								ZNF238 (288700 upstream) : C1orf100 (6461 downstream)																							GTTATGTTGGTTAGAACTAAG	0.373													4	2	---	---	---	---	
TRIM58	25893	broad.mit.edu	37	1	248036039	248036040	+	Intron	DEL	GA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248036039_248036040delGA	uc001ido.2	+						OR2W3_uc001idp.1_Intron	NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58							intracellular	zinc ion binding			skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			ggagtgaggtgagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16644539	16644539	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16644539delC								MYCN (557411 upstream) : FAM49A (89362 downstream)																							AAACAAAAAACCCACGCCCTT	0.393													4	2	---	---	---	---	
KCNS3	3790	broad.mit.edu	37	2	18084324	18084324	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18084324delC	uc002rcv.2	+						KCNS3_uc002rcw.2_Intron	NM_002252	NP_002243	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel						energy reserve metabolic process|regulation of insulin secretion	Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium channel regulator activity			ovary(4)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TCTGTGGTGACCACCATTTCA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20280178	20280178	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20280178delG								LAPTM4A (28389 upstream) : SDC1 (120380 downstream)																							AAGGTGGAGAGGGGGCTTGAA	0.522													4	2	---	---	---	---	
C2orf84	653140	broad.mit.edu	37	2	24400411	24400412	+	Intron	INS	-	T	T	rs141426860	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24400411_24400412insT	uc002rfc.2	+						C2orf84_uc010eyc.2_Intron	NM_001040710	NP_001035800	Q86W67	CB084_HUMAN	hypothetical protein LOC653140												0						GCTATCAGGGATTTTTTTTAAA	0.337													5	5	---	---	---	---	
CEBPZ	10153	broad.mit.edu	37	2	37442333	37442334	+	Intron	DEL	AG	-	-	rs3217142		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37442333_37442334delAG	uc002rpz.2	-							NM_005760	NP_005751	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein zeta						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding			pancreas(1)	1		all_hematologic(82;0.21)				CATAGCTGTCAGTGCCGTTACA	0.401													4	3	---	---	---	---	
CEBPZ	10153	broad.mit.edu	37	2	37442339	37442340	+	Intron	DEL	GT	-	-	rs3841525		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37442339_37442340delGT	uc002rpz.2	-							NM_005760	NP_005751	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein zeta						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding			pancreas(1)	1		all_hematologic(82;0.21)				TGTCAGTGCCGTTACAGTGAAA	0.386													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43077376	43077376	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43077376delT								HAAO (57625 upstream) : ZFP36L2 (372166 downstream)																							TGAGCCCCGGTCCTCCTCCCT	0.607													4	2	---	---	---	---	
SRBD1	55133	broad.mit.edu	37	2	45644386	45644386	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45644386delA	uc002rus.2	-						SRBD1_uc010yoc.1_Intron	NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			agtctatgataaatctgtaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	59182185	59182186	+	Intron	INS	-	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59182185_59182186insC	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																		GTGCCTCGTTTCCCCTGACTTT	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60931010	60931010	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60931010delT								BCL11A (150377 upstream) : PAPOLG (52373 downstream)																							ttgatggttgttttttttttc	0.035													3	3	---	---	---	---	
PUS10	150962	broad.mit.edu	37	2	61192800	61192800	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61192800delT	uc010fci.2	-						PUS10_uc002sao.2_Intron|PUS10_uc010ypk.1_Intron	NM_144709	NP_653310	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(2)|large_intestine(1)|kidney(1)	4			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			AATAGTTTTGTTTTTTTTTTT	0.299													5	3	---	---	---	---	
VAX2	25806	broad.mit.edu	37	2	71157377	71157378	+	Intron	INS	-	A	A	rs144792191	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71157377_71157378insA	uc002shh.2	+							NM_012476	NP_036608	Q9UIW0	VAX2_HUMAN	ventral anterior homeobox 2						ectoderm development|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						ttcaaaacaccaactcacatct	0.178													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82542761	82542762	+	IGR	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82542761_82542762insT								None (None upstream) : None (None downstream)																							TTTTATACTTGTTTTTTTACCA	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	83201091	83201092	+	IGR	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83201091_83201092insT								None (None upstream) : None (None downstream)																							GCTGATAGATCTTTTTTTTTTA	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92317886	92317886	+	IGR	DEL	T	-	-	rs71254507		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92317886delT								FKSG73 (187392 upstream) : None (None downstream)																							gagttgaacctttcttttgag	0.000													20	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106221835	106221835	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106221835delA	uc002tdf.2	-											Homo sapiens hypothetical protein LOC285000, mRNA (cDNA clone IMAGE:3925223), partial cds.																		CTTGCCCTGCAAAAAAATAAA	0.204													4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	110015641	110015641	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110015641delG	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						gattttcagtggtccagggaa	0.229													4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	110027313	110027313	+	Intron	DEL	A	-	-	rs59358067		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110027313delA	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						AGAGATTTCCATTGGATGATC	0.483													3	5	---	---	---	---	
ZC3H8	84524	broad.mit.edu	37	2	112991123	112991125	+	Intron	DEL	TCT	-	-	rs142308039		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112991123_112991125delTCT	uc002thp.2	-							NM_032494	NP_115883	Q8N5P1	ZC3H8_HUMAN	zinc finger CCCH-type containing 8						apoptosis|negative regulation of T cell differentiation in thymus|negative regulation of transcription, DNA-dependent|positive regulation of thymocyte apoptosis|response to antibiotic|T cell homeostasis	nucleus	RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						CTGCTTAAAATCTTCTTAAGTCC	0.192													9	5	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	116280487	116280487	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116280487delT	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						AGAATCAGTGTTGACCAAGAT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	117710449	117710449	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117710449delT								None (None upstream) : DDX18 (861806 downstream)																							actttctaggttttatagctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	127693689	127693689	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127693689delT								GYPC (239444 upstream) : BIN1 (111918 downstream)																							CAGCCAGCACTTTTTTTTTCT	0.358													4	2	---	---	---	---	
UGGT1	56886	broad.mit.edu	37	2	128933982	128933982	+	Intron	DEL	A	-	-	rs71731988		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128933982delA	uc002tps.2	+						UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1						'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						actctgtctcaaaaaaaaaaa	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130115387	130115388	+	IGR	DEL	AC	-	-	rs150207522		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130115387_130115388delAC								None (None upstream) : LOC389033 (565047 downstream)																							GCATCTGGAAACACACACACAC	0.465													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132817202	132817204	+	IGR	DEL	AGA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132817202_132817204delAGA								C2orf27B (257968 upstream) : NCRNA00164 (87960 downstream)																							CTTATCAAGGAGAAGAACTCAAG	0.310													4	4	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	133007618	133007618	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133007618delA	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						cacattctacaaaaacaccat	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133036797	133036798	+	IGR	INS	-	AGC	AGC	rs142957672		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133036797_133036798insAGC								NCRNA00164 (21255 upstream) : GPR39 (137349 downstream)																							caggatcaaaaaacatccctat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133093581	133093581	+	IGR	DEL	A	-	-	rs112636531		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133093581delA								NCRNA00164 (78039 upstream) : GPR39 (80566 downstream)																							ttacaataacaaaaagggcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134813443	134813443	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134813443delC								NCKAP5 (487412 upstream) : MGAT5 (198387 downstream)																							TCAGAAGTCACCAGCagcaga	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	137411593	137411594	+	IGR	DEL	TG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137411593_137411594delTG								CXCR4 (535868 upstream) : THSD7B (111521 downstream)																							GGTGTTCAGCTGTGTGTGTACT	0.455													4	2	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	137870342	137870343	+	Intron	INS	-	GTGTGT	GTGTGT	rs148763110	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137870342_137870343insGTGTGT	uc002tva.1	+						THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		TGTTAAtgtacgtgtgtgtgtg	0.302													3	3	---	---	---	---	
PRPF40A	55660	broad.mit.edu	37	2	153513134	153513135	+	Intron	DEL	AG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153513134_153513135delAG	uc002tyh.3	-						PRPF40A_uc002tyg.3_Intron	NM_017892	NP_060362	O75400	PR40A_HUMAN	formin binding protein 3						mRNA processing|RNA splicing	nuclear matrix|nuclear speck	protein binding				0						ttgttgagacagagtcttgttc	0.134													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	158222213	158222214	+	IGR	INS	-	T	T	rs140170666	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158222213_158222214insT								ERMN (38067 upstream) : CYTIP (48917 downstream)																							CCTttcctctcttttttttttc	0.342													4	3	---	---	---	---	
CCDC148	130940	broad.mit.edu	37	2	159038322	159038322	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159038322delG	uc002tzq.2	-						CCDC148_uc002tzr.2_Intron|CCDC148_uc010foh.2_Intron	NM_138803	NP_620158	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148											ovary(2)	2						gctggactgtgGGGGTTTTGA	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	168297716	168297716	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168297716delG								XIRP2 (181457 upstream) : B3GALT1 (377466 downstream)																							AAAGTTGCCTGGGACATGATT	0.433													4	2	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171259144	171259144	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171259144delA	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						ctactgcttgaaaaaaaaaag	0.239													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177885871	177885871	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177885871delT								MIR1246 (420091 upstream) : HNRNPA3 (191551 downstream)																							TCCAGCCACCTTTTTAATGGC	0.398													4	2	---	---	---	---	
ZNF804A	91752	broad.mit.edu	37	2	185648300	185648300	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185648300delT	uc002uph.2	+							NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A							intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11						TCTCAGTCACTTTTCTCTGGC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	190804144	190804144	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190804144delA								PMS1 (61790 upstream) : MSTN (116283 downstream)																							ctagcagtggaaaaaaaaagt	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201833365	201833365	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201833365delA								ORC2L (4955 upstream) : FAM126B (5077 downstream)																							aggattaattaaaaaaaaaag	0.000													4	2	---	---	---	---	
CREB1	1385	broad.mit.edu	37	2	208397937	208397938	+	Intron	INS	-	T	T	rs140311533	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208397937_208397938insT	uc002vcc.2	+						CREB1_uc010ziz.1_Intron|CREB1_uc002vcd.2_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)	GTTTTGAATGATTTTTTTTTTG	0.292			T	EWSR1	clear cell sarcoma|angiomatoid fibrous histiocytoma								3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	216536921	216536921	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216536921delT	uc002vfm.1	-						uc002vfn.1_Intron					Homo sapiens cDNA FLJ34546 fis, clone HLUNG2008959.																		tgtatggaaatttttttttgt	0.035													4	3	---	---	---	---	
SMARCAL1	50485	broad.mit.edu	37	2	217280531	217280531	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217280531delT	uc002vgc.3	+						SMARCAL1_uc010fvf.2_Intron|SMARCAL1_uc002vgd.3_Intron|SMARCAL1_uc010fvg.2_Intron	NM_014140	NP_054859	Q9NZC9	SMAL1_HUMAN	SWI/SNF-related matrix-associated						chromatin modification|DNA metabolic process|regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity			ovary(3)|breast(3)|skin(1)	7		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		tgaacagcagtttttttgaaa	0.124									Schimke_Immuno-Osseous_Dysplasia				4	2	---	---	---	---	
VIL1	7429	broad.mit.edu	37	2	219299818	219299819	+	Intron	DEL	CT	-	-	rs67794207		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219299818_219299819delCT	uc002via.2	+						VIL1_uc010zke.1_Intron|VIL1_uc002vib.2_Intron	NM_007127	NP_009058	P09327	VILI_HUMAN	villin 1						actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTGAAAAGACTCTCTAGTTTC	0.490													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	220837874	220837875	+	IGR	INS	-	T	T	rs144684724	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220837874_220837875insT								SLC4A3 (331173 upstream) : None (None downstream)																							aacttaatgcattttttttaga	0.000													2	4	---	---	---	---	
DNER	92737	broad.mit.edu	37	2	230266274	230266275	+	Intron	INS	-	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230266274_230266275insA	uc002vpv.2	-							NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		acgctgagtagaaaaaaaaatc	0.000													4	2	---	---	---	---	
DNER	92737	broad.mit.edu	37	2	230291647	230291648	+	Intron	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230291647_230291648insT	uc002vpv.2	-							NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		CAGAGCATTCGTTGGTGTGTGG	0.322													4	2	---	---	---	---	
TRIP12	9320	broad.mit.edu	37	2	230667606	230667607	+	Intron	INS	-	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230667606_230667607insA	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron|TRIP12_uc010zlz.1_Intron	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ACACTGCCACCAAAAAAAAAAC	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239915784	239915784	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239915784delC								TWIST2 (83547 upstream) : HDAC4 (54081 downstream)																							atctgctacacccagatgaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	240839264	240839264	+	IGR	DEL	A	-	-	rs5839824		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240839264delA								HDAC4 (515918 upstream) : NDUFA10 (60894 downstream)																							acCAGCCCAGAAAGCCCACCC	0.303													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	241239593	241239594	+	IGR	DEL	GA	-	-	rs10540873		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241239593_241239594delGA								OTOS (159520 upstream) : GPC1 (135521 downstream)																							agaaagagaggagagagagaga	0.307													4	2	---	---	---	---	
CMC1	152100	broad.mit.edu	37	3	28280321	28280321	+	5'Flank	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28280321delA	uc003cea.2	+							NM_182523	NP_872329	Q7Z7K0	COXAM_HUMAN	COX assembly mitochondrial protein homolog							mitochondrion	metal ion binding				0						TACATTTGCCAAAAAAAGGAA	0.378													4	2	---	---	---	---	
ANO10	55129	broad.mit.edu	37	3	43444583	43444583	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43444583delT	uc003cmv.2	-						ANO10_uc011azs.1_Intron|ANO10_uc003cmw.2_Intron|ANO10_uc010hil.2_Intron|ANO10_uc011azt.1_Intron	NM_018075	NP_060545	Q9NW15	ANO10_HUMAN	transmembrane protein 16K						cell death	chloride channel complex	chloride channel activity			ovary(2)	2						TGTTAGATTATTTTTTCTTCC	0.453													4	2	---	---	---	---	
DNAH1	25981	broad.mit.edu	37	3	52402599	52402599	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52402599delA	uc011bef.1	+							NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1						ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ATGTGACACCAAAAAAATCCC	0.483													4	2	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52588818	52588818	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52588818delG	uc003des.2	-	27	4543	c.4531delC	c.(4531-4533)CAGfs	p.Q1511fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Intron|PBRM1_uc003der.2_Frame_Shift_Del_p.Q1424fs|PBRM1_uc003det.2_Intron|PBRM1_uc003deu.2_Intron|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.Q1456fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.Q1431fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.Q1404fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.Q1455fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1511	Pro-rich.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TGAAGTGGCTGCATGCTGCCC	0.592			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								26	24	---	---	---	---	
FLNB	2317	broad.mit.edu	37	3	58041141	58041142	+	Intron	DEL	GG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58041141_58041142delGG	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GGTGGTGGGCGGGCCATATTTG	0.292													4	2	---	---	---	---	
FHIT	2272	broad.mit.edu	37	3	61052321	61052321	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61052321delA	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)		agaaaacagcaaaaagtatta	0.045			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	74964511	74964512	+	IGR	DEL	CA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74964511_74964512delCA								CNTN3 (394168 upstream) : FAM86D (506193 downstream)																							CATGTTTGTTCACAAATGAATA	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	80450403	80450404	+	IGR	DEL	GT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80450403_80450404delGT								ROBO1 (633344 upstream) : None (None downstream)																							tgggcagatggtgaatatcttt	0.248													4	2	---	---	---	---	
GBE1	2632	broad.mit.edu	37	3	81719609	81719609	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81719609delC	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)		ATCAATTTCACCCGACCTCTT	0.343									Glycogen_Storage_Disease_type_IV				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	87812672	87812672	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87812672delT								POU1F1 (486935 upstream) : HTR1F (219054 downstream)																							tcctctgaccttttttttcta	0.144													4	2	---	---	---	---	
EPHA3	2042	broad.mit.edu	37	3	89376883	89376883	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89376883delT	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)		AGAACTGTGCTTTTTTTTTGT	0.363										TSP Lung(6;0.00050)			2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	94003850	94003850	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94003850delA								NSUN3 (158220 upstream) : LOC255025 (653257 downstream)																							AATAAAGCCCAATAAAGAAGT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	95191017	95191017	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95191017delT								LOC255025 (295938 upstream) : None (None downstream)																							gaaaaaaaggttacaggagtt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	95892609	95892610	+	IGR	INS	-	T	T	rs143058712	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95892609_95892610insT								LOC255025 (997530 upstream) : EPHA6 (640815 downstream)																							ttgaagcggtcttttttttaac	0.000													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105677805	105677805	+	IGR	DEL	C	-	-	rs137874592		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105677805delC								CBLB (89539 upstream) : LOC100302640 (877855 downstream)																							TCTTTAAGGACGCAGTTtccc	0.239													3	4	---	---	---	---	
PVRL3	25945	broad.mit.edu	37	3	110833649	110833650	+	Intron	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110833649_110833650insT	uc003dxt.1	+						PVRL3_uc003dxu.1_Intron	NM_015480	NP_056295	Q9NQS3	PVRL3_HUMAN	poliovirus receptor-related 3 precursor						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane	cell adhesion molecule binding|protein homodimerization activity			upper_aerodigestive_tract(2)	2						ttatacatggatttttttttca	0.084													4	2	---	---	---	---	
WDR52	55779	broad.mit.edu	37	3	113141496	113141496	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113141496delT	uc003eae.1	-							NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2											central_nervous_system(1)	1						TGCCCACCGGTTTTTTTCTTT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	113822046	113822046	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113822046delT								QTRTD1 (14780 upstream) : DRD3 (25511 downstream)																							ggtaagaagcttttttttgtc	0.159													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	115309834	115309835	+	IGR	INS	-	T	T	rs113983981		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115309834_115309835insT								ZBTB20 (443707 upstream) : GAP43 (32316 downstream)																							CCCTGTACTCATTTTTTTTTTT	0.272													3	3	---	---	---	---	
LSAMP	4045	broad.mit.edu	37	3	115721398	115721398	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115721398delA	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		CATCCCTTGGAAAAAAAAATC	0.483													3	3	---	---	---	---	
NR1I2	8856	broad.mit.edu	37	3	119501307	119501308	+	Intron	DEL	GA	-	-	rs2276706	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119501307_119501308delGA	uc003edj.2	+						NR1I2_uc003edi.2_Intron|NR1I2_uc003edk.2_5'Flank	NM_003889	NP_003880	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2						drug export|exogenous drug catabolic process|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|steroid metabolic process|xenobiotic metabolic process|xenobiotic transport	nucleoplasm	drug binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(114;0.175)	Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Rifampin(DB01045)|Vitamin E(DB00163)	TTCTAGGGTGGAAAAAAAAAAG	0.436													4	2	---	---	---	---	
EPHB1	2047	broad.mit.edu	37	3	134846775	134846776	+	Intron	INS	-	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134846775_134846776insC	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron|EPHB1_uc003equ.2_Intron	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						CCAACCACACTCCCTCCTCACC	0.475													4	2	---	---	---	---	
STAG1	10274	broad.mit.edu	37	3	136161037	136161038	+	Intron	DEL	CA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136161037_136161038delCA	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						aagactcAATCACACACACACA	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145708951	145708954	+	IGR	DEL	CTGT	-	-	rs5853251		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145708951_145708954delCTGT								None (None upstream) : PLOD2 (78274 downstream)																							gtttgtttgcctgtctgtctttgt	0.020													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	150221082	150221082	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150221082delA								TSC22D2 (43469 upstream) : SERP1 (38699 downstream)																							aaggagtgacaaaaaaccaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	167724037	167724038	+	IGR	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167724037_167724038insT								SERPINI1 (180681 upstream) : GOLIM4 (3616 downstream)																							TTTATAGACTATTTTTTTTCCA	0.243													4	2	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	168936746	168936747	+	Intron	DEL	GT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168936746_168936747delGT	uc011bpj.1	-						MECOM_uc003ffl.2_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform c						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						ATATAGCTGCGTGTGTGTGTGT	0.485													4	2	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170372145	170372145	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170372145delT	uc011bpt.1	+						uc003fha.1_Intron	NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			AAGGCGACTATTTTTTTTTTA	0.433													4	3	---	---	---	---	
FNDC3B	64778	broad.mit.edu	37	3	171759789	171759789	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171759789delA	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fhx.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)		ATAGTTGATTAAAAAAAAAAT	0.363													4	2	---	---	---	---	
FNDC3B	64778	broad.mit.edu	37	3	171870369	171870369	+	Intron	DEL	T	-	-	rs71931144		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171870369delT	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fia.2_Intron|FNDC3B_uc003fhx.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)		TGGGAAGGGCTTTTTTTTTTT	0.443													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177835432	177835434	+	IGR	DEL	GAA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177835432_177835434delGAA								TBL1XR1 (920384 upstream) : KCNMB2 (418790 downstream)																							gcctcttcctgaagcactttagc	0.143													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	179842325	179842325	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179842325delT								PEX5L (87808 upstream) : TTC14 (477593 downstream)																							ttgtgactcctttttttctct	0.000													4	2	---	---	---	---	
KNG1	3827	broad.mit.edu	37	3	186432807	186432810	+	5'Flank	DEL	ACAC	-	-	rs112328658		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186432807_186432810delACAC	uc011bsa.1	+						KNG1_uc003fqr.2_5'Flank	NM_001102416	NP_001095886	P01042	KNG1_HUMAN	kininogen 1 isoform 1						blood coagulation, intrinsic pathway|elevation of cytosolic calcium ion concentration|inflammatory response|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|positive regulation of renal sodium excretion|positive regulation of urine volume|smooth muscle contraction|vasodilation	extracellular space|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding			skin(1)	1	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)	Ouabain(DB01092)	acacacacagacacacacacacac	0.333													5	4	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	187904077	187904077	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187904077delA	uc011bsg.1	+							NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		AAGTTTTCATAAGGGACTGCT	0.453			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195490839	195490841	+	Intron	DEL	TCC	-	-	rs63306962		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195490839_195490841delTCC	uc011bto.1	-						MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTACTCCTTATCCAGATGCCACC	0.626													4	4	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195490843	195490846	+	Intron	DEL	GATG	-	-	rs34858176		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195490843_195490846delGATG	uc011bto.1	-						MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TCCTTATCCAGATGCCACCTCCCG	0.632													2	4	---	---	---	---	
LMLN	89782	broad.mit.edu	37	3	197761637	197761637	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197761637delA	uc011buo.1	+						LMLN_uc003fyt.2_Intron|LMLN_uc010iar.2_Intron|LMLN_uc010ias.2_Intron|LMLN_uc003fyu.2_Intron	NM_033029	NP_149018	Q96KR4	LMLN_HUMAN	leishmanolysin-like isoform 2						cell adhesion|cell division|mitosis|proteolysis	cytoplasm|membrane	metalloendopeptidase activity|zinc ion binding			skin(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		AGGTCTGGATAAAATTCCTGT	0.353													4	2	---	---	---	---	
ZFYVE28	57732	broad.mit.edu	37	4	2418216	2418217	+	Intron	INS	-	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2418216_2418217insC	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						GCTGCTGCACGCCCCCAAAACG	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6239041	6239041	+	RNA	DEL	G	-	-	rs34405068		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6239041delG	uc003giw.1	+	5		c.1544delG								Homo sapiens cDNA FLJ33698 fis, clone BRAWH2004779.																		TGGAGGAAGAGGAGGGACAAA	0.522													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	11274685	11274686	+	IGR	DEL	TT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11274685_11274686delTT								CLNK (588299 upstream) : MIR572 (95765 downstream)																							tctctgcctcttgaacatcaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	19143763	19143765	+	IGR	DEL	TTG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19143763_19143765delTTG								None (None upstream) : None (None downstream)																							CTCTGGATTTTTGTTGTTGTTGT	0.384													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	26067513	26067513	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26067513delG								C4orf52 (136013 upstream) : RBPJ (253819 downstream)																							CTGGAGCAaagggctgcgagg	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	26299111	26299111	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26299111delG								C4orf52 (367611 upstream) : RBPJ (22221 downstream)																							GGAAGATGCTGGCCTTCGCTT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	42109789	42109790	+	IGR	DEL	CC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42109789_42109790delCC								SLC30A9 (20239 upstream) : BEND4 (3082 downstream)																							GAACAAGTTGCCCAGTAAAGCT	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49155702	49155703	+	IGR	INS	-	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49155702_49155703insG								CWH43 (91609 upstream) : None (None downstream)																							attccattccattcattccatt	0.000													3	3	---	---	---	---	
SLC4A4	8671	broad.mit.edu	37	4	72240502	72240503	+	Intron	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72240502_72240503insT	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron|SLC4A4_uc003hgc.3_Intron|SLC4A4_uc003hga.2_Intron|SLC4A4_uc003hgb.3_Intron	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)			TTGTAAAACAGTTTTTTTTTTT	0.337													5	3	---	---	---	---	
SLC4A4	8671	broad.mit.edu	37	4	72426133	72426134	+	Intron	INS	-	TCTT	TCTT	rs142450272	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72426133_72426134insTCTT	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron|SLC4A4_uc003hgc.3_Intron|SLC4A4_uc010iid.2_Intron	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)			TTTATATTCTCTGGTTTTTTAT	0.317													10	10	---	---	---	---	
ANKRD17	26057	broad.mit.edu	37	4	73963152	73963152	+	Intron	DEL	T	-	-	rs55834843		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73963152delT	uc003hgp.2	-						ANKRD17_uc003hgo.2_Intron|ANKRD17_uc003hgq.2_Intron|ANKRD17_uc003hgr.2_Intron	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a						interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATAGAGAGCCttttttttttt	0.134													6	6	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79238878	79238879	+	Intron	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79238878_79238879insT	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron|FRAS1_uc003hky.1_Intron|FRAS1_uc003hkz.2_Intron|FRAS1_uc003hla.1_Intron	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						AAGTGTTATGATTTTTTTTTCT	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	80201749	80201749	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80201749delT	uc003hlr.1	+						uc003hls.2_Intron					Homo sapiens full length insert cDNA clone YY75G10.																		ATTTTGATACTTTTTTTTTCC	0.373													4	2	---	---	---	---	
AFF1	4299	broad.mit.edu	37	4	88056446	88056446	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88056446delT	uc003hqj.3	+						AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926	P51825	AFF1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TGCTTTTAACTTTTTTTTTTC	0.269													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	105706043	105706044	+	IGR	INS	-	T	T	rs149343945	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105706043_105706044insT								CXXC4 (289985 upstream) : TET2 (361899 downstream)																							atattcttcagttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	128272021	128272021	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128272021delA								None (None upstream) : INTU (282099 downstream)																							cgtaaaagttaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153541657	153541657	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153541657delT								FBXW7 (85314 upstream) : TMEM154 (5614 downstream)																							TGACTGAAACTtttttttgtt	0.234													6	3	---	---	---	---	
PDGFC	56034	broad.mit.edu	37	4	157866940	157866940	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157866940delA	uc003iph.1	-						PDGFC_uc003ipi.1_Intron|PDGFC_uc011cis.1_Intron	NM_016205	NP_057289	Q9NRA1	PDGFC_HUMAN	platelet-derived growth factor C precursor						central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		attctctctgaaaaacATCCA	0.194													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164449736	164449737	+	3'UTR	INS	-	TGTT	TGTT	rs144407064	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164449736_164449737insTGTT	uc003iqs.1	-	8					MARCH1_uc003iqr.1_3'UTR	NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GGCATTTGGTCTGTTTGTTTTT	0.371													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	176268830	176268830	+	IGR	DEL	T	-	-	rs36019040		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176268830delT								ADAM29 (369500 upstream) : GPM6A (285259 downstream)																							GCCTTATACATTTTTTTTTTC	0.358													4	2	---	---	---	---	
GPM6A	2823	broad.mit.edu	37	4	176556193	176556193	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176556193delC	uc003iuf.2	-	7	1504	c.700delG	c.(700-702)GTTfs	p.V234fs	GPM6A_uc011ckj.1_Frame_Shift_Del_p.V227fs|GPM6A_uc003iug.2_Frame_Shift_Del_p.V234fs|GPM6A_uc003iuh.2_Frame_Shift_Del_p.V223fs	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2	234	Helical; (Potential).					cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		GCAGACAGAACCATAAGGTAG	0.413													87	47	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	178553740	178553740	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178553740delT	uc003iux.1	+											Homo sapiens cDNA FLJ37626 fis, clone BRCOC2014748.																		aagagagagcttttttttttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180278361	180278361	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180278361delA								None (None upstream) : None (None downstream)																							caagagtgctagaagctgtga	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180953739	180953740	+	IGR	INS	-	GT	GT			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180953739_180953740insGT								None (None upstream) : None (None downstream)																							gggcagagcaggtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190818022	190818022	+	Intron	DEL	A	-	-	rs113369235		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190818022delA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		ttgtgatggtaggggggtggc	0.000													6	4	---	---	---	---	
ZNF622	90441	broad.mit.edu	37	5	16467767	16467767	+	5'Flank	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16467767delA	uc003jfq.2	-							NM_033414	NP_219482	Q969S3	ZN622_HUMAN	zinc finger protein 622							cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1						ctgtggctggagagtctccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24162787	24162787	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24162787delT	uc003jgq.1	+											Homo sapiens cDNA FLJ34836 fis, clone NT2NE2010400.																		AGAATCAGTGTTTTGTGGGGG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	34013003	34013004	+	IGR	INS	-	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34013003_34013004insA								AMACR (4797 upstream) : C1QTNF3 (4960 downstream)																							GGCATAAATACAaaaaaaaaag	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42745817	42745818	+	IGR	INS	-	A	A	rs140946194	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42745817_42745818insA								GHR (23892 upstream) : CCDC152 (11102 downstream)																							TAGAAAAAGGTAAAAAATTGTC	0.317													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	53630129	53630129	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53630129delC								ARL15 (23726 upstream) : HSPB3 (121316 downstream)																							atcaacctgtccccacttacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	57546976	57546976	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57546976delA								ACTBL2 (768340 upstream) : PLK2 (202836 downstream)																							gataaccaggaaggggacaga	0.025													4	2	---	---	---	---	
JMY	133746	broad.mit.edu	37	5	78608021	78608021	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78608021delT	uc003kfx.3	+						JMY_uc003kfw.1_Intron	NM_152405	NP_689618	Q8N9B5	JMY_HUMAN	junction-mediating and regulatory protein						'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		ACTAAAACTGTGTATTAAAAA	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	106276729	106276729	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106276729delA								None (None upstream) : EFNA5 (435862 downstream)																							agcctcctttaaaaaaacctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	109266292	109266292	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109266292delA								MAN2A1 (62863 upstream) : TMEM232 (358642 downstream)																							TTCACAATTGAAAAAAAAATG	0.279													4	2	---	---	---	---	
YTHDC2	64848	broad.mit.edu	37	5	112894853	112894854	+	Intron	INS	-	G	G	rs141909278	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112894853_112894854insG	uc003kqn.2	+						YTHDC2_uc010jcf.1_Intron	NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2								ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		aggagcctggaggtaagtcaga	0.000													2	5	---	---	---	---	
ZNF608	57507	broad.mit.edu	37	5	123987062	123987062	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123987062delA	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)		TGGTTTTCTCATCATCTTCTC	0.453													4	2	---	---	---	---	
SPOCK1	6695	broad.mit.edu	37	5	136558832	136558834	+	Intron	DEL	GGC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136558832_136558834delGGC	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)			ataacaactgggcaggaagagac	0.153													4	2	---	---	---	---	
PKD2L2	27039	broad.mit.edu	37	5	137225971	137225971	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137225971delA	uc003lby.2	+						PKD2L2_uc010jep.1_Intron|PKD2L2_uc003lbw.1_Intron|PKD2L2_uc003lbx.2_Intron	NM_014386	NP_055201	Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2							integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			actccgtctcaaaaaaaaaaT	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	137824440	137824440	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137824440delA								EGR1 (19436 upstream) : ETF1 (17348 downstream)																							acagcagggcaaaaaggacaa	0.239													4	2	---	---	---	---	
NRG2	9542	broad.mit.edu	37	5	139378582	139378582	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139378582delC	uc003lex.1	-						NRG2_uc003lev.1_Intron|NRG2_uc003lew.1_Intron|NRG2_uc003ley.1_Intron	NM_004883	NP_004874	O14511	NRG2_HUMAN	neuregulin 2 isoform 1						embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ttcagatccacttcctgcttg	0.070													4	2	---	---	---	---	
GNPDA1	10007	broad.mit.edu	37	5	141394116	141394117	+	5'Flank	INS	-	TTTTG	TTTTG	rs143783926	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141394116_141394117insTTTTG	uc003lmf.3	-						GNPDA1_uc003lmg.3_5'Flank|GNPDA1_uc010jgh.2_5'Flank|GNPDA1_uc003lmh.3_5'Flank	NM_005471	NP_005462	P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1						generation of precursor metabolites and energy|glucosamine catabolic process|N-acetylglucosamine metabolic process|single fertilization	cytoplasm	glucosamine-6-phosphate deaminase activity|hydrolase activity				0		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTCAGTGttattttgttttgt	0.406													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	143364576	143364576	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143364576delA								HMHB1 (164294 upstream) : YIPF5 (173155 downstream)																							tccaacacagaaaaaaatctt	0.000													4	2	---	---	---	---	
AFAP1L1	134265	broad.mit.edu	37	5	148693849	148693850	+	Intron	DEL	GT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148693849_148693850delGT	uc003lqh.2	+						AFAP1L1_uc010jgy.2_Intron|AFAP1L1_uc003lqi.1_5'Flank	NM_152406	NP_689619	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1								protein binding			breast(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGTGTGTGAGTGTGTGTGTGT	0.530													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	150392751	150392751	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150392751delA								LOC134466 (66605 upstream) : GPX3 (7248 downstream)																							TTGAGTTGGGAAAGGGCTAAG	0.358													4	2	---	---	---	---	
GLRA1	2741	broad.mit.edu	37	5	151228714	151228714	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151228714delT	uc003lut.2	-						GLRA1_uc003lur.2_Intron|GLRA1_uc003lus.2_Intron	NM_001146040	NP_001139512	P23415	GLRA1_HUMAN	glycine receptor, alpha 1 isoform 1 precursor						muscle contraction|negative regulation of transmission of nerve impulse|neuropeptide signaling pathway|positive regulation of acrosome reaction|regulation of membrane potential|startle response	cell junction|chloride channel complex|integral to plasma membrane|intracellular membrane-bounded organelle|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|protein binding|receptor activity|taurine binding|transmitter-gated ion channel activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	tctttctttcttttcttttct	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	152371078	152371078	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152371078delA								NMUR2 (586238 upstream) : GRIA1 (498097 downstream)																							AGTGTACGGCAAAAAAGGTGA	0.403													4	2	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156803127	156803128	+	Intron	INS	-	C	C	rs34321927		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156803127_156803128insC	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_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)			CTGCCCCTCCTCTCAGGCCCAT	0.480													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168692160	168692161	+	Intron	INS	-	AAAC	AAAC	rs141431756	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168692160_168692161insAAAC	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron|MIR585_hsa-mir-585|MI0003592_5'Flank	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCATGCTCAAaaacaaacaaa	0.356													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8864367	8864367	+	IGR	DEL	A	-	-	rs35509239		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8864367delA								HULC (210290 upstream) : None (None downstream)																							AAGAGAAAGTAAATTAAACAA	0.174													4	2	---	---	---	---	
KIF13A	63971	broad.mit.edu	37	6	17944590	17944590	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17944590delA	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			AGTATGCCCCAAATCCATTTA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	29240692	29240692	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29240692delT								OR2J2 (98342 upstream) : OR14J1 (33775 downstream)																							CCCATCCAAGTTTGCTCCTGT	0.358													4	2	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38987309	38987309	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38987309delT	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						tgaactgtggtgatggtggct	0.000													4	2	---	---	---	---	
PAQR8	85315	broad.mit.edu	37	6	52237225	52237225	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52237225delC	uc003pao.3	+							NM_133367	NP_588608	Q8TEZ7	MPRB_HUMAN	progestin and adipoQ receptor family member						cell differentiation|multicellular organismal development|oogenesis	integral to membrane|plasma membrane	receptor activity|steroid binding				0	Lung NSC(77;0.0875)					GTGAAGTTCTCCATGTGTTTA	0.458													4	2	---	---	---	---	
COL21A1	81578	broad.mit.edu	37	6	56014506	56014507	+	Intron	INS	-	AG	AG			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56014506_56014507insAG	uc003pcs.2	-						COL21A1_uc003pct.1_Intron|COL21A1_uc011dxi.1_Intron|COL21A1_uc003pcu.1_Intron	NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			tatccaatagatcagcaagtcc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57553541	57553542	+	IGR	DEL	AG	-	-	rs113085434		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57553541_57553542delAG								PRIM2 (40166 upstream) : GUSBL2 (692617 downstream)																							agtgacctacagagtcaatgca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57563307	57563307	+	IGR	DEL	G	-	-	rs67382068		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57563307delG								PRIM2 (49932 upstream) : GUSBL2 (682852 downstream)																							GGAGAAATTAGCCTTCAGGAT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	63037253	63037254	+	IGR	DEL	TC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63037253_63037254delTC								KHDRBS2 (41153 upstream) : LGSN (948603 downstream)																							TGCctctctgtctctctctccc	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	76872112	76872113	+	IGR	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76872112_76872113insT								IMPG1 (89777 upstream) : None (None downstream)																							CAAAGCCACTGTTTTTTTTTCA	0.347													4	2	---	---	---	---	
KIAA1919	91749	broad.mit.edu	37	6	111583284	111583284	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111583284delA	uc003puv.3	+							NM_153369	NP_699200	Q5TF39	NAGT1_HUMAN	sodium-dependent glucose transporter 1						carbohydrate transport|sodium ion transport	apical plasma membrane|integral to membrane	symporter activity			ovary(3)	3		all_cancers(87;2.35e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.055)|all cancers(137;0.0871)|Epithelial(106;0.0884)		GTGTCAAAACAAAAAAAAAAT	0.284													16	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	119711678	119711678	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119711678delA								MAN1A1 (40752 upstream) : None (None downstream)																							tgagaatctgaagccataggg	0.000													4	2	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	124216209	124216209	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124216209delT	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010kep.1_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		CCTACACCCCTTTTTTTTTTG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	142543208	142543208	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142543208delT								VTA1 (1125 upstream) : GPR126 (79848 downstream)																							ttctggcggcttttttttagg	0.000													2	4	---	---	---	---	
C6orf72	116254	broad.mit.edu	37	6	149904869	149904870	+	Intron	INS	-	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149904869_149904870insG	uc003qmq.1	+							NM_138785	NP_620140	Q9NU53	CF072_HUMAN	hypothetical protein LOC116254 precursor							integral to membrane					0		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.66e-12)|GBM - Glioblastoma multiforme(68;0.171)		ATCTATTATGTGGGGGGAAATA	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	155845389	155845390	+	IGR	DEL	AA	-	-	rs35376844		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155845389_155845390delAA								NOX3 (68352 upstream) : MIR1202 (422541 downstream)																							AAGCAGTGAGAAAAAAAGAGAA	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	157006260	157006261	+	IGR	INS	-	AGATAGAT	AGATAGAT			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157006260_157006261insAGATAGAT								MIR1202 (738247 upstream) : ARID1B (92825 downstream)																							ACAagataggcagatagataga	0.020													4	2	---	---	---	---	
TULP4	56995	broad.mit.edu	37	6	158834462	158834462	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158834462delT	uc003qrf.2	+						TULP4_uc011efo.1_Intron|TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1						intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		ACTCTCCAACTTTCAAACTTT	0.403													4	2	---	---	---	---	
FNDC1	84624	broad.mit.edu	37	6	159635396	159635396	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159635396delA	uc010kjv.2	+						FNDC1_uc010kjw.1_Intron	NM_032532	NP_115921	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1							extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TGTAGCAAGTAAAAAAAACAA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160266950	160266950	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160266950delT								PNLDC1 (25215 upstream) : MAS1 (61024 downstream)																							TAATCCTTTCTTTTTTTTTTT	0.308													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165688412	165688412	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165688412delA								None (None upstream) : C6orf118 (4743 downstream)																							CGCACCTTAGAAAAAAAATTG	0.363													4	2	---	---	---	---	
SMOC2	64094	broad.mit.edu	37	6	169047682	169047682	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169047682delC	uc003qws.1	+						SMOC2_uc003qwr.1_Intron|SMOC2_uc011egu.1_Intron	NM_022138	NP_071421	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2						signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		GCTTATTATTCCCCCCAGGAG	0.463													2	4	---	---	---	---	
GPER	2852	broad.mit.edu	37	7	1130606	1130607	+	Intron	INS	-	CT	CT	rs149305678	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1130606_1130607insCT	uc010ksd.1	+						C7orf50_uc003sju.2_Intron|C7orf50_uc011jvt.1_Intron|C7orf50_uc011jvu.1_Intron|GPER_uc003sjz.1_Intron|GPER_uc003ska.1_Intron|GPER_uc003skb.2_Intron	NM_001098201	NP_001091671	Q99527	GPER_HUMAN	G protein-coupled receptor 30							endoplasmic reticulum membrane|Golgi membrane|integral to plasma membrane	G-protein coupled receptor activity			ovary(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;2.32e-16)		TTCTGGACCCACTCTCTCTCTC	0.455													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4444920	4444920	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4444920delA								SDK1 (136291 upstream) : FOXK1 (238468 downstream)																							acacagagccaaaccatatca	0.000													4	2	---	---	---	---	
RSPH10B2	728194	broad.mit.edu	37	7	5983261	5983262	+	Intron	INS	-	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5983261_5983262insC	uc003sph.1	-						RSPH10B2_uc003spg.1_Intron|RSPH10B2_uc010ktd.1_Intron|RSPH10B2_uc011jwk.1_Intron	NM_173565	NP_775836	B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B											ovary(1)|pancreas(1)|skin(1)	3						tgcaacctccgccccccaggct	0.025													15	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	6712525	6712525	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6712525delT	uc003sqr.1	+											Homo sapiens cDNA FLJ41306 fis, clone BRAMY2042549.																		GCTGACCTCATTTTTTTAGTT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17711642	17711643	+	IGR	INS	-	A	A	rs112456451		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17711642_17711643insA								AHR (325867 upstream) : SNX13 (118743 downstream)																							CACCAGTTCTTAAAAAAAAAAA	0.426													4	2	---	---	---	---	
DNAH11	8701	broad.mit.edu	37	7	21607893	21607893	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21607893delG	uc003svc.2	+							NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						TGTTTGTGCTGGTACCATTGA	0.368									Kartagener_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	23119668	23119668	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23119668delA								FAM126A (65898 upstream) : KLHL7 (25685 downstream)																							CCTCTTAGTTAAAAAAACAAA	0.144													4	2	---	---	---	---	
CRHR2	1395	broad.mit.edu	37	7	30702684	30702684	+	Intron	DEL	T	-	-	rs77710158		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30702684delT	uc003tbn.2	-						CRHR2_uc010kvw.1_Intron|CRHR2_uc010kvx.1_Intron|CRHR2_uc010kvy.1_Intron|CRHR2_uc003tbo.2_Intron|CRHR2_uc003tbp.2_Intron	NM_001883	NP_001874	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2						G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(2)|ovary(1)|skin(1)	4						ggccaacgtgttttttttaac	0.000													5	3	---	---	---	---	
ANLN	54443	broad.mit.edu	37	7	36461893	36461894	+	Intron	DEL	TC	-	-	rs34997991		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36461893_36461894delTC	uc003tff.2	+						ANLN_uc011kaz.1_Intron|ANLN_uc003tfg.2_Intron|ANLN_uc010kxe.2_Intron	NM_018685	NP_061155	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein						cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3						ACACATACATtctctctctctc	0.272													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	38010887	38010887	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38010887delG								EPDR1 (19348 upstream) : STARD3NL (207046 downstream)																							TTTTCCTCCTGGGACACCAAA	0.423													4	2	---	---	---	---	
C7orf10	79783	broad.mit.edu	37	7	40513239	40513239	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40513239delA	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13								transferase activity			ovary(2)	2						GGAGGAGCAGAAAAAAAAAAT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41613542	41613543	+	IGR	INS	-	T	T	rs143920916	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41613542_41613543insT								C7orf10 (713185 upstream) : INHBA (115060 downstream)																							ATGCCACCCCCACCTCACTATT	0.426													2	4	---	---	---	---	
PKD1L1	168507	broad.mit.edu	37	7	47882381	47882381	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47882381delC	uc003tny.1	-							NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						CTGCTCTTCACCCTGACAGAT	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57728682	57728683	+	IGR	DEL	TG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57728682_57728683delTG								ZNF716 (195417 upstream) : None (None downstream)																							cctttatatatgttttctccac	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61660842	61660843	+	IGR	INS	-	AA	AA			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61660842_61660843insAA								None (None upstream) : None (None downstream)																							ATTTCCTTTTTAAAAAAAATCA	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65080809	65080809	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65080809delC								ZNF92 (214812 upstream) : INTS4L2 (31968 downstream)																							CCACTTTTGTCCCCATATGGA	0.403													4	2	---	---	---	---	
ABCB4	5244	broad.mit.edu	37	7	87039692	87039692	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87039692delA	uc003uiv.1	-						ABCB4_uc003uiw.1_Intron|ABCB4_uc003uix.1_Intron	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4						cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					GAGGTATAGTAAAACTTTCCT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	88230541	88230542	+	IGR	DEL	TG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88230541_88230542delTG								STEAP4 (294332 upstream) : ZNF804B (158211 downstream)																							GTAGGTTGTATGTGTGTGTGTG	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	93582640	93582640	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93582640delA								GNG11 (26816 upstream) : BET1 (9445 downstream)																							gcatcccagTAAAATTCATCT	0.169													4	2	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103191328	103191328	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103191328delC	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AATCTACCTTCCAACTAGAAA	0.408													4	2	---	---	---	---	
MDFIC	29969	broad.mit.edu	37	7	114648353	114648353	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114648353delT	uc003vhf.2	+							NM_199072	NP_951038	Q9P1T7	MDFIC_HUMAN	MyoD family inhibitor domain containing protein						activation of JUN kinase activity|interspecies interaction between organisms|negative regulation of protein import into nucleus|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|regulation of Wnt receptor signaling pathway|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleolus|nucleolus|nucleus	cyclin binding|Tat protein binding			ovary(1)	1						GGCAGTGCTGTTTTTTTTTTT	0.403													4	3	---	---	---	---	
CAV1	857	broad.mit.edu	37	7	116023297	116023298	+	Intron	INS	-	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116023297_116023298insA	uc010lkd.1	+						CAV2_uc003vhv.2_Intron|CAV2_uc003vhw.2_Intron|CAV2_uc003vhx.2_Intron|CAV2_uc010lkb.1_Intron|CAV2_uc010lkc.2_Intron|CAV2_uc003vib.2_Intron|CAV2_uc003vhz.2_Intron|CAV2_uc003via.2_Intron|CAV1_uc010lke.1_Intron	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)			GAACAAAACTTAAAAAAAAAAA	0.218													4	2	---	---	---	---	
C7orf58	79974	broad.mit.edu	37	7	120782441	120782441	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120782441delA	uc003vjq.3	+						C7orf58_uc003vjs.3_Intron|C7orf58_uc003vjt.3_Intron	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1							endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)					GTTAATGTTCAAAAAAAATGT	0.368													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128227088	128227088	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128227088delT								METTL2B (84111 upstream) : FLJ45340 (54207 downstream)																							ttttgacttctttttttgtat	0.000													4	2	---	---	---	---	
FLJ43663	378805	broad.mit.edu	37	7	130669690	130669691	+	Intron	INS	-	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130669690_130669691insG	uc011kpk.1	-						FLJ43663_uc003vqo.1_Intron|FLJ43663_uc003vqp.2_Intron|FLJ43663_uc003vqq.2_Intron	NR_024153				Homo sapiens cDNA FLJ43663 fis, clone SYNOV4005989.												0						AAATTCACGGCAGATTGCTCAG	0.366													5	3	---	---	---	---	
LRGUK	136332	broad.mit.edu	37	7	133856358	133856358	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133856358delG	uc003vrm.1	+							NM_144648	NP_653249	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain								ATP binding|kinase activity			lung(2)|skin(2)|kidney(1)	5						CTTTGGGGATGGGGGTGTGGA	0.488													4	2	---	---	---	---	
KRBA1	84626	broad.mit.edu	37	7	149421062	149421062	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149421062delC	uc003wfz.2	+						KRBA1_uc010lpj.2_Intron|KRBA1_uc003wga.2_Intron|KRBA1_uc003wgb.2_Intron	NM_032534	NP_115923	A5PL33	KRBA1_HUMAN	KRAB A domain containing 1											ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GTGGCCCCCACCACAAACACT	0.632													20	9	---	---	---	---	
SSPO	23145	broad.mit.edu	37	7	149520153	149520153	+	Intron	DEL	A	-	-	rs67616784		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149520153delA	uc010lpk.2	+						SSPO_uc010lpm.1_Intron|SSPO_uc003wgg.2_Intron|SSPO_uc003wgh.2_Intron|SSPO_uc003wgi.1_Intron	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor						cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AGCACCTGCCAAGGCCCCTCA	0.637													3	3	---	---	---	---	
ACTR3C	653857	broad.mit.edu	37	7	150000094	150000095	+	5'Flank	DEL	GA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150000094_150000095delGA	uc003wgu.1	-							NM_001040135	NP_001035225	Q9C0K3	ARP3C_HUMAN	actin-related protein 3-beta isoform 2						regulation of actin filament polymerization	cytoskeleton	actin binding|ATP binding				0						tCATGCCTTTGAGTGACACCAC	0.287													4	2	---	---	---	---	
LRRC61	65999	broad.mit.edu	37	7	150021062	150021062	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150021062delT	uc003wgv.2	+						LRRC61_uc003wgx.2_Intron|LRRC61_uc003wgw.2_Intron	NM_023942	NP_076431	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61												0			OV - Ovarian serous cystadenocarcinoma(82;0.011)			CTTTGTGTCATTTTTTTTGCA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	151588763	151588764	+	IGR	INS	-	CTT	CTT	rs3036154		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151588763_151588764insCTT								PRKAG2 (14447 upstream) : GALNTL5 (64747 downstream)																							taacgaataAACTCACTTTTAG	0.193													6	5	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151944708	151944708	+	Intron	DEL	T	-	-	rs113407913		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151944708delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		ACTAAAAGAATTTTTAAAGTT	0.264			N		medulloblastoma								5	5	---	---	---	---	
RBM33	155435	broad.mit.edu	37	7	155495625	155495626	+	Intron	INS	-	C	C	rs142672680	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155495625_155495626insC	uc010lqk.1	+						RBM33_uc011kvv.1_Intron	NM_053043	NP_444271	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33								nucleotide binding|RNA binding			ovary(1)	1	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		ACAAATGGGGGCTTTCCCCAAC	0.460													2	4	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157884395	157884398	+	Intron	DEL	GATA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157884395_157884398delGATA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		AGGGACAGGTgatagatagatgag	0.029													3	3	---	---	---	---	
ERICH1	157697	broad.mit.edu	37	8	591104	591104	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:591104delG	uc011kwh.1	-						ERICH1_uc003wpe.1_Intron|uc003wpf.1_RNA	NM_207332	NP_997215	Q86X53	ERIC1_HUMAN	glutamate-rich 1											large_intestine(2)	2		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		TTCTGGAGGTGGTTACTTACC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	4858879	4858879	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4858879delT								CSMD1 (6551 upstream) : None (None downstream)																							AACTGGCATGTTGTTACCAAT	0.423													4	2	---	---	---	---	
XKR6	286046	broad.mit.edu	37	8	10829758	10829758	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10829758delA	uc003wtk.1	-							NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		GCTCTCTAGGAAAAAAACAAC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20509794	20509796	+	IGR	DEL	AAG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20509794_20509796delAAG								LZTS1 (396991 upstream) : None (None downstream)																							TTACAAAGGAAAGAAGGTCTAAC	0.468													4	4	---	---	---	---	
ESCO2	157570	broad.mit.edu	37	8	27644932	27644933	+	Intron	INS	-	TAAAATGT	TAAAATGT	rs151089506	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27644932_27644933insTAAAATGT	uc003xgg.2	+						ESCO2_uc010luy.1_Intron	NM_001017420	NP_001017420	Q56NI9	ESCO2_HUMAN	establishment of cohesion 1 homolog 2						cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding			central_nervous_system(1)	1		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		CATTGCCCAGGTGCTGGGTCAT	0.356									SC_Phocomelia_syndrome				4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	32731623	32731624	+	IGR	DEL	AC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32731623_32731624delAC								NRG1 (109065 upstream) : FUT10 (496722 downstream)																							ACACACATATACACACACACTG	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	33126400	33126400	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33126400delA								NRG1 (503842 upstream) : FUT10 (101946 downstream)																							ACCCATGAGGAAGACAACCTT	0.428													4	2	---	---	---	---	
DDHD2	23259	broad.mit.edu	37	8	38099572	38099572	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38099572delA	uc003xlb.2	+						DDHD2_uc003xlc.2_Intron|DDHD2_uc011lbl.1_Intron	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1						lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			actccatctcaaaaaaaaaaa	0.139													12	8	---	---	---	---	
ADAM18	8749	broad.mit.edu	37	8	39515255	39515255	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39515255delT	uc003xni.2	+						ADAM18_uc010lww.2_Intron|ADAM18_uc010lwx.2_Intron	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18						cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			GATACGTTCATTTTAAAGGTA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	47830034	47830034	+	IGR	DEL	C	-	-	rs66764103		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47830034delC								BEYLA (62627 upstream) : KIAA0146 (343508 downstream)																							agccaggctgcccccagagcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	57397983	57397983	+	Intron	DEL	A	-	-	rs34350009		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57397983delA	uc003xtb.1	+											Homo sapiens cDNA FLJ34244 fis, clone FCBBF3028794.																		aaaaccacagaaaacctagtc	0.000													4	6	---	---	---	---	
FAM110B	90362	broad.mit.edu	37	8	58913935	58913936	+	Intron	DEL	GT	-	-	rs72424818		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58913935_58913936delGT	uc003xtj.1	+							NM_147189	NP_671722	Q8TC76	F110B_HUMAN	hypothetical protein LOC90362							microtubule organizing center|mitochondrion|nucleus				large_intestine(1)	1		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)				GTGTGTGCAGGTGTGTGTGTGT	0.436													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	62867192	62867193	+	IGR	DEL	TC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62867192_62867193delTC								ASPH (239993 upstream) : NKAIN3 (294308 downstream)																							tctgtctctgtctctctctctc	0.257													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	64329408	64329408	+	Intron	DEL	T	-	-	rs11353267		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64329408delT	uc003xvb.1	-											Homo sapiens cDNA FLJ36051 fis, clone TESTI2018083.																		TCCTGGGCTATCCAGATGAAA	0.209													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	76772909	76772909	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76772909delA								HNF4G (293850 upstream) : LOC100192378 (750206 downstream)																							GAGATGTGCCAAGTTCAGAGT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	78348716	78348716	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78348716delT								PEX2 (436192 upstream) : None (None downstream)																							agttcaaaaattttttaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	80311963	80311964	+	IGR	INS	-	T	T	rs141429247	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80311963_80311964insT								IL7 (594205 upstream) : STMN2 (211416 downstream)																							GCTTTATCATCCTCTGGGGGTG	0.515													4	2	---	---	---	---	
MRPS28	28957	broad.mit.edu	37	8	80831586	80831586	+	Intron	DEL	A	-	-	rs34441760		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80831586delA	uc003ybp.2	-						MRPS28_uc003ybo.2_Intron|TPD52_uc010lzr.2_Intron	NM_014018	NP_054737	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S28							mitochondrial small ribosomal subunit					0	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)			TTTTGTTTTGAAAAAAAAAAA	0.164													8	4	---	---	---	---	
ZNF704	619279	broad.mit.edu	37	8	81666907	81666907	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81666907delT	uc003yby.1	-							NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			TCACAAGGCctcctccttcca	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	87100614	87100614	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87100614delT								PSKH2 (18763 upstream) : ATP6V0D2 (10525 downstream)																							cagagctctcttttttttttt	0.100													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	92855649	92855649	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92855649delA								SLC26A7 (445269 upstream) : RUNX1T1 (115503 downstream)																							CATACACTGTAAAAAAAAATA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94252532	94252533	+	IGR	DEL	AC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94252532_94252533delAC								C8orf83 (222631 upstream) : FAM92A1 (460240 downstream)																							GAAAAAGTATacacacacacac	0.351													4	3	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	103114459	103114459	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103114459delA	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)			caggtaatacaaaaaaaaatt	0.199													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	108856416	108856425	+	IGR	DEL	ACATCACATC	-	-	rs36226129		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108856416_108856425delACATCACATC								ANGPT1 (346162 upstream) : RSPO2 (55120 downstream)																							ACTATCCACAacatcacatcacatcacatc	0.257													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	110237540	110237561	+	IGR	DEL	TGTCACTGGGATTTTTCAGATT	-	-	rs143825616		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110237540_110237561delTGTCACTGGGATTTTTCAGATT								TRHR (105730 upstream) : NUDCD1 (15588 downstream)																							ATCTGAGGGCTGTCACTGGGATTTTTCAGATTTAAGCAGATT	0.455													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116392810	116392810	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116392810delA								None (None upstream) : TRPS1 (27915 downstream)																							TTAACCATTTAAAATGTAAGA	0.378													4	2	---	---	---	---	
SAMD12	401474	broad.mit.edu	37	8	119467508	119467509	+	Intron	DEL	CT	-	-	rs113092622		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119467508_119467509delCT	uc003yom.2	-						SAMD12_uc010mda.1_Intron|SAMD12_uc010mdb.1_Intron	NM_207506	NP_997389	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			gctttcaCACctctctctctct	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	122260868	122260868	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122260868delA								SNTB1 (436559 upstream) : HAS2 (364403 downstream)																							AGGACATCAGAAAAAAAAAGA	0.363											OREG0018947	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ZHX2	22882	broad.mit.edu	37	8	123908479	123908479	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123908479delC	uc003ypk.1	+							NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2							cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			TTTTTTTTTTCTTAAGGGCAT	0.323													4	2	---	---	---	---	
NSMCE2	286053	broad.mit.edu	37	8	126301610	126301611	+	Intron	DEL	CT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126301610_126301611delCT	uc003yrw.2	+							NM_173685	NP_775956	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			ctaagtgcccctctctcagcca	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128263912	128263912	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128263912delT								FAM84B (693446 upstream) : LOC727677 (38150 downstream)																							GACTCCTCCCTTTTTTTCTAT	0.393													4	2	---	---	---	---	
TG	7038	broad.mit.edu	37	8	134108167	134108167	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134108167delC	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron|SLA_uc003ytz.2_Intron|SLA_uc011lje.1_Intron|SLA_uc011ljf.1_Intron|SLA_uc011ljg.1_Intron|SLA_uc010mea.2_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CTGCCTTCCTCACCCACCTAC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136207497	136207500	+	IGR	DEL	TTAC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136207497_136207500delTTAC								MIR30D (390309 upstream) : LOC286094 (38874 downstream)																							ATGTATCATATTACTTATTTCGTC	0.250													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138696949	138696949	+	IGR	DEL	A	-	-	rs71703020		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138696949delA								None (None upstream) : FAM135B (445319 downstream)																							ATTATATTTGAAAAAAAAAGT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138818149	138818149	+	IGR	DEL	G	-	-	rs72189185		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138818149delG								None (None upstream) : FAM135B (324119 downstream)																							ACATGAGCCTGGTTAGGCTGA	0.408													2	4	---	---	---	---	
FAM135B	51059	broad.mit.edu	37	8	139273090	139273090	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139273090delT	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GGTCTCCTCCTTCTGTCCTGA	0.498										HNSCC(54;0.14)			4	2	---	---	---	---	
EIF2C2	27161	broad.mit.edu	37	8	141553951	141553951	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141553951delG	uc003yvn.2	-						EIF2C2_uc010men.2_Intron|EIF2C2_uc010meo.2_Intron	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1						mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)			TCTGGGGTTCGGGGCTGTGTC	0.443													4	2	---	---	---	---	
SUGT1P1	441394	broad.mit.edu	37	9	33283995	33283995	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33283995delC	uc010mjq.1	-							NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0						CCCCCCACATCCACCATATAG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66471182	66471182	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66471182delG								FAM74A4 (976796 upstream) : LOC442421 (25288 downstream)																							gtgaggctttgcaataaactc	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68356752	68356752	+	IGR	DEL	C	-	-	rs75577840		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68356752delC								FAM27B (562563 upstream) : MIR1299 (645487 downstream)																							GAAGTCTCATCCCCATATTTT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68418028	68418029	+	IGR	DEL	AG	-	-	rs71861265		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68418028_68418029delAG								FAM27B (623839 upstream) : MIR1299 (584210 downstream)																							ATCTAGTAACAGGGTAACATTT	0.272													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	77806517	77806517	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77806517delT								OSTF1 (44404 upstream) : PCSK5 (699043 downstream)																							AGTCTTACTCTTTTGGTGATA	0.333													4	2	---	---	---	---	
ZCCHC6	79670	broad.mit.edu	37	9	88917247	88917250	+	Intron	DEL	ACAA	-	-	rs151269506		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88917247_88917250delACAA	uc004aoq.2	-						ZCCHC6_uc010mqe.2_Intron|ZCCHC6_uc011ltf.1_Intron|ZCCHC6_uc004aor.2_Intron|ZCCHC6_uc004aos.2_Intron|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Intron	NM_024617	NP_078893	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6						RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2						TAAGTGGAATACAAACAAAGAGTG	0.412													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	104663606	104663607	+	IGR	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104663606_104663607insT								GRIN3A (162744 upstream) : None (None downstream)																							TCTCAATCTCCTTTTTTTTGTT	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107894555	107894555	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107894555delT								ABCA1 (204119 upstream) : SLC44A1 (112374 downstream)																							AGAGTTAGGCttttttttttc	0.244													5	3	---	---	---	---	
COL27A1	85301	broad.mit.edu	37	9	116987273	116987273	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116987273delC	uc011lxl.1	+						COL27A1_uc004bii.2_Intron	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor						cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4						GTtaaggttgccagataaaat	0.139													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119559684	119559684	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119559684delT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						agaaaagaggtttttttttct	0.338													4	2	---	---	---	---	
CEP110	11064	broad.mit.edu	37	9	123837749	123837750	+	Intron	DEL	CA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123837749_123837750delCA	uc004bkw.2	+									Q7Z7A1	CNTRL_HUMAN	SubName: Full=Centrosomal protein 110kDa;						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						GACGGGTTGTCACGGTATCGGA	0.530													4	2	---	---	---	---	
ZER1	10444	broad.mit.edu	37	9	131524768	131524769	+	Intron	INS	-	TCT	TCT	rs139534165	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131524768_131524769insTCT	uc004bwa.1	-							NM_006336	NP_006327	Q7Z7L7	ZER1_HUMAN	zyg-11 homolog B (C. elegans)-like						ATP hydrolysis coupled proton transport|regulation of ubiquitin-protein ligase activity	Cul2-RING ubiquitin ligase complex|vacuolar proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism|ubiquitin-protein ligase activity			ovary(1)	1						ttgggcaagtgtctccacctct	0.010													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	133030103	133030103	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133030103delG								NCS1 (30520 upstream) : ASS1 (289991 downstream)																							CAACCAAGCTGGGGGTTGTGA	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2369909	2369909	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2369909delA								ADARB2 (590191 upstream) : PFKP (739843 downstream)																							GCTAAGTCTTAAAAAGTTAGG	0.438													4	2	---	---	---	---	
TAF3	83860	broad.mit.edu	37	10	7911489	7911490	+	Intron	DEL	TG	-	-	rs139105476	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7911489_7911490delTG	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						agttccctgttgtgacatttag	0.000													4	2	---	---	---	---	
ARL5B	221079	broad.mit.edu	37	10	18957250	18957250	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18957250delA	uc001iqd.1	+							NM_178815	NP_848930	Q96KC2	ARL5B_HUMAN	ADP-ribosylation factor-like 8						small GTPase mediated signal transduction	intracellular	GTP binding			ovary(1)	1						TCCTTCCGTTAAAAAAAAAAA	0.353													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	23828302	23828303	+	IGR	DEL	TG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23828302_23828303delTG								OTUD1 (96994 upstream) : KIAA1217 (155372 downstream)																							AATAGGTCTTTGACGTTGATCA	0.450													4	2	---	---	---	---	
YME1L1	10730	broad.mit.edu	37	10	27434219	27434219	+	Intron	DEL	A	-	-	rs72362930		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27434219delA	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						gaaaaattGCAAAAAAAAAAA	0.159													13	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31005791	31005791	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31005791delA	uc010qdx.1	+											SubName: Full=cDNA FLJ59642, highly similar to Supervillin;																		tCCTGCAGTCAAAAAAAAAAA	0.254													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38817517	38817518	+	IGR	INS	-	AATGT	AATGT			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38817517_38817518insAATGT								LOC399744 (76437 upstream) : None (None downstream)																							aaatggtatagaatggaatgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44232655	44232655	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44232655delT								ZNF32 (88329 upstream) : HNRNPA3P1 (50205 downstream)																							AGCATGTGTCTGGAAGTCGTC	0.552													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47058662	47058663	+	Intron	DEL	AT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47058662_47058663delAT	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						acagccacacatatcacacaca	0.050													2	4	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	55974013	55974016	+	Intron	DEL	TGTT	-	-	rs140103577		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55974013_55974016delTGTT	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				AAATGGAAAATGTTTGGATGATTT	0.265										HNSCC(58;0.16)			4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	67392923	67392923	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67392923delA								ANXA2P3 (806289 upstream) : CTNNA3 (286802 downstream)																							CTAAGACCACAAAAAACACCT	0.214													4	2	---	---	---	---	
CDH23	64072	broad.mit.edu	37	10	73563299	73563299	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73563299delA	uc001jrx.3	+						CDH23_uc001jsg.3_Intron|CDH23_uc001jsh.3_Intron|CDH23_uc001jsi.3_Intron	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						TAGCTCCAGGaaaaaaaaaac	0.299													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80023903	80023909	+	Intron	DEL	CTTGGCA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80023903_80023909delCTTGGCA	uc010qlp.1	+											SubName: Full=cDNA FLJ57363;																		CCTAGACTGGCTTGGCACTTGAAGGAG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85656040	85656041	+	IGR	INS	-	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85656040_85656041insA								NRG3 (909105 upstream) : GHITM (243144 downstream)																							AAAGAATGAAGAAAAGAAACTG	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85867999	85867999	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85867999delA								None (None upstream) : GHITM (31186 downstream)																							gtctagtaacaaaaagcaaac	0.119													4	2	---	---	---	---	
SLIT1	6585	broad.mit.edu	37	10	98790808	98790809	+	Intron	DEL	TG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98790808_98790809delTG	uc001kmw.2	-							NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		ACTGAAACACTGTGTTTACATT	0.569													6	4	---	---	---	---	
SLIT1	6585	broad.mit.edu	37	10	98838415	98838416	+	Intron	DEL	CT	-	-	rs140909861		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98838415_98838416delCT	uc001kmw.2	-						SLIT1_uc009xvh.1_Intron	NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TAGCTTCGTCCTCTTCAACTCT	0.550													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113701497	113701497	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113701497delT								ADRA2A (860837 upstream) : GPAM (208125 downstream)																							acttacctgcttttctccaaa	0.010													4	2	---	---	---	---	
ATRNL1	26033	broad.mit.edu	37	10	117589136	117589136	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117589136delA	uc001lcg.2	+						ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor							integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CTTTTAAGCCAAAAAAAGATA	0.378													4	2	---	---	---	---	
C10orf119	79892	broad.mit.edu	37	10	121602280	121602280	+	Intron	DEL	T	-	-	rs71935400		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121602280delT	uc001ler.2	-						C10orf119_uc001leq.1_Intron|C10orf119_uc001les.1_Intron	NM_024834	NP_079110	Q9BTE3	MCMBP_HUMAN	chromosome 10 open reading frame 119						cell division|DNA-dependent DNA replication|mitosis|S phase of mitotic cell cycle|sister chromatid cohesion	nucleus	chromatin binding				0		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.0044)		TGCATCCTCCttttttttttt	0.199													6	3	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127583269	127583269	+	Intron	DEL	C	-	-	rs10709545		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127583269delC	uc001ljg.1	-						FANK1_uc010quk.1_5'Flank|FANK1_uc001ljh.3_5'Flank|FANK1_uc009yan.2_5'Flank	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				AATACTAATGCTAATCCTTTA	0.303													7	5	---	---	---	---	
HRAS	3265	broad.mit.edu	37	11	534410	534415	+	Intron	DEL	CCCAGC	-	-	rs61877782		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:534410_534415delCCCAGC	uc001lpv.2	-						HRAS_uc010qvw.1_Intron|HRAS_uc010qvx.1_Intron|HRAS_uc010qvy.1_Intron	NM_005343	NP_005334	P01112	RASH_HUMAN	v-Ha-ras Harvey rat sarcoma viral oncogene						activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding			urinary_tract(174)|thyroid(155)|skin(126)|upper_aerodigestive_tract(112)|soft_tissue(37)|prostate(29)|salivary_gland(24)|cervix(23)|stomach(14)|pituitary(10)|lung(9)|haematopoietic_and_lymphoid_tissue(9)|breast(6)|testis(5)|endometrium(4)|bone(3)|large_intestine(2)|oesophagus(2)|penis(2)|kidney(1)|adrenal_gland(1)|thymus(1)	749		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Sulindac(DB00605)	CAGGCCCAGGCCCAGCCCCAGGCCCC	0.699		6	Mis		infrequent sarcomas|rare other types	rhadomyosarcoma|ganglioneuroblastoma|bladder			Costello_syndrome	HNSCC(11;0.0054)			10	5	---	---	---	---	
STIM1	6786	broad.mit.edu	37	11	3987268	3987268	+	Intron	DEL	A	-	-	rs12276603		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3987268delA	uc001lyv.2	+						STIM1_uc009yef.2_Intron	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor						activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		acaaaaaaccaaaaaaaacCC	0.199													4	2	---	---	---	---	
SPON1	10418	broad.mit.edu	37	11	14116249	14116250	+	Intron	DEL	GA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14116249_14116250delGA	uc001mle.2	+							NM_006108	NP_006099	Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)		atGAATGAATGAGAAGCAGTTA	0.243													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	18613646	18613646	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18613646delT								UEVLD (3365 upstream) : SPTY2D1 (14303 downstream)																							TGAAATTGGCTTTTTTTTTTA	0.363													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	20744286	20744287	+	Intron	DEL	AC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20744286_20744287delAC	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						gagaacaaatacaagagagttc	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	26005631	26005632	+	IGR	DEL	TT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26005631_26005632delTT								LUZP2 (901449 upstream) : ANO3 (205197 downstream)																							TTTCTTCCTCTTTTTGGGTGGT	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49009777	49009777	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49009777delA								OR4A47 (498505 upstream) : FOLH1 (158411 downstream)																							ACATTTTTTTAATTTCACtat	0.274													11	5	---	---	---	---	
PYGM	5837	broad.mit.edu	37	11	64515643	64515643	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64515643delC	uc001oax.3	-						RASGRP2_uc009ypw.2_5'Flank|PYGM_uc001oay.3_Intron	NM_005609	NP_005600	P11217	PYGM_HUMAN	muscle glycogen phosphorylase isoform 1						glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)	AATCTCTAATCCCTCGTGCGA	0.602													4	2	---	---	---	---	
POLA2	23649	broad.mit.edu	37	11	65030407	65030407	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65030407delC	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)	AAGCTAATTGCCTGAGCTGTC	0.478													4	2	---	---	---	---	
MYO7A	4647	broad.mit.edu	37	11	76904299	76904301	+	Intron	DEL	TGG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76904299_76904301delTGG	uc001oyb.2	+						MYO7A_uc010rsm.1_Intron|MYO7A_uc001oyc.2_Intron|MYO7A_uc009yus.1_Intron|MYO7A_uc009yut.1_Intron	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1						actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4						atgttagtgatggtggtggtggt	0.000													4	5	---	---	---	---	
NOX4	50507	broad.mit.edu	37	11	89290633	89290633	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89290633delC	uc009yvq.2	-							NM_001143837	NP_001137309	Q9NPH5	NOX4_HUMAN	NADPH oxidase 4 isoform c						cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				TTAATTCATGCCACATCACTG	0.403													4	2	---	---	---	---	
CASP5	838	broad.mit.edu	37	11	104871386	104871386	+	Intron	DEL	T	-	-	rs45440097		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104871386delT	uc010rva.1	-						CASP5_uc010ruz.1_Intron|CASP5_uc010rvb.1_Intron|CASP5_uc010rvc.1_Intron|CASP5_uc009yxh.2_Intron|CASP5_uc010rvd.1_Intron	NM_004347	NP_004338	P51878	CASP5_HUMAN	caspase 5 isoform a precursor						apoptosis|cellular response to mechanical stimulus|proteolysis|regulation of apoptosis	intracellular	cysteine-type endopeptidase activity|protein binding			ovary(2)|lung(1)	3		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		TTTTGTTTTGTTTTTTTTTTC	0.363													7	4	---	---	---	---	
CWF19L2	143884	broad.mit.edu	37	11	107328852	107328852	+	5'Flank	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107328852delT	uc010rvp.1	-							NM_152434	NP_689647	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control								catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		CCGGAGTAAGTTACAAGCTCT	0.398													4	2	---	---	---	---	
SLC35F2	54733	broad.mit.edu	37	11	107686320	107686320	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107686320delA	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron|SLC35F2_uc001pjs.2_Intron	NM_017515	NP_059985	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2						transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		acacacacacaaaaaaaaaaa	0.149													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	109960615	109960615	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109960615delC								C11orf87 (660777 upstream) : ZC3H12C (3311 downstream)																							GGTCAATTCTCCCATATTAGC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112289782	112289783	+	IGR	DEL	TG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112289782_112289783delTG								PTS (149105 upstream) : NCAM1 (542212 downstream)																							TATGTGTGCATGTGTGTGTGTG	0.351													4	2	---	---	---	---	
NCAM1	4684	broad.mit.edu	37	11	112984733	112984733	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112984733delT	uc009yyq.1	+						NCAM1_uc001pno.2_Intron	NM_001076682	NP_001070150	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		TAGCGATGTATTCTGATGCCC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128524137	128524138	+	IGR	INS	-	AG	AG			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128524137_128524138insAG								ETS1 (66684 upstream) : FLI1 (32292 downstream)																							ataaaaaaacaagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134587029	134587029	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134587029delC								B3GAT1 (305217 upstream) : None (None downstream)																							acccttttatcccccatcatc	0.095													4	2	---	---	---	---	
ADIPOR2	79602	broad.mit.edu	37	12	1851262	1851263	+	Intron	INS	-	TC	TC			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1851262_1851263insTC	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827	Q86V24	ADR2_HUMAN	adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			TTTGTCACttttctctctctct	0.168													4	2	---	---	---	---	
FAM90A1	55138	broad.mit.edu	37	12	8382986	8382986	+	5'Flank	DEL	C	-	-	rs142178842		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8382986delC	uc001qui.2	-						FAM90A1_uc001quh.2_5'Flank	NM_018088	NP_060558	Q86YD7	F90A1_HUMAN	hypothetical protein LOC55138								nucleic acid binding|zinc ion binding			ovary(1)	1				Kidney(36;0.0866)		TTGATGTGCACCCCCCCCAGG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8968022	8968027	+	IGR	DEL	AAACCC	-	-	rs113104838		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8968022_8968027delAAACCC								RIMKLB (32337 upstream) : A2ML1 (7123 downstream)																							GGAGATTATTAAACCCTGGACATTTC	0.417													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8968028	8968029	+	IGR	INS	-	GGTG	GGTG	rs146218175		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8968028_8968029insGGTG								RIMKLB (32343 upstream) : A2ML1 (7121 downstream)																							TATTAAACCCTGGACATTTCCT	0.426													4	2	---	---	---	---	
LMO3	55885	broad.mit.edu	37	12	16737520	16737520	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16737520delG	uc001rdk.1	-						LMO3_uc001rdj.1_Intron|LMO3_uc010shy.1_Intron|LMO3_uc001rdl.1_Intron|LMO3_uc009zii.1_Intron|LMO3_uc010shz.1_Intron|LMO3_uc001rdm.1_Intron|LMO3_uc001rdo.1_Intron|LMO3_uc001rdp.1_Intron|LMO3_uc001rdn.1_Intron|LMO3_uc009zij.1_Intron|LMO3_uc009zik.1_Intron	NM_018640	NP_061110	Q8TAP4	LMO3_HUMAN	LIM domain only 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent		zinc ion binding				0		Hepatocellular(102;0.244)				GTGGAGGAGTGGGGGGGGTAA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	20160588	20160589	+	IGR	INS	-	T	T	rs150406668	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20160588_20160589insT								AEBP2 (485415 upstream) : PDE3A (361608 downstream)																							AATTTAAAACATTTTTTTTTTA	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	25833457	25833457	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25833457delT								IFLTD1 (31969 upstream) : RASSF8 (278512 downstream)																							cttctgcccattttttctccg	0.000													4	2	---	---	---	---	
TMTC1	83857	broad.mit.edu	37	12	29725490	29725490	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29725490delT	uc001rjb.2	-						TMTC1_uc001riz.2_Intron|TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					TTCCTGAGGCTTTTTTTTGGG	0.448													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30491998	30491998	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30491998delT								TMTC1 (554306 upstream) : IPO8 (289925 downstream)																							TCAGACCCACTTTTAATCCAC	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30980928	30980928	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30980928delT								CAPRIN2 (73480 upstream) : TSPAN11 (98434 downstream)																							ACATCCTGCCTTTGGAATTCT	0.517													4	2	---	---	---	---	
BICD1	636	broad.mit.edu	37	12	32276497	32276497	+	Intron	DEL	T	-	-	rs2683474	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32276497delT	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			TGGGAAAAAATTAAAGATGAA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	37880402	37880402	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37880402delG								None (None upstream) : ALG10B (830155 downstream)																							ATATGCAAAAGAAAATCCATG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38524714	38524714	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38524714delA								None (None upstream) : ALG10B (185843 downstream)																							ATCTGTGACTAAATCCTGATG	0.418													4	2	---	---	---	---	
TMEM117	84216	broad.mit.edu	37	12	44393992	44393993	+	Intron	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44393992_44393993insT	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632	Q9H0C3	TM117_HUMAN	transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)		gcaatgtacccgggtaagttca	0.059													4	2	---	---	---	---	
RND1	27289	broad.mit.edu	37	12	49255474	49255474	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49255474delC	uc001rsn.2	-							NM_014470	NP_055285	Q92730	RND1_HUMAN	GTP-binding protein RHO6 precursor						actin filament organization|axon guidance|negative regulation of cell adhesion|neuron remodeling|small GTPase mediated signal transduction	adherens junction|cytoskeleton|cytosol	GTP binding|GTPase activity|receptor binding			ovary(1)	1						TCCAAAAGGTCCCATGCCTGA	0.552													4	2	---	---	---	---	
LIMA1	51474	broad.mit.edu	37	12	50640635	50640635	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50640635delC	uc001rwj.3	-						LIMA1_uc001rwk.3_Intron|LIMA1_uc010smr.1_Intron|LIMA1_uc010sms.1_Intron	NM_016357	NP_057441	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1 isoform b						actin filament bundle assembly|negative regulation of actin filament depolymerization|ruffle organization	cytoplasm|focal adhesion|stress fiber	actin filament binding|actin monomer binding|zinc ion binding			ovary(1)	1						CTCCACAAGTCCATCCCTTCC	0.254													4	2	---	---	---	---	
SOAT2	8435	broad.mit.edu	37	12	53502221	53502222	+	Intron	INS	-	T	T	rs145718124	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53502221_53502222insT	uc001sbv.2	+						SOAT2_uc009zms.2_Intron	NM_003578	NP_003569	O75908	SOAT2_HUMAN	acyl-CoA:cholesterol acyltransferase 2						cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|macrophage derived foam cell differentiation|very-low-density lipoprotein particle assembly	brush border|endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			ovary(1)	1						tcttattgtactatgcaaataa	0.000													2	4	---	---	---	---	
FLJ12825	440101	broad.mit.edu	37	12	54503918	54503918	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54503918delG	uc001sey.2	+							NR_026655				Homo sapiens cDNA FLJ12825 fis, clone NT2RP2002800.												0						CCGGAGGTCAGGAACAAGGGA	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	60839418	60839418	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60839418delC								SLC16A7 (664011 upstream) : None (None downstream)																							catcctgtagccctacccagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	64575780	64575780	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64575780delA								SRGAP1 (34167 upstream) : C12orf66 (10640 downstream)																							CCAAGAGGTCAAAAAAAAAAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	74511369	74511371	+	IGR	DEL	AAC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74511369_74511371delAAC								None (None upstream) : ATXN7L3B (420180 downstream)																							AATGTCTCCTAACAACAACAACA	0.360													4	2	---	---	---	---	
PTPRQ	374462	broad.mit.edu	37	12	81035631	81035632	+	Intron	DEL	TC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81035631_81035632delTC	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0						cttctctctttctctctctctc	0.158													4	2	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	81826805	81826805	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81826805delA	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6						AACAAAAATTAAAAAAAAAAC	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82979250	82979251	+	IGR	DEL	AC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82979250_82979251delAC								C12orf26 (106309 upstream) : TMTC2 (101683 downstream)																							CTTCTACCCAACACACACACAT	0.243													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	87342548	87342549	+	IGR	INS	-	A	A	rs138936058	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87342548_87342549insA								MGAT4C (109867 upstream) : None (None downstream)																							AGTAAACTAGTAAAAAAATAAT	0.312													3	3	---	---	---	---	
POC1B	282809	broad.mit.edu	37	12	89853185	89853185	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89853185delA	uc001tbc.2	-						POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc010sun.1_Intron|POC1B_uc009zsp.2_Intron|POC1B_uc009zsq.2_Intron	NM_172240	NP_758440	Q8TC44	POC1B_HUMAN	WD repeat domain 51B						cell projection organization	centriole|microtubule basal body				ovary(1)	1						cttaaagtataaaaaaaaaaa	0.149													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	94430293	94430294	+	IGR	INS	-	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94430293_94430294insG								CRADD (141677 upstream) : PLXNC1 (112205 downstream)																							AGAACAGCACTGGAAATTTGAG	0.243													4	2	---	---	---	---	
NEDD1	121441	broad.mit.edu	37	12	97311847	97311848	+	Intron	INS	-	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97311847_97311848insA	uc001teu.3	+						NEDD1_uc001tev.3_Intron|NEDD1_uc010svc.1_Intron|NEDD1_uc001tew.2_Intron|NEDD1_uc001tex.2_Intron	NM_152905	NP_690869	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally						cell division|G2/M transition of mitotic cell cycle|mitosis	cytosol					0						GGGCCAGGTGGAAAAAATGAGA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97661691	97661691	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97661691delA								NEDD1 (314230 upstream) : RMST (197108 downstream)																							aaCAGGCACCAAAAAATAACA	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	98217614	98217614	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98217614delA								RMST (258821 upstream) : LOC100128191 (689139 downstream)																							CCAAGTGGTTAAAAAAAAAAT	0.368													4	4	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	100002183	100002184	+	Intron	DEL	AC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100002183_100002184delAC	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GGCACAAGAAACAAAGAGGATG	0.292													4	2	---	---	---	---	
NUAK1	9891	broad.mit.edu	37	12	106501334	106501335	+	Intron	INS	-	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106501334_106501335insG	uc001tlj.1	-							NM_014840	NP_055655	O60285	NUAK1_HUMAN	AMPK-related protein kinase 5								ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2						AAACTTTCCTAGGGGAAAGGCA	0.500													4	2	---	---	---	---	
TCP11L2	255394	broad.mit.edu	37	12	106711971	106711973	+	Intron	DEL	CAA	-	-	rs34594208		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106711971_106711973delCAA	uc001tln.2	+						TCP11L2_uc001tll.2_Intron|TCP11L2_uc001tlm.2_Intron	NM_152772	NP_689985	Q8N4U5	T11L2_HUMAN	t-complex 11 (mouse) like 2											ovary(3)	3						ATAATGCATTCAACAAGAAAAAT	0.177													17	24	---	---	---	---	
RBM19	9904	broad.mit.edu	37	12	114290338	114290338	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114290338delT	uc009zwi.2	-						RBM19_uc001tvn.3_Intron|RBM19_uc001tvm.2_Intron	NM_001146699	NP_001140171	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19						multicellular organismal development|positive regulation of embryonic development	chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|RNA binding			skin(3)|ovary(1)|liver(1)|central_nervous_system(1)	6	Medulloblastoma(191;0.163)|all_neural(191;0.178)					AATTCCTGAATTTGCTTTCGG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115837861	115837861	+	IGR	DEL	A	-	-	rs1009975	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115837861delA								TBX3 (715892 upstream) : MED13L (558522 downstream)																							aatggaactcatcagtgttaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	124755972	124755972	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124755972delT								ZNF664 (256005 upstream) : FAM101A (17738 downstream)																							ttcttcttccttttttttttg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126327238	126327240	+	IGR	DEL	GCA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126327238_126327240delGCA								TMEM132B (183649 upstream) : LOC100128554 (599787 downstream)																							CCGATCTATTGCAGCAGCAGCAC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127788705	127788705	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127788705delA								LOC100128554 (831375 upstream) : None (None downstream)																							GGATTTTTTTAAAAAAACAGA	0.338													4	2	---	---	---	---	
TMEM132C	92293	broad.mit.edu	37	12	128970792	128970792	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128970792delT	uc001uhs.3	+							NM_001136103	NP_001129575	Q8N3T6	T132C_HUMAN	transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1						CGTTACCATCTTTATTCAGAG	0.463													4	2	---	---	---	---	
MRP63	78988	broad.mit.edu	37	13	21751528	21751529	+	3'UTR	INS	-	C	C	rs140863639	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21751528_21751529insC	uc001unw.2	+	2					SKA3_uc001unt.2_5'Flank|SKA3_uc001unv.2_5'Flank|SKA3_uc001unu.2_5'Flank	NM_024026	NP_076931	Q9BQC6	RT63_HUMAN	mitochondrial ribosomal protein 63												0		all_cancers(29;2.76e-20)|all_epithelial(30;2.97e-18)|all_lung(29;4.58e-16)|Lung SC(185;0.0262)|Breast(139;0.147)		all cancers(112;9.43e-05)|Epithelial(112;0.000285)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|Lung(94;0.0932)		AGAGCTCTAAACCCCCAATACT	0.371													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	25205039	25205040	+	IGR	INS	-	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25205039_25205040insC								LOC374491 (33229 upstream) : ATP12A (49655 downstream)																							CAGGAGTCTTTCCCCTATCAGC	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31572123	31572123	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31572123delG								C13orf26 (22972 upstream) : HSPH1 (138642 downstream)																							ctggagtcaagggcagtgcat	0.025													4	2	---	---	---	---	
STARD13	90627	broad.mit.edu	37	13	33829766	33829767	+	Intron	INS	-	A	A			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33829766_33829767insA	uc001uuw.2	-						STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron|STARD13_uc010abh.1_Intron	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GCTAGAGACAGAAAAAAATCAG	0.416													4	2	---	---	---	---	
NBEA	26960	broad.mit.edu	37	13	35632677	35632677	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35632677delT	uc001uvb.2	+							NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TAACTGATCATTTTTCCCAAA	0.249													4	2	---	---	---	---	
LHFP	10186	broad.mit.edu	37	13	40106434	40106434	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40106434delC	uc001uxf.2	-						uc001uxg.2_RNA	NM_005780	NP_005771	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner precursor							integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		TCACAGCCCTCCACAAAACAG	0.428			T	HMGA2	lipoma								4	2	---	---	---	---	
THSD1P1	374500	broad.mit.edu	37	13	52803642	52803642	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52803642delT	uc001vgm.1	-						uc001vgn.2_Intron					Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						CAGTTTTCCCTTTTTTTTTTT	0.328													11	7	---	---	---	---	
DIAPH3	81624	broad.mit.edu	37	13	60471373	60471373	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60471373delA	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)		AAGTAGATATAATTAATAGGG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	81342756	81342756	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81342756delG								SPRY2 (427670 upstream) : None (None downstream)																							GTCTTAAACTGGGGGGGGAAC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	89350581	89350581	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89350581delT								None (None upstream) : None (None downstream)																							atatttttccttttttttttt	0.000													3	3	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109810543	109810543	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109810543delC	uc001vqt.1	+						MYO16_uc010agk.1_Intron	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			GTCCGTTCTGCCAGGTTTCTT	0.507													4	2	---	---	---	---	
DAAM1	23002	broad.mit.edu	37	14	59817573	59817573	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59817573delT	uc001xdz.1	+						DAAM1_uc001xea.1_Intron	NM_014992	NP_055807	Q9Y4D1	DAAM1_HUMAN	dishevelled-associated activator of						actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)		tcagccctgctttttttctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	71732527	71732535	+	IGR	DEL	TGTGAAGAT	-	-	rs141239115		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71732527_71732535delTGTGAAGAT								PCNX (150428 upstream) : SNORD56B (132519 downstream)																							aaagagtgaatgtgaagattgtgaagata	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	76970342	76970343	+	IGR	INS	-	G	G	rs147646877	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76970342_76970343insG								ESRRB (2164 upstream) : VASH1 (257892 downstream)																							cgaaatggaatgggggaggccc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	80410226	80410226	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80410226delT								NRXN3 (79468 upstream) : DIO2 (253644 downstream)																							ACTTTAAGACTTTAGGAGACA	0.383													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20614996	20614999	+	Intron	DEL	TTTG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20614996_20614999delTTTG	uc001ytg.2	-						uc010tyx.1_Intron|uc001yth.3_Intron					RecName: Full=Putative HERC2-like protein 3;																		CCCTCACTTATTTGTTTGTTTAtt	0.216													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20863420	20863420	+	IGR	DEL	T	-	-	rs111525382		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20863420delT								GOLGA8C (82394 upstream) : BCL8 (6636 downstream)																							ATTTTCTTTCttttttttaaa	0.174													6	5	---	---	---	---	
BCL8	606	broad.mit.edu	37	15	20877736	20877737	+	Intron	DEL	AT	-	-	rs149802357		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20877736_20877737delAT	uc010tze.1	-						BCL8_uc010tzd.1_5'Flank	NR_027992				RecName: Full=Putative protein BCL8;												0						TGAAGTCTGAATATAAGTTTAA	0.351													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21216004	21216004	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21216004delC								NF1P1 (81379 upstream) : LOC646214 (716510 downstream)																							TGCACAGTGTCCCCCTGGAGA	0.682													16	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23791858	23791859	+	IGR	DEL	AA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23791858_23791859delAA								GOLGA8E (343435 upstream) : MKRN3 (18595 downstream)																							aaccgtctgtaaaccatgactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30428885	30428885	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30428885delT	uc010azm.1	+											Homo sapiens cDNA, FLJ17568.																		TGCCTTTTTCTTTTTTTTTTC	0.418													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37546474	37546475	+	IGR	INS	-	TAT	TAT	rs147091078	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37546474_37546475insTAT								MEIS2 (152974 upstream) : TMCO5A (680352 downstream)																							aaaattGATTCTATTATACTTA	0.262													4	4	---	---	---	---	
DNAJC17	55192	broad.mit.edu	37	15	41079433	41079433	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41079433delG	uc001zms.1	-						DNAJC17_uc010bbz.1_Intron|DNAJC17_uc010bca.1_Intron|DNAJC17_uc010bcb.1_Intron	NM_018163	NP_060633	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17						protein folding		heat shock protein binding|nucleotide binding|RNA binding|unfolded protein binding				0		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		caaataaagtggatgtacttA	0.045													4	2	---	---	---	---	
EXD1	161829	broad.mit.edu	37	15	41521081	41521081	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41521081delA	uc001znk.2	-						CHP_uc001znl.2_5'Flank|EXD1_uc010ucv.1_Intron	NM_152596	NP_689809	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding			ovary(1)	1						AACATTAAAGAAAAAAAAATT	0.264													4	2	---	---	---	---	
CAPN3	825	broad.mit.edu	37	15	42692884	42692884	+	Intron	DEL	A	-	-	rs79160618		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42692884delA	uc001zpn.1	+						CAPN3_uc001zpk.1_Intron|CAPN3_uc001zpl.1_Intron|CAPN3_uc010udf.1_Intron|CAPN3_uc010udg.1_Intron|CAPN3_uc001zpo.1_Intron|CAPN3_uc001zpp.1_Intron|CAPN3_uc001zpq.1_5'Flank	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a						muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		accctgcctcaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	49017373	49017373	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49017373delA								FBN1 (79455 upstream) : CEP152 (12976 downstream)																							GCGTCACAAGAAAAAAAAAAT	0.214													8	4	---	---	---	---	
SHC4	399694	broad.mit.edu	37	15	49136095	49136096	+	Intron	INS	-	A	A	rs147281731	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49136095_49136096insA	uc001zxb.1	-						SHC4_uc010uey.1_Intron|SHC4_uc010uez.1_Intron	NM_203349	NP_976224	Q6S5L8	SHC4_HUMAN	rai-like protein						intracellular signal transduction	cell junction|postsynaptic membrane				ovary(3)|pancreas(2)	5		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		AAAGAGGGCTGATAGTCTCAGC	0.495													4	3	---	---	---	---	
COPS2	9318	broad.mit.edu	37	15	49429190	49429190	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49429190delA	uc001zxf.2	-						COPS2_uc001zxh.2_Intron|COPS2_uc010ufa.1_Intron	NM_004236	NP_004227	P61201	CSN2_HUMAN	COP9 constitutive photomorphogenic homolog						cullin deneddylation|transcription from RNA polymerase II promoter	cytoplasm|signalosome	protein binding|signal transducer activity			lung(1)	1		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		cctctctctcaaaaaaaaaaa	0.065													4	5	---	---	---	---	
SPPL2A	84888	broad.mit.edu	37	15	51011920	51011920	+	Intron	DEL	T	-	-	rs67581503		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51011920delT	uc001zyv.2	-							NM_032802	NP_116191	Q8TCT8	PSL2_HUMAN	signal peptide peptidase-like 2A							integral to membrane	aspartic-type endopeptidase activity				0				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		TCCTCTGCTGTTTTTTTTTTT	0.358													8	6	---	---	---	---	
MYO5C	55930	broad.mit.edu	37	15	52524531	52524532	+	Intron	DEL	AA	-	-	rs56101752		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52524531_52524532delAA	uc010bff.2	-						MYO5C_uc010uga.1_Intron|MYO5C_uc010ugb.1_Intron	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)		ggaaggagagaaagaaagaaga	0.134													2	4	---	---	---	---	
GCOM1	145781	broad.mit.edu	37	15	57928152	57928152	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57928152delG	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						ggacccttctggggaacagat	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	60104330	60104331	+	IGR	INS	-	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60104330_60104331insC								BNIP2 (122688 upstream) : FOXB1 (192090 downstream)																							ATAAACGCTTTCCCCCGTCTCT	0.421													4	2	---	---	---	---	
MEGF11	84465	broad.mit.edu	37	15	66253293	66253293	+	Intron	DEL	T	-	-	rs76210418		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66253293delT	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821	A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1						AAATCATTCCTTTTTTTTTTT	0.343													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	67287601	67287601	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67287601delA								SMAD6 (213266 upstream) : SMAD3 (70594 downstream)																							aaggttgcataaacacactac	0.000													4	2	---	---	---	---	
ACSBG1	23205	broad.mit.edu	37	15	78485853	78485853	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78485853delG	uc002bdh.2	-	5	714	c.658delC	c.(658-660)CTGfs	p.L220fs	ACSBG1_uc010umw.1_Frame_Shift_Del_p.L216fs|ACSBG1_uc010umx.1_Intron|ACSBG1_uc010umy.1_Frame_Shift_Del_p.L113fs	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin	220					long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1						CAAACCTTCAGGATCTTTTCC	0.577													93	51	---	---	---	---	
CHRNB4	1143	broad.mit.edu	37	15	78927090	78927090	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78927090delG	uc002bed.1	-						CHRNB4_uc002bee.1_Intron|CHRNB4_uc010blh.1_Intron	NM_000750	NP_000741	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4						regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0						CCCTGTGGATGGGGACATGGG	0.562													4	2	---	---	---	---	
UBE2Q2P1	388165	broad.mit.edu	37	15	85105420	85105421	+	Intron	INS	-	G	G	rs1828575		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85105420_85105421insG	uc002bkn.1	-							NR_003661				Homo sapiens cDNA FLJ43276 fis, clone KIDNE2011532, moderately similar to Homo sapiens melanoma-associated chondroitin sulfate proteoglycan 4.												0						AAAGGCAACACATTAAATTCAT	0.391													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88169689	88169689	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88169689delT								NCRNA00052 (46772 upstream) : NTRK3 (250299 downstream)																							CTAAGAAAACTAAGGAAATAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	89027856	89027856	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89027856delT								MRPS11 (6362 upstream) : DET1 (26932 downstream)																							TTAGTATATATTTGGACACAC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	90048112	90048112	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90048112delA								RHCG (8313 upstream) : LOC283761 (50 downstream)																							acaaaatcttaaaaaaaaacg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93811449	93811449	+	IGR	DEL	A	-	-	rs11335008		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93811449delA								RGMA (179016 upstream) : MCTP2 (963352 downstream)																							ctttgcaaagaaaaAAAAAAA	0.209													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96768148	96768148	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96768148delC								LOC145820 (717074 upstream) : NR2F2 (101009 downstream)																							AACAGAGTTGCCAGGTCGGTG	0.478													4	2	---	---	---	---	
LOC91948	91948	broad.mit.edu	37	15	98310939	98310939	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98310939delA	uc002buh.1	-						LOC91948_uc002bug.1_Intron	NR_024173				SubName: Full=Putative uncharacterized protein ENSP00000381347;												0						tctagtcagtaaaaaggcagg	0.000													4	2	---	---	---	---	
IGF1R	3480	broad.mit.edu	37	15	99393881	99393881	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99393881delA	uc002bul.2	+						IGF1R_uc010urq.1_Intron|IGF1R_uc010bon.2_Intron	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor						anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)	GAGAAGTCAGAAAAGCATAAC	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102078338	102078338	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102078338delC								PCSK6 (48151 upstream) : TM2D3 (94842 downstream)																							GAAATGCTATCCACTCAGAGA	0.478													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7669381	7669382	+	Intron	DEL	GC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7669381_7669382delGC	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		GGCAGTGTGTGCGAGTATGTGT	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8055482	8055483	+	IGR	DEL	GT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8055482_8055483delGT								A2BP1 (292142 upstream) : TMEM114 (564020 downstream)																							TAGGTGTGCCGTGTGTGTGTGT	0.396													4	2	---	---	---	---	
GRIN2A	2903	broad.mit.edu	37	16	10218336	10218337	+	Intron	DEL	TT	-	-	rs71402433		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10218336_10218337delTT	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TTGATAACTCTTTGTTTATCCG	0.426													4	4	---	---	---	---	
CIITA	4261	broad.mit.edu	37	16	10982371	10982372	+	Intron	DEL	GA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10982371_10982372delGA	uc002dai.3	+						CIITA_uc002daj.3_Intron|CIITA_uc002dak.3_Intron|CIITA_uc002dag.2_Intron|CIITA_uc002dah.2_Intron|CIITA_uc010bup.1_Intron	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator						interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1						TCCCTCGGGGGAGAGAGAGGTG	0.436			T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|								4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12204500	12204501	+	Intron	DEL	CC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12204500_12204501delCC	uc002dby.3	+						SNX29_uc010uyx.1_Intron	NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						TTTAAAAACACCCTGCTCCAGG	0.500													4	2	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14676791	14676791	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14676791delA	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						TACCTGAGGCAACCCTCCCCC	0.254													4	2	---	---	---	---	
XYLT1	64131	broad.mit.edu	37	16	17376817	17376818	+	Intron	INS	-	C	C	rs138423148	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17376817_17376818insC	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						gcaataagtcaccccccccaag	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27038975	27038975	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27038975delA								HS3ST4 (889967 upstream) : C16orf82 (39244 downstream)																							aaaaaggactaatataGTTTG	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28251264	28251264	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28251264delT								XPO6 (28074 upstream) : SBK1 (52576 downstream)																							ATTCGACAGGTTTTTCCAGGC	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28271405	28271406	+	IGR	INS	-	TGTG	TGTG	rs138931229	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28271405_28271406insTGTG								XPO6 (48215 upstream) : SBK1 (32434 downstream)																							GTGTATTTGCTtgtgtgtgtgt	0.421													5	5	---	---	---	---	
ZNF688	146542	broad.mit.edu	37	16	30581350	30581351	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30581350_30581351insC	uc002dyt.2	-	3	1495_1496	c.717_718insG	c.(715-720)GGGCGGfs	p.G239fs	ZNF688_uc002dys.2_Frame_Shift_Ins_p.G225fs|uc002dyu.2_5'Flank	NM_145271	NP_660314	P0C7X2	ZN688_HUMAN	zinc finger protein 688 isoform a	239_240					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CGGCCCCGCCGCCCCCCGGAGC	0.708													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33946421	33946422	+	IGR	INS	-	A	A	rs112464617		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33946421_33946422insA								None (None upstream) : MIR1826 (19086 downstream)																							caaacagcatcacatgctacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33946503	33946503	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33946503delC								None (None upstream) : MIR1826 (19005 downstream)																							ccttcagcagcccccacactg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34180461	34180461	+	IGR	DEL	T	-	-	rs80312899		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34180461delT								MIR1826 (214869 upstream) : UBE2MP1 (223341 downstream)																							ACAGTTTTAGTGGGTTTTGGT	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51749006	51749006	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51749006delA								SALL1 (563823 upstream) : TOX3 (722912 downstream)																							ATACTTAAGGAAATGTACAGA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52039554	52039554	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52039554delA								SALL1 (854371 upstream) : TOX3 (432364 downstream)																							ctgctgcaagaaaaaaaaata	0.000													5	3	---	---	---	---	
BBS2	583	broad.mit.edu	37	16	56521107	56521107	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56521107delA	uc002ejd.2	-							NM_031885	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2 protein						adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1						aatttgatttaaaaaaaAAAA	0.174									Bardet-Biedl_syndrome				4	2	---	---	---	---	
MT1F	4494	broad.mit.edu	37	16	56689391	56689391	+	5'Flank	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56689391delA	uc002ejt.2	+							NM_005949	NP_005940	P04733	MT1F_HUMAN	metallothionein 1F							cytoplasm	cadmium ion binding|copper ion binding|zinc ion binding				0						CAACCTGCCTAAGACCATGGA	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64706207	64706207	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64706207delA								None (None upstream) : CDH11 (274478 downstream)																							GTGAAAGAACAGGAGACAGAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	70407635	70407635	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70407635delT								DDX19A (356 upstream) : ST3GAL2 (5703 downstream)																							acaatgaacattttttttttc	0.000													4	2	---	---	---	---	
HYDIN	54768	broad.mit.edu	37	16	70858436	70858436	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70858436delT	uc002ezr.2	-						HYDIN_uc010cfy.2_Intron	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)				TTTGATTCACttttttttttt	0.119													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73897923	73897923	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73897923delT								HTA (770253 upstream) : PSMD7 (432758 downstream)																							AAGCCAGGGCTTTTTAAGTTA	0.413													4	2	---	---	---	---	
BCAR1	9564	broad.mit.edu	37	16	75273111	75273111	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75273111delC	uc002fdv.2	-						BCAR1_uc002fdt.2_5'Flank|BCAR1_uc002fdu.2_5'Flank|BCAR1_uc010cgu.2_Intron|BCAR1_uc010vna.1_Intron|BCAR1_uc010vnb.1_Intron|BCAR1_uc002fdw.2_Intron|BCAR1_uc010vnc.1_Intron|BCAR1_uc010vnd.1_Intron|BCAR1_uc002fdx.2_Intron	NM_014567	NP_055382	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1						actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway	cytosol|focal adhesion|membrane fraction|ruffle	protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity			central_nervous_system(5)|breast(2)|prostate(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.169)		ACACCTGAGACCCCACTAGCA	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86628067	86628068	+	IGR	DEL	TG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86628067_86628068delTG								FOXL1 (12764 upstream) : FBXO31 (734876 downstream)																							GCGgtgtgtctgtgtgtgtgtg	0.366													3	3	---	---	---	---	
ZNF778	197320	broad.mit.edu	37	16	89296977	89296977	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89296977delG	uc010vpf.1	+						uc010vph.1_5'Flank			Q96MU6	ZN778_HUMAN	Homo sapiens cDNA FLJ31875 fis, clone NT2RP7002450, weakly similar to ZINC FINGER PROTEIN 84.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0269)		aaacagaccagggacacggct	0.055													4	2	---	---	---	---	
GLOD4	51031	broad.mit.edu	37	17	681631	681631	+	Intron	DEL	T	-	-	rs34763747		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:681631delT	uc002frv.2	-						GLOD4_uc002frt.2_5'Flank|GLOD4_uc002fru.2_Intron|GLOD4_uc010vqc.1_Intron	NM_016080	NP_057164	Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							mitochondrion					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		gacagccggctggtgttagag	0.169													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	10582182	10582182	+	IGR	DEL	T	-	-	rs11334426		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10582182delT								MYH3 (22717 upstream) : SCO1 (1469 downstream)																							gcagggtttgttttttttttt	0.000													4	2	---	---	---	---	
TNFRSF13B	23495	broad.mit.edu	37	17	16844614	16844614	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16844614delA	uc002gqs.1	-						TNFRSF13B_uc010vwt.1_Intron|TNFRSF13B_uc002gqt.1_Intron|TNFRSF13B_uc010vwu.1_3'UTR	NM_012452	NP_036584	O14836	TR13B_HUMAN	tumor necrosis factor receptor 13B						cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding|receptor activity			kidney(2)	2						CCAGGACAGCAGGTGCCAACC	0.423									IgA_Deficiency_Selective				4	2	---	---	---	---	
PIGS	94005	broad.mit.edu	37	17	26886007	26886007	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26886007delT	uc002hbo.2	-						PIGS_uc002hbn.2_Intron|PIGS_uc010wap.1_Intron	NM_033198	NP_149975	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			breast(2)|urinary_tract(1)|kidney(1)	4	Lung NSC(42;0.00431)					tcttcacatcttttttttttg	0.000													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35097964	35097965	+	IGR	DEL	TA	-	-	rs60115188		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35097964_35097965delTA								MRM1 (132558 upstream) : LHX1 (196534 downstream)																							tgtgctggtgtatgtgtgtgta	0.139													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39463870	39463870	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39463870delC								KRTAP9-9 (51255 upstream) : KRTAP17-1 (7301 downstream)																							CTAGCTAAGTCATAATGAGCT	0.453													4	2	---	---	---	---	
ITGB3	3690	broad.mit.edu	37	17	45329412	45329412	+	5'Flank	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45329412delA	uc002ilj.2	+						ITGB3_uc002ili.1_5'Flank|ITGB3_uc010wkr.1_5'Flank	NM_000212	NP_000203	P05106	ITB3_HUMAN	integrin beta chain, beta 3 precursor						activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|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|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)	gccagtagagaaaaaaaaatt	0.000													4	2	---	---	---	---	
B4GALNT2	124872	broad.mit.edu	37	17	47236696	47236697	+	Intron	INS	-	TTTGT	TTTGT	rs139717167	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47236696_47236697insTTTGT	uc002ion.2	+						B4GALNT2_uc010wlt.1_Intron|B4GALNT2_uc010wlu.1_Intron	NM_153446	NP_703147	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2						lipid glycosylation|negative regulation of cell-cell adhesion|UDP-N-acetylgalactosamine metabolic process	integral to Golgi membrane	acetylgalactosaminyltransferase activity			large_intestine(1)|ovary(1)	2			all cancers(6;0.000316)			gtgtgtgtttgtttgttttgtt	0.188													11	6	---	---	---	---	
ABCC3	8714	broad.mit.edu	37	17	48743833	48743833	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48743833delA	uc002isl.2	+						ABCC3_uc002isk.3_Intron	NM_003786	NP_003777	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C, member 3						bile acid metabolic process	integral to plasma membrane|membrane fraction	ATP binding|bile acid-exporting ATPase activity|organic anion transmembrane transporter activity			skin(3)|central_nervous_system(1)	4			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Glibenclamide(DB01016)	actccgtctcaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	50988717	50988717	+	IGR	DEL	A	-	-	rs113307667		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50988717delA								CA10 (751340 upstream) : KIF2B (911522 downstream)																							atattgctggaaaaaaaaagg	0.030													4	3	---	---	---	---	
SMURF2	64750	broad.mit.edu	37	17	62547477	62547477	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62547477delA	uc002jep.1	-						SMURF2_uc002jeq.1_Intron|SMURF2_uc002jer.1_Intron	NM_022739	NP_073576	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2						BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			cctgtctcagaaaaaaaaaaa	0.169													7	4	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71417422	71417422	+	Intron	DEL	C	-	-	rs11337646		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71417422delC	uc010dfm.2	-						SDK2_uc010dfn.2_Intron	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						GATTGTTTGACCCCAGTGGTG	0.473											OREG0031507	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76521380	76521381	+	IGR	INS	-	C	C	rs137895113	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76521380_76521381insC								DNAH17 (52524 upstream) : CYTH1 (148750 downstream)																							TACAACGGTGTCCCACCTGGAG	0.663													4	4	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77260756	77260757	+	Intron	INS	-	C	C			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77260756_77260757insC	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			CCTCATAGCTTCCCCAGTTCAC	0.396													4	2	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78709237	78709237	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78709237delT	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|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						AATTCAAATGTTTTTTAACAA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	214519	214520	+	IGR	INS	-	TTG	TTG	rs142588910		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:214519_214520insTTG								USP14 (780 upstream) : THOC1 (2 downstream)																							CTGTACAACAATTGTTATAAAA	0.351													6	9	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13387957	13387957	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13387957delA	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		TAGCAGTTTGAAAAAGTGTTT	0.423													4	2	---	---	---	---	
GREB1L	80000	broad.mit.edu	37	18	18929188	18929189	+	Intron	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18929188_18929189insT	uc010xam.1	+						GREB1L_uc002ktf.1_Intron|GREB1L_uc010dlp.1_Intron	NM_001142966	NP_001136438	Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast							integral to membrane					0						taattatgttattttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	19812269	19812272	+	IGR	DEL	ATCC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19812269_19812272delATCC								GATA6 (30042 upstream) : CTAGE1 (181292 downstream)																							acatacatctatccatccatccat	0.000													4	2	---	---	---	---	
ZNF521	25925	broad.mit.edu	37	18	22800317	22800317	+	Intron	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22800317delG	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)					CCTGGGCAATGGGTGAGGGAA	0.473			T	PAX5	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	28751025	28751027	+	IGR	DEL	ATT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28751025_28751027delATT								DSC1 (8206 upstream) : DSG1 (147025 downstream)																							gaaaagtgacattatcacagtaa	0.049													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	56835677	56835677	+	IGR	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56835677delT								SEC11C (9616 upstream) : GRP (51723 downstream)																							tgaaagaaagttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	584136	584136	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:584136delG								BSG (644 upstream) : HCN2 (5757 downstream)																							TGGTCTGAGCGGGGGTCTCAG	0.607											OREG0025106	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SMARCA4	6597	broad.mit.edu	37	19	11170665	11170666	+	Intron	INS	-	G	G			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11170665_11170666insG	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc010dxq.2_Intron|SMARCA4_uc010dxr.2_Intron|SMARCA4_uc002mqj.3_Intron|SMARCA4_uc010dxs.2_Intron|SMARCA4_uc002mqh.3_Intron	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity			lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CCCCTTGCTGTGGGGGTGCTGC	0.663			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				4	2	---	---	---	---	
ZNF333	84449	broad.mit.edu	37	19	14805551	14805555	+	Intron	DEL	AAAAG	-	-	rs75337291		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14805551_14805555delAAAAG	uc002mzn.2	+						ZNF333_uc010dzq.2_Intron|ZNF333_uc002mzk.3_Intron|ZNF333_uc002mzl.3_Intron|ZNF333_uc002mzm.2_Intron|ZNF333_uc010dzr.1_Intron	NM_032433	NP_115809	Q96JL9	ZN333_HUMAN	zinc finger protein 333						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						TCCAAATGTTAAAagaaagtaaaca	0.210													8	8	---	---	---	---	
CASP14	23581	broad.mit.edu	37	19	15163609	15163610	+	Intron	INS	-	CA	CA	rs140888936	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15163609_15163610insCA	uc010dzv.1	+						CASP14_uc002naf.2_Intron	NM_012114	NP_036246	P31944	CASPE_HUMAN	caspase 14 precursor						apoptosis|cell differentiation|epidermis development|proteolysis	cytoplasm|nucleus	cysteine-type endopeptidase activity			skin(2)|ovary(1)|lung(1)	4						atcttcaaaatcacacacacac	0.163													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	15830920	15830920	+	IGR	DEL	T	-	-	rs68070556		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15830920delT								CYP4F12 (22936 upstream) : OR10H2 (7914 downstream)																							Attttttttcttttttttttt	0.373													4	2	---	---	---	---	
HAPLN4	404037	broad.mit.edu	37	19	19383501	19383502	+	Intron	INS	-	GT	GT			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19383501_19383502insGT	uc002nmc.2	-						TM6SF2_uc002nmd.1_Intron	NM_023002	NP_075378	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4						cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding			pancreas(1)	1			Epithelial(12;0.00575)			AATGGAGTAGGgtgtgtgtgtg	0.436													5	3	---	---	---	---	
ZNF626	199777	broad.mit.edu	37	19	20806648	20806649	+	3'UTR	DEL	CA	-	-	rs71893877		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20806648_20806649delCA	uc002npb.1	-	4					ZNF626_uc002npc.1_3'UTR	NM_001076675	NP_001070143	Q68DY1	ZN626_HUMAN	zinc finger protein 626 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						TATGCTTTGCCACATTCTTCAC	0.203													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30544400	30544400	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30544400delG								C19orf2 (37789 upstream) : ZNF536 (318928 downstream)																							CCCGTGGAGTGGGTGTGCTGC	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	32162824	32162825	+	IGR	DEL	AC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32162824_32162825delAC								TSHZ3 (322634 upstream) : ZNF507 (673689 downstream)																							GCACTCATATACACACACACAC	0.475													4	2	---	---	---	---	
GPI	2821	broad.mit.edu	37	19	34862117	34862117	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34862117delA	uc002nvg.1	+						GPI_uc002nvf.2_Intron|GPI_uc010xrv.1_Intron|GPI_uc010xrw.1_Intron|GPI_uc010edl.1_Intron	NM_000175	NP_000166	P06744	G6PI_HUMAN	glucose phosphate isomerase						angiogenesis|gluconeogenesis|glycolysis|hemostasis|humoral immune response	cytosol|extracellular space|nucleus|plasma membrane	cytokine activity|glucose-6-phosphate isomerase activity|growth factor activity			ovary(1)|kidney(1)	2	Esophageal squamous(110;0.162)					TTTATAGTTCAAAAAAAGTTG	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	35076554	35076554	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35076554delG								LOC643719 (7958 upstream) : SCGBL (7793 downstream)																							gatgcttggtgggcaggggac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	39470553	39470553	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39470553delG								FBXO17 (4173 upstream) : FBXO27 (44111 downstream)																							TGCATTGCCTGGGCCCATCAT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	43807803	43807808	+	IGR	DEL	TGTGTG	-	-	rs66685229	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43807803_43807808delTGTGTG								PSG9 (34121 upstream) : PRG1 (45400 downstream)																							AGAGAGAGAAtgtgtgtgtgtgtgtg	0.330													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	44686849	44686849	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44686849delA								ZNF226 (5013 upstream) : ZNF227 (29842 downstream)																							aatgggctttaaaaaaaaatt	0.000													4	2	---	---	---	---	
SLC8A2	6543	broad.mit.edu	37	19	47975113	47975114	+	5'UTR	DEL	AG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47975113_47975114delAG	uc002pgx.2	-	1					SLC8A2_uc010xyq.1_5'UTR|SLC8A2_uc010xyr.1_5'UTR	NM_015063	NP_055878	Q9UPR5	NAC2_HUMAN	solute carrier family 8 member 2 precursor						cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(1)	4		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		TCCGCCCGAAAGAGAGAGAGAG	0.441													4	2	---	---	---	---	
PPP2R1A	5518	broad.mit.edu	37	19	52704783	52704783	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52704783delA	uc002pyp.2	+						PPP2R1A_uc010ydk.1_Intron|PPP2R1A_uc010epm.1_Intron|PPP2R1A_uc002pyq.2_5'UTR	NM_014225	NP_055040	P30153	2AAA_HUMAN	alpha isoform of regulatory subunit A, protein						ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity			endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		GGATGTGTTTAGCCGAGGACC	0.254			Mis		clear cell ovarian carcinoma								4	2	---	---	---	---	
NLRP2	55655	broad.mit.edu	37	19	55512434	55512438	+	3'UTR	DEL	CTTAT	-	-	rs4200	byFrequency	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55512434_55512438delCTTAT	uc002qij.2	+	13					NLRP2_uc010yfp.1_3'UTR|NLRP2_uc010esn.2_3'UTR|NLRP2_uc010eso.2_3'UTR|NLRP2_uc010esp.2_3'UTR	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2						apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TGCACACATCCTTATCTTTGTTACA	0.415													10	5	---	---	---	---	
SNPH	9751	broad.mit.edu	37	20	1245278	1245278	+	5'Flank	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1245278delA	uc002wes.2	+						SNPH_uc002wet.2_5'Flank	NM_014723	NP_055538	O15079	SNPH_HUMAN	syntaphilin						synaptic vesicle docking involved in exocytosis	cell junction|integral to membrane|synapse|synaptosome	syntaxin-1 binding			ovary(2)	2						CATTTGTTGCAAAAAAAGTAA	0.279													4	2	---	---	---	---	
SIRPD	128646	broad.mit.edu	37	20	1535429	1535429	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1535429delA	uc002wfi.2	-							NM_178460	NP_848555	Q9H106	SIRPD_HUMAN	signal-regulatory protein delta precursor							extracellular region				ovary(1)|kidney(1)|skin(1)	3						CTCCCAGAGTAAACACTGAGG	0.294													4	2	---	---	---	---	
ITPA	3704	broad.mit.edu	37	20	3190767	3190768	+	Intron	DEL	GC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3190767_3190768delGC	uc002wid.2	+						ITPA_uc002wie.2_Intron|ITPA_uc002wif.2_Intron	NM_033453	NP_258412	Q9BY32	ITPA_HUMAN	inosine triphosphatase isoform a						nucleotide metabolic process	cytoplasm	metal ion binding|nucleoside-triphosphate diphosphatase activity|nucleotide binding			ovary(1)	1						caggacatttgcttcacagcgc	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	4566007	4566008	+	IGR	INS	-	C	C	rs144659328	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4566007_4566008insC								ADRA1D (336348 upstream) : PRNP (100789 downstream)																							agctggggctgactcatctgaa	0.000													1	5	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17425417	17425418	+	Intron	DEL	GG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17425417_17425418delGG	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	taatgccactgggaaacttcag	0.000													4	2	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17444611	17444612	+	Intron	DEL	CA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17444611_17444612delCA	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron|PCSK2_uc002wpn.2_5'UTR	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	tgcagctcagcacacacacaca	0.069													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	20816142	20816143	+	IGR	DEL	TC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20816142_20816143delTC								RALGAPA2 (122876 upstream) : PLK1S1 (290481 downstream)																							GGAGGAGACTTCTAAAGGGTGG	0.465													4	2	---	---	---	---	
PLK1S1	55857	broad.mit.edu	37	20	21208034	21208035	+	Intron	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21208034_21208035insT	uc002wsb.2	+						PLK1S1_uc010zsh.1_Intron|PLK1S1_uc010zsi.1_Intron|PLK1S1_uc010zsj.1_Intron|PLK1S1_uc002wsd.2_Intron	NM_018474	NP_060944	Q2M2Z5	KIZ_HUMAN	polo-like kinase 1 substrate 1 isoform 1						spindle organization	centrosome	protein kinase binding				0						GAAGCTGCTCCTTTTTTTTCAA	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22079334	22079334	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22079334delA								PAX1 (382714 upstream) : LOC284788 (301637 downstream)																							TCAGGGGAGGAAAAAAAATCC	0.453													4	2	---	---	---	---	
RBM39	9584	broad.mit.edu	37	20	34306205	34306205	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34306205delA	uc002xeb.2	-						RBM39_uc002xdz.2_Intron|RBM39_uc002xea.2_Intron|RBM39_uc010gfn.2_Intron|RBM39_uc010zvm.1_Intron|RBM39_uc002xeg.2_Intron|RBM39_uc002xec.2_Intron|RBM39_uc002xed.2_Intron|RBM39_uc002xee.2_Intron|RBM39_uc002xef.2_Intron|RBM39_uc010zvn.1_Intron	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a						mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					aaaacaaaacaaaaaaaaaAC	0.313													3	4	---	---	---	---	
SRC	6714	broad.mit.edu	37	20	35988305	35988306	+	Intron	INS	-	TT	TT			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35988305_35988306insTT	uc002xgx.2	+						SRC_uc002xgy.2_Intron	NM_005417	NP_005408	P12931	SRC_HUMAN	proto-oncogene tyrosine-protein kinase SRC						axon guidance|bone resorption|cell junction assembly|cellular membrane organization|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular protein kinase cascade|leukocyte migration|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of integrin activation|Ras protein signal transduction|regulation of bone resorption|regulation of vascular permeability|response to interleukin-1|signal complex assembly|T cell costimulation	caveola|cytosol|mitochondrial inner membrane	ATP binding|heme binding|integrin binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|SH3/SH2 adaptor activity			large_intestine(10)|lung(1)|central_nervous_system(1)|endometrium(1)	13		Myeloproliferative disorder(115;0.00878)			Dasatinib(DB01254)	AGGGCCAAGCATTTTTTTTTTC	0.272													4	2	---	---	---	---	
BLCAP	10904	broad.mit.edu	37	20	36150582	36150583	+	5'Flank	INS	-	A	A	rs149299117		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36150582_36150583insA	uc002xha.2	-						BLCAP_uc002xhb.2_Intron|BLCAP_uc002xhc.2_Intron|NNAT_uc002xhd.2_Intron|NNAT_uc002xhe.2_Intron	NM_006698	NP_006689	P62952	BLCAP_HUMAN	bladder cancer associated protein						apoptosis|cell cycle	integral to membrane					0		Myeloproliferative disorder(115;0.00878)				AATTGCTTTACaaaaaaaaaaa	0.292													6	3	---	---	---	---	
RALGAPB	57148	broad.mit.edu	37	20	37117833	37117833	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37117833delT	uc002xiw.2	+						RALGAPB_uc010zvz.1_Intron|RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2						TTGCTGtttctttttttttga	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	40459330	40459330	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40459330delC								CHD6 (212197 upstream) : PTPRT (242063 downstream)																							ccataaaagtccaggtgagtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	47103830	47103830	+	IGR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47103830delA								LOC284749 (104449 upstream) : PREX1 (136963 downstream)																							AACTGGCTCCAACCCAGGTCT	0.468													4	2	---	---	---	---	
PREX1	57580	broad.mit.edu	37	20	47368267	47368267	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47368267delC	uc002xtw.1	-							NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CTCAGGATTTCCAGGGCTGCC	0.502													3	4	---	---	---	---	
PTPN1	5770	broad.mit.edu	37	20	49160154	49160154	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49160154delA	uc002xvl.2	+						PTPN1_uc010zys.1_Intron	NM_002827	NP_002818	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type						blood coagulation|interferon-gamma-mediated signaling pathway|negative regulation of insulin receptor signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytosol|endoplasmic reticulum membrane	protein tyrosine phosphatase activity|zinc ion binding				0		Lung NSC(126;0.163)			Clodronate(DB00720)|Tiludronate(DB01133)	TAAGCTGACCAAGCCAGAAGA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52349960	52349960	+	IGR	DEL	G	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52349960delG								ZNF217 (139159 upstream) : SUMO1P1 (141082 downstream)																							aagccagagtgggagacatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53647775	53647776	+	IGR	INS	-	CTT	CTT			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53647775_53647776insCTT								DOK5 (380066 upstream) : CBLN4 (924721 downstream)																							gcagtgaataacttctatctcc	0.000													4	2	---	---	---	---	
PCK1	5105	broad.mit.edu	37	20	56140965	56140967	+	3'UTR	DEL	ATC	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56140965_56140967delATC	uc002xyn.3	+	10					PCK1_uc010zzm.1_3'UTR	NM_002591	NP_002582	P35558	PCKGC_HUMAN	cytosolic phosphoenolpyruvate carboxykinase 1						gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			skin(1)	1	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CACCATAATAATCATCACCACAC	0.429													3	4	---	---	---	---	
PMEPA1	56937	broad.mit.edu	37	20	56236037	56236038	+	Intron	DEL	CA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56236037_56236038delCA	uc002xyq.2	-						PMEPA1_uc002xyr.2_Intron|PMEPA1_uc002xys.2_Intron|PMEPA1_uc002xyt.2_Intron	NM_020182	NP_064567	Q969W9	PMEPA_HUMAN	transmembrane prostate androgen-induced protein						androgen receptor signaling pathway	integral to membrane|plasma membrane	WW domain binding			pancreas(1)	1						cacacgtgcccacacacacaca	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58974368	58974368	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58974368delT	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																		atccatcatgttttttatata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59564523	59564524	+	IGR	DEL	GT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59564523_59564524delGT								MIR646 (680898 upstream) : CDH4 (263035 downstream)																							cttgttacaggtgtgtgtgtgt	0.040													4	3	---	---	---	---	
DNAJC5	80331	broad.mit.edu	37	20	62525560	62525561	+	5'Flank	DEL	CA	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62525560_62525561delCA	uc002yhf.2	+						DNAJC5_uc002yhg.1_5'Flank	NM_025219	NP_079495	Q9H3Z4	DNJC5_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5						neurotransmitter secretion|protein folding	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|melanosome|plasma membrane	heat shock protein binding|unfolded protein binding			pancreas(1)	1	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTTGGCAATTCAAGACCGGCAT	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10705050	10705050	+	IGR	DEL	T	-	-	rs140544697		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10705050delT								None (None upstream) : TPTE (201693 downstream)																							tgcattcatctcacagagttg	0.000													4	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11037537	11037537	+	Intron	DEL	T	-	-	rs57142183		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11037537delT	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AAACAAAAAATACTTACTGGA	0.274													3	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11056763	11056763	+	Intron	DEL	T	-	-	rs111350938		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11056763delT	uc002yit.1	-							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)		CATTGAGTAATAAAATGTTCC	0.299													5	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11087766	11087766	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11087766delT	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)		TAAGACTGTATTTTTTATGGA	0.134													6	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11093095	11093095	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11093095delA	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)		GTTACCATGCAAAAAAATATA	0.328													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11096543	11096544	+	Intron	DEL	AG	-	-	rs142805951		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11096543_11096544delAG	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)		tttttgagacagagtctccctc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11144773	11144774	+	IGR	DEL	TG	-	-	rs72428671		TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11144773_11144774delTG								BAGE (45836 upstream) : None (None downstream)																							TGGAtgtgtctgtgtgtgtgtg	0.371													4	2	---	---	---	---	
NCAM2	4685	broad.mit.edu	37	21	22436306	22436306	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22436306delC	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)		ATTTGGACATCCaggaagtgg	0.189													4	2	---	---	---	---	
APP	351	broad.mit.edu	37	21	27489207	27489207	+	Intron	DEL	T	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27489207delT	uc002ylz.2	-						APP_uc010glk.2_Intron|APP_uc002yma.2_Intron|APP_uc011ach.1_Intron|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.1_Intron|APP_uc011acj.1_Intron	NM_000484	NP_000475	P05067	A4_HUMAN	amyloid beta A4 protein isoform a precursor						adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)				AATCTCAGTAtttttttttgg	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	28157367	28157368	+	IGR	DEL	AG	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28157367_28157368delAG								CYYR1 (211786 upstream) : ADAMTS1 (51240 downstream)																							ACAACTAGGAAGAGAGGAAGAA	0.431													2	4	---	---	---	---	
KRTAP23-1	337963	broad.mit.edu	37	21	31722574	31722574	+	5'Flank	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31722574delA	uc002yny.1	-							NM_181624	NP_853655	A1A580	KR231_HUMAN	keratin associated protein 23-1							intermediate filament					0						gagaggccacaaaaaaaatcc	0.065													4	2	---	---	---	---	
HSF2BP	11077	broad.mit.edu	37	21	45001538	45001538	+	Intron	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45001538delA	uc002zdi.2	-						HSF2BP_uc011aey.1_Intron	NM_007031	NP_008962	O75031	HSF2B_HUMAN	heat shock transcription factor 2 binding						spermatogenesis|transcription from RNA polymerase II promoter	cytosol	binding			skin(1)	1				STAD - Stomach adenocarcinoma(101;0.18)		caagaaaggcaaaaaaaacac	0.000													4	2	---	---	---	---	
PRMT2	3275	broad.mit.edu	37	21	48073849	48073850	+	Intron	DEL	TT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:48073849_48073850delTT	uc002zjx.2	+						PRMT2_uc002zjw.2_Intron|PRMT2_uc002zjy.2_Intron|PRMT2_uc010gqm.2_Intron|PRMT2_uc011aga.1_Intron|PRMT2_uc011agb.1_Intron|PRMT2_uc011agc.1_Intron|PRMT2_uc002zjz.1_Intron	NM_206962	NP_996845	P55345	ANM2_HUMAN	HMT1 hnRNP methyltransferase-like 1						developmental cell growth|induction of apoptosis|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of androgen receptor signaling pathway	cytosol|nucleus	androgen receptor binding|estrogen receptor binding|histone-arginine N-methyltransferase activity|peroxisome proliferator activated receptor binding|progesterone receptor binding|protein homodimerization activity|retinoic acid receptor binding|signal transducer activity|thyroid hormone receptor binding|transcription coactivator activity			ovary(1)	1	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)		tcttttcttgtttttttttttt	0.391													3	4	---	---	---	---	
PRODH	5625	broad.mit.edu	37	22	18921414	18921414	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18921414delC	uc010grl.2	-						PRODH_uc002zoj.3_Intron|PRODH_uc002zol.3_Intron|PRODH_uc002zok.3_Intron	NM_016335	NP_057419	O43272	PROD_HUMAN	proline dehydrogenase 1						glutamate biosynthetic process|induction of apoptosis by oxidative stress|proline catabolic process	mitochondrial inner membrane|mitochondrial matrix	proline dehydrogenase activity			breast(1)	1					L-Proline(DB00172)	TACACTTGTACCCCCTGTGAA	0.547													4	2	---	---	---	---	
HIRA	7290	broad.mit.edu	37	22	19344237	19344237	+	Intron	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19344237delC	uc002zpf.1	-						HIRA_uc011agx.1_Intron|HIRA_uc010grn.1_Intron|HIRA_uc010gro.1_Intron|HIRA_uc010grp.2_Intron	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective						chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)					TACCCCTCAGCCCTCAGCCTA	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	34767045	34767046	+	IGR	INS	-	T	T	rs137881755	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34767045_34767046insT								LARGE (448461 upstream) : ISX (695083 downstream)																							ATGTCCTTCTGTTTTATCTCAA	0.431													3	3	---	---	---	---	
ATXN10	25814	broad.mit.edu	37	22	46172039	46172039	+	Intron	DEL	A	-	-	rs74852502	by1000genomes	TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46172039delA	uc003bgm.1	+						ATXN10_uc011aqt.1_Intron|ATXN10_uc003bgn.1_Intron	NM_013236	NP_037368	Q9UBB4	ATX10_HUMAN	ataxin 10						cell death|neuron projection development	dendrite|neuronal cell body|perinuclear region of cytoplasm				ovary(1)|kidney(1)	2		Ovarian(80;0.00973)|all_neural(38;0.0417)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0223)		TTTGCAGAATAAAAAAACACC	0.259													4	2	---	---	---	---	
DDX3X	1654	broad.mit.edu	37	X	41203543	41203544	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41203543_41203544insT	uc004dfe.2	+	10	1771_1772	c.916_917insT	c.(916-918)ATTfs	p.I306fs	DDX3X_uc010nhf.1_Frame_Shift_Ins_p.I290fs|DDX3X_uc004dff.2_Frame_Shift_Ins_p.I306fs|DDX3X_uc011mkq.1_Frame_Shift_Ins_p.I290fs|DDX3X_uc011mkr.1_Frame_Shift_Ins_p.I306fs|DDX3X_uc011mks.1_Intron|DDX3X_uc004dfg.2_RNA|DDX3X_uc011mkt.1_RNA	NM_001356	NP_001347	O00571	DDX3X_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3	306	Necessary for interaction with XPO1.|Helicase ATP-binding.				interspecies interaction between organisms	cytoplasm|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding|RNA binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6						TGGTGCCGATATTGGTCAGCAG	0.406										HNSCC(61;0.18)			271	370	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	68159193	68159193	+	IGR	DEL	C	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68159193delC								EFNB1 (93164 upstream) : PJA1 (221389 downstream)																							TGAGGCTCCTCCCCACATCCT	0.488													4	2	---	---	---	---	
NHSL2	340527	broad.mit.edu	37	X	71156583	71156584	+	Intron	DEL	GT	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71156583_71156584delGT	uc011mqa.1	+							NM_001013627	NP_001013649	Q5HYW2	NHSL2_HUMAN	NHS-like 2												0	Renal(35;0.156)					GATGATGGTGGTGTGTGTGTGT	0.426													4	3	---	---	---	---	
ATRX	546	broad.mit.edu	37	X	76763680	76763680	+	3'UTR	DEL	A	-	-			TCGA-CZ-5456-01A-01D-1501-10	TCGA-CZ-5456-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76763680delA	uc004ecp.3	-	35					ATRX_uc004ecq.3_3'UTR|ATRX_uc004eco.3_3'UTR	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1						DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	TGCCCTATTTAAAAAAAAAAA	0.313			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						12	7	---	---	---	---	
